CASE REPORT | doi:10.20944/preprints202208.0155.v1
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Antrograde Amnesia; repetitive questioning; Transient global amnesia
Online: 8 August 2022 (10:55:46 CEST)
Transient global amnesia (TGA) is an uncommon clinical syndrome characterized by a loss of short-term memory and disorientation that resolves in twenty-four hours. The etiology is unknown and the diagnosis is made by exclusion of other possible etiologies that may cause similar patterns and the reversibility of the condition in less than 24 hours. Here we report a 60-year-old male presented with sudden onset of disorientation and short-term memory loss early in the morning while at home and started to ask his whereabouts and what happened. He had no history of significant medical or psychiatric disease. There was no history of previous similar episodes. He had no recent history of sleep problems, head trauma, substance abuse, or loss of consciousness. He had no history of seizure disorder, or migraine. A neurologic examination revealed a normal wakefulness state with mild disorientation, and short-term memory impairment. He had score of 18/30 on mini-mental state examination (which later returned to normal baseline in 24 hours). Extensive lab investigations did not show any abnormal findings. Brain MRI did not show any acute cerebral pathology. The EEG was negative for any abnormal cerebral activity. His memory improved and returned to normal baseline over the course of a 20-hour from the onset. After exclusion of potential causes and the patient returned to normal state of memory, the diagnosis of transient global amnesia was made. At the follow-up visit, the patient was in a state of normal function without a recurrence of memory impairment. Here we presented this interesting case of transient global amnesia. TGA is diagnosis of exclusion and important to keep in mind when evaluating a patient with acute onset of short-term memory impairment, especially when etiological investigation revealed no potential cause.
ARTICLE | doi:10.20944/preprints201811.0503.v1
Subject: Engineering, Control And Systems Engineering Keywords: robust control; preview control; repetitive control; controller design; uncertain systems
Online: 20 November 2018 (12:30:14 CET)
A robust guaranteed cost preview repetitive controller is proposed for a class of polytopic uncertain discrete-time systems. In order to improve the tracking performance, the repetitive controller combined with preview compensator is inserted in the forward channel. By using the L-order forward difference operator, an augmented dynamic system is constructed. Then, the guaranteed cost preview repetitive control problem is transformed into the guaranteed cost control problem for the augmented dynamic system. For given performance index, the sufficient condition of asymptotic stability for the closed-loop system is derived by combining parameter-dependent Lyapunov function method with linear matrix inequality (LMI) techniques. By incorporating the controller obtained into the original system, the guaranteed-cost preview repetitive controller is derived. A numerical example is also included to show the effectiveness of the proposed method.
ARTICLE | doi:10.20944/preprints201610.0041.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: RNA; DNA; Repetitive sequences; RNA stem loops; RNA group identities
Online: 12 October 2016 (10:58:59 CEST)
Current knowledge of the RNA world indicates two different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share – as main characteristics – a non-repetitive syntax. The differences in their syntax structure is coherent with the difference of the functions they represent. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. The DNA genomes themselves are rather inactive, whereas the non-coding RNA domain is highly active, even as non-random genetic innovation operators. This indicates that repetitive syntax is the essential pre-requisite for RNA interactions to install variable RNA-group-identities, whereas the non-repetitive syntax serves as a stable conservation tool for successful selection processes out of RNA-groups cooperation and competition. The interaction opportunities of RNA loops with repetitive syntax are higher than with non-repetitive ones. Interestingly, these two genetic codes resemble the function of all natural languages, i.e., (a) everyday language use for organization and coordination of biotic group behavior, and (b) artificial (instrumental) language use for conservation of blueprints for complex protein-body constructions.
REVIEW | doi:10.20944/preprints202111.0448.v2
Subject: Social Sciences, Behavior Sciences Keywords: non-invasive brain stimulation; sequence learning; statistical learning; repetitive TMS; DLPFC
Online: 9 February 2023 (02:41:04 CET)
Predictive processes and numerous cognitive, motor, and social skills depend heavily on sequence and statistical learning. The visuomotor Serial Reaction Time Task (SRTT) can measure these fundamental cognitive processes. In this review, we sought to answer whether repetitive transcranial magnetic stimulation (rTMS) is suitable for modulating visuomotor sequence learning and which factors mediate its efficacy. We systematically analyzed the eligible records (n = 17) that attempted to modulate the performance of the SRTT with rTMS. The purpose of the analysis was to determine how the following factors affected SRTT performance: (1) stimulated brain areas, (2) rTMS protocols, (3) stimulated hemisphere, (4) timing of the stimulation, (5) SRTT sequence properties, and (6) other methodological features. The primary motor cortex (M1) and the dorsolateral prefrontal cortex (DLPFC) were found to be the most promising stimulation targets. Low-frequency protocols over the M1 usually weaken performance, but the results are less consistent for the DLPFC. These inconsistencies (at least in part) may be due to the current frequency-based heuristics of rTMS effects developed for explaining local stimulation effects in the motor cortex. Although this review cannot provide an ultimate answer about the optimal stimulation and task parameters, it comprehensively discusses the behavioral effects of six factors that are crucial for designing future studies to modulate sequence learning with rTMS. Moreover, we conclude that synergistically combining functional neuroimaging with rTMS could adequately link the rTMS-induced network effects with the behavioral findings that are crucial to develop a unified cognitive model of visuomotor sequence learning.
