Miracle-dz/UniFAR-FTUs huggingface dataset:
Poor Immune Reconstitution in HIV-Infected Patients Associates with High Percentage of Regulatory CD4+ T Cells

CD4+ regulatory T cells (Tregs) are essential for the maintenance of the immune system's equilibrium, by dampening the activation of potential auto-reactive T cells and avoiding excessive immune activation. To correctly perform their function, Tregs must be maintained at the right proportion with respect to effector T cells. Since this equilibrium is frequently disrupted in individuals infected with the human immunodeficiency virus (HIV), we hypothesize that its deregulation could hamper immune reconstitution in patients with poor CD4+ T cell recovery under highly active antiretroviral therapy (HAART). We analysed Tregs percentages amongst CD4+ T cells in 53 HIV-infected patients under HAART, with suppression of viral replication and distinct levels of immune reconstitution. As controls, 51 healthy individuals were also analysed. We observed that amongst the patients with Nadir values (the lowest CD4+ T cell counts achieved) <200 cells/µL, the individuals with high Tregs percentages (≥10% of total CD4+ T cells) had the worse CD4+ T cell reconstitution. In accordance, the well-described direct correlation between the Nadir value and CD4+ T cell reconstitution is clearly more evident in individuals with high Tregs proportions. Furthermore, we observed a strong negative correlation between Tregs percentages and CD4+ T cell recovery among immunological non-responder HIV+ individuals. All together, this work shows that high Tregs frequency is an important factor associated with sub-optimal CD4+ T cell recovery. This is particularly relevant for immunological non-responders with low Nadir values. Our results suggest that the Tregs proportion might be of clinical relevance to define cut-offs for HAART initiation.
English as Lingua Franca ( ELF ) as Medium of Learning in a Hotel Management Educational Program : an applied linguistic approach

(Applied) linguists started to show interest in English as a Lingua Franca (ELF) a good decade ago, which almost immediately sparked off strong and thriving research activities at various universities; not least at our own department, as readers of VIEWS are very aware of (Seidlhofer 2000). This contribution outlines a new research project in this area. As it is in its initial stages, comments are particularly welcome. The paper is a slightly abridged version of the project proposal I submitted earlier this year to the FWF (Austrian Fund for the Promotion of Scientific Research), on the basis of which I was granted a two-year research grant (Charlotte-Bühler-Habilitationsstipendium). Section 1 provides a summarylike overview of the basic considerations, underlying rationale and research questions of the project. This is followed by a discussion of the most relevant theoretical and disciplinary background information (sections 2 and 3), which paves the way for a more detailed presentation of the research questions pursued and research methods used (section 4). Section 5 concludes this paper by describing some anticipated results.
Protease-Activated Receptor 2 Sensitizes the Capsaicin Receptor Transient Receptor Potential Vanilloid Receptor 1 to Induce Hyperalgesia

