Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we used admixture and genetic relatedness analysis of northern highbush (NHB, V. corymbosum) and southern highbush (SHB, V. darrowii) blueberry genotypes and F2 progenies of the V. corymbosum × V. darrowii cross. Using genotyping-by-sequencing (GBS), we generated ~3.34 billion reads (75 bp). The GBS reads were aligned to the Vaccinium corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single nucleotide polymorphisms (SNPs), which were used for principal component, haplotype, and admixture analysis. PCA formed three main groups: 1) NHB cultivars, 2) SHB cultivars, and 3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB, indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mix of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived SNP markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.

Kersting’s groundnut is an important source of protein and essential nutrients that contribute to food security in West Africa. However, the crop is still underexploited by the populations and under-researched by the scientific community. This study aimed to investigate the genetic diversity and population structure of 217 Kersting’s groundnut accessions from five origins using 886 DArTseq markers. Gene diversity was low and ranged from 0.049 to 0.064. The number of private alleles greatly varied among populations (42–192) and morphotypes (40–339). Moderate to very high levels of selfing and inbreeding were observed among populations (s=56–85%, F_IS=0.389–0.736) and morphotypes (s=57–82%, F_IS=0.400–0.691). Moreover, little to very high genetic differentiations were observed among populations (0.006≤F_IS≤0.371) and morphotypes (0.029≤F_IS≤0.307). Analysis of molecular variance partitioned 38.5% of the genetic variation among and 48.7% within populations (P<0.001). Significant isolations by distance were detected between populations (R²=0.612, P=0.011) and accessions (R²=0.499, P<0.001). Discriminant analysis of principal components and neighbour joining consistently distinguished eight distinct clusters. These data provide a global picture of the existing genetic diversity for Kersting’s groundnut and will guide the choice of breeding strategies to increase production.

Meloidogyne javanica causing root-knot nematode in soybean is an important problem in soybean areas, leading to several yield losses. Some accessions have been identified carrying resistance loci to this nematode specie. In this study, a set of 317 soybean accessions were characterized for resistance to M. javanica. Genome-wide association study (GWAS) was performed using SNPs from genotyping-by-sequencing (GBS), and a region of 29.2 Kbp on chromosome 13 was identified. The haplotype analysis showed that SNPs were able to discriminate susceptible and resistant accessions, leading to 25 accessions sharing the resistance locus. Furthermore, 5 accessions may be new M. javanica resistance sources. The screening of the SNPs in the USDA soybean germplasm showed that several accessions previous reported as resistance to other nematodes also showed the resistance haplotype on chromosome 13. High levels of concordance among the phenotypes of Brazilian cultivars and the SNPs in chromosome 13 were observed. A in silico analysis of the mapped region on soybean genome revealed a presence of 5 genes with structural similarity with major resistance genes. The expression levels of the candidate genes in the interval demonstrated a potential pseudogene, and other two model genes up-regulated in the resistance source after pathogen infection. The SNPs associated to the region conferring resistance is a important tool for introgression of the resistance by marker-assisted selection in soybean breeding programs.

Limiting harm to organisms via genetic sampling is an important consideration for rare species. Nondestructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the Unionid freshwater mussel, Texas Pigtoe (Fusconaia askewi). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared to swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence) while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.

Pasmo (Septoria linicola) is a fungal disease causing major losses in seed yield and quality, and stem fibre quality in flax. Pasmo resistance (PR) is quantitative and has low heritability. To improve PR breeding efficiency, the accuracy of genomic prediction (GP) was evaluated using a diverse worldwide core collection of 370 accessions. Four marker sets, including three defined by 500, 134, and 67 previously identified quantitative trait loci (QTL) and one of 52,347 PR-correlated genome-wide single nucleotide polymorphisms, were used to build ridge regression best linear unbiased prediction (RR-BLUP) models using pasmo severity (PS) data collected from field experiments performed during five consecutive years. With five-fold random cross-validation, GP accuracy as high as 0.92 was obtained from the models using the 500 QTL when the average PS was used as the training dataset. GP accuracy increased with training population size, reaching values >0.9 with training population size greater than 185. Linear regression of the observed PS with the number of positive-effect QTL in accessions provided an alternative GP approach with an accuracy of 0.86. The results demonstrate the GP models based on marker information from all identified QTL and the 5-year PS average is highly effective for PR prediction.

Next-generation sequencing (NGS) has actualized human papillomavirus (HPV) virome profiling for in-depth investigation of viral evolution and pathogenesis. However, viral computational analysis remains a bottleneck due to semantic discrepancies between computational tools and curated reference genomes. To address this, we developed and tested automated workflows for HPV taxonomic profiling and visualization using a customized Papillomavirus database in CLC Microbial Genomics Module. HPV genomes from Papilloma Virus Episteme were customized and incorporated into CLC “ready-to-use” workflows for stepwise data processing to include: 1) Taxonomic Analysis, 2) Estimate Alpha/Beta Diversities, and 3) Map Reads to Reference. Low-grade (n = 95) and high-grade (n = 60) Pap smears were tested with ensuing collective runtimes: Taxonomic Analysis (36 min); Alpha/Beta Diversities (5 sec); Map Reads (45 min). Tabular output conversion to visualizations entailed 1-2 keystrokes. Biodiversity analysis between low- (LSIL) and high-grade squamous intraepithelial lesions (HSIL) revealed loss of species richness and gain of dominance by HPV-16 in HSIL. Integrating clinically relevant, taxonomized HPV reference genomes within automated workflows proved to be an ultra-fast method of virome profiling. The entire process named “HPV DeepSeq” provides a simple, accurate and practical means of NGS data analysis for a broad range of applications in viral research.

A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 QTL for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48-73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8-14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.

Bacterial wilt (BW), caused by Ralstonia solanacearum is one of the major biotic factors limiting tomato production in the humid tropics. Pyramiding of resistance genes through marker-assisted selection is an efficient way to develop durable BW resistant cultivars. Tomato line ‘Hawaii 7996’ (H7996) is a stable and robust resistance source against various R. solanacearum strains. Major BW resistance quantitative trait loci (QTLs) Bwr-12 and Bwr-6, and several minor or strain specific QTLs have been coarse-mapped in this line, but none has been fine-mapped and validated. The objective of the current study was to construct a high density genetic map using single-nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing, fine-map Bwr-12 and Bwr-6 and determine the effects of these QTLs using a near isogenic line (NIL) population. A high density genetic map using 1,604 SNP markers with an average distance of 0.82 cM was developed for 188 F9 recombinant inbred lines derived from the cross H7996 × WVa700. A total of seven QTLs associated with BW resistance to race 1-phylotype I or/and race 3-phylotype II strains were located on chromosomes 6 (Bwr-6.1, 6.2, 6.3 and 6.4) and 12 (Bwr-12.1, Bwr-12.2 and Bwr-12.3) with logarithm of odds (LOD) scores of 6.2-15.6 and 6.2-31.1, explaining 14.2-33.4% and 15.9-53.9% of the total phenotypic variation contributed from H7996, respectively. To validate the genetic effects of the two QTL regions, a set of 80 BC3F3 NILs containing different sections of Bwr-6 with or without Bwr-12 was phenotyped for disease severity after challenge with either race 1-phylotype I Pss4 or race 3-phylotype II Pss1632 BW strains over two seasons. Bwr-6.1 specific to Pss4 and Bwr-6.3 specific to Pss1632 were mapped to an interval of 5.0 cM (P < 0.05) between 6_33,444,000_SLM6-47 and 6_33,868,000_SLM6-124 SNP marker, and to 2.7 cM (P < 0.01) between positions 6_35,949,000 _SLM6-107 to 6_36,750,000_SLM6-82 marker, respectively. In addition, the specific effect of Bwr-12 for resistance to Pss4 (LOD score of 5.8-16.1, P < 0.01) was confirmed and markers for this QTL have already been made available previously.

Piscine lactococcosis is a disease caused by Lactococcus garvieae, L. petauri and L. formosensis. It is considered to be an emerging disease and poses a risk to global aquaculture production. Studies of the genetic diversity of Lactococcus spp. strains have epidemiological importance since they provide information on the genetic relationships between isolates and indicate geographic and temporal distribution. The aim of this study was to evaluate the genetic diversity of Brazilian Lactococcus spp. isolates obtained from native fish species using PCR-based DNA fingerprinting techniques. For this, 36 isolates were selected and submitted to gyrB sequencing, molecular serotyping, REP-, BOX-, and RAPD-PCR approaches. The discriminatory power and the congruence between the typing methods were calculated. After the correct taxonomic discrimination of the isolate, a total of 14, 5 and 17 isolates were reclassified as L. garvieae, L. formosensis and L. petauri, respectively. L. garvieae and L. petauri are related to serotype I, while L. formosensis strains were classified as serotype II. The typing methods tested are useful for evaluating the genetic diversity of isolates and a comprehensive indication of the diversity was found. Heterogeneous and homogeneous populations were observed for L. garvieae and L. petauri, respectively. RAPD-PCR demonstrated a greater discriminatory power for L. formosensis and L. petauri, while REP-PCR showed better results for L. garvieae strains, thus these methodologies are recommended for genotyping these bacterial species. In conclusion, Brazilian isolates of Lactococcus spp. obtained from native fish species constitute a genetically diverse population and the techniques used in this study allowed a better genetic characterization of the isolates.

Bacillus anthracis, the causative agent of anthrax, has two virulence plasmids: pXO1 and pXO2. Plasmid pXO2 carries the genes of an antiphagocytic capsule synthesis. Plasmid pXO1 carries the genes pagA, lef, and cya encoding anthrax toxins, as well as atxA, which encodes the main regulator of pathogenicity factor expression. In the present paper, we evaluated the polymorphism of the pagA, lef, cya, and atxA genes for 85 B. anthracis strains belonging to different evolutionary lineages and canSNP groups and three B. cereus strains possessing pXO1-like plasmids. We found 19 genotypes (GT) strongly correlated with the main evolutionary lineages; they were mainly correlated with the canSNP group within these lines. In some cases, one GT combined the strains of several canSNP groups, and some canSNP groups were divided into several GTs. The most interesting of such cases were 1) the formation of a separate GT by strains of the A.Br.008/009 group isolated in the former USSR; 2) the presence of a unique GT in some American strains of the A.Br.Aust94 group; 3) the division of the A.Br.001/002 group into two subgroups, one of which may be a transitional link to the group A.Br.Ames; 4) the fact that European isolates of the B.Br.CNEVA group and Arctic strains of the B.Br.001/002 group have a common GT.

Recent climatic disasters (dzudzs) and uncontrolled massive breeding endangered valuable ge-netic resources of Mongolian goats labored by five thousand years of evolution in extremes of Al-tai mountains and Gobi deserts. Meanwhile, Mongolian goats has never been characterized by genomic data. We used Illumina Goat SNP50 to investigate phylogenic relationships and genetic risks in 5 local Mongolian populations: Erchim (N=37) from geographically remote Darkhat Valley in the northern mountains, Ulgii Red (N=35) and Dorgon (N=28) from the western mountain region, Buural (N=34) from the western steppe and mountain areas and Gobi Gurvan Saikhan (N=33) from semi-arid steppe area in the South Gobi region. ROH analyses, estimated populations sizes and Fst values showed South Gobi and Darkhat Valley goats to be of a high risk of inbreed-ing that however appear to be of distinct origin (artificial selection vs geographical isolation). In-dices of genetic differentiations between Mongolian goats were relatively low compared to Euro-pean breeds. Meanwhile, we suggest direct comparison is not fully appropriate given that Mongo-lian breeds were not subjected to intense selection. Darkhat Valley goats were clearly differentiat-ed from other Mongolian breeds according to various types of analyses. Phylogenetic relationships within XXX breeds of the rest of the world plotted Mongolian goats between some Russian (Altai, Orenburg) and Chinese populations (Nanjiang and Qinggeli). Thus, present study (i) highlights demographic history Mongolian goats and (ii)provides unified SNP-data called for support deci-sions in conservational genetics. Finally, our work (iii) raises a question of how exactly these data should be compared to make objective choices.

