Miracle-dz/UniFAR-FTUs huggingface dataset:
Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes

Metagenomics is the study of microorganisms in environmental and clinical samples using high-throughput sequencing of random fragments of their DNA. Since metagenomics does not require any prior culturing of isolates, entire microbial communities can be studied directly in their natural state. In metagenomics, the abundance of genes is quantified by sorting and counting the DNA fragments. The resulting count data are high-dimensional and affected by high levels of technical and biological noise that make the statistical analysis challenging. In this article, we introduce an hierarchical overdispersed Poisson model to explore the variability in metagenomic data. By analyzing three comprehensive data sets, we show that the gene-specific variability varies substantially between genes and is dependent on biological function. We also assess the power of identifying differentially abundant genes and show that incorrect assumptions about the gene-specific variability can lead to unacceptable high rates of false positives. Finally, we evaluate shrinkage approaches to improve the variance estimation and show that the prior choice significantly affects the statistical power. The results presented in this study further elucidate the complex variance structure of metagenomic data and provide suggestions for accurate and reliable identification of differentially abundant genes.
A Mild Form of SLC29A3 Disorder: A Frameshift Deletion Leads to the Paradoxical Translation of an Otherwise Noncoding mRNA Splice Variant

We investigated two siblings with granulomatous histiocytosis prominent in the nasal area, mimicking rhinoscleroma and Rosai-Dorfman syndrome. Genome-wide linkage analysis and whole-exome sequencing identified a homozygous frameshift deletion in SLC29A3, which encodes human equilibrative nucleoside transporter-3 (hENT3). Germline mutations in SLC29A3 have been reported in rare patients with a wide range of overlapping clinical features and inherited disorders including H syndrome, pigmented hypertrichosis with insulin-dependent diabetes, and Faisalabad histiocytosis. With the exception of insulin-dependent diabetes and mild finger and toe contractures in one sibling, the two patients with nasal granulomatous histiocytosis studied here displayed none of the many SLC29A3-associated phenotypes. This mild clinical phenotype probably results from a remarkable genetic mechanism. The SLC29A3 frameshift deletion prevents the expression of the normally coding transcripts. It instead leads to the translation, expression, and function of an otherwise noncoding, out-of-frame mRNA splice variant lacking exon 3 that is eliminated by nonsense-mediated mRNA decay (NMD) in healthy individuals. The mutated isoform differs from the wild-type hENT3 by the modification of 20 residues in exon 2 and the removal of another 28 amino acids in exon 3, which include the second transmembrane domain. As a result, this new isoform displays some functional activity. This mechanism probably accounts for the narrow and mild clinical phenotype of the patients. This study highlights the ‘rescue’ role played by a normally noncoding mRNA splice variant of SLC29A3, uncovering a new mechanism by which frameshift mutations can be hypomorphic.
Isolation and characterization of a promoter responsive to salt, osmotic and dehydration stresses in soybean

Abstract Drought stress is the main limiting factor of soybean yield. Currently, genetic engineering has been one important tool in the development of drought-tolerant cultivars. A widely used strategy is the fusion of genes that confer tolerance under the control of the CaMV35S constitutive promoter; however, stress-responsive promoters would constitute the best alternative to the generation of drought-tolerant crops. We characterized the promoter of α-galactosidase soybean (GlymaGAL) gene that was previously identified as highly up-regulated by drought stress. The β-glucuronidase (GUS) activity of Arabidopsis transgenic plants bearing 1000- and 2000-bp fragments of the GlymaGAL promoter fused to the uidA gene was evaluated under air-dried, polyethylene glycol (PEG) and salt stress treatments. After 24 h of air-dried and PEG treatments, the pGAL-2kb led to an increase in GUS expression in leaf and root samples when compared to the control samples. These results were corroborated by qPCR expression analysis of the uidA gene. The pGAL-1kb showed no difference in GUS activity between control and treated samples. The pGAL-2kb promoter was evaluated in transgenic soybean roots, leading to an increase in EGFP expression under air-dried treatment. Our data indicates that pGAL-2kb could be a useful tool in developing drought-tolerant cultivars by driving gene expression.
Documents of learning: graduate students’ experiences of tensions when studying qualitative data analysis approaches

This reflective article discusses the learning processes and experiences associated with qualitative data analysis as presented in students’ reflection journals. Fourteen doctoral students in a qualitative data analysis course shared their reflective journals with the research team. Data analysis included: (1) analysis of tension type and contexts; and (2) critical discourse analysis of students’ texts. The data illustrated various types and contexts of tensions such as: (1) desire for mastery and positioning oneself as a lifelong learner; (2) time required for analysis and time available to complete the research project; (3) holistic and detail oriented analysis; and (4) individual perception of an analysis and group consensus. Based on the findings, the use of reflective journaling can facilitate student learning and instructors’ understandings of students’ professional growth. The article concludes with some benefits and limitations of reflective journaling as documents of learning in the context of research training.
Spécificités des coopérations en R&D subventionnées et non subventionnées dans la stratégie partenariale d’EDF R&D