Inflammatory proteases (mast cell tryptase and trypsins) cleave protease-activated receptor 2 (PAR2) on spinal afferent neurons and cause persistent inflammation and hyperalgesia by unknown mechanisms. We determined whether transient receptor potential vanilloid receptor 1 (TRPV1), a cation channel activated by capsaicin, protons, and noxious heat, mediates PAR2-induced hyperalgesia. PAR2 was coexpressed with TRPV1 in small- to medium-diameter neurons of the dorsal root ganglia (DRG), as determined by immunofluorescence. PAR2 agonists increased intracellular [Ca2+] ([Ca2+]i) in these neurons in culture, and PAR2-responsive neurons also responded to the TRPV1 agonist capsaicin, confirming coexpression of PAR2 and TRPV1. PAR2 agonists potentiated capsaicin-induced increases in [Ca2+]i in TRPV1-transfected human embryonic kidney (HEK) cells and DRG neurons and potentiated capsaicin-induced currents in DRG neurons. Inhibitors of phospholipase C and protein kinase C (PKC) suppressed PAR2-induced sensitization of TRPV1-mediated changes in [Ca2+]i and TRPV1 currents. Activation of PAR2 or PKC induced phosphorylation of TRPV1 in HEK cells, suggesting a direct regulation of the channel. Intraplantar injection of a PAR2 agonist caused persistent thermal hyperalgesia that was prevented by antagonism or deletion of TRPV1. Coinjection of nonhyperalgesic doses of PAR2 agonist and capsaicin induced hyperalgesia that was inhibited by deletion of TRPV1 or antagonism of PKC. PAR2 activation also potentiated capsaicin-induced release of substance P and calcitonin gene-related peptide from superfused segments of the dorsal horn of the spinal cord, where they mediate hyperalgesia. We have identified a novel mechanism by which proteases that activate PAR2 sensitize TRPV1 through PKC. Antagonism of PAR2, TRPV1, or PKC may abrogate protease-induced thermal hyperalgesia.
Geographical Analysis of Aneurysmal Subarachnoid Hemorrhage in Japan Utilizing Publically-Accessible DPC Database

Since the launch of the novel medical reimbursement system Diagnosis Procedure Combination (DPC) in 2003 in Japan, inpatient data has been accumulated over time as part of a Japanese governmental nationwide database. This is partially accessible by the public, and this study examined the adequacy of this database as epidemiological research material by extracting the data relating to aneurysmal subarachnoid hemorrhage (aSAH) with special attention given to the limitations that this involves. Datasets after 2010 are considered suitable for analysis because of the numbers of participating hospitals and the analysis term. Extracting the data by prefecture, those with a continuously high aSAH incidence were Aomori, Iwate, Akita, Yamagata, Kochi and Kumamoto Prefectures, and those with low aSAH incidence were Kanagawa, Shiga, Kyoto, Shimane and Ehime Prefectures. Although these obtained results are informative, a publically-accessible DPC database has several limitations. Some limitations have been resolved: the analyzed term each year is now 12-months and the number of participating hospitals seems to have stabilized around 1700. However, other limitations such as masking the numbers in each hospital reporting less than 10 patients still exist, so careful and critical interpretation is necessary in utilizing a publically-accessible DPC database. Considering the potential of this database as material for epidemiological research, future analysis of the entire DPC database by qualified researchers is desirable.
In God We Trust. All Others Must Bring Data. - W. Edwards Deming. Using Word Embeddings to Recognize Idioms

Expressions, such as add fuel to the ﬁre , can be interpreted literally or idiomatically depending on the context they occur in. Many Natural Language Processing applications could improve their performance if idiom recognition were improved. Our approach is based on the idea that idioms violate cohesive ties in local contexts, while literal expressions do not. We propose two approaches: 1) Compute inner product of context word vectors with the vector representing a target expression. Since literal vectors predict well local contexts, their inner product with contexts should be larger than idiomatic ones, thereby telling apart literals from idioms; and (2) Compute literal and idiomatic scatter (covariance) matrices from local contexts in word vector space. Since the scatter matrices represent context distributions, we can then measure the difference between the distributions using the Frobenius norm. For comparison, we implement Fazly et al. (2009)’s, Sporleder and Li (2009)’s, and Li and Sporleder (2010b)’s methods and apply them to our data. We provide experimental results validating the proposed techniques.
Integrated Analysis of Mutation Data from Various Sources Identifies Key Genes and Signaling Pathways in Hepatocellular Carcinoma