Cryptosporidium is comprised an apicomplexan parasitic protist, which infects a wide range of hosts, causing cryptosporidiosis. In cattle farms, the incidence of cryptosporidiosis results in high mortality in calves leading to considerable economic loss in the livestock industry. Infected animals may also act as a major reservoir of Cryptosporidium spp., in particular C. parvum, the most common cause of cryptosporidiosis in calves. This poses a significant risk to other farms via breeding centres, to trading of livestock and to human health. This study, funded by the Interreg-2-seas programme, is a part of a global project aimed at strategies to tackle cryptosporidiosis. To reach this target, it was essential to determine whether prevalence was dependent on the studied countries or if the issue was borderless. Indeed, C. parvum occurrence was assessed across dairy farms in certain regions of Belgium, France and the Netherlands. At the same time, the animal-to-animal transmission of the circulating C. parvum subtypes was studied. To accomplish this, 1084 faecal samples, corresponding to 57 dairy-farms from all three countries, were analysed. Well-established protocols amplifying the 18S rDNA and gp60 genes fragments, followed by DNA sequencing, were used for the detection and subtyping C. parvum; the DNA sequences obtained were further characterised using a combination of bioinformatics and phylogenetics methods. Our results show 25.7%, 24.9% and 20.8% prevalence of Cryptosporidium spp. in Belgium, France and the Netherlands respectively. Overall, 93% of the farms were Cryptosporidium positive. The gp60 subtyping demonstrated a significant number of the C. parvum positives belonged to the IIa allelic family, which has been also detected in humans. Consequently, this study highlights how widespread is C. parvum in dairy farms and endorses cattle as a major carrier of zoonotic C. parvum subtypes, which subsequently pose a significant threat to human health.

The world has now entered into a replacement era of genomics due to the continued advancements within the next generation high throughput sequencing technologies, which incorporates sequencing by synthesis-fluorescent in place sequencing (FISSEQ), pyrosequencing, sequencing by ligation using polony amplification, supported oligonucleotide detection (SOLiD), sequencing by hybridization alongside sequencing by ligation, and nanopore technology. Great impacts of those methods are often seen for solving the genome related problems of plant and Animalia which will open the door of a replacement era of genomics. This might ultimately overcome the Sanger sequencing that ruled for 30 years. NGS is predicted to advance and make the drug discovery process more rapid.

DNA sequencing methods were first developed more than 20 years ago with the publication of two approaches to sequencing methodology that became known as Sanger sequencing (1), based on enzymatic synthesis from a single-stranded DNA template with chain termination using dideoxynucleotides (ddNTPs) and Maxim-Gilbert sequencing (2),which involved chemical degradation ofend-radio-labeled DNA fragments. Both methods relied on four-lane,high resolution polyacrylamide gel electrophoresis to separate the labeled fragment and allow the base sequence to be read in a staggered ladder-like fashion. Sanger sequencing was technically easier and faster, and thus became the main DNA sequencing method for the vast majority of applications.

A novel process design for damage-free and highly accurate positional integration of an optical multi-axial force sensor into a hollow tube by means of rotary swaging is introduced. Numerical simulations reveal relevant process phenomena of thin disc joining inside a pre-toothed hollow tube and help to find an optimal process design. Experimental trials show a significant effect of axial material flow and the number of tools in a rotary swaging process. By taking these effects into account, a successful form- and force-fit joining of the sensor carrying discs into the tube can be achieved. A successful joining of an optical sensor for bending forces and torque measurement shows hysteresis-free sensory behavior and thus backlash-free joining of the sensor carrier discs. The paper finishes with presenting an approach for closed-loop position controlling during the joining process and numerically investigation of the process design.

Background: Human papillomavirus (HPV) is diagnosed in most cervical cancers and is the fourth cause of cancer worldwide. Currently, fourteen HPV types are considered carcinogenic (HPV 16/18/31/33/35/39/45/51/52/56/58/59/66/68) with different oncogenicity. Cervical lesions might be due to HR (high risk)-HPV for what is important to identify new methods to genotype cervical lesions. The main goal was to identify, for the first time, HPV-HR in cervical lesions using Anyplex™ Detection kit in paraffin-embedded tissue. (2) Methods: It was performed a retrospective study in 45 women from Academic Hospital of Cova da Beira (CHUCB). DNA extraction was performed and through Anyplex™ II HPV-HR Detection kit HPV-HR were genotyped. (3) Results: HPV-HR were identified in 38 women; HPV-16 (55,26%), HPV-18/39/56/58/59 (5,26%), HPV-31 (21,05%), HPV-35 (7,89%), HPV-51/6 (2,63%) and HPV-52 (10,53%). (4) Conclusions: Our results reflect that Anyplex™ II HPV-HR Detection kit, designed for HR-HPV genotyping of cervical cancer screening, might be properly used to HR-HPV genotyping in histology. The proposed methodology allows an easy and cheaper technique that should be used as a future cervical risk stratification. It is a strong tool to be implemented in clinical practice in order to detect HR-HPV detection in cervical lesions, contributing to a more accurate diagnosis.

Chronic Kidney Disease (CKD) is one of the worldwide health threats, kidneys may be affected by internal pathologies and environmental factors as well as a number of genes are also involved in the kidney dysfunctioning, so UMOD is one of these genes which has significant effect in regulating urea and creatinine level in blood and decreased excretion of uric acid which causes interstitial damages in kidney and may result CKD. Hence, the present study is envisaged to observe the association of this gene locus (r.1264T>C) with CKD in Pakistani population using ARMS-PCR genotyping, for the purpose, a total of 75 samples were investigated, out of which 45 were found homozygous wild-type, 21 heterozygous and 09 homozygous mutants. PLINK data analysis toolset showed that our sampled population does not obeys Hardy-Weinberg Equilibrium by χ² (2, N = 75) = 18.87, p = and Chi-square statistics with p = 1.40×10^-005 showing a significant genotypic association with the subject phenotype with an alternative allele frequency of 0.15 and 0.48 within cases & controls respectively. Furthermore, an odds-ratio of 0.2 predicts that the risk of wild-type allele (A) is 0.8 times higher in patient as compared to controls and mutant allele is 0.2 times preventive in patients. Additionally, a few bioinformatics tools e.g., ProtParam, PsiPred, TMHMM-2.0, Motif Scan, ScanProsite, NetPhos3.1, GPS PAIL2.0, NetOGlyc4.0, PRmePRed, PDB-RCSB and STRING were applied to predict different characteristics of Uromodulin protein including physicochemical properties, secondary/transmembrane structures, protein conserved domains and posttranslational modifications respectively. This pilot scale study provided a comprehensive insight of the association of aforementioned genetic variant with CKD to identify and evaluate the genetic risk factors along with functional effects of the subject variant which may be used as CKD prevention by adopting DNA screening and genetic counselling recommendations.

Dairy cattle predicted by genomic breeding values to be heat tolerant are known to have less milk production decline and lower core body temperature increases in response to elevated temperatures. In a study conducted at the University of Melbourne’s Dookie Robotic Dairy Farm during summer, we identified the most 20 heat-susceptible and 20 heat-tolerant cows in a herd of 150 Holstein Friesian lactating cows based on their phenotypic responses (changes in respiration rate, surface body temperature, panting score, and milk production). Hair samples were collected from the tip of the cows' tail following standard genotyping protocols. The results indicated variation in feed saved and HT genomic estimated breeding values (GEBVs) (P≤0.05) across age, indicating a potential for their selection. As expected, the thermotolerant group had higher GEBVs for HT and feed saved but lower for milk production. In general, younger cows had superior GEBVs for Balanced Performance Index (BPI), Type Weighted Index (TWI) and Australian Selection Index (ASI), whilst older cows were superior in fertility, feed saved (FS) and HT. The study demonstrated highly significant (P≤ 0.001) negative correlations (-0.28 to -0.74) between HT and GEBVs for current Australian Dairy cattle selection indices (BPI, TWI, ASI, HWI) and significant (P≤ 0.05) positive correlations between HT and GEBVs for traits like FS (0.45) and fertility (0.25). Genomic selection for HT will help improve cow efficiency and sustainability of dairy production under hot summer conditions. However, a more extensive study involving more lactating cows across multiple farms is recommended to confirm the associations between the phenotypic predictors of HT and GEBVs.

Cryptosporidium parvum is one of the major causes of neonatal calf diarrhoea resulting in reduced farm productivity and compromised animal welfare worldwide. Livestock act as a major reservoir of this parasite, which can be transmitted to humans directly and/or indirectly, posing a public health risk. Research reports on Cryptosporidium prevalence from the east Mediterranean region are scarce with even less originating from Cyprus. This study is the first to explore occurrence of Cryptosporidium spp. in young dairy calves on the island. A total of 242 faecal samples were collected from 10 dairy cattle farms in Cyprus, all of which were screened for Cryptosporidium spp. using nested-PCR amplification targeting the small subunit of the ribosomal RNA (18S rRNA) gene. The 60 kDa glycoprotein (gp60) gene was also sequenced for the samples identified as C. parvum positive to determine the subtypes present. Occurrence of Cryptosporidium was 43.8% (106/242) with at least one positive isolate in each farm sampled. Prevalence per farm ranged from 20¬‒64%, while C. bovis, C. ryanae and C. parvum were the only species identified. Amongst those, the latter was the predominant species, representing 51.8% of all positive samples. Four zoonotic subtypes were identified – IIaA14G1R1, IIaA15G1R1, IIaA15G2R1 and IIaA18G2R1. IIaA14G1R1 was the most abundant; representing 48.2% of all C. parvum positive samples and was also the most widespread. This is the first report of zoonotic subtypes of C. parvum circulating in Cyprus. These results highlight the need for further research into the parasite focusing on its diversity, prevalence, host-range and transmission dynamics on the island.

Anemia is a well-developed discipline where the concepts of precision medicine have, in part and being studied extensively. This review discusses the treatment of EPO-deficient anemia and resistance in Chronic Kidney Disease (CKD). Traditionally, erythropoietin-stimulating agents (ESA) and iron supplementation have been used to manage anemia in CKD. However, these treatments have potential risks, including cardiovascular and thromboembolic events. Newer treatments have emerged to address these risks, such as slow-release and low-dosage intravenous iron, oral iron, and erythropoietin-iron combination therapy. Another novel approach is using hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHI). This review highlights the need for precision medicine targeting genetic components of EPO-deficient anemia in CKD and discusses individual variability of genes such as the erythropoietin gene (EPO), Interleukin-β gene (IL-β), and hypoxia-inducible factor gene (HIF). Pharmacogenomics testing aims to provide targeted therapies and interventions that are tailored to the specific characteristics of an individual, optimizing treatment outcomes and minimizing resistance and adverse effects. The article concludes by suggesting the potential of receptor modification to revolutionize treatment outcome of erythropoietin deficiency anemia through integration of the mentioned approach.

High resolution information on nucleotide arrangement in the genome of any or-ganism is critical to understand its genetic makeup, function, and evolutionary his-tory. For years, DNA sequencing has provided crucial breakthroughs in the field of genomics and molecular biology. With the advent of technology, Next Generation Sequencing has now transformed the whole genome sequencing prospects, thus unveiling the novel and interesting features of an organism genome that can behold. Next generation sequencing platforms offer realistic approach to identify and anal-yses whole genome with high throughput, accuracy, scalability in a very short time span. Information obtained can be further used in improving our existing healthcare systems, designing novel and personalized therapeutic modules, making the envi-ronment sustainable and proactively preparing ourselves for future pandemics and outbreaks. This article discusses the various NGS technologies and approaches, their advantages, drawbacks, and futuristic usage in different fields. Though still in nascent stages and marred with flaws, with ongoing advancement, NGS will indeed have promising impacts in the future.

In this study, a structural profiling of equid alphaherpesvirus 1 (EHV-1) transcriptome was carried out using next-generation (Illumina) and third-generation (Oxford Nanopore Technologies) sequencing platforms. We annotated the canonical mRNA molecules and their isoforms, including transcript start and end site isoforms, and splice variants. Additionally, a number of putative 5′-truncated mRNAs containing shorter in-frame ORFs were detected. We also demonstrated that EHV-1 produces a high number of non-coding transcripts, including antisense and intergenic RNAs. One of the most remarkable features of the EHV-1 is the generation of abundant fusion transcripts some of which encoding chimeric polypeptides. We observed a higher number of splicing and transcriptional overlaps than in related viruses. Additionally, we found that many upstream genes of tandem gene clusters have their own transcript end sites (TESs) besides the co-terminal TESs, which is rare in other alphaherpesviruses. We show here that the replication origins (OriS and OriL) of the virus are co-localized with promoter sequences and overlap with specific RNA molecules. Furthermore, we discovered a novel non-coding RNA (designated as NOIR) that overlaps the 5′-ends of the longer transcript variants encoded by the two main transactivator genes ORF64 and 65 bracketing the OriL. These all suggest the existence of a central regulatory system which controls the genome-wide transcription and the replication through a mechanism based on the interference between the machineries carrying out the synthesis of DNA and RNA.