Ce travail analyse la place respective des cooperations en R&D subventionnees versus non subventionnees dans les strategies d’accords technologiques des entreprises. Nous avancons que les ressources additionnelles apportees par les subventions gouvernementales favorisent la creation d’un portefeuille de cooperation ambidextre, les accords subventionnes etant plus exploratoires que les seconds, lesquels sont plutot a visee d’exploitation. Puis nous elaborons une serie de propositions theoriques permettant de differencier les deux types d’accords suivant deux logiques organisationnelles distinctes, en termes d’incitation, de coordination et d’apprentissage. L’ensemble de nos propositions est confronte de maniere probante au cas de la strategie partenariale d’EDF R&D.
InGaAs channel HEMTs for photonic frequency double mixing conversion over the sub-THz band

We report on photonic frequency double-mixing conversion utilizing an InGaAs channel HEMT. A 1-GHz modulation signal on a 112.5-GHz carrier is electrically input to the gate, whereas a 1.58-μm dual wavelength CW laser beam having a frequency difference of 87.5-GHz local signal are irradiated to the channel. The InGaAs HEMT works as a photomixer generating a 87.5-GHz local signal which is then electrically mixed to the 5-GHz modulated 112.5-GHz carrier signal, resulting in the down-conversion of the 5-GHz signal to a 25-GHz intermediate frequency (IF) band.
Constructing discussion tasks in university tutorials: shifting dynamics and identities

This article examines task-setting sequences in university tutorial sessions. Classes from three higher education institutions were audio- and video-recorded. The resulting data, which included both tutor-led and peer group discussions, were transcribed and analysed using conversation analysis (CA). A number of themes emerged from our analysis. First, we found that the tutor's opening turns routinely followed a three-part sequence, the interpersonal and metadiscursive functions of which, we argue, are crucial components in the educative process. Second, we found that students displayed discursively their reluctance to engage in discussion activities and a resistance towards academic or intellectual identities. In contrast to findings from previous studies of tutor—student interaction, we found that interactional power was negotiated in complex and contradictory ways. This, in turn, may embody a range of complex social functions including attention to the `face' concerns of the group, category membership and orientation to broader cultural trends.
Awareness of Stress-Reduction Interventions on Work Attitudes: The Impact of Tenure and Staff Group in Australian Universities

This study explored the impact of staff group role and length of organizational tenure in the relationship between the awareness of stress interventions (termed intervention awareness: IA) and the work-related attitudinal outcomes of university employees. A two-wave longitudinal study of a sample of 869 employees from 13 universities completed a psychosocial work factors and health questionnaire. Hierarchical regression analyses examined the contribution of staff role and different lengths of organizational tenure with IA and employees' reports of job satisfaction, affective organizational commitment, trust in senior management, and perceived procedural justice. Employees' length of tenure affected the relation between IA and work attitudes, and there were also differences between academic and non-academic staff groups. For non-academic employees, IA predicted job satisfaction, affective organizational commitment, trust in senior management, and perceived procedural justice. However, for academics, IA only predicted job satisfaction and trust which identifies a need to increase the visibility of organizational interventions. Across the tenure groups, IA predicted: (1) perceived procedural justice for employees with five or less years of tenure; (2) job satisfaction for employees with 0–19 years of tenure; (3) trust in senior management for employees with 6–19 years of tenure; and (4) affective organizational commitment for employees with a tenure length of 6–10 years. Employees working at the university for an intermediate period had the most positive perceptions of their organization in terms of IA, job satisfaction, trust in senior management, and affective organizational commitment, whereas employees with 20–38 years of tenure had the least positive perceptions. Results suggest that employees in the middle of their careers report the most positive perceptions of their university. The findings highlight the need to attend to contextual issues in organizational stress and wellbeing interventions and suggest that management may need to implement new strategies and/or promote existing stress-management and reduction strategies to academics, and employees whom are either new to the university or those who have been working for the organization for longer periods of time to ensure that they are aware of organizational strategies to promote employee wellbeing and morale within their work environments.
Advantages and applications of CAR-expressing natural killer cells