REVIEW | doi:10.20944/preprints202106.0145.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Repetitive element; Transposable element; Non-coding RNA; ncRNA; Functional element; Bioinformatics
Online: 4 June 2021 (15:33:17 CEST)
With a large number of annotated non-coding RNAs (ncRNAs), repetitive sequences are found to constitute functional components (termed as repetitive elements) in ncRNAs that perform specific biological functions. Bioinformatics analysis is a powerful tool for improving our understanding of the role of repetitive elements in ncRNAs. This chapter summarizes recent findings that reveal the role of repetitive elements in ncRNAs. Furthermore, relevant bioinformatics approaches are systematically reviewed, which promises to provide valuable resources for studying the functional impact of repetitive elements on ncRNAs.
ARTICLE | doi:10.20944/preprints202008.0548.v1
Subject: Biology And Life Sciences, Biophysics Keywords: promoter sequences; repetitive sequences; pausing; abortive initiation; RNA polymerase; dsDNA rigidity
Online: 25 August 2020 (11:28:21 CEST)
In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences enriched with thymine bases represent the signal inducing abortive transcription. On the other hand, certain repetitive sequence elements broadly embedded in promoter regions constitute the signal inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we also suggest that repetitive sequence elements of promoter DNA modulate the rigidity of its double-stranded form, which profoundly influences the reaction coordinates of the productive initiation via pausing.
ARTICLE | doi:10.20944/preprints201803.0145.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: repetitive elements; RNA-Seq; genomics; evolution; cytogenetics; supernumerary elements; extra chromosomes
Online: 19 March 2018 (08:33:48 CET)
B chromosomes (B) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). Bs origin is generally linked to the A chromosome complement (A). The first report of a B chromosome in African cichlids was on Astatotilapia latifasciata, which can harbor 0, 1 or 2 B chromosomes. Classical cytogenetics studies found high TE content on the species B chromosome. In this study, we aim to understand TE composition and expression on A. latifasciata genome and its relation to the B chromosome. We use bioinformatics analysis to explore TEs genome organization and also their composition on the B chromosome. Bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq) we showed that all major TE classes are transcribed in brain, muscle and male/female gonads. The evaluation of TE expression between B- and B+ individuals showed that few elements have differential expression among groups and expanded B elements were not highly transcribed. Putative silencing mechanisms may the acting on the B chromosome of A. latifasciata to prevent adverse consequences of repeat transcription and mobilization in the genome.
REVIEW | doi:10.20944/preprints202010.0388.v1
Subject: Engineering, Automotive Engineering Keywords: Autism Spectrum Disorder; activity analysis; automated detection; repetitive behavior; abnormal gait; visual saliency
Online: 19 October 2020 (14:49:24 CEST)
Autism Spectrum Disorder (ASD) is a neuro-developmental disorder that limits social interactions, cognitive skills, and abilities. Since ASD can last during an affected person's entire life cycle, the diagnosis at the early onset can yield a significant positive impact. The current medical diagnostic systems (e.g., DSM-5/ICD-10) are somewhat subjective; rely purely on the behavioral observation of symptoms, and hence, some individuals often go misdiagnosed or late-diagnosed. Therefore, researchers have focused on developing data-driven automated diagnosis systems with less screening time, low cost, and improved accuracy while significantly reducing professional intervention. Human Activity Analysis (HAA) is considered one of the most promising niches in computer vision research. This paper aims to analyze its potentialities in the automated detection of autism by tracking the exclusive characteristics of autistic individuals such as repetitive behavior, atypical walking style, and unusual visual saliency. This review provides a detailed inspection of HAA-based autism detection literature published in 2011 on-wards depicting core approaches, challenges, probable solutions, available resources, and scopes of future exploration in this arena. According to our study, deep learning outperforms machine learning in ASD detection with a classification accuracy of 76\% to 95\% on different datasets comprise of video, image, or skeleton data that recorded participants performing a large number of actions. However, machine learning provides satisfactory results on datasets with a small number of action classes and has a range of 60\% to 93\% accuracy among numerous studies. We hope this extensive review will provide a comprehensive guideline for researchers in this field.
