Miracle-dz/UniFAR-FTUs huggingface dataset:
Primary HPV testing verification: A retrospective ad‐hoc analysis of screening algorithms on women doubly tested for cytology and HPV

To evaluate human papillomavirus (HPV) testing as a primary screening tool, we retrospectively analyzed data comparing (1) HPV testing to the algorithms of the ATHENA Study: (2) cytology alone, (3) cytology with ASCUS triage in women 25–29 and (4) cotesting ≥ 30 or (5) cotesting ≥ 25.
The DSM5/RDoC debate on the future of mental health research: implication for studies on human stress and presentation of the signature bank

Abstract In 2008, the National Institute of Mental Health (NIMH) announced that in the next few decades, it will be essential to study the various biological, psychological and social “signatures” of mental disorders. Along with this new “signature” approach to mental health disorders, modifications of DSM were introduced. One major modification consisted of incorporating a dimensional approach to mental disorders, which involved analyzing, using a transnosological approach, various factors that are commonly observed across different types of mental disorders. Although this new methodology led to interesting discussions of the DSM5 working groups, it has not been incorporated in the last version of the DSM5. Consequently, the NIMH launched the “Research Domain Criteria” (RDoC) framework in order to provide new ways of classifying mental illnesses based on dimensions of observable behavioral and neurobiological measures. The NIMH emphasizes that it is important to consider the benefits of dimensional measures from the perspective of psychopathology and environmental influences, and it is also important to build these dimensions on neurobiological data. The goal of this paper is to present the perspectives of DSM5 and RDoC to the science of mental health disorders and the impact of this debate on the future of human stress research. The second goal is to present the “Signature Bank” developed by the Institut Universitaire en Santé Mentale de Montréal (IUSMM) that has been developed in line with a dimensional and transnosological approach to mental illness.
The Footprint of Genome Architecture in the Largest Genome Expansion in RNA Viruses

The small size of RNA virus genomes (2-to-32 kb) has been attributed to high mutation rates during replication, which is thought to lack proof-reading. This paradigm is being revisited owing to the discovery of a 3′-to-5′ exoribonuclease (ExoN) in nidoviruses, a monophyletic group of positive-stranded RNA viruses with a conserved genome architecture. ExoN, a homolog of canonical DNA proof-reading enzymes, is exclusively encoded by nidoviruses with genomes larger than 20 kb. All other known non-segmented RNA viruses have smaller genomes. Here we use evolutionary analyses to show that the two- to three-fold expansion of the nidovirus genome was accompanied by a large number of replacements in conserved proteins at a scale comparable to that in the Tree of Life. To unravel common evolutionary patterns in such genetically diverse viruses, we established the relation between genomic regions in nidoviruses in a sequence alignment-free manner. We exploited the conservation of the genome architecture to partition each genome into five non-overlapping regions: 5′ untranslated region (UTR), open reading frame (ORF) 1a, ORF1b, 3′ORFs (encompassing the 3′-proximal ORFs), and 3′ UTR. Each region was analyzed for its contribution to genome size change under different models. The non-linear model statistically outperformed the linear one and captured >92% of data variation. Accordingly, nidovirus genomes were concluded to have reached different points on an expansion trajectory dominated by consecutive increases of ORF1b, ORF1a, and 3′ORFs. Our findings indicate a unidirectional hierarchical relation between these genome regions, which are distinguished by their expression mechanism. In contrast, these regions cooperate bi-directionally on a functional level in the virus life cycle, in which they predominantly control genome replication, genome expression, and virus dissemination, respectively. Collectively, our findings suggest that genome architecture and the associated region-specific division of labor leave a footprint on genome expansion and may limit RNA genome size.
Interaction between the canopy dwelling echinoid Holopneustes purpurescens and its host kelp Ecklonia radiata

I examined the interaction between the unusual, canopy dwelling echinoid Holopneustes purpurescens and its main host plant, the kelp Ecklonia radiata. During a 4 yr study at Cape Banks, New South Wales, Australia, H. purpurescens reached densities as high as 1 ind. per thallus of E. rad~ata nd > l 7 mw2, with densities declining strongly in the latter years of the study. These sea urchins also occurred, although at lower densities, on the dictyotalean alga Homoeostrichus sinclairii. H. purpurescens consumed laminae of E. radiata in the field at the rate of -1 g large ind. -l (diameter >40 mm) d'l Consumption by the sea urchins was not affected by variation in phlorotannin levels among laminae. The impact of feeding by H. purpurescens on E. radiata, measured as (1) changes in the biomass of the kelps and (2) changes in thallus elongation rates, was examined in field experiments done in 2 seasons in which different numbers and sizes of sea urchins were caged with individual E. radiata. In spring, all densities and sizes of H. purpurescens caused significant damage (biomass) to E. radiata after 4 wk, and higher densities (2 per kelp thallus) of large sea urch~ns resulted in kelp mortality. No measurable damage occurred in autumn, with all kelps losing large amounts of biomass. No significant effect on thallus elongation rates was seen in either season after 4 wk. However, elongation rates varied among treatments after 2 wk in autumn. Grazing by H purpurescens did not result in compensatory growth by E. radjata, nor did levels of phlorotannins in the kelps increase in response to grazing (chemical induction).
Evaluation of seminal plasma proteomics and relevance of FSH in identification of nonobstructive azoospermia: A preliminary study