We have been encouraging practicing gynecologists to adopt molecular diagnostics tests, PCR, and cancer biomarkers, as an alternative enabled by these platforms to traditional Papanicolaou and colposcopy tests, respectively. An aliquot of liquid-based cytology was used for the molecular test [high-risk HPV types, (HR HPV)], another for the PAP test and still one more for the p16/Ki67 dual stain cytology. A total of 4,499 laboratory samples were evaluated, and we found that 25.1% of low-grade samples and 47.9% of high-grade samples after PAP testing had a negative HR HPV-PCR result. In those cases, reported as Pap-negative, 22.1% got a positive HR HPV-PCR result. Dual staining with the p16/Ki67 biomarkers in samples was positive for HR HPV, and 31.7% were also positive for these markers. Of the PCR results positive for any of these high-risk HPV subtypes, n 68.3% we did not to find evidence for the presence of cancerous cells, highlighting the importance of performing dual staining with p16/Ki67 after PCR, to avoid unnecessary colposcopies. Encountered challenges are a deep-rooted social reluctance in Mexico to abandon traditional Pap smears and the opinion of many specialists, we still believe that colposcopy continues to be a preferred procedure over dual staining protocol.

Orthohantaviruses can cause two types of human infections: hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). HFRS is a zoonotic disease transmitted by multiple rodent species. Yunnan Province in southwest China is the natural foci of HFRS, and Dali Prefecture in Yunnan Province has the highest incidence of HFRS; however, the precise status of orthohantavirus infection in Dali Prefecture remains unknown. To this end, we obtained clinical data of HFRS patients from the medical records of the People's Hospital of Xiangyun County in Dali Prefecture from July 2019 to August 2021. We collected epidemiological data of HFRS patients through interviews and investigated host animals using the night clip or night cage method. We systematically performed epidemiological analyses of patients and host animals. The differences in the presence of rodent activity at home (2=8.75, P=0.031&lt;0.05), of rodent-proof equipment in the food (2=9.19, P=0.025&lt;0.05), and of rodents or rodent excrement in the workplace (2=10.35, P=0.014&lt;0.05) were statistically different in the four clinical types, including mild, medium, severe, and critical HFRS-associated diseases. Furthermore, we conducted molecular detection of orthohantavirus in host animals. The total orthohantavirus infection rate of rodents was 2.7% (9/331); the specific infection rate of specific animal species was 6.1% (5/82) for the Apodemus chevrieri, 100% (1/1) for the Rattus nitidus, 3.8% (2/53) for the Rattus norvegicus, and 12.5% (1/8) for the Crocidura dracula. In this study, a total of 21 strains of orthohantavirus were detected in patients and rodents. The 12 orthohantavirus strains from patients showed a closer relationship with Seoul orthohantavirus (SEOOV) L0199, DLR2, and GZRn60 strains; the six orthohantavirus strains from Rattus norvegicus and Apodemus chevrieri were closely related to SEOOV GZRn60 strain; One strains (XYRn163) from Rattus norvegicus and one strain (XYR.nitidus97) from Rattus nitidus were closely related to SEOOV DLR2 strain; the orthohantavirus strain from Crocidura dracula was closely related to the Luxi orthohantavirus (LUXV) LX309 strain. In conclusion, patients with HFRS in Xuangyun County of Dali Prefecture are predominantly affected by SEOOV, with multiple genotypes of orthohantavirus in host animals, and most importantly, these orthohantavirus strains constantly demonstrated zoonotic risk in humans.

Genomic selection (GS) is a predictive approach that was build up to increase the rate of genetic gain per unit of time in breeding programs. It has emerged as a valuable method for improving complex traits that are controlled by many genes with small effect. GS enables the prediction of breeding value of candidate genotypes for selection. In this work we address important issues related to GS and its implementation in tomato breeding context. Genomic constrains and critical parameters affecting the accuracy of prediction in such crop such as phenotyping, genotyping training population composition and size and statistical method should be carefully evaluated. Comparison of GS approaches for facilitating the selection of tomato superior genotypes during breeding program are also discussed. GS applied to tomato breeding has already shown to be feasible. We illustrated how GS can improve the rate of gain in elite lines selection, descendent and in backcross schemes. The GS schemes begin to be delineated and computer science can provide support for future selection strategies. A new breeding framework is beginning to emerge for optimizing tomato improvement procedures.

Late blight caused by the oomycete pathogen Phytophthora infestans is a devastating disease of potato and tomato worldwide, including Israel. The population structure of this pathogen was monitored in potato and tomato fields in Israel during a 36-year period of 1983-2019. Isolates of the pathogen were tested for sensitivity to phenylamide fungicides, mating type, race structure, and genotype. The phenotypic and genotypic structure of the population from potato have changed greatly from one year to another, from one season to the next, within a season and within a single field. Major changes also occurred in the population collected from tomato crops. The mechanisms driving these multiple changes and the heterogeneous nature of the population in Israel are shown to derive from multiple migration events of the pathogen via seed tubers from Europe and from fitness-driven selection processes.

Given of the outstanding versatile properties, the multilayered anti-corrosion coatings have drawn great interests in academic and engineering fields. However, the application of multilayered coatings is restricted by some limitations such as low interlayer compatibilities, harsh preparation process, etc. This work introduced a composite film fabricated on 2A12 aluminum alloy surface, including an anodic oxide film, a sol-gel film as well as a layer-by-layer (LBL) self-assembling film from bottom to top. The microstructure and elemental characterization indicated that the finish of the coating with the LBL film resulted in a closely connected multilayered coating with a smoother surface. The anticorrosion performance was systematically evaluated in the simulated corrosive medium and neutral salt-spray environment. The intergrated coating with the LBL film presented an excellent anticorrosion ability with the system impedance over 108 Ω•cm² and the self-corrosion current density two orders of magnitude lower than that of the other coatings. After the acceleration test in salt-spray environment, the multilayered coatings could still show a good protective performance with almost no cracks and no penetration of chloride ions. It is believed that the as-constructed multilayered coating with high corrosive properties and fine surface state will have promising applications in the field of anticorrosion engineering.

African swine fever virus (ASFV) is the causative agent of African swine fever, an economically important disease of pigs, often with a high case fatality rate. ASFV has demonstrated low genetic diversity among isolates collected within Eurasia. To explore the influence of viral variants on clinical outcomes and infection-dynamics in pigs experimentally infected with ASFV, we have designed a deep sequencing strategy. Variant analysis revealed 3 distinct SNPs present in the virus inoculum (at 2.4%, 0.7%, and 13% frequency, respectively) that were maintained within all infected pigs (1-6 % frequency, and the latter at 16-21%). Several pigs displayed other unique SNPs at &lt;10% frequency. In addition, a deletion of 10487 bp (resulting in the complete loss of 21 genes) was present at nearly 100% frequency in the ASFV DNA from one pig at position 6362-16849. This deletion was also found to be present at low levels in the virus inoculum and in two other infected pigs. The current methodology can be used for the currently circulating Eurasian ASFVs and also adapted to other ASFV strains and genotypes. Comprehensive deep sequencing is critical for following ASFV molecular evolution, especially for identification of modifications that affect virus virulence.

(1) Background: The prediction of cervical lesions evolution is a challenge for clinicians. The prospective study aimed to determine and compare the predictive accuracy of cytology, HPV genotyping, and p16/Ki67 dual staining alone or in combination with personal risk factors for the prediction of progression, regression or persistence of cervical lesions in human papillomavirus (HPV)-infected patients; (2) Methods: This prospective study included HPV-positive patients with or without cervical lesions that underwent follow-up. Descriptive statistics and sensitivity analysis for individual or combined index tests were used for data analysis; (3) Results: The highest predictive performance for the progression of cervical lesions was achieved by a model that comprised a Pap smear suggestive of high-grade squamous intraepithelial lesion (HSIL), the presence of 16/18 HPV strains, a positive p16/Ki67 dual staining result along with the presence of at least 3 clinical risk factors, which had a sensitivity (Se) of 74.42%, a specificity of 97.92%, an area under the receiver operating curve (AUC) of 0.961, and an accuracy of 90.65%. The prediction of cervical lesions regression or persistence was modest; (4) Conclusions: Multiple testing or new biomarkers should be used to improve HPV-positive patient surveillance, especially for cervical lesion regression or persistence prediction.

Background: Obesity and its attendant conditions have become major health problems worldwide and is currently ranked as the fifth most common leading cause of death globally. Complex environmental and genetic factors are the cause of the current obesity epidemic. Diet, lifestyle, chemical exposures, and other confounding factors are difficult to manage in humans. The mice model is helpful in researching genetics BW gain because genetic and environmental risk factors can be controlled in mice. Studies in mouse strains with various genetic backgrounds and established genetic structures provide unparalleled opportunities to find and analyze trait-related genomic loci. In this study, we used the Collaborative Cross (CC), a large panel of recombinant inbred mouse strains, to present a predictive study using CC mice SMAD4 knockout profiles to understand and effectively identify predisposition to body weight gain. Materials and Methods: Male C57Bl / 6J Smad4+/- mice were mated with female mice from 10 different CC lines to create F1 mice (Smad4+/- x CC). Body weight (BW) was measured weekly until week 16, then monthly until the end (week 48). The heritability H2 of the assessed traits was estimated and presented. Comparative analysis of various machine learning algorithms for predicting the BW changes and genotype of mice was conducted. Results and conclusions: Our data showed that the body weight records of F1 mice with different CC lines differed between wildtype and mutant Smad4 mice during the experiment. Genetic background affects weight gain and some lines gained more weight in the presence of Smad4 knockout, while others gained less, but in general, the mutation caused overweight mice, except for a few lines. In both control and mutant groups, female %BW had a higher heritability H2 value than males. Additionally, both sexes with wildtype genotypes showed higher heritability values than the mutant group. Logistic Regression provides the most accurate mouse genotype predictions using machine learning. We plan to validate the proposed method on more CC lines and mice per line to expand machine learning for BW prediction.

This study aimed to evaluate the hazards posed by foodborne bacteria of the Listeria genus by analyzing prevalence, diversity and virulence of Listeria spp. in food and food manufacturing plants. Seventy five isolates obtained from the routine analysis of 653 samples by three diagnostic laboratories in Northern Italy were genotipically differentiated by Repetitive Extragenic Palindrome (rep) PCR with the GTG5 primer, identified by sequencing the 16S rRNA gene and examined by specific PCR tests for the presence of L. monocytogenes virulence determinants occasionally found to occur in other species of the genus. The identity of the amplification products was confirmed by sequencing. Fifty seven isolates were identified as L. innocua, 12 as L. monocytogenes, 5 as L. welshimeri and one as L. seeligeri. All L. monocytogenes isolates belonged to the serotype 1/2a and were predicted to be virulent for the presence of the inlJ internalin gene. Potentially virulent strains of L. innocua, L. seeligeri and L. welshimeri, carrying the L. monocytogenes inlA gene and/or hly gene, were identified, and most isolates were found to possess the toxin-antitoxin system mazEF for efficient adaptation to heat shock. Results indicated the need to reinforce food contamination prevention measures against all Listeria species by efficiently defining their environmental distribution.

Hepatitis-C is one of the most common viral diseases caused by hepatitis C virus (HCV). It is responsible for millions of deaths each year in the developing world. The common dissemination paths of HCV include the use of contaminated water and transfusion of infected blood. Control of this virus has become a challenge for scientists and health professionals due to its versatility and adaptability in different host environments. Along with other problems, lack of efficient diagnosis, quantification and genotyping of viral strains are the major hindrances in a management of this notorious epidemic. The knowledge of HCV genotype and an amount of virus in patient’s blood are pre-requisites to determine the duration and method of treatment. In this review, we discuss the implications of HCV molecular diagnostic methods and their clinical applications. We conclude that while, several commercial and home-brewed methods are available for this purpose, and there is a visible vacuum for cost effective, robust, sensitive assays that can detect multiple viral genotypes in a single reaction. We are of the view that the level of sensitivity offered by Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) technique is unequivocal as compared to other techniques. Therefore, researchers may explore further possibilities using this technique in the management of HCV.

