Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of the basement membrane in invasive epithelial clusters in Drosophila

The basement membrane (BM) represents a barrier to cell migration, which has to be degraded to promote invasion. However, the role and behaviour of the BM during the development of pre-invasive cells is only poorly understood. Drosophila border cells (BCs) provide an attractive genetic model in which to study the cellular mechanisms underlying the migration of mixed cohorts of epithelial cells. BCs are made of two different epithelial cell types appearing sequentially during oogenesis: the polar cells and the outer BCs. Here, we show that the pre-invasive polar cells undergo an unusual and asymmetrical apical capping with major basement membrane proteins, including the two Drosophila Collagen IV α chains, Laminin A and Perlecan. Capping of polar cells proceeds through a novel, basal-to-apical transcytosis mechanism that involves the small GTPase Drab5. Apical capping is transient and is followed by rapid shedding prior to the initiation of BC migration, suggesting that the apical cap blocks migration. Consistently, non-migratory polar cells remain capped. We further show that JAK/STAT signalling and recruitment of outer BCs are required for correct shedding and migration. The dynamics of the BM represents a marker of migratory BC, revealing a novel developmentally regulated behaviour of BM coupled to epithelial cell invasiveness.
Early Outcomes of Roux-en-Y Gastric Bypass in a Publically Funded Obesity Program

Background. There is limited literature assessing the outcomes of bariatric surgery in a publically funded, North American, multidisciplinary bariatric program. Our objective was to assess outcomes of roux-en-Y gastric bypass (RYGB) in a publically funded bariatric program through a retrospective review of patient records. Methods. 293 patients spent a median of 13 months attending a multidisciplinary obesity clinic prior to undergoing laparoscopic RYGB surgery. The hospital was a Canadian, publically funded, level 2 trauma center with university teaching services. Results. 79% of the patients were female and the average BMI at first visit to clinic was 55.3 kg/m2. The average decrease in BMI was 19.2 ± 0.9 kg/m2. This was an average absolute weight loss of 56.1 kg or 35.5% of initial weight. The average excess weight loss was 63.4 ± 20.4%. Improvement or resolution of obesity related comorbidities occurred in 65.9% of type 2 diabetics and in 50% of hypertensive patients. Conclusion. Despite this being an unconventional setting of a publically funded program in a large Canadian teaching hospital, early outcomes following RYGB were appropriate in severely obese patients. Ongoing work will identify areas of improvement for enhanced efficiencies within this system.
Misaligned Principal Components Analysis: Application to gene expression time series analysis

Principal Component Analysis (PCA) is a widely applied method for extracting structure from samples of high dimensional biological data. Often there exist misalignments between different samples and this can cause severe problems in PCA if not properly taken into account. For example, subject-dependent temporal differences in gene expression response to a treatment will create relative time shifts in the samples that decohere the PCA analysis. Depending on the characteristics of the underlying signal, the sensitivity of PCA to such misalignments is severe, leading to a phase transition phenomenon that can be studied using the spectral theory of autocorrelation matrices. With this as motivation, we propose a new method of PCA, called MisPCA, that explicitly accounts for the effects of misalignments in the samples. We illustrate MisPCA on clustering longitudinal temporal gene expression data.
Isolobal Series of Chemical Fragments

During the study of carbonyl clusters using 14n and 4n rules, it was discovered that fragments and atoms could be categorized. This paper presents the categorization of isolobal fragments, molecules and ions using the 14n and 4n rules. In the process of categorization, the conventional periodic table was recreated. A new method of categorizing clusters using fragments and series has been introduced for the first time and this immensely simplifies the categorization of clusters from simple to more complex ones including boranes, carboranes, transition metal carbonyls and metalloboranes. The paper also introduces a simple algebra of cluster series.
Bipolar Disorder and the TCI: Higher Self-Transcendence in Bipolar Disorder Compared to Major Depression

Personality traits are potential endophenotypes for genetic studies of psychiatric disorders. One personality theory which demonstrates strong heritability is Cloninger's psychobiological model measured using the temperament and character inventory (TCI). 277 individuals who completed the TCI questionnaire as part of the South Island Bipolar Study were also interviewed to assess for lifetime psychiatric diagnoses. Four groups were compared, bipolar disorder (BP), type 1 and 2, MDD (major depressive disorder), and nonaffected relatives of a proband with BP. With correction for mood state, total harm avoidance (HA) was higher than unaffected in both MDD and BP groups, but the mood disorder groups did not differ from each other. However, BP1 individuals had higher self-transcendence (ST) than those with MDD and unaffected relatives. HA may reflect a trait marker of mood disorders whereas high ST may be specific to BP. As ST is heritable, genes that affect ST may be of relevance for vulnerability to BP.
Clinical and Biomarkers Difference in Prepartum and Postpartum Eclampsia

Background There is a large body of literature which assessed the incidence and risk factors of eclampsia, but little was done in assessing the association of clinical features and biological markers with prepartum and postpartum eclampsia. Methods A total of 361 eclamptic women admitted to three teaching hospitals between 2008 and 2013 were included in this analysis. A comparative analysis was done for several clinical and biological variables to assess their association with prepartum and postpartum eclampsia. Results The overall incidence of eclampsia was 1.2% (prepartum 71% and postpartum 29%). The majority of women with prepartum eclampsia were young, primigravida, more hypertensive, symptomatic and proteinuric. Conversely, the majoritys of the women with post-partum eclampsia were adult, multiparous, carrying pregnancy to term, anemic, thrombocytopenic, and with hepatic dysfunction. The commonest severity symptom (headache) was less common in postpartum eclamptic women. Conclusion The incidence of eclampsia was among the highest in the world. And, the analysis has shown that the clinical and biochemical spectrum of prepartum and postpartum eclampsia were apparently different. The majority of the women who developed postpartum eclampsia were multiparous and adult. Derangement of biomarkers was also more common in women with postpartum eclampsia.
Clonal Origin of Germ Cell Colonies after Spermatogonial Transplantation in Mice1