Background Recently, a number of studies have performed genome or exome sequencing of hepatocellular carcinoma (HCC) and identified hundreds or even thousands of mutations in protein-coding genes. However, these studies have only focused on a limited number of candidate genes, and many important mutation resources remain to be explored. Principal Findings In this study, we integrated mutation data obtained from various sources and performed pathway and network analysis. We identified 113 pathways that were significantly mutated in HCC samples and found that the mutated genes included in these pathways contained high percentages of known cancer genes, and damaging genes and also demonstrated high conservation scores, indicating their important roles in liver tumorigenesis. Five classes of pathways that were mutated most frequently included (a) proliferation and apoptosis related pathways, (b) tumor microenvironment related pathways, (c) neural signaling related pathways, (d) metabolic related pathways, and (e) circadian related pathways. Network analysis further revealed that the mutated genes with the highest betweenness coefficients, such as the well-known cancer genes TP53, CTNNB1 and recently identified novel mutated genes GNAL and the ADCY family, may play key roles in these significantly mutated pathways. Finally, we highlight several key genes (e.g., RPS6KA3 and PCLO) and pathways (e.g., axon guidance) in which the mutations were associated with clinical features. Conclusions Our workflow illustrates the increased statistical power of integrating multiple studies of the same subject, which can provide biological insights that would otherwise be masked under individual sample sets. This type of bioinformatics approach is consistent with the necessity of making the best use of the ever increasing data provided in valuable databases, such as TCGA, to enhance the speed of deciphering human cancers.
Habitat collapse due to overgrazing threatens turtle conservation in marine protected areas

Marine protected areas (MPAs) are key tools for combatting the global overexploitation of endangered species. The prevailing paradigm is that MPAs are beneficial in helping to restore ecosystems to more ‘natural’ conditions. However, MPAs may have unintended negative effects when increasing densities of protected species exert destructive effects on their habitat. Here, we report on severe seagrass degradation in a decade-old MPA where hyper-abundant green turtles adopted a previously undescribed below-ground foraging strategy. By digging for and consuming rhizomes and roots, turtles create abundant bare gaps, thereby enhancing erosion and reducing seagrass regrowth. A fully parametrized model reveals that the ecosystem is approaching a tipping point, where consumption overwhelms regrowth, which could potentially lead to complete collapse of the seagrass habitat. Seagrass recovery will not ensue unless turtle density is reduced to nearly zero, eliminating the MPA's value as a turtle reserve. Our results reveal an unrecognized, yet imminent threat to MPAs, as sea turtle densities are increasing at major nesting sites and the decline of seagrass habitat forces turtles to concentrate on the remaining meadows inside reserves. This emphasizes the need for policy and management approaches that consider the interactions of protected species with their habitat.
Functional Analysis of Vif Protein Shows Less Restriction of Human Immunodeficiency Virus Type 2 by APOBEC3G

ABSTRACT Viral infectivity factor (Vif) is one of the human immunodeficiency virus (HIV) accessory proteins and is conserved in the primate lentivirus group. This protein is essential for viral replication in vivo and for productive infection of nonpermissive cells, such as peripheral blood mononuclear cells (PBMC). Vif counteracts an antiretroviral cellular factor in nonpermissive cells named CEM15/APOBEC3G. Although HIV type 1 (HIV-1) Vif protein (Vif1) can be functionally replaced by HIV-2 Vif protein (Vif2), its identity is very small. Most of the functional studies have been carried out with Vif1. Characterization of functional domains of Vif2 may elucidate its function, as well as differences between HIV-1 and HIV-2 infectivity. Our aim was to identify the permissivity of different cell lines for HIV-2 vif-minus viruses. By mutagenesis specific conserved motifs of HIV-2 Vif protein were analyzed, as well as in conserved motifs between Vif1 and Vif2 proteins. Vif2 mutants were examined for their stability, expression, and cellular localization in order to characterize essential domains of Vif2 proteins. Viral replication in various target cells (PBMC and H9, A3.01, U38, and Jurkat cells) and infectivity in single cycle assays in the presence of APOBEC3G were also analyzed. Our results of viral replication show that only PBMC have a nonpermissive phenotype in the absence of Vif2. Moreover, the HIV-1 vif-minus nonpermissive cell line H9 does not show a similar phenotype for vif-negative HIV-2. We also report a limited effect of APOBEC3G in a single-cycle infectivity assay, where only conserved domains between HIV-1 and HIV-2 Vif proteins influence viral infectivity. Taken together, these results allow us to speculate that viral inhibition by APOBEC3G is not the sole and most important determinant of antiviral activity against HIV-2.
Meta-Analysis of Criterion Validity for Curriculum-Based Measurement in Written Language