In contrast to donor T cells, natural killer (NK) cells are known to mediate anti-cancer effects without the risk of inducing graft-versus-host disease (GvHD). In order to improve cytotoxicity against resistant cancer cells, auspicious efforts have been made with chimeric antigen receptor (CAR) expressing T- and NK cells. These CAR-modified cells express antigen receptors against tumor-associated surface antigens, thus redirecting the effector cells and enhancing tumor-specific immunosurveillance. However, many cancer antigens are also expressed on healthy tissues, potentially leading to off tumor/on target toxicity by CAR-engineered cells. In order to control such potentially severe side effects, the insertion of suicide genes into CAR-modified effectors can provide a means for efficient depletion of these cells. While CAR-expressing T cells have entered successfully clinical trials, experience with CAR-engineered NK cells is mainly restricted to pre-clinical investigations and predominantly to NK cell lines. In this review we summarize the data on CAR expressing NK cells focusing on the possible advantage using these short-lived effector cells and discuss the necessity of suicide switches. Furthermore, we address the compliance of such modified NK cells with regulatory requirements as a new field in cellular immunotherapy.
Named Entity Recognition in Broadcast News Using Similar Written Texts

We propose a new approach to improving named entity recognition (NER) in broadcast news speech data. The approach proceeds in two key steps: (1) we detect block alignments between highly similar blocks of the speech data and corresponding written news data that are easily obtainable from the Web, (2) we employ term expansion techniques commonly used in information retrieval to recover named entities that were initially missed by the speech transcriber. We show that our method is able to find the named entities missing in the transcribed speech data, but also to correct incorrectly assigned named entity tags. Consequently, our novel approach improves state-of-the-art results of NER from speech data both in terms of recall and precision.
Cardiovascular Recovery From Acute Laboratory Stress: Reliability and Concurrent Validity

Objective We assessed the value of laboratory measures of cardiovascular recovery across four criteria: reliability across multiple tasks, reliability across a 3-year time interval, ability to predict daily ambulatory blood pressure, and interrelationships with coronary risk factors and psychosocial variables. Methods Three hundred twenty-nine healthy adults (mean age = 27.1 years) completed a two-part protocol consisting of 1 day of laboratory testing and 1 day of ambulatory monitoring. The laboratory protocol included a 15-minute baseline assessment followed by three 5-minute laboratory challenges (mental arithmetic, speech, and handgrip). Five-minute recovery periods followed each exercise. One hundred twenty-five participants returned after 3 years to repeat the protocol. Results When aggregated across tasks, cardiovascular recovery showed acceptable levels of internal consistency (&agr; values = 0.7) and proved relatively stable across time (r values = 0.22–0.35). Recovery values statistically improved the prediction of daily ambulatory readings above baseline and stress reactivity laboratory values (p values < .001) but were largely unrelated to coronary risk factors or psychosocial measures. Conclusion These results suggest that cardiovascular recovery from acute laboratory stress can be treated as a stable individual difference variable that can improve standard laboratory-based predictor models of ambulatory readings.
‘Negative symptoms’, health, depression, and level of functioning among nursing home residents

A six‐month longitudinal design was used to assess the relations among functinal ability, medically disabling conditions, cognitive function, depression, and negative psychiatric symptoms in a nursing home sample. Seventy intermediate and skilled care residents were interviewed, with 51 completing the six‐month follow‐up. Negative symptoms were found to be related approximately equally to physical disability, boredom, and depression, but were not strongly predicted by any study variables. The most stable relationship observed was that between negative symptoms and functioning in the realm of activities of daily living (ADL). Negative symptoms predicted change in ADL functioning across the six‐month period of the study. The findings have possible implications for predicting mortality and focusing interventions on what appears to be a general decline syndrome in nursing home elderly.
Cards, Money and Two Hacking Forums: An Analysis of Online Money Laundering Schemes

The emergence of the internet as a global, borderless communication platform afforded a wide range ofsocial and economic opportunities to people throughout theworld. Criminals have exploited the ability to communicateinstantaneously around the globe to facilitate crossjurisdictionalcyber-fraud and subsequently, online moneylaundering. Coordinating international fraud and moneylaundering schemes requires a medium of communication, suchas online hacking and carding forums, where offenders meet toexchange information and to engage in their illegal business. Forthe study presented in this paper, publicly available onlinecarding and hacking forums were downloaded and keywords ofinterest pertaining to online money laundering were extracted. This study undertakes an analysis of two large Russian-speakinghacking and carding forums by qualitatively analyzing andquantifying contexts of keyword usage. Findings indicate thatcyber-fraudsters are primarily interested in cashing outdigitally stolen funds and do so mainly by resorting to theservices of money mules and virtual casinos.
Acid-sensing Ion Channel 2 (ASIC2) Modulates ASIC1 H+-activated Currents in Hippocampal Neurons*