Nonobstructive azoospermia (NOA) patients present with high levels of serum FSH. At the protein level, the aetiology and pathways underlying different subtypes of NOA are unclear. The aim was to evaluate quantitatively differences in proteomic profiles of NOA patients presenting with normal serum FSH and normal testicular volume and high serum FSH and small testicular volume. The study comprised of 14 nonobstructive azoospermic men (N = 4; normal FSH and normal testicular volume and N = 10; high FSH and small testicular volume) and seven normozoospermic men. Proteomic analysis was done using LC‐MS. GSTM3 and PGK2 were less abundant in the normal and high FSH group compared to controls. HSPA4L and HSPA4 were exclusively present in control group whereas HSP90AB1, HSPA1B, HSP90AA1 and HSPA2 were less abundant and exclusive to the normal and high FSH group. We have identified six heat‐shock proteins that may have a role in the pathology of NOA. FSH and testicular volume by itself are not good markers of NOA. The inverse association of GSTM3 and PGK2 regulation with FSH levels along with 12 proteins exclusively in NOA groups suggests further evaluation of their predictive potential in a larger cohort of patients.
Sunlight-Exposed Biofilm Microbial Communities Are Naturally Resistant to Chernobyl Ionizing-Radiation Levels

Background The Chernobyl accident represents a long-term experiment on the effects of exposure to ionizing radiation at the ecosystem level. Though studies of these effects on plants and animals are abundant, the study of how Chernobyl radiation levels affect prokaryotic and eukaryotic microbial communities is practically non-existent, except for a few reports on human pathogens or soil microorganisms. Environments enduring extreme desiccation and UV radiation, such as sunlight exposed biofilms could in principle select for organisms highly resistant to ionizing radiation as well. Methodology/Principal Findings To test this hypothesis, we explored the diversity of microorganisms belonging to the three domains of life by cultivation-independent approaches in biofilms developing on concrete walls or pillars in the Chernobyl area exposed to different levels of radiation, and we compared them with a similar biofilm from a non-irradiated site in Northern Ireland. Actinobacteria, Alphaproteobacteria, Bacteroidetes, Acidobacteria and Deinococcales were the most consistently detected bacterial groups, whereas green algae (Chlorophyta) and ascomycete fungi (Ascomycota) dominated within the eukaryotes. Close relatives to the most radio-resistant organisms known, including Rubrobacter species, Deinococcales and melanized ascomycete fungi were always detected. The diversity of bacteria and eukaryotes found in the most highly irradiated samples was comparable to that of less irradiated Chernobyl sites and Northern Ireland. However, the study of mutation frequencies in non-coding ITS regions versus SSU rRNA genes in members of a same actinobacterial operational taxonomic unit (OTU) present in Chernobyl samples and Northern Ireland showed a positive correlation between increased radiation and mutation rates. Conclusions/Significance Our results show that biofilm microbial communities in the most irradiated samples are comparable to non-irradiated samples in terms of general diversity patterns, despite increased mutation levels at the single-OTU level. Therefore, biofilm communities growing in sunlight exposed substrates are capable of coping with increased mutation rates and appear pre-adapted to levels of ionizing radiation in Chernobyl due to their natural adaptation to periodical desiccation and ambient UV radiation.
Incorporating World Knowledge to Document Clustering via Heterogeneous Information Networks

One of the key obstacles in making learning protocols realistic in applications is the need to supervise them, a costly process that often requires hiring domain experts. We consider the framework to use the world knowledge as indirect supervision. World knowledge is general-purpose knowledge, which is not designed for any specific domain. Then the key challenges are how to adapt the world knowledge to domains and how to represent it for learning. In this paper, we provide an example of using world knowledge for domain dependent document clustering. We provide three ways to specify the world knowledge to domains by resolving the ambiguity of the entities and their types, and represent the data with world knowledge as a heterogeneous information network. Then we propose a clustering algorithm that can cluster multiple types and incorporate the sub-type information as constraints. In the experiments, we use two existing knowledge bases as our sources of world knowledge. One is Freebase, which is collaboratively collected knowledge about entities and their organizations. The other is YAGO2, a knowledge base automatically extracted from Wikipedia and maps knowledge to the linguistic knowledge base, WordNet. Experimental results on two text benchmark datasets (20newsgroups and RCV1) show that incorporating world knowledge as indirect supervision can significantly outperform the state-of-the-art clustering algorithms as well as clustering algorithms enhanced with world knowledge features.
Practice parameter for electrodiagnostic studies in carpal tunnel syndrome: Summary statement