(1) Background: Transcription factors (TFs) are main regulators of eukaryotic gene expression. The cooperative binding of at least two TFs to genomic DNA is the widespread mechanism of transcription regulation. Massive analysis of co-occurrence of overrepresented pairs of motifs (composite elements, CEs) for different target TFs studied in ChIP-seq experiments can clarify the mechanisms of TF cooperation. (2) Methods: We focused on homotypic CEs representing the same motif models and considered only CEs with spacers. We improved the capability of the Motifs Co-Occurrence Tool (MCOT) to predict asymmetric homotypic CEs in which one of par-ticipating motifs has higher conservation than the other. We categorized the target TFs from the data of M. musculus ChIP-seq and A. thaliana ChIP-seq/DAP-seq according to the structure of DNA-binding domains (DBDs) into classes. (3) Results: For all TF classes the predominance of asymmetric CEs over both symmetric and those with no enrichment in both directions was re-vealed. Target TFs from classes Basic helix-loop-helix factors (bHLH) and Basic leucine zipper factors (bZIP) showed the highest fractions of datasets with asymmetric CEs. We showed that pioneer TFs, despite their DBD types, have a higher significance of asymmetry within homotyp-ic CEs compared to other TFs. (4) Conclusion: Asymmetry within homotypic CEs is a promising new feature decrypting the mechanisms of gene transcription regulation.

Over the last several years, large-scale cancer genomics studies involving multi region, multi-sample sequencing indicate that most or at least many cancer patients may have one or more “clonal" mutations in their tumors. Clonal mutations are those that are present in all of a patient’s cancer cells. They can be identified via multiregion, multisample biopsies - or circulating tumor cells/cell-free DNA. Achilles Therapeutics is currently the only company targeting patient-specific, clonal mutations. They have opted to utilize an immunotherapy approach. However, I recently devised another approach for exploiting clonal mutations called “Oncolytic Vector Replication Contingent on Omnipresent Mutation Engagement” (OVERCOME). It is based on the identification of patient-specific, clonal mutations and targeting them using a bioengineered facultative intracellular bacterium. It would be initially non-replicating, but transiently regain the ability to replicate (and also transiently become hyper-virulent) upon mutation detection via molecular switches.

Indiana Vesiculovirus (IVV; formerly as Vesicular stomatitis virus and Vesicular stomatitis Indiana virus) causes a disease in livestock that is very similar to the foot and mouth disease thereby an outbreak may lead to significant economic loss. Long-read sequencing (LRS) -based approaches revealed a hidden complexity of the transcriptomes in several viruses already. This technique was utilized already for the sequencing of the IVV genome, but our study is the first for the application of this technique for the profiling of IVV transcriptome. Since LRS is able to sequence full-length RNA molecules, and thereby providing more accurate annotation of the transcriptomes than the traditional short-read sequencing methods. The objectives of this study were to assemble the complete transcriptome of using nanopore sequencing, to ascertain cell-type specificity and dynamics of viral gene expression and to evaluate host gene expression changes induced by the viral infection. We carried out a time-course analysis of IVV gene expression in human glioblastoma and primate fibroblast cell lines using a nanopore-based LRS approach and applied both amplified and direct cDNA sequencing, as well as cap-selection for a fraction of samples. Our investigations revealed that, although the IVV genome is simple, it generates a relative complex transcriptomic architecture. In this study, we also demonstrated that IVV transcripts vary in structure and exhibit differential gene expression patterns in the two examined cell types.

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell Acute Lymphoblastic Leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.

Perfluorinated compounds (PFCs) are used in the manufacturing process of the semiconductor and display industries, and the need for emission reduction is growing as a greenhouse gas with a very large global warming potential. The decomposition characteristics of etch type and water film (WF) type plasma-wet scrubbers were investigated. The PFCs used in the study were CF4, SF6, NF3, CHF3, C2F6, C3F8, and C4F8, and the destruction removal efficiency (DRE) and by-product gas generation rate according to the changes in the parameters (total flow rate and power) of the plasma-wet scrubber were confirmed. When the total flow rate was 100 L/min and the measured maximum power (11 kW), the reduction efficiency of CF4 in the etch type was 95.60 % and the DRE of other PFCs was 99.99 %. And, in the WF type, the DRE of CF4 was 90.06 %, that of SF6 was 96.44 %, and that of other PFCs was 99.99 %. When the total flow rate was 300 L/min and 11 kW, the DRE of SF6 in the etch type was 99 %, and the DRE of NF3, CHF3, C2F6, C3F8, and C4F8 were 99.80 %, 95.34 %, 85.38 %, 88.49 %, and 98.22 %, respectively. And, in the WF type, the DRE of SF6 was 94.39 %, and the DRE of NF3, CHF3, C2F6, C3F8, and C4F8 were 99.80 %, 95.34 %, 85.38 %, 88.49 %, and 98.22 %, respectively. The by-product gas generation rate was significantly lower in the WF type.

As β-glucosidases represent the major bottleneck for industrial degradation of plant biomass, great efforts are being devoted both to discover novel and robust versions of these enzymes, as well as to develop efficient and inexpensive ways to produce them. In this work, raw glycerol from chemical production of biodiesel was tested as carbon source for the fungus Talaromyces amestolkiae with the aim of producing enzyme cocktails rich in this activity. Approximately 11 U/mL β-glucosidase were detected in these cultures, constituting the major cellulolytic activity. Proteomic analysis revealed BGL-3 as the most abundant protein and the main β-glucosidase. This enzyme crude was successfully used to supplement a basal commercial cellulolytic cocktail (Cellu-clast 1.5L) for saccharification of pretreated wheat straw, corroborating that even hardly exploitable industrial wastes, such as glycerol, can be used as secondary raw materials to produce valuable enzymatic preparations in a framework of circular economy

In recent years, demand for consumption of marine foods, and especially fish, has substantially increased worldwide. The majority of collagen available is sourced from mammalian-derived products. Although fish derived gelatine is a viable alternative to mammalian sourced gelatine, there are some challenges related to the use of fish gelatine including odour, colour, gelling and film forming properties as well as consistency in gelatine amino acid composition. Chemicals used for pre-treatment, as well as extraction conditions such as temperature and time, can influence the length of polypeptide chains that result and the functional properties of the gelatine. Compared to mammalian sources, gelatines derived from fish show notable differences in physical and chemical properties, and great care should be paid to optimization of the production process in order to obtain a product with the best properties for intended applications. The focus of this review is to explore the feasibility of producing gelatine sourced from marine processing by-products using different pre-treatment and extraction strategies with the aim of improving the techno-functional properties of the final product and improving the clean-label status of gelatines. The bioactivities of gelatine hydrolysates are also discussed.

In recent years, demand for consumption of marine foods, and especially fish, has substantially increased worldwide. The majority of collagen available is sourced from mammalian-derived products. Although fish derived gelatine is a viable alternative to mammalian sourced gelatine, there are some challenges related to the use of fish gelatine including odour, colour, gelling and film forming properties as well as consistency in gelatine amino acid composition. Chemicals used for pre-treatment, as well as extraction conditions such as temperature and time, can influence the length of polypeptide chains that result and the functional properties of the gelatine. Compared to mammalian sources, gelatines derived from fish show notable differences in physical and chemical properties, and great care should be paid to optimization of the production process in order to obtain a product with the best properties for intended applications. The focus of this review is to explore the feasibility of producing gelatine sourced from marine processing by-products using different pre-treatment and extraction strategies with the aim of improving the techno-functional properties of the final product and improving the clean-label status of gelatines. The bioactivities of gelatine hydrolysates are also discussed.

Understanding microbial composition in upper respiratory infections (URIs) is critical for effective diagnosis and treatment. Precision Metagenomic next-generation sequencing p(mNGS) can provide a comprehensive yet clinically relevant profile of respiratory infection. The hybridization capture-based targeted sequencing generated a precision metagenomics profile of 29 patients with acute URIs. Nasopharyngeal samples were collected from the subjects suspected of respiratory infection, and p(mNGS) was performed using the Illumina®/IDbyDNA Respiratory Pathogen ID/AMR Panel (RPIP). The dataset obtained from the mNGS analysis contains a wealth of information on the composition of acute URI microbiota, including the relative abundance of known pathogens and potential clinical implications. The dataset represents a valuable resource for future research endeavors in respiratory medicine, infectious disease epidemiology, and therapeutic interventions. In addition, the dataset offers significant potential for reuse and integration with other omics datasets. The comprehensive nature of the mNGS data allows the exploration of associations between the respiratory microbiota and host factors such as clinical outcomes, immune responses, or genetic predisposition. Combining this dataset with other relevant datasets, such as transcriptomics or metabolomics, could provide a deeper understanding of the complex interactions between the microbiota and the host in acute URIs.

We performed a comprehensive analysis of angiosarcoma (AS) genomic biomarkers and their associations with the site of origin. We aimed to describe the genomic landscape of AS in a cohort of 143 cases of AS profiled by Caris Life Sciences. Data of Next Generation Sequencing (NGS) with a 592 gene panel was available for the entire cohort. Fifty-three cases had data of Whole Exome Sequencing (WES) which we used to study the microenvironment phenotype. Immuno-therapy (IO) response biomarkers: Tumor Mutation Burden (TMB), Microsatellite Instability (MSI) and PD-L1 status were included. IO-response markers were present in 36.4% of the cohort and in 65% of head and neck AS (H/N-AS) (p<0.0001). H/N-AS cases had predominantly muta-tions in TP53 (50.0%, p=0.0004), POT1 (40.5%, p<0.0001) and ARID1A (33.3%, p=0.5875). In breast AS, leading alterations were MYC amplification (63.3%, p<0.0001), HRAS (16.1%, p=0.0377), and PI3KCA (16.1%, p=0.2352). A microenvironment with a high immune signature, associated with better response to IO, was present in 13% of the cases. This signature was evenly distributed among different primary sites. We found that the molecular biology for AS varies significantly according to the primary site. Our findings can facilitate the design and optimiza-tion of therapeutic strategies for AS to overcome resistance to IO and targeted therapies.

In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencings with our earlier data generated by other LRS and short-read sequencing techniques. As a result, we identified a number of novel genes, transcripts, and transcript isoforms, including splice and length variants, and also confirmed earlier annotated RNA molecules. One of the major findings of this study is the discovery of a large number of 5’-truncated putative mRNAs embedded into larger host mRNAs. A large fraction of these RNA molecules contain in-frame ORFs, which may encode N-terminally truncated polypeptides. These study demonstrates that the PRV transcriptome is much more complex than previously appreciated.

RaTG13 (a bat derived SARS-like CoV) is the closest relative sequence of SARS-CoV-2 reported till date. The sample from which RaTG13 was sequenced was a bat fecal swab collected in 2013 from Tongguan, Mojiang, Yunnan province, China. The Illumina based sequence of RaTG13, MN996532.1, was deposited on 27^th Jan 2020 and the raw data (Illumina), https://www.ncbi.nlm.nih.gov/sra/SRX7724752[accn]. There are discrepancies in dates about when the metagenome sequencing of RaTG13 sample was done (2018 or 2020), both stated by the same corresponding author. Comparison of the RNA Seq data of RaTG13 fecal swab to the corresponding data from the bat fecal swabs deposited by the same working group using the same methods indicated that the RaTG13 raw data seemed to be different in various aspects. The fecal swab sample showed abnormally less read of bacterial reads in the swab was exceptionally low, i.e. 0.7%, compared to the 20-90% abundance in other fecal swabs from bats processed by similar methods. Also, another raw data in the form of amplicon sequences was deposited in May 2020; however, the dates mentioned on the files of the sequenced amplicons were older (2017, 2018). The genome assembly of RaTG13 could not be done de-novo and the average coverage of the genome ~8%. Also, literature indicates that RaTG13 RBD cannot bind to Rhinolophus ACE-2 receptors. Collectively, the anomalies in the raw data of RaTG13 and other issues pose an important question about the overall authenticity of the RaTG13 genome sequence.

To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called “-omics”, have made genetic sequencing readily available across fields in biology from applications in non-traditional study organisms to precision medicine. Thus, understanding these tools is critical for any biologist, especially those early in their career. This comprehensive review discusses the chronological development of different sequencing methods, the bioinformatics steps to analyzing this data, and social and ethical issues raised by these techniques that must be discussed and evaluated.