ARTICLE | doi:10.20944/preprints201811.0066.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Alu; LINE-1 (L1); X-chromosome inactivation (XCI); repetitive sequences; RNA binding strength
Online: 8 November 2018 (11:10:53 CET)
Two X chromosomes of female mammals randomly inactivate one of paternal or maternal X chromosome in early embryonic development and all the daughter cells produced from these cells retain the same feature of X chromosome inactivation, which is called X chromosome inactivation (XCI). Studying the mechanisms of XCI is important for understanding epigenetic that plays an important role in age-associated diseases. The previous studies have demonstrated that binding of RNAs and DNAs may play a role in activating gene expression. In this paper, our study aims to explore whether the mechanisms of XCI involve the RNA binding strength to X chromosome DNAs. The bioinformatics analyses based on big data were used to analyze the simulated binding strength of RNAs (RNA binding strength) to 23 chromosomes (including X chromosome and 22 human autosomes) and the characteristics of repetitive sequences in the X-inactivation centre. The results revealed that RNA binding strength of the long arm of the X chromosome that is almost entirely inactivated in XCI was significantly lower than that of all autosomes and the short arm of X chromosome, meanwhile the RNA binding strengths of inactivation regions in X chromosome were significantly lower than that of regions escaping from XCI. Different repetitive sequence clusters within the center of XCI presented a cross distribution characteristic. To further prove whether the repetitive sequences in human X chromosome involve in XCI, we cloned long interspersed element (LINE-1, L1) and short interspersed element (Alu) from human Xq13, the center of XCI, and constructed expression vectors carrying sense-antisense combination repetitive sequences (L1s or Alus). Effects of combined L1 or combined Alu sequences on expression of EGFP reporter gene were examined in stably transfected HeLa cells, which simulates the effects of repetitive sequences located on chromosomes. The results of experiments revealed transcribed L1 repetitive sequences activated EGFP reporter gene expression, so did the Alus. The experiment results suggested repetitive sequences activated genes by interaction of transcribed RNAs and DNAs. Since the binding of RNAs and DNAs can activate gene, so the low RNA binding strength of human X chromosome may be one of reasons of XCI. The cross distribution characteristics of different repetitive sequence clusters leading to a cascade of gene activation or gene inactivation may be the reason of transcriptional silencing one of the X chromosomes in female mammals.
ARTICLE | doi:10.20944/preprints202211.0342.v1
Subject: Social Sciences, Behavior Sciences Keywords: neuroethology; methodology; sexual differences; aging; Alzheimer’s disease; marble burying test; burrowing test; repetitive behavior
Online: 18 November 2022 (01:08:33 CET)
Burying and burrowing are promising rodent-typical behaviors to model neuropsychiatric symptoms (NPS). However, the original tests could be insufficient to conclude which NPS are modeled. Here, we propose methodological modifications such as the two-zone configuration and dual analysis in the Marble Burying Test (MB). Also, a new Brief Burrowing Test (BB), a 20 min brief version of the Deacon’s Burrowing Test (DB). We comprehensively studied these behaviors in 12-month-old male and female mice with normal and Alzheimer’s disease (AD)-pathological aging. The results: 1) confirm our precedent report of sexual dimorphism, with enhanced burying in male 3xTg-AD mice; 2) describe for the first time burrowing behavior in 3xTg-AD mice and its sex dependence; 3) regardless of the pattern, MB and BB reflected a goal-directed rather than an indiscriminate digging; 4) using the MB and BB to model anxiety-like behavior it’s not recommended; 5) burying and burrowing represent a repetitive rather than a stereotyped-like or perseverative behavior. In addition: 1) burying and burrowing behavioral patterns are alike, connected by several correlations; 2) the two-zones configuration is a useful tool to assess the intentionality of the burying and burrowing behaviors and to perform a more accurate screening of the NPS modeled by them.
ARTICLE | doi:10.20944/preprints202108.0569.v1
Subject: Social Sciences, Cognitive Science Keywords: visual short-term memory; repetitive transcranial magnetic stimulation; visual memory precision; serial memory effects
Online: 31 August 2021 (11:43:33 CEST)
We investigated the role of the human medio-temporal complex (hMT+) in the memory encoding and storage of a sequence of four coherently moving RDKs by applying repetitive transcranial magnetic stimulation (rTMS) during an early or late phase of the retention interval. Moreover, in a second experiment we also tested whether disrupting the functional integrity of hMT+ during the early phase impaired the precision of the encoded motion directions. Overall, results showed that both recognition accuracy and precision were worse in middle serial positions, suggesting the occurrence of primacy and recency effects. We found that rTMS delivered during the early (but not the late) phase of the retention interval was able to impair not only recognition of RDKs, but also the precision of the retained motion direction. However, such impairment occurred only for RDKs presented in middle positions along the presented sequence, where performance was already closer to chance level. Altogether these findings suggest an involvement of hMT+ in the memory encoding of visual motion direction. Given that both position sequence and rTMS modulated not only recognition but also precision of the stored information, these findings are in support of a model of visual short-term memory with a variable resolution of each stored item, consistent with the assigned amount of memory resources, and that such item-specific memory resolution is supported by the functional integrity of area hMT+.