Carpal tunnel syndrome (CTS) is a common clinical problem and frequently requires surgical therapy. The results of electrodiagnostic (EDX) studies have been found to be highly sensitive and specific for the diagnosis of CTS. This document defines the standards, guidelines, and options for EDX studies of CTS based on a critical review of the literature published in 1993 and recently updated by a review of the literature through the year 2000. The reader is referred to the updated review for a detailed discussion of the literature and the EDX techniques for the assessment of CTS which are summarized here. Both reviews addressed the following key clinical questions:
Identification of Novel PTPRQ and MYO1A Mutations in An Iranian Pedigree with Autosomal Recessive Hearing Loss

Autosomal recessive non-syndromic hearing loss (ARNSHL) is defined as a genetically heterogeneous disorder. The aim of the present study was to screen for pathogenic variants in an Iranian pedigree with ARNSHL. Next-generation targeted sequencing of 127 deafness genes in the proband detected two novel variants, a homozygous missense variant in PTPRQ (c.2599 T>C, p.Ser867Pro and a heterozygous missense variant in MYO1A (c.2804 T>C, p.Ile935Thr), both of which were absent in unaffected sibs and two hundred unaffected controls. Our results suggest that the homozygous PTPRQ variant maybe the pathogenic variant for ARNSHL due to the recessive nature of the disorder. Nevertheless, the heterozygous MYO1A may also be involved in this disorder due to the multigenic pattern of ARNSHL. Our data extend the mutation spectrum of PTPRQ and MYO1A, and have important implications for genetic counseling in unaffected sibs of this family. In addition, PTPRQ and MYO1A pathogenic variants have not to date been reported in the Iranian population.
ILLUMINATING THE STRUCTURE AND FUNCTION OF CYS‐LOOP RECEPTORS

1 Cys‐loop receptors are an important class of ligand‐gated ion channels. They mediate fast synaptic neurotransmission, are implicated in various ‘channelopathies’ and are important pharmacological targets. Recent progress in X‐ray crystallography and electron microscopy has provided a considerable insight into the structure of Cys‐loop receptors. However, data from these experiments only provide ‘snapshots’ of the proteins under investigation. They cannot provide information about the various conformations the protein adopts during transition from the closed to the open and desensitized states. 2 Voltage‐clamp fluorometry helps overcome this problem by simultaneously monitoring movements at the channel gate (through changes in current) and conformational rearrangements in a domain of interest (through changes in fluorescence) in real time. Thus, the technique can provide information on both transitional and steady state conformations and serves as a real time correlate of the channel structure and its function. 3 Voltage‐clamp fluorometry experiments on Cys‐loop receptors have yielded a large body of data concerning the mechanisms by which agonists, antagonists and modulators act on these receptors. They have shed new light on the conformational mobility of both the ligand‐binding and the transmembrane domain of Cys‐loop receptors.
Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis

A model system for investigating how developmental regulatory networks determine cell fate is spore formation in Bacillus subtilis. The master regulator for sporulation is Spo0A, which is activated by phosphorylation via a phosphorelay that is subject to three positive feedback loops. The ultimate decision to sporulate is, however, stochastic in that only a portion of the population sporulates even under optimal conditions. It was previously assumed that activation of Spo0A and hence entry into sporulation is subject to a bistable switch mediated by one or more feedback loops. Here we reinvestigate the basis for bimodality in sporulation. We show that none of the feedback loops is rate limiting for the synthesis and phosphorylation of Spo0A. Instead, the loops ensure a just-in-time supply of relay components for rising levels of phosphorylated Spo0A, with phosphate flux through the relay being limiting for Spo0A activation and sporulation. In addition, genes under Spo0A control did not exhibit a bimodal pattern of expression as expected for a bistable switch. In contrast, we observed a highly heterogeneous pattern of Spo0A activation that increased in a nonlinear manner with time. We present a computational model for the nonlinear increase and propose that the phosphorelay is a noise generator and that only cells that attain a threshold level of phosphorylated Spo0A sporulate.
Brain-released alarmins and stress response synergize in accelerating atherosclerosis progression after stroke