Klebsiella pneumoniae, a major cause of both hospital and community-acquired infections, is listed by the World Health Organization as a critical priority antibiotic- resistant bacterial pathogen. With the appearance of sequencing techniques such as Next-generation Sequencing (NGS), there is the possibility to obtain the whole genome of the bacteria, getting to know all antimicrobial resistance determinants. The purpose of this study has been to apply this new technology to clinical microbiology, in order to characterize the resistome present in carbapenem-resistant K.pneumoniae strains isolated in a tertiary hospital in Valencia, Spain. A total of 234 isolates were prepared for whole-genome sequencing with Ilumina MiSeq, and sequences were later studied for antimicrobial resistance genes, sequence-typing and plasmids. Sequence-typing showed four major circulating clones in our hospital settings: ST11, ST307, ST101 and ST147, carrying different plasmids and different resistance determinants such as OXA-48 and NDM-1 carbapenemase. Application of new technologies such as whole-genome sequencing in clinical microbiology gives advantages when it comes to rapid therapy adjustment, consequently improving the patient’s clinical outcomes.

The decomposition of straw is a dynamic process, which is reflected in the decomposing microbial consortia, however, this process is poorly understood. Here we performed an experiment on the gradual colonization of oat straw by the soil microbial community. The results showed that soil respiration and bacterial diversity were negatively correlated – while the first decreased, the latter increased. In accordance with the dynamics of diversity and respiration, succession was divided into early, middle, and late decomposition phases. Analysis of 16S rRNA and ITS2 amplicon sequencing data revealed three jointly changing groups of phylotypes, corresponding with distinguished phases of decomposition. The presence of cellulolytic members of Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota for bacteria and Ascomycota for fungi had been detected since the early phase, but most of the initial phylotypes were gone by the end of the phase. The second phase marked the functional core with a constant set of other phylotypes from these phyla, persisting in the community. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major members of this consortium had GH genes, connected to cellulose and chitin degradation. The appearance of non-cellulolytic members from Bdellovibrio, Myxococcota, Chloroflexi, and Crenarchaeota characterized the last phase of the mature community.

Among all economically important plant species in the world, grapevine (Vitis vinifera L.) is the most cultivated fruit plant. It has a significant impact on the economies of many countries through wine and fresh and dried fruit production. In recent years, the grape and wine industry has been facing outbreaks of known and emerging viral diseases across the world. Although high-throughput sequencing (HTS) has been used extensively in grapevine virology, the application and potential of third-generation sequencing have not been explored in understanding grapevine viruses and their impact on the grapevine. Nanopore sequencing, a third-generation technology, can be used for direct sequencing of both RNA and DNA with minimal infrastructure. Compared to other HTS methods, the MinION nanopore platform is faster and more cost-effective and allows for long-read sequencing. Due to the size of the MinION device, it can be easily carried for field viral disease surveillance. This review article discusses grapevine viruses and their diagnostic methods, the principle of nanopore sequencing technology and its application in grapevine virus detection, virus–plant interactions, as well as the characterization of viral RNA modifications.

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME and an in house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 and R9.2 were compared.

MicroRNAs (miRNAs) are crucial regulatory RNAs, originated from hairpin precursors. For the past decade, researchers are focusing extensively on miRNA profiles in various plants. However studies on precursor miRNAs (pre-miRNAs) global profiling stay static even in model plants. Here, for the first time in a non-model plant, Abelmoschus esculentus with negligible genome information, we are reporting the global profiling to characterize the miRNAs and their associated pre-miRNAs by applying next generation sequencing approach. Preliminarily we performed sRNA (small RNA) sequencing with five biological replicates of leaf samples to attain 207,285,863 reads and data analysis using miRPlant keyed out 128 known and 845 novel miRNA candidates. With the objective to seize their associated hairpin precursors, we accomplished pre-miRNA sequencing to attain 83,269,844 reads. The paired end reads are merged, adaptor trimmed and the resulting 40-241 nt (nucleotide) sequences were picked out for analysis by using perl scripts from miRGrep tool and in-house built shell script for Minimum Fold Energy Index (MFEI) calculation. Applying stringent criteria of dicer cleavage pattern and perfect stem loop structure revealed precursors for 57 known miRNAs of 15 families and 18 novel miRNAs. Quantitative Real Time (qRT) PCR was performed to determine the expression of selected miRNAs.

Applying a procedure similar to that of E.S. Bring, by using a 4^th degree Tschirnhaus transformation, it was possible to transform the Bring-Jerrard normal quintic (BJQ) equation into a De Moivre form (DMQ), so that it could be solved by radicals. The general solution by radicals of the De Moivre equations of any degree is presented. By the same procedure the BJSx (normal sextic) equation was taken to another one without the 2^nd, 4^th and 6^th terms which was transformed into a cubic (solvable) equation. By applying a 6^th degree Tschirnhaus transformation to the BJSp (normal septic) equation its binormal (without the 2^nd, 3^rd, 4^th and 5^th terms) form was obtained.

Applying a procedure similar to that of E.S. Bring, by using a 4^th degree Tschirnhaus transformation, it was possible to transform the Bring-Jerrard normal quintic (BJQ) equation into a De Moivre form (DMQ), so that it could be solved by radicals. The general solution by radicals of the De Moivre equations of any degree is presented. By the same procedure the BJSx (normal sextic) equation was taken to another one without the 2^nd, 4^th and 6^th terms which was transformed into a cubic (solvable) equation. By applying a 6^th degree Tschirnhaus transformation to the BJSp (normal septic) equation its binormal (without the 2^nd, 3^rd, 4^th and 5^th terms) form was obtained.

Applying a procedure similar to that of E.S. Bring, by using a 4^th degree Tschirnhaus transformation, it was possible to transform the Bring-Jerrard normal quintic (BJQ) equation into a De Moivre form (DMQ), so that it could be solved by radicals. The general solution by radicals of the De Moivre equations of any degree is presented. By the same procedure the BJSx (normal sextic) equation was taken to another one without the 2^nd, 4^th and 6^th terms which was transformed into a cubic (solvable) equation. By applying a 6^th degree Tschirnhaus transformation to the BJSp (normal septic) equation its binormal (without the 2^nd, 3^rd, 4^th and 5^th terms) form was obtained.

Applying a procedure similar to that of E.S. Bring, by using a 4^th degree Tschirnhaus transformation, it was possible to transform the Bring-Jerrard normal quintic (BJQ) equation into a De Moivre form (DMQ), so that it could be solved by radicals. The general solution by radicals of the De Moivre equations of any degree is presented. By the same procedure the BJSx (normal sextic) equation was taken to another one without the 2^nd, 4^th and 6^th terms which was transformed into a cubic (solvable) equation. By applying a 6^th degree Tschirnhaus transformation to the BJSp (normal septic) equation its Bring-Jerrard binormal (without the 2^nd, 3^rd, 4^th and 5^th terms) form was obtained.

The skin is the largest organ in the human body and serves multiple functions such as barrier protection and thermoregulation. The maintenance of its integrity and healthy structure is of paramount importance. Accordingly, technological advances in cosmetic sciences have been directed towards optimizing these factors. Plant-derived ingredients have been explored for their bioactivity profiles and sustainable sources. Grape by-products carry a group of bioactive molecules that display important biological activities. Nonetheless, many of these molecules (e.g., phenolic compounds) are unstable and susceptible to degradation. So, its encapsulation using nano/microsystems (i.e. liposomes) has been explored as a promising solution. In this work, two grape seed extracts were obtained, one from a single grape variety (GSE-Ov), and another from a mix of five grape varieties (GSE-Sv). These extracts were analysed for their antioxidant and antimicrobial activities, as well as for their chemical composition and molecular structure. The extract that showed the most promising properties was the GSE-Ov with a DPPH IC₅₀ of 0.079 mg.mL^-1. This extract was encapsulated in soy lecithin liposomes coated with pectin, with an encapsulation efficiency of 88.8%. These showed an in vitro release of polyphenols of 59.4% during 24 h. The particles displayed a zeta potential of -20.3 mV, and an average diameter of 13.6 µm. Loaded liposomes proved to be safe under 5 and 2.5 mg.mL^-1, in HaCaT and HDF cell models, respectively. Additionally, they demonstrated anti-inflammatory activity against IL-1α when tested at 2 mg.mL^-1. This work enabled the valorization of a by-product from the wine industry, by using natural extracts in skincare products.

China faces a persistent deficiency in feed protein resources. Enhancing the utilization efficiency of indigenous feed protein resources emerges as a viable strategy to alleviate the current deficit in protein feed supply. Corn gluten meal (CGM), characterized by high proportion of crude protein and glutamine, is predominantly employed in animal feed. Nonetheless, the water-insolubility of CGM protein hampers its protein bioavailability when utilized as feed material. This study aimed to augment protein bioavailability, liberate glutamine peptides from CGM, and produce gluta-mine-enriched CGM fermented feed. We executed a co-fermentation protocol using Bacillus subtilis A5, Lactobacillus 02002, and acid protease to generate the CGM fermented feed. Subsequent in vivo experiment with broilers were conducted to assess the efficacy of the fermented product. Findings revealed that the soluble protein, glutamine, small peptides, and lactic acid contents in the fer-mented feed increased by 69.1%, 700%, 47.6%, and 125.9%, respectively. Incorporating CGM fermented feed into the diet markedly enhanced the growth performance and intestinal health of broilers, positively modulated the cecal microbiota structure, and augmented the population of beneficial bacteria, specifically Lactobacillus. These results furnish both experimental and theoretical foundations for deploying CGM fermented feed as an alternative protein feed resource.

Development and redevelopment are important drivers of tree removal and canopy loss in urban landscapes. Local ordinances are often used to curtail tree removal, but punitive regulations alone may not be enough to reduce urban tree canopy loss in land development. In Florida (US), efforts to balance trees and development have so far focused on fees and fines, but with a recent backlash against tree regulations and the fast pace of urban growth, we explored the possible role of incentives in urban tree policies. We interviewed 20 land developers across Florida to understand their perspectives on current barriers and potential incentives for tree preservation and planting. We collected data from developers, whose perspectives on tree preservation are often unknown or overlooked, despite their significant role in tree planting, removal, and retention in and around cities. Our results show that major barriers to tree preservation and planting include requirements to grade sites for stormwater management, site constraints, and monetary costs. Most developers did not know of any existing incentives beyond intrinsic motivations but said that financial incentives would be most appealing to them. Top incentive suggestions include increasing building density, reducing impact fees and tax liability, and changing tree mitigation policies. Another promising finding is that developers are willing to work with regulators to find solutions that benefit both parties. Future research should consider evaluating the level of support and viability of different incentives by gathering feedback from policymakers, land developers, and the public.

One main objective of this study was to increase the utilization of the raw material in the rose (Rosa damascena Mill.) essential oil industry by application of membrane technologies. A new ultrafiltration-based process for green recovery of polyphenols from distilled (de-aromatized) rose petals, the primary by-product in essential oil production, was created. The process includes enzyme-assisted extraction and subsequent membrane separation for partial concentration. Following a green membrane technology strategy, the newly developed process proposes an environmentally-friendly alternative to the conventional processing, comprising organic solvent ex-traction and adsorber resin purification. The results showed that the permeate flux decreased with volume reduction ratio’s rise and increased with the transmembrane pressure and feed flow rate rises. At the beginning of the process the highest flux was with UF1-PAN membrane, but at the end of the process with UF10-PAN membrane. Total polyphenols of the retentates in-creased by 27-39% and 26-67% during ultrafiltration with UF1-PAN and UF10-PAN membrane, respectively, with the highest value obtained for UF10-PAN membrane at VRR 6. The highest concentration factor and rejection of total solids, total polyphenols, redox-active antioxidants and radical scavenging antioxidants were obtained at VRR 6 with UF10-PAN membrane. This membrane and concentration level at transmembrane pressure of 0.4 MPa and feed flow rate of 330 dm3/h are recommended to be used for application of ultrafiltration of rose-petals by-product for potential use in the food industry.

In an increasingly resource-constrained era, the utilization approach of waste and by-products from grain processing, is attractive widely, considering both nutritive value and economic aspects and move towards more sustainable food systems. Following the fundamentals of a circular economy, the need of the hour lies in its effective utilization as a grain waste and by-products conversion into value-added products in food industry. The aim of this study is twofold: 1. Understanding the progress of grain waste and by-products to valorization in human nutrition, using bibliometrics; different literature databases namely Google Scholar, Web of Science and Elsevier Scopus have been evaluated for their merits and values; 2. Exploration of knowledge-based strategies, by reviewing the literature concerning the possible use of grain waste and by-products for food processing industry, reducing burden on virgin raw materials. The review allowed to unlock the latest-advances of upcycling side streams and waste from grain processing industry.