We used meta-analysis to examine the criterion validity of four scoring procedures used in curriculum-based measurement of written language. A total of 22 articles representing 21 studies (N = 21) met the inclusion criteria. Results indicated that two scoring procedures, correct word sequences and correct minus incorrect sequences, have acceptable criterion validity with commercially developed and state- or locally developed criterion assessments. Results indicated trends for scoring procedures at each grade level. Implications for researchers and practitioners are discussed.
Improving a Bimanual Motor Skill Through Unimanual Training

When we learn a bimanual motor skill (e.g., rowing a boat), we often break it down into unimanual practices (e.g., a rowing drill with the left or right arm). Such unimanual practice is thought to be useful for learning bimanual motor skills efficiently because the learner can concentrate on learning to perform a simpler component. However, it is not so straightforward to assume that unimanual training (UT) improves bimanual performance. We have previously demonstrated that motor memories for reaching movements consist of three different parts: unimanual-specific, bimanual-specific, and overlapping parts. According to this scheme, UT appears to be less effective, as its training effect is only partially transferred to the same limb for bimanual movement. In the present study, counter-intuitively, we demonstrate that, even after the bimanual skill is almost fully learned by means of bimanual training (BT), additional UT could further improve bimanual skill. We hypothesized that this effect occurs because UT increases the memory content in the overlapping part, which might contribute to an increase in the memory for bimanual movement. To test this hypothesis, we examined whether the UT performed after sufficient BT could improve the bimanual performance. Participants practiced performing bimanual reaching movements (BM) in the presence of a novel force-field imposed only on their left arm. As an index for the motor performance, we used the error-clamp method (i.e., after-effect of the left arm) to evaluate the force output to compensate for the force-field during the reaching movement. After sufficient BT, the training effect reached a plateau. However, UT performed subsequently improved the bimanual performance significantly. In contrast, when the same amount of BT was continued, the bimanual performance remained unchanged, highlighting the beneficial effect of UT on bimanual performance. Considering memory structure, we also expected that BT could improve unimanual performance, which was confirmed by another experiment. These results provide a new interpretation of why UT was useful for improving a bimanual skill, and propose a practical strategy for enhancing performance by performing training in various contexts.
The Informal Sector, Firm Dynamics and Institutional Participation

The informal microfirm sector is believed to be large, accounting for 20-40 percent of employment in many developing countries. The literature tends to view the sector as the disadvantaged sector of a segmented labor market, as existing to evade government regulations, or as constrained by lack of access to government services. The authors offer a unique theoretical framework to analyze informality and microfirm growth behavior -- one that emphasizes the entrepreneurial nature of informal firms and sees informality as a secondary characteristic. First, they assume that informal firms in developing countries have dynamics similar to firms in industrial countries: entrepreneurs have unobserved, differing cost structures that determine their long-run size and survival -- structures that they can only discover by going into business. Second, informality can be thought of as a decision to participate in societal institutions. Access to mechanisms that ensure property rights, pool risk, or enforce contracts become more important as a firm grows, and the entrepreneur will be willing to pay for them through"taxes"in a way that was not the case as a small firm. The combination of these assumptions generates several of the stylized facts emerging from cross-sectional data and identified in existing models -- informal firms tend to remain small and have high rates of mortality, and lower productivity -- without recourse to government-induced distortions in labor or product markets. Further, the framework predicts that firms whose cost structures dictate that they should expand will make the transition to formality as they grow. Using detailed observations from Mexico, the authors find their view consistent with patterns of formality and growth of microfirms.
Skipping politics: Measuring avoidance of political content in social media