Hippocampal neurons express subunits of the acid-sensing ion channel (ASIC1 and ASIC2) and exhibit large cation currents that are transiently activated by acidic extracellular solutions. Earlier work indicated that ASIC1 contributed to the current in these neurons and suggested its importance for normal behavior. However, the specific contribution of ASIC1 and ASIC2 subunits to acid-evoked currents in hippocampal neurons remained uncertain. To decipher the individual role of the ASIC subunits, we studied H+-gated currents in neurons from both ASIC1 and ASIC2 null mice. We found that much of the current was produced by ASIC1a/2a heteromultimeric channels, and individual subunits made distinct contributions. The ASIC1a subunit was key in establishing current amplitude. The ASIC2a subunit had little effect on amplitude but influenced desensitization, recovery from desensitization, pH sensitivity, and the response to modulatory agents. We also found heterogeneity in the contribution of ASIC2 throughout the neuronal population, with individual neurons expressing both ASIC1a homomultimeric and ASIC1a/2a heteromultimeric channels. Studies of neurons heterozygous for disrupted ASIC alleles indicated that the properties of H+-gated currents are dependent on the proportion of the individual subunits. These findings indicate that the absolute and relative amounts of ASIC subunits determine the amplitude and properties of hippocampal H+-gated currents and therefore may contribute to normal physiology and pathophysiology.
History by Diversity: Helping Historians search News Archives

Longitudinal corpora like newspaper archives are of immense value to historical research, and time as an important factor for historians strongly influences their search behaviour in these archives. While searching for articles published over time, a key preference is to retrieve documents which cover the important aspects from important points in time which is different from standard search behavior. To support this search strategy, we introduce the notion of a Historical Query Intent to explicitly model a historian's search task and define an aspect-time diversification problem over news archives. We present a novel algorithm, HistDiv, that explicitly models the aspects and important time windows based on a historian's information seeking behavior. By incorporating temporal priors based on publication times and temporal expressions, we diversify both on the aspect and temporal dimensions. We test our methods by constructing a test collection based on The New York Times Collection with a workload of 30 queries of historical intent assessed manually. We find that HistDiv outperforms all competitors in subtopic recall with a slight loss in precision. We also present results of a qualitative user study to determine wether this drop in precision is detrimental to user experience. Our results show that users still preferred HistDiv's ranking.
An Extension of the Consensus-Based Bundle Algorithm for Multi-agent Tasks with Task Based Requirements

This paper addresses the problem of multi-agent, multi-task assignment with multiple agent requirements on tasks for unmanned aerial vehicles by presenting the Consensus Based Grouping Algorithm. The algorithm is an extension of the Consensus Based Bundle Algorithm that converges to a conflict free, feasible solution of which previous algorithms are unable to account for. Furthermore the algorithm creates a framework to take into account task based requirements, deadlocking and a method to store assignments for a dynamical environment.
Endothelial Arginine Resynthesis Contributes to the Maintenance of Vasomotor Function in Male Diabetic Mice

Aim Argininosuccinate synthetase (ASS) is essential for recycling L-citrulline, the by-product of NO synthase (NOS), to the NOS substrate L-arginine. Here, we assessed whether disturbed arginine resynthesis modulates endothelium-dependent vasodilatation in normal and diabetic male mice. Methods and Results Endothelium-selective Ass-deficient mice (Assfl/fl/Tie2Cretg/− = Ass-KOTie2) were generated by crossing Assfl/fl mice ( = control) with Tie2Cre mice. Gene ablation in endothelial cells was confirmed by immunohistochemistry. Blood pressure (MAP) was recorded in 34-week-old male mice. Vasomotor responses were studied in isolated saphenous arteries of 12- and 34-week-old Ass-KOTie2 and control animals. At the age of 10 weeks, diabetes was induced in control and Ass-KOTie2 mice by streptozotocin injections. Vasomotor responses of diabetic animals were studied 10 weeks later. MAP was similar in control and Ass-KOTie2 mice. Depletion of circulating L-arginine by arginase 1 infusion or inhibition of NOS activity with L-NAME resulted in an increased MAP (10 and 30 mmHg, respectively) in control and Ass-KOTie2 mice. Optimal arterial diameter, contractile responses to phenylephrine, and relaxing responses to acetylcholine and sodium nitroprusside were similar in healthy control and Ass-KOTie2 mice. However, in diabetic Ass-KOTie2 mice, relaxation responses to acetylcholine and endothelium-derived NO (EDNO) were significantly reduced when compared to diabetic control mice. Conclusions Absence of endothelial citrulline recycling to arginine did not affect blood pressure and systemic arterial vasomotor responses in healthy mice. EDNO-mediated vasodilatation was significantly more impaired in diabetic Ass-KOTie2 than in control mice demonstrating that endothelial arginine recycling becomes a limiting endothelial function in diabetes.