The sample data are used from Shaanxi Statistical Yearbook （1999-2018）and poverty population in X County of Southern Shaanxi in 2018. By using Eviews and Excel, this report focuses on analyzing the relationship between education investment and economic growth, education for poverty population, per capita income and poverty caused by education in X county, which can explain reasons for the phenomenon of poverty caused by education. The countermeasures are proposed to solve the phenomenon of poverty caused by education, including establishing scientific education view, correctly understanding education investment and benefit, and improving the aid mechanism for poor students to realize the effective connect among poverty alleviation through education, accurate poverty alleviation and rural revitalization.

There have been several developments in the field of nanopore biosensor development and sequencing applications that address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making these platforms a mainstay in contemporary research labs. Equipped with the ability to provide long and short-read sequencing information with quick turn-around times and simple sample preparation, nanopore sequencers are quickly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We conclude with examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.

Clinical metagenomics (CMg), referred to as the application of next-generation sequencing (NGS) to clinical samples, is a promising tool for the diagnosis of hospital-acquired pneumonia (HAP). Indeed, CMg allows identifying pathogens and antibiotic resistance genes (ARGs), thereby providing the information required for the optimization of the antibiotic regimen. Hence, provided that CMg would be faster than conventional culture, the probabilistic regimen used in HAP could be tailored faster, which should lead to an expected decrease of mortality and morbidity. While the inference of the antibiotic susceptibility testing from metagenomic or even genomic data is challenging, a limited number of antibiotics are used in the probabilistic regimen of HAP (namely beta-lactams, aminoglycosides, fluoroquinolones, glycopeptides and oxazolidinones). Accordingly in the perspective of applying CMg to the early diagnostic of HAP, we aimed at reviewing the performances of whole genomic sequencing (WGS) of the main HAP-causing bacteria (Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia and Staphylococcus aureus) for the prediction of susceptibility to the antibiotic families advocated in the probabilistic regimen of HAP.

Neurofibromatosis type1 (NF1) is an autosomal dominant disorder caused by mutations in the NF1gene. Although congenital pseudarthrosis of the tibia (CPT) has frequently been associated with NF1, the underlying molecular mechanism of CPT in these NF1 patients is yet ill-understood. The aim of the present study was to detect NF1 mutations from genomic DNA and to harbor variants associated with CPT in NF1 patients. Whole-exome sequencing was first carried out with samples from two patients with CPT in one NF1 family, and a novel mutation c.2324A>G (p.E775G) in NF1 gene was identified. Additionally, a missense variant c.455C>T (p.P152L) in BCOR gene completely co-segregated with the CPT phenotype within this family. Subsequently, NF1 and NF2 genes in four other unrelated patients with both NF1 and CPT were screened using targeted sequencing. Four mutations in NF1 gene, including two known mutations (c.2288T>C/p.L763P, c.574 C>T/p.R192*) and two novel mutations (c.768delT/p.F256Lfs*25, c.2229_2230delTG/ p.V744Qfs*23) were detected. Further study confirmed that CPT was present in NF1 families, and NF1 mutations were closely associated with these complex phenotypes. Moreover, the data from the current study indicated that male gender might be a susceptibility factor for CPT in NF1. Therefore, we speculated that BCOR variants might be related to CPT phenotype among male NF1 patients.

In terms of sustainability, there is a pressing need to evaluate agricultural and forestry leafy biomass that has no current economic value or may pose a threat to the environment. In this aspect, leafy biomass, which represents around 5% of the total tree, can be used for purposes that would be more profitable and ecofriendly. To this end, biorefinery of leafy biomass in the way of extracting valuable health compounds such as phenolics would ensure a valuable societal health ingredient besides alleviating waste disposal problem. However, during the biorefinery process, the primary challenges start with ensuring the feedstock to produce phenol rich leaves extract followed by their isolation and commercialization of this leaves extract. This current review aims to detail the types of biomasses, biorefinery approach of leafy biomass towards the phenolic extraction, leaves commercialization followed by the marketing strategy of the application of phenol rich leaves extract. The outcome of this overview will serve researchers and relevant industries in understanding the process for feedstock collection and the suitable sectors to apply leafy biomass derived healthy compounds.

Cashew (Anacardium occidentale) processing generates a by-product (CB) with potential for health benefits and could be a favorable ingredient to be added to a probiotic food matrix. This study aimed to assess the functional attributes of CB in fermented milk with a probiotic and a starter culture using in vitro- gastrointestinal conditions. Using a standardized fermentability assay, two strains more adapted to the dehydrated CB were chosen and applied in: Test Formulation (TF, with CB) and Control Formulation (CF, without CB). TF and CF were fermented by the probiotic strain Lacticaseibacillus paracasei subsp. paracasei F19® and the starter Streptococcus thermophilus ST-M6®. During a 28-day refrigerated (6-8 °C) shelf-life study, both strains used in CF and TF were resistant and maintained a population above 8.0 log CFU/mL in the fermented milk. TF had significant increase in total phenolic compounds and greater antioxidant potential during shelf life, along with improved survival of F19® after in vitro-simulated gastrointestinal conditions. The cashew by-product revealed to be promising as a substrate for the strains studied and the presence of CB increased the content of phenolics and antioxidant activity during storage, as well as the gastric resistance to the probiotic., leading to a promising healthy product.

The aim of this study was to assess precipitation (P) by analyzing data from in situ stations compared with those from solely remote sensing products CHIRP and CMORPH, with a reference station in the city. The evapotranspiration (ET) was analyzed directly using SSEBop. The region chosen for this study was the Metropolitan Area of Belem (MAB), close to the estuary of the Amazon River and the mouth of the Tocantins River. Belem is the rainiest state capital of Brazil, which causes a myriad of problems for the local population. The monthly best fit is shown here. In this study, we analyzed P and ET from local stations and compared them with those from satellite products. The main metrics RMSE, NRMSE, MBE, R2, Slope, and NS were used. For the reference station, the automatic and conventional CHIRP and CMORPH results, in mm/month, were as follows: automatic CHIRP: RMSE = 93,3, NRMSE = 0.32, MBE = −33,54, R2 = 0.7048, Slope = 0.945, NS = 0.5668; CMORPH: RMSE = 195,93, NRMSE = 0.37, MBE = −52,86, R2 = 0.6731, Slope = 0.93, NS = 0.4344; conventional station CHIRP: RMSE = 94.87, NRMSE = 0.32, MBE = −33.54, R2 = 0.7048, Slope = 0.945, NS = 0.5668; CMORPH: RMSE = 105.58, NRMSE = 0.38, MBE = −59.46 R2 = 0.7728, Slope = 1.007, NS = 0.4308. This was compared with the pixel and in situ station data. The ET ranges, on average, between 83 mm/month in the Amazonian summer and 112 mm/month in the Amazonian winter. This work concludes that, although CMORPH has a coarser resolution of 0.25° compared to CHIP’s 0.05° for MAB at a monthly resolution, the remote sensing products were reliable. SSEBop also showed reliable performance. For analyses of the consistency of precipitation time series, these products could provide more accurate information.

Augmented and Virtual Reality have been experiencing a rapidly growth in recent years, but there is not still a deep knowledge on their capabilities and where they could be explored. In that sense, this paper presents a study on the accuracy and repeatability of the Microsoft's HoloLens 2 (Augmented Reality device) and HTC Vive (Virtual Reality device) using an OptiTrack system as ground truth. For the HoloLens 2, the method used was hand tracking, while in HTC Vive, the object tracked was the system's hand controller. A series of tests in different scenarios and situations were performed to explore what could influence the measures. The HTC Vive obtained results in the millimetre scale, while the HoloLens 2 revealed not so accurate measures (around 2 centimetres). Although the difference can seem to be considerable, the fact that HoloLens 2 was tracking the user's hand and not an inherit controller made a huge impact. The results were considered a significant step for the on going project of developing a human-robot interface to program by demonstration an industrial robot using Extended Reality, which shows great potential to succeed based on this data.

Rural landscapes all over the world are subject to great transformations, first of all the continuous and slow depopulation of land and villages. It is a dramatic phenomenon that causes devastating consequences for environmental systems and for the tangible and intangible heritage of entire territories. The situation becomes more ambiguous when it comes to cultural landscapes, especially those internationally recognized as exceptional (i.e. inscribed on the UNESCO World Heritage List). In this case, the risk is to abandon agricultural production in favor of consumerist tourist economies, which can damage the territorial authenticity. In this paper we question the role of the landscape project in strengthening territorial resilience. In particular, a composite and interdependent action is proposed between landscape design and implementation of a multifunctional agriculture model, oriented towards teaching and tourism. To undertake this investigation, a master's thesis work on Landscape Architecture is examined, as an opportunity for a research-by-design method. The application case is the Italian UNESCO site of Vignale Monferrato, a depopulated rural village, characterized by abandoned land and buildings. The paper concludes by outlining replicability application scenarios for the proposed model.

In tracking-by-detection paradigm for multi-target tracking, target association is modeled as an optimization problem that is usually solved through network flow formulation. In this paper, we proposed combinatorial optimization formulation and used a bipartite graph matching for associating the targets in the consecutive frames. Usually, the target of interest is represented in a bounding box and track the whole box as a single entity. However, in the case of humans, the body goes through complex articulation and occlusion that severely deteriorate the tracking performance. To partially tackle the problem of occlusion, we argue that tracking the rigid body organ could lead to better tracking performance compared to the whole body tracking. Based on this assumption, we generated the target hypothesis of only the spatial locations of person’s heads in every frame. After the localization of head location, a constant velocity motion model is used for the temporal evolution of the targets in the visual scene. Qualitative results are evaluated on four challenging video surveillance dataset and promising results has been achieved.

Mill scale is the by-product of iron and steel industry. It can be recycled via sinter plant or solid as sinter feed materials. 85 to 90% of the constituent particles are more than 0.008 inches. The iron content is near around 70 %, with a very small amount of alkaline compounds and non-ferrous metals. Mill scale is polluted and contaminated with lubricants, oils and greases from the equipment. In this experiment for recovering of oil from mill scale, it is treated with three different methods. Then all methods were compared according to the ability of oil elimination and iron recovered. After washing and boiling with surfactants, large amount of polluted waste water becomes a problem for environment so this wastewater was utilized for making of Microbial Fuel Cells (MFCs), production of electricity in MFC depends on the biodegradation of organic materials, so different waste were added in wastewater for making MFC. The remaining of MFC was converted in bioethanol, biodiesel and biofertilizer. So this research is economical and environmentally friendly and fulfilled the important aspect of green environment with zero waste. It will be a mile stone in the research of metallurgy, environmental engineering, recycling technology and zero waste management.

For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, and mechanistic studies of virus infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses, and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes.

Legume plants enter symbiosis with soil nitrogen-fixing bacteria (rhizobia), thereby gaining access to the assimilable atmospheric nitrogen. This symbiosis is important for agriculture, thus, biofertilizers with effective strains of rhizobia are created for crop legumes to increase their yield and minimize the amounts of mineral fertilizers used. In this work, we sequenced and characterized the genome of Rhizobium leguminosarum bv. viciae strain RCAM1022, a component of the ‘Rhizotorfin’ biofertilizer produced in Russia and used for pea (Pisum sativum L.).

Objective Our objective was to observe the benefits and limitations of WES (Whole Exome Sequencing) in the prenatal setting, in the Romanian population. The scope was to observe the diagnostic yield in comparison to molecular karyotyping testing, which had negative results, as well as a case of consanguinity. Methods The first criteria was selecting pregnancies with abnormal ultrasound findings. These findings would not lead the medical team to a certain known syndrome. Second, we performed SNP-array, which tested negative in all cases, except for Case number 9 which had an abnormal result. The ulterior testing method was WES, using Massive Parallel Sequencing of the whole coding region of the human genome on Next Generation Sequencing Platform, NovaSeq 6000 (average coverage >100X, read length: 2x100bp). The Twist Human Core Exome kit RefSeq & Mitochondrial panel (Twist Bioscience) was used for the library preparation. Bioinformatic analysis was performed by direct comparison of the genome of the test sample with the human reference sequence (hg38). Results Our small cohort of 10 patients, resulted in a 50% diagnostic yield. After receiving the results whether a diagnose or a negative result, 2 couples chose to terminate the pregnancy, 5 were born affirmatively without symptoms, and are still monitored up to date. One of the pregnancies led to a stillbirth. We have also found 3 incidental findings that helped the multidisciplinary team better manage the patient as well as the members at risk. Conclusion In this article we present 10 cases which were tested through prenatal WES, showing the great diagnostic yield in comparison to SNP-array in our selected cases. As a closing remark, we wish to highlight the benefits of WES testing in prenatal cases. Further testing is needed to get a clearer picture of the prenatal diagnostic yield in the Romanian population.