REVIEW | doi:10.20944/preprints202202.0009.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: satellite DNA; repetitive DNA; tandem repeats; classical human satellites; HSATI; HSATII; HSATIII; HSat1; HSat2; HSat3
Online: 28 April 2022 (10:18:37 CEST)
The classical human satellite DNAs, also referred to as human satellites 1, 2 and 3 (HSat1, HSat2, HSat3, collectively HSat1-3) constitute the largest individual arrays of tandemly repeated DNA sequences in the genome. Even though they were among the first human DNA sequences to be isolated and characterized at the dawn of molecular biology, HSat1-3 have been left behind in the genomics era and remain among the most enigmatic sequences in the human genome. Although HSat1-3 total roughly 3% of the genome on average, they were almost entirely missing from the human genome reference assembly for 20 years. Recently, the Telomere-to-Telomere Consortium produced the first truly complete assembly of a human genome, including the enormous HSat1-3 arrays, opening them up for a new wave of discovery. Towards this end, here, I provide an account of the history and current understanding of HSat1-3 genomics, evolution, and roles in disease.
ARTICLE | doi:10.20944/preprints202101.0045.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Kombucha tea; microbial diversity; bacterial cellulose; Komagataeibacter xylinus; repetitive elements sequence-based rep-PCR; typing
Online: 4 January 2021 (13:24:41 CET)
Bacterial cellulose (BC) is receiving great attention due to its unique properties such as high purity, water retention capacity, high mechanical strength, and biocompatibility. However, the production of BC has been limited because of high cost and low productivity. In this light, the isolation of new BC producing bacteria and selection of high productive strains became a promising issue. Kombucha tea is a fermented beverage in which the bacteria fraction of the microbial community is composed mostly by strains belonging to the genus Komagataeibacter. In this study Kombucha tea production trials were performed starting from a previous batch, and bacterial isolation was conducted along cultivation time. From the whole microbial pool, 46 isolates were tested for their ability in producing BC. The obtained BC yield ranged from 0.59 g/L, for the isolate K2G36, to 23 g/L for K2G30 used as the reference strain. The genetic intraspecific diversity of the 46 isolates was investigated using two repetitive-sequence-based PCR typing methods, which are the enterobacterial repetitive intergenic consensus (ERIC) elements and the (GTG)5 sequences, respectively. The results obtained using two different approaches revealed the suitability of the fingerprints techniques, showing a discrimination power, calculated as D index, of 0.94 for (GTG)5 rep-PCR and 0.95 for ERIC rep-PCR. In order to improve the sensitivity of the applied method, a combined model from the two genotyping experiments was performed, allowing to discriminate among strains.
REVIEW | doi:10.20944/preprints202310.1603.v1
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: chronic traumatic encephalopathy (CTE); Alzheimer’s disease (AD); traumatic encephalopathy syndrome (TES); traumatic brain injury (TBI); repetitive head impacts (RHI)
Online: 25 October 2023 (08:57:48 CEST)
Chronic traumatic encephalopathy (CTE) is a unique neurodegenerative disease that is associated with repetitive head impacts (RHI) in both civilian and military settings. In 2014, the research criteria for the clinical manifestation of CTE, traumatic encephalopathy syndrome (TES) were proposed to improve the clinical identification and understanding of the complex neuropathological phenomena underlying CTE. This review provides a comprehensive overview of the current understanding of the neuropathological and clinical features of CTE, proposed biomarkers of traumatic brain injury (TBI) in both research and clinical settings, and a range of treatments based on previous preclinical and clinical research studies. Due to the heterogeneity of TBI, there is no universally agreed-upon serum, CSF, or neuroimaging marker for its diagnosis. However, as our understanding of this complex disease continues to evolve, it is likely that there will be more robust, early diagnostic methods and effective clinical treatments. This is especially important given the increasing evidence of a correlation between TBI and neurodegenerative conditions, such as Alzheimer's disease and CTE1. As public awareness of these conditions grows, it is imperative to prioritize both basic and clinical research, as well as the implementation of necessary safe and preventative measures.