Selective exposure is a growing concern as people become more reliant on social media for political information. While self-reports often ask about exposure to political content on social media, existing research does not account for the fact that even those exposed to political content may still choose to ignore it. To effectively account for this, we employ corneal eye tracking software, such that we can observe users’ gaze and the amount of time they actually spend with political content. Consistent with expectations, the earlier a cue that a post is political, the faster a user skips over it. This trend is concentrated among those least interested in politics. Implications for how we think about social media and political information flows in the modern media environment are discussed.
Subrings of singular cohomology associated to spectra

This paper extends the relation established for group cohomology by Green, Hunton and Schuster between chromatic phenomena in stable homotopy theory and certain natural subrings of singular cohomology. This exploits the theory due to Henn, Lannes and Schwartz of unstable algebras over the Steenrod algebra localized away from nilpotents.
Aetiological overlap between anxiety and attention deficit hyperactivity symptom dimensions in adolescence

Background Anxiety and attention‐deficit/hyperactivity (ADH) problems are common in adolescence, often co‐occur, and are characterised by high heterogeneity in their phenotypic expressions. Although it is known that anxiety and ADH problems correlate, the relationships between subtypes of anxiety and ADH problems have been scarcely investigated. Methods Using a large population sample of adolescent twins and siblings we explored the phenotypic and aetiological association between anxiety subtypes (panic/agoraphobia, separation anxiety, social anxiety, physical injury fears, obsessive‐compulsive symptoms and generalised anxiety) and the two ADH dimensions (attention problems and hyperactivity/impulsivity). Both phenotypes were assessed using self‐report questionnaires. Results The association between ADH problems and anxiety could be entirely attributed to attention problems, not hyperactivity/impulsivity. Most of the correlations between anxiety subtypes and attention problems showed an approximately equal role of genetic and nonshared environmental factors. Conclusions The high heterogeneity within anxiety and ADH problems should be taken into account in order to better understand comorbidity between them.
Upper Airway Collapsibility and Patterns of Flow Limitation at Constant End-expiratory Lung 1 Volume 2 3 Key Words 57 Obstructive Sleep Apnea, Pharyngeal Critical Closing Pressure, Starling Resistor 58 59

34 The passive pharyngeal critical closing pressure (Pcrit) is measured using a series of pressure 35 drops. However, pressure drops also lower end-expiratory lung volume (EELV), which 36 independently affects Pcrit. We describe a technique to measure Pcrit at a constant EELV. 37 CPAP treated obstructive sleep apnea (OSA) patients and controls were instrumented with an 38 epiglottic catheter, magnetometers (to measure change in EELV), and nasal 39 mask/pneumotachograph and slept supine on nasal CPAP. Pcrit was measured in standard 40 fashion and using our novel “biphasic technique” in which expiratory pressure only was lowered 41 for one minute prior to dropping the inspiratory pressure; this allowed EELV to decrease to the 42 drop level before performing the pressure drop. 7 OSA and 3 controls were studied. The 43 biphasic technique successfully lowered EELV prior to the inspiratory pressure drop. Pcrit was 44 similar between the standard and biphasic techniques (-0.4±2.6 vs. -0.6±2.3cmH2O, respectively, 45 p=0.84). Interestingly, we noted three different patterns of flow limitation: 1) classic Starling 46 resistor type – flow fixed and independent of downstream pressure, 2) negative effort 47 dependence within breaths – substantial decrease in flow, sometimes with complete collapse, as 48 downstream pressure decreased 3) and negative effort dependence across breaths – progressive 49 reductions in peak flow as respiratory effort on successive breaths increased. Overall, EELV 50 changes do not influence standard passive Pcrit measurements if breaths 3-5 of pressure drops 51 are used. These results also highlight the importance of inspiratory collapse in OSA 52 pathogenesis. The cause of negative effort dependence within and across breaths is not known 53 and requires further study. 54