The Arbas cashmere goat is a unique biological resource that plays a vital role in livestock husbandry in China. LCDM is a medium with special small molecules (consisting of human LIF, CHIR99021, (S)-(+)-dimethindene maleate, and minocycline hydrochloride) for generation pluripotent stem cells (PSCs) with bidirectional developmental potential in mice, humans, pigs, and bovines. However, there is no report on whether LCDM can support for generation of PSCs with the same ability in Arbas cashmere goats. In this study, we applied LCDM to generation goat induced PSCs (giPSCs) from goat fetal fibroblasts (GFFs) by reprogramming. The derived giPSCs exhibited stem cell morphology, expressing pluripotent markers, and could differentiate into three germ layers. Moreover, the giPSCs differentiated into the trophectoderm lineage by spontaneous and directed differentiation in vitro. The giPSCs contributed to embryonic and extraembryonic tissue in preimplantation blastocysts and postimplantation chimeric embryos. RNA-sequencing analysis showed that the giPSCs were very close to goat embryos at the blastocyst stage and giPSCs have similar properties to typical extended PSCs (EPSCs). The establishment of giPSCs with LCDM provides a new way to generate high quality of PSCs from domestic animals and lays the foundation for basic and applied research in biology and agriculture.

Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol – the RAPIDprep assay – with the aim to provide cause agnostic laboratory diagnosis of infection within 24 hours of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities and extraction kits using a single protocol without input nucleic acid quantification or quality assessment. Furthermore, we demonstrate the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift towards integration of modern genomic techniques to infectious disease investigations.

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities’ response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and CO1 amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using DNA Subway, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r>0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi:bacteria (F:B) proportions between different trails (p=2*10^-16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema, and Tremella. Chlorellales algae, and pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella, were associated with the cluster. There was functional redundancy in clusters that were differently composed, but shared similar ecological functions. These results implied a set of traits for post fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, pathogenicity and parasitism, antimicrobials, and N-metabolism.

High-quality chromosome-scale haplotype sequences— of diploid genomes, polyploid genomes and metagenomes — provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information that spans whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent methodological progress in these areas and discuss perspectives that could enable routine high-quality haplotype reconstruction in clinical and evolutionary studies.

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It also has been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler— SMARTdenovo, which is an SMS assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a fast assembler that did not require highly accurate raw reads for error correction, unlike other, contemporaneous SMS assemblers. It has performed well for evaluating congeneric assemblers and has been successful for a variety of assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015, and here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.

Kiwifruit vines are generally sensitive to waterlogging stress. So far, molecular responses of different kiwifruit genotypes for waterlogging stress are less well-explored. In this study, using RNA-sequencing, we examined transcriptional regulation in the roots of a waterlogging-tolerant genotype KR5 (Actinidia valvata), and a sensitive genotype ‘Hayward’ (Actinidia deliciosa) subjected to 0, 12, 24, and 72 h of waterlogging. Compared with 0 h, transcriptional adjustments of these two genotypes occurred as early as 12 h and became notably pronounced 72 h after waterlogging. Waterlogging stress for 72 h promoted the expression of genes involved in ethylene biosynthesis, sucrose and hexose transport, anaerobic fermentation, nitrate reduction, alanine accumulation, and reactive oxygen scavenging in both genotypes. The differential regulation of genes encoding 9-cis-epoxycarotenoid dioxygenase, phosphoglucomutase, alanine-glyoxylate transaminase, and other enzymes pointed to their diverse strategies upon waterlogging in these two genotypes. In addition, more sucrose and trehalose contents, as well as a higher activity of alcohol dehydrogenase and manganese superoxide dismutases were stimulated in KR5 roots after 72h of waterlogging than that in ‘Hayward’. Overall, our results provided more insights into the molecular basis of the waterlogging response in kiwifruit.

New challenges arise in the face of global climate change which impact every ecosystem on earth, including aquatic systems. This is evident in observations made in regard to the world’s oceans, which show trends of incremental changes in ocean surface temperatures, sea levels, and ocean acidity. These environmental shifts impact human resources such as fisheries and aquaculture. In addition, according to the World Bank, the increase in human population will also require more food and nutrient production, which include industries such as aquaculture. With this increasing demand in aquaculture and fisheries, we must develop efficient and productive methods to operate these industries. We can use genetic methods, specifically transcriptomic information to better understand the biology of our source of nutrition. With the advent of RNASeq techniques, we can provide a better understanding about growth and development, immune function and stress, and adaptations. The use of population genetics or (genomics) to detect Single Nucleotide Polymorphisms (SNPs) between populations or closely related species can provide greater insight from stock structure to fishery-induced evolution. In addition, candidate loci can be investigated further to better understanding evolutionary processes, which provide clues on physiological adaptations and gene expression patterns that can help elucidate how these organisms respond to their current environment. In addition, the use of transcriptomic analyses such as differential gene expression can be used to determine resilience in various environmental conditions such as pollution, hypoxic/anoxic conditions, fluctuations in salinity, and temperature extremes. There has been an increase in transcriptomic studies for many aquaculture species, which has aimed at improving our understanding of growth, development, and metabolism, providing vital information for fisheries and aquaculture industries to make adjustments to environmental conditions such as oxygen availability, nutrition, and salinity. All of these aspects provide insightful information for advancing our knowledge of aquaculture, fisheries and conservation management.

Abstract Objective: Endometriosis is a chronic disease characterized by the growth of endometrial cells outside the uterine cavity. The dysfunction of the immune system is strongly associated with the progression of endometriosis, and is also correlated to the diversity of microbiota in the genital tract. According to previous studies, the microbiota significantly contributes to multi-systemic function, but the evidence of endometriosis and adenomyosis remains insufficient. Thus, the present study attempted to identify the characteristics of microbiota in endometriosis patients, and the connection between microbiota and immunological dysfunction. Methods: In order to compare and explore the potential microbiota correlated to endometriosis and adenomyosis in the genital tract, 134 samples obtained from the cervical canal, posterior fornix and uterine cavity were analyzed by 16s-rRNA sequencing. The raw data was filtered, analyzed and visualized, and bio-information methods were used to identify the different and distinctive characteristics of microbiota. Results: Two different locations near the cervix, cervical canal and posterior fornix, exhibited no differences in alpha diversity. Among the different disease groups, five microbiota were distinctive in the genus level, and Atopobium presented with the greatest significance in adenomyoisis-endometriosis patients. The LEfSe analysis failed to identify the special biomarkers, while several characteristic functions were identified through PICRUSt. Conclusion: Lactobacillus is dominant in the female lower genital tract, and Atopobium is distinctively higher in patients with endometriosis combined with adenomyosis. Several different functions of microbiota were explored, and these are found to be associated with endometriosis and adenomyosis. These findings may provide a new concept of microbiota/immune system/endometriosis system. There is an urgent need to investigate the potential microbial biomarkers of endometriosis in the future.

MicroRNAs (miRNAs) dysregulation contribute the cancer pathogenesis. However, the miRNA profile of canine oral melanoma (COM), one of the frequent malignant melanoma in dog is still unrevealed. The aim of this study is to reveal the miRNA profile in canine oral melanoma. MicroRNAs profile of oral tissues from normal healthy dogs and COM patients were compared by next-generation sequencing. Along with tumour suppressor microRNAs (miRNAs), we report 30 oncogenic miRNAs in COM. Expression of miRNAs were further confirmed by quantitative real-time PCR (qPCR). Pathway analysis showed that deregulated miRNAs impact on cancer and signalling pathways. Three oncogenic miRNAs targets (miR-450b, 301a, and 223) from human study also were down-regulated in COM and had significant negative co-relation with their respective miRNA. Furthermore, we found that miR-450b expression is higher in metastatic cells and regulated MMP9 expression through a PAX9-BMP4-MMP9 axis. In silico analysis indicated that miR-126, miR-20b, and miR-106a regulated the highest numbers of differentially expressed transcription factors in respect to human melanoma. Chromosomal enrichment analysis revealed the X chromosome was enriched with oncogenic miRNAs. We comprehensively analyzed the miRNA’s profile in COM which will be a useful resource for developing therapeutic interventions in both species.

Data on the KIT mutation rate in skin melanoma in the central European region is missing. Accordingly, in a cohort of 79 double wild type (BRAF/NRAS) skin melanoma KIT mutation was assessed by Sanger sequencing of exons 9,11,13,17 and 18. In this skin melanoma cohort KIT mutation frequency was found to be 34/79 (43%) with a significantly higher rate in acrolentiginous melanoma (ALM) as compared to UV-induced common variants (20/34, 58.8% versus 14/45, 31.1%, p=0.014). Exon 11 was the most frequent mutation site (44.7%) followed by exon 9 (21.1%) equally characterizing UV-induced common histotypes and ALM tumors. KIT mutation hotspots were identified in exon 9 (c491/492), in exon 11 (c559,c572, c570), in exon 13 (c642), in exon 17 (c822) and in exon 18 (c853). The relatively high KIT mutation rate in skin melanoma in this central-European cohort justifies regular testing of this molecular target.

Sutherlandia frutescens (S. frutescens) has been traditionally used as an herbal medicine to ameliorate symptoms associated with cancer, infectious diseases, as well as inflammation. The objective of this investigation was to explore the impact of S. frutescens on the expression of genes in a murine macrophage cell line (i.e., RAW 264.7). We found that treatment with an ethanolic-extract of S. frutescens (SFE) 1 h prior to the stimulation with LPS and IFNγ for 24 h significantly affected the expression of 715 genes in RAW 264.7 cells. When the post-stimulation period was shortened to 8 h, the number of genes that were significantly impacted by SFE diminished to 50. Pathway analysis revealed that inflammatory signaling pathways, such as NF-κB, MAPK, and TNF, as well as signaling pathways associated with immune-related responses, were inhibited by SFE treatment. These findings are consistent with previously reported anti-inflammatory activity of SFE and enable better understanding of the immune-modulating properties of this botanical. To our knowledge, this represents the first report on the impact of S. frutescens on global gene expression in an immune cell population.

Throughout history, the pursuit of diagnosing and predicting crop yields has evidenced genetics, environment, and management practices' intertwined roles in achieving food security. However, the sensitivity of crop phenotypes and genetic responses to weather and climate remains unclear, hampering the identification of the underlying abilities of plants to adapt to climate change. We hypothesize that the PAWN global sensitivity analysis (GSA) coupled with a genetic by environment (GxE) model -built of environmental covariance and genetic markers structures- can evidence the contributions of climate on the predictability of maize yields in the U.S. and Ontario, Canada (US-CA). The GSA-GxE modeling framework estimates the relative contribution of climate variables such as solar radiation, temperature, rainfall, and relative humidity on improving maize yield predictions in US-CA. We use an improved version of the Genomes to Fields (G2F) initiative multi-dimensional database to build the environmental covariance matrices for the proposed GSA-GxE framework. The PAWN indices show that the aggregated GxE model’s highest sensitivity levels over US-CA were attributed to solar radiation, temperature, rainfall, and relative humidity. In one-third of the locations, rainfall was the primary climate variable responsible for maize yield predictability. Also, a consistent pattern of top sensitivity indices by location indicates that Relative Humidity, Solar Radiation, and Temperature were distributed as the main or the second most relevant drivers of maize yield predictability.

Introduction: Determination of radiological bone age (BA) is a diagnostic method that consists of estimating chronological age (CA) from the bone maturation of children. Although environmental and hormonal factors can interfere with bone ossification, the process is essentially dependent on ancestral inheritance. These ethnic backgrounds are not usually considered, which can lead to biased interpretations and inadequate decision-making by pediatricians or forensic experts. The objective of this study was to determine the precision and accuracy of these radiological procedures among different ethnic groups. Methods: A qualitative systematic review carried out following MOOSE statement and previously registered in the International Prospective Registry of Systematic Reviews PROSPERO (CRD42023449512). Search was performed in MEDLINE (PubMed) (n=561), Cochrane Library (n=261), CINAHL (n=103), Web of Science (WOS) (n=181) and public institutional repositories (n=37) from inception to 31st December 2022 using Mesh as “Diagnostic Techniques and Procedures”, “Diagnostic imaging”, “Radiography”, “Age Determination by Skeleton” and free terms combining with booleans “AND” and “OR”. PEDro scale, and Risk of Bias in non-randomized Studies of Exposure (ROBINS-E) were used to assess methodological quality and risk of bias of included studies respectively. Results: 51 articles (n=19,531) were included according to the inclusion criteria previously established. There was a good to moderate methodological quality and a high to very high risk of bias. Skeletal methods for determining BA were precised in terms of intra-observer and inter-observer reliability in all ethnic groups. Regarding to accuracy of Skeletal methods in Caucasians and Hispanic children, GPA was accurate at all ages, but in youths, TW3 RUS could be a consistent alternative. In Asian and Arab, GPA and TW3 overestimated BA in adolescents near adulthood. In African youths, GPA overestimated BA while TW3 was more accurate in estimating CA. Dental and Cervical radiographic methods are equally precise but lesser accurate than Skeletal BA determination. Conclusion: Skeletal radiographic methods GPA and TW3 are both precise for BA determination among all ethnical groups, but their accuracy in estimating CA can be altered by racial bias.