Atherosclerosis is exacerbated after stroke because of synergy of catecholaminergic stress response and alarmin-dependent signaling. An alarmin(g) consequence of stroke Patients surviving a stroke are at an increased risk for subsequent cardiovascular events. Preclinical models have shown accelerated atherosclerosis after stroke; however, the mechanisms underlying this enhanced plaque formation and inflammation in arteries have not been investigated. Now, Roth et al. have discovered that stroke-induced alarmin high-mobility group box 1 (HMGB1) release and sympathetic stress response activation exert a synergistic effect, resulting in exacerbation of atherosclerotic plaques in mice. The authors suggest that interfering with these processes after stroke might reduce the risk of secondary cardiovascular events. Stroke induces a multiphasic systemic immune response, but the consequences of this response on atherosclerosis—a major source of recurrent vascular events—have not been thoroughly investigated. We show that stroke exacerbates atheroprogression via alarmin-mediated propagation of vascular inflammation. The prototypic brain-released alarmin high-mobility group box 1 protein induced monocyte and endothelial activation via the receptor for advanced glycation end products (RAGE)–signaling cascade and increased plaque load and vulnerability. Recruitment of activated monocytes via the CC-chemokine ligand 2–CC-chemokine receptor type 2 pathway was critical in stroke-induced vascular inflammation. Neutralization of circulating alarmins or knockdown of RAGE attenuated atheroprogression. Blockage of β3-adrenoreceptors attenuated the egress of myeloid monocytes after stroke, whereas neutralization of circulating alarmins was required to reduce systemic monocyte activation and aortic invasion. Our findings identify a synergistic effect of the sympathetic stress response and alarmin-driven inflammation via RAGE as a critical mechanism of exacerbated atheroprogression after stroke.
Job stressors, personality and burnout in primary school teachers.

BACKGROUND Teaching is considered a highly stressful occupation. Burnout is a negative affective response occurring as a result of chronic work stress. While the early theories of burnout focused exclusively on work-related stressors, recent research adopts a more integrative approach where both environmental and individual factors are studied. Nevertheless, such studies are scarce with teacher samples. AIMS The present cross-sectional study sought to investigate the association between burnout, personality characteristics and job stressors in primary school teachers from Cyprus. The study also investigates the relative contribution of these variables on the three facets of burnout - emotional exhaustion, depersonalization and reduced personal accomplishment. SAMPLE A representative sample of 447 primary school teachers participated in the study. METHOD Teachers completed measures of burnout, personality and job stressors along with demographic and professional data. Surveys were delivered by courier to schools, and were distributed at faculty meetings. RESULTS Results showed that both personality and work-related stressors were associated with burnout dimensions. Neuroticism was a common predictor of all dimensions of burnout although in personal accomplishment had a different direction. Managing student misbehaviour and time constraints were found to systematically predict dimensions of burnout. CONCLUSIONS Teachers' individual characteristics as well as job related stressors should be taken into consideration when studying the burnout phenomenon. The fact that each dimension of the syndrome is predicted by different variables should not remain unnoticed especially when designing and implementing intervention programmes to reduce burnout in teachers.
The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1w⃞

To understand the gene network controlling tolerance to cold stress, we performed an Arabidopsis thaliana genome transcript expression profile using Affymetrix GeneChips that contain ∼24,000 genes. We statistically determined 939 cold-regulated genes with 655 upregulated and 284 downregulated. A large number of early cold-responsive genes encode transcription factors that likely control late-responsive genes, suggesting a multitude of transcriptional cascades. In addition, many genes involved in chromatin level and posttranscriptional regulation were also cold regulated, suggesting their involvement in cold-responsive gene regulation. A number of genes important for the biosynthesis or signaling of plant hormones, such as abscisic acid, gibberellic acid, and auxin, are regulated by cold stress, which is of potential importance in coordinating cold tolerance with growth and development. We compared the cold-responsive transcriptomes of the wild type and inducer of CBF expression 1 (ice1), a mutant defective in an upstream transcription factor required for chilling and freezing tolerance. The transcript levels of many cold-responsive genes were altered in the ice1 mutant not only during cold stress but also before cold treatments. Our study provides a global picture of the Arabidopsis cold-responsive transcriptome and its control by ICE1 and will be valuable for understanding gene regulation under cold stress and the molecular mechanisms of cold tolerance.
Coloring Random and Semi-Random k-Colorable Graphs

Abstract The problem of coloring a graph with the minimum number of colors is well known to be NP-hard, even restricted to k -colorable graphs for constant k ≥ 3. On the other hand, it is known that random k -colorable graphs are easy to k -color. The algorithms for coloring random k -colorable graphs require fairly high edge densities, however. In this paper we present algorithms that color randomly generated k -colorable graphs for much lower edge densities than previous approaches. In addition, to study a wider variety of graph distributions, we also present a model of graphs generated by the semi-random source of Santha and Vazirani (M. Santha and U. V. Vazirani, J. Comput. System Sci. 33 (1986), 75-87) that provides a smooth transition between the worst-case and random models. In this model, the graph is generated by a "noisy adversary"-an adversary whose decisions (whether or not to insert a particular edge) have some small (random) probability of being reversed. We show that even for quite low noise rates, semi-random k -colorable graphs can be optimally colored with high probability.