Grape pomace is one of the main by-products in the wine industry and contains some high added-value compounds such as polysaccharides. Considering the wide application possibilities of polysaccharides in wine and in the food industry, the revalorization of grape pomace to extract polysaccharides presents itself as an opportunity for by-product management. Therefore, the aim of this study was to characterize polysaccharide extracts obtained from pomace by-products of different white grape varieties. The type and content of polysaccharides, proteins and phenols were analyzed. Statistically significant differences were found between the varietal extracts in the types and concentrations of polysaccharides. The extracts obtained from the Verdejo and Puesta en Cruz varieties showed the highest polysaccharide purity and contents, but the type of polysaccharides was different in each case. The Verdejo provided extracts richer in non pectic polysaccharides, while the Puesta en Cruz in pectic polysaccharides. Protein and polyphenol contents were low in all extracts, below 2.5% and 3.7%, respectively. These results open up a new possibility for the revalorization of grape pomace by-products to obtain polysaccharide-rich extracts, although it would be interesting to improve both the yield and the purity of the extracts obtained by studying other extraction techniques or processes.

Tree ordinances can be an effective means of preserving urban forests in the face of development pressures. Despite this, they also have the potential to be divisive among the public - especially when applied to privately-owned land. In this study we surveyed 1,716 Florida urban residents to understand how they value regulation and management of the urban forest. Specifically, we asked about: tree protection ordinances, incentive programs to manage or plant trees, justification for tree removal, and development. Most respondents supported tree protections, even when applied to trees on their own property or when they had the potential to limit development activities. Additionally, there was limited support for removing healthy trees for development. Respondents supported the use of funds for urban forestry efforts – particularly at the local or state level.

The assessment of caprock integrity for underground storage of CO2 and/or enhanced oil recovery (EOR) systems is a multiscale endeavor. Caprock sealing behavior depends on coupled processes that operate over a broad range of length and time scales including nanoscale heterogeneity in capillary and wettability properties to depositional heterogeneity that is basin wide. Larger-scale sedimentary architecture, fractures, and faults can govern properties of potential “seal-bypass” systems that may be difficult to assess. We present a multiscale investigation of geologic sealing integrity of the caprock system that overlies the Morrow B sandstone reservoir, Farnsworth Unit, Texas, USA. The Morrow B sandstone is the target geologic unit for an on-going combined CO2 storage–EOR project by the Southwest Regional Partnership on Carbon Sequestration (SWP). Methods and/or data encompass small-to-large scales, including: petrography using electron and optical microscopy; mercury porosimetry; core examinations of sedimentary architecture and fractures; well logs; a suite of geomechanical testing; and a noble gas profile through sealing lithologies into the reservoir, as preserved from fresh core. The combined data set allows a comprehensive examination of sealing quality by scale, by primary features that control sealing behavior, and an assessment of sealing behavior over geologic time.

Multiple myeloma (MM) is an incurable, diverse cancer in which abnormal plasma cells produce and release monoclonal immunoglobulin (Ig), also known as monoclonal protein or M protein. MM is always preceded by monoclonal gammaglobulinemia of unknown significance (MGUS) and smoldering multiple myeloma (SMM). Diagnosis of MM is made from a bone marrow sample, which involves analysis of the appearance of plasma cells. Quantification of CD138+ plasma cells in core biopsies is performed using techniques such as immunohistochemistry, flow cytometry, fluorescence in situ hybridization (FISH) and conventional cytogenetics. Urinalysis includes total protein by immunofixation and 24-hour urine by serum protein electrophoresis. FISH probes should detect the presence of at least del 13, del 17p, t(4;14), t(11;14), t(14;16), and 1q21 amplifications. Indeed, next-generation sequencing (NGS) has become an increasingly important tool in the diagnosis and treatment of MM. It can be used to identify genetic mutations, copy number changes, and clonal structures to help determine disease prognosis and treatment strategies. NGS can identify subclonal populations of cancer cells that are resistant to therapy and may lead to disease relapse, and can be used to identify potential targets for personalized therapy. For example, NGS can identify mutations in genes involved in drug resistance, enabling the selection of drugs that may be more effective in treating a patient's cancer. This systematic review analyzes 182 papers to determine the position and role of NGS in the diagnosis of MM. We first analyze the platforms and sample types used in the selected studies, and then start discussing the results.

There is a growing trend among consumers to seek out natural foods and products with natural ingredients. This shift in consumer preferences had a direct impact on both food and pharmaceutical industries, leading to a focus of scientific research and commercial efforts to meet these new demands. The aim of this work is to review recent available scientific data on foods of interest, such as artichoke, gooseberry, and polygonoideae plants, as well as olive oil and red raspberries. Interestingly, the urgency of solutions to the climate change emergency has brought new attention to by-products of grapevine bunch stem and cane, which have been found to contain bioactive compounds with potential health benefits. There is a pressing need for a faster process of translating scientific knowledge from the laboratory to real-world applications, especially in the face of the increasing societal burden associated to non-communicable diseases (NCDs), environmental crises, the post-pandemic world, and ongoing violent conflicts around the world.

Breeding for low hydrogen cyanide (HCN) varieties is a major objective of programmes targeting boiled cassava food product. To enhance breeding for low HCN, knowledge on genetic variation and trait heritability is essential. In this study, 64 cassava clones established across four locations and evaluated for HCN using three HCN assessment methods; 1 to 9 scale, 0 ppm to 800 ppm scale and a quantitative assay based on spectrophotometer readings (HCN_Spec). Data were also collected on the weather variables precipitation, relative humidity, and temperature. Significant differences were observed among clones (P &lt; 0.001) and locations (p &lt; 0.001). There were also significant (p &lt; 0. 001) clone by environment interactions. Locations Arua and Serere posted higher HCN scores among clones and were associated with significantly higher (p &lt; 0.001) mean daily temperature (K) and lower relative humidity (%) across 12-hour and 18-hour intervals. Within locations HCN broad sense heritability estimates ranged 0.22 – 0.64 while combined location heritability estimates ranged 0.14 to 0.32. Relationships between the methods were positive and strong (R2 = 0.75 – 0.92). It is expected that the information herein will accelerate efforts towards breeding for low HCN cassava varieties.

Spatio-temporal variability and dynamics in Sahelian agro-pastoral zones make each local situation a special case. These specificities must be considered to guide the dissemination of agricultural options with a view to sustainable development. The territorial scale of municipalities is not sufficient for this necessary contextualization; the scale of the “village terroir” seems to be a better option. This is the hypothesis put forward by the Global Collaboration for Resilient Food Systems program. By analyzing the links between farm managers and their cultivated land, as well as the spatio-temporal dynamics of “village terroirs” in three regions of Niger (Maradi, Dosso and Tillabéri), this study provides evidence of the existence and functional usefulness of the village terroir for farmers, their land management and their activities. It demonstrates the usefulness of contextualizing agricultural options at this scale. It is based on data collected through participatory mapping and surveys. Their analysis elucidates the links between “terroirs village” and the specific functioning of the agro-socio-ecosystems acting on each of them, thus laying the systemic and geographical foundations for a model of the spatio-temporal dynamics of “village terroirs”. This initial work has opened up new perspectives in modeling and sustainable development.

In the past years, consumers have increased their interest to buy healthier food products, rejecting those products with more additives and giving preference to the fresh ones. Moreover, the current environmental situation has made society more aware of the importance of reducing the production of plastic and food waste. In this way and considering the Food Industry need of reducing the food spoilage along the food chain, edible coating has been considered as an eco-friendly food packaging that can replace traditional plastic packaging providing an improvement in the product’s shelf-life. Edible coating are thin layers applied straightaway on the food materials’ surface, that are made of biopolymers that usually incorporate other elements, such as nanoparticles or essential oils, to improve their physicochemical properties. These materials must provide a barrier that can prevent the pass of water vapor and other gasses, the microbial growth, the moisture loss, and the oxidation, so the shelf-life could be extended. The aim of this review was to compile the current data available to give a global vision of the formulation process and the different ways to improve the characteristics of the coats applied in both fruits and vegetables. In this way, the suitability of compounds in by-products produced during the Food Industry chain were also considered for the edible coating production.

Clinical trials are research studies performed on people that are aimed at evaluating a medical, surgical, or behavioural intervention. It is a primary way that researchers find out if a new treatment, like a new drug or diet, or medical device is safe and effective in people. In this paper blockchain technology is embedded in a digital twin aiming to improve the quality of clinical trials through the boost of data integrity among the quality-related activities, and to promote participants' safety. First, a blockchain-embedded quality-enabled digital twin is proposed and the interactions among the enablers and peers are highlighted. Then, a prototype of the proposed system is developed, and the data of a pilot trial is used to justify the applicability of the system. The results showed that the proposed system is efficient, and hence it is feasible to adopt into a clinical trial. With the successful development of the proposed system, it is promising to provide effective data integration and knowledge management for improving participant safety.

Coffee pulp, obtained from wet coffee processing, is the major by-product accumulating in the coffee producing countries. One of the many approaches valorising this underestimated agricultural residue is the production of distillates. This research project deals with the production of spirits from coffee pulp using three different Coffea arabica varieties as a substrate. Coffee pulp was fermented for 72 hours with a selected yeast strain (Saccharomyces cerevisiae L.), acid, pectin lyase, and water. Several parameters, such as temperature, pH, sugar concentration and alcoholic strength were measured to monitor the fermentation process. Subsequently, the alcoholic mashes were double distilled with stainless steel pot stills and a sensory evaluation of the products was conducted. Furthermore, the chemical composition of fermented mashes and produced distillates were evaluated. It showed that elevated methanol concentrations were present in mashes and products of all three varieties. The sensory evaluation found the major aroma descriptor for the coffee pulp spirits as being stone fruit. The fermentation and distillation experiments revealed that coffee pulp can be successfully used as a raw material for the production of fruit spirits. However, the spirit quality and its flavour characteristics can be improved with optimised process parameters and distillation equipment.

The purpose of this research has been to provide information about the psychological effects of confinement forced by a prolonged quarantine in a suitable adult sample of 596 Bolivians of both sexes. It was sought to explore the perceptions of the participants about their own emotional state: fears, anxieties, depressions, while they were in isolation to reduce the probability of contagion of COVID 19. Additionally, we were interested in verifying the modulating effects of resilience and self-efficacy on such emotional states. The results indicated, in the same direction of similar studies, significant relationships between high perceived loneliness, high levels of stress and anxiety, with relatively high levels of depression. Likewise, it was clear that stress, perceived loneliness, and anxiety are predictors of depression among those in conditions of forced isolation. Finally, it was found that both resilience and self-efficacy exert a clear moderating effect by attenuating the relationships of perceived loneliness and anxiety, on depression.

Collagen is the most abundant protein in the animal kingdom. Industrial collagen is mainly bovine and porcine origin. However, due to religious beliefs, allergic issues, and infectious diseases, alternative sources of collagen as marine are gaining increasing interest. In this work, the acid-soluble collagen (ASC) were extracted from salt-cured Atlantic cod (Gadus morhua) skin and characterized. The extraction yield was about 2.0%, equivalent to the extraction yield reported for other fish skins. The electrophoretic pattern showed the typical type I structure (α, β and γ chains). UV-VIS and FTIR absorbance spectra suggested a very pure ASC with an intact triple helical structure. The integrity and the adequate porosity required for different applications were then confirmed by electron micrograph. Our findings allow us to say that, for the first time, we extracted acid-soluble type I collagen from salt-cured Atlantic cod skin, with characteristics suitable for application in various fields, such as biomedical.