Abstract Spermatogenesis originates from a small number of spermatogonial stem cells that can reinitiate spermatogenesis and produce germ cell colonies following transplantation into infertile recipient testes. Although several previous studies have suggested a single-cell origin of germ cell colonies, only indirect evidence has been presented. In this investigation, we tested the clonal origin hypothesis using a retrovirus, which could specifically mark an individual spermatogonial stem cell. Spermatogonial stem cells were infected in vitro with an enhanced green fluorescence protein-expressing retrovirus and subsequently transplanted into infertile recipient mice. Live haploid germ cells were recovered from individual colonies and were microinjected into eggs to create offspring. In total, 45 offspring were produced from five colonies, and 23 (51%) of the offspring were transgenic. Southern blot analysis indicated that the transgenic offspring from the single colony carried a common integration site, and the integration site was different among the transgenic offspring from different colonies. These results provide evidence that germ cell colonies develop from single spermatogonial stem cells.
Bayesian Neural Word Embedding

Recently, several works in the domain of natural language processing presented successful methods for word embedding. Among them, the Skip-Gram with negative sampling, known also as word2vec, advanced the state-of-the-art of various linguistics tasks. In this paper, we propose a scalable Bayesian neural word embedding algorithm. The algorithm relies on a Variational Bayes solution for the Skip-Gram objective and a detailed step by step description is provided. We present experimental results that demonstrate the performance of the proposed algorithm for word analogy and similarity tasks on six different datasets and show it is competitive with the original Skip-Gram method.
Using Word Embeddings for Automatic Query Expansion

In this paper a framework for Automatic Query Expansion (AQE) is proposed using distributed neural language model word2vec. Using semantic and contextual relation in a distributed and unsupervised framework, word2vec learns a low dimensional embedding for each vocabulary entry. Using such a framework, we devise a query expansion technique, where related terms to a query are obtained by K-nearest neighbor approach. We explore the performance of the AQE methods, with and without feedback query expansion, and a variant of simple K-nearest neighbor in the proposed framework. Experiments on standard TREC ad-hoc data (Disk 4, 5 with query sets 301-450, 601-700) and web data (WT10G data with query set 451-550) shows significant improvement over standard term-overlapping based retrieval methods. However the proposed method fails to achieve comparable performance with statistical co-occurrence based feedback method such as RM3. We have also found that the word2vec based query expansion methods perform similarly with and without any feedback information.
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods.
What Makes a Good Bug Report?

In software development, bug reports provide crucial information to developers. However, these reports widely differ in their quality. We conducted a survey among developers and users of APACHE, ECLIPSE, and MOZILLA to find out what makes a good bug report. The analysis of the 466 responses revealed an information mismatch between what developers need and what users supply. Most developers consider steps to reproduce, stack traces, and test cases as helpful, which are, at the same time, most difficult to provide for users. Such insight is helpful for designing new bug tracking tools that guide users at collecting and providing more helpful information. Our CUEZILLA prototype is such a tool and measures the quality of new bug reports; it also recommends which elements should be added to improve the quality. We trained CUEZILLA on a sample of 289 bug reports, rated by developers as part of the survey. The participants of our survey also provided 175 comments on hurdles in reporting and resolving bugs. Based on these comments, we discuss several recommendations for better bug tracking systems, which should focus on engaging bug reporters, better tool support, and improved handling of bug duplicates.
ApoA-II modulates the association of HDL with class B scavenger receptors SR-BI and CD36 Published, JLR Papers in Press, January 16, 2004. DOI 10.1194/jlr.M300417-JLR200

The class B scavenger receptors SR-BI and CD36 exhibit a broad ligand binding specificity. SR-BI is well characterized as a HDL receptor that mediates selective cholesteryl ester uptake from HDL. CD36, a receptor for oxidized LDL, also binds HDL and mediates selective cholesteryl ester uptake, although much less efficiently than SR-BI. Apolipoprotein A-II (apoA-II), the second most abundant HDL protein, is considered to be proatherogenic, but the underlying mechanisms are unclear. We previously showed that apoA-II modulates SR-BI-dependent binding and selective uptake of cholesteryl ester from reconstituted HDL. To investigate the effect of apoA-II in naturally occurring HDL on these processes, we compared HDL without apoA-II (from apoA-II null mice) with HDLs containing differing amounts of apoA-II (from C57BL/6 mice and transgenic mice expressing a mouse apoA-II transgene). The level of apoA-II in HDL was inversely correlated with HDL binding and selective cholesteryl ester uptake by both scavenger receptors, particularly CD36. Interestingly, for HDL lacking apoA-II, the efficiency with which CD36 mediated selective uptake reached a level similar to that of SR-BI. These results demonstrate that apoA-II exerts a marked effect on HDL binding and selective lipid uptake by the class B scavenger receptors and establishes a potentially important relationship between apoA-II and CD36.
Analytical Evaluation of the Diazyme Glycated Serum Protein Assay on the Siemens ADVIA 1800

Background: Hemoglobin A1c (HbA1c) is considered the gold standard for assessment of glycemic control in diabetic patients. HbA1c is inadequate in individuals homozygous or compound heterozygous for hemoglobin variants or in conditions with an altered red blood cell turnover. In these cases glycated albumin (GA) is proposed as an alternative assay. We aimed to evaluate the analytical performance of the Diazyme glycated serum protein (GSP) assay on an automated analyzer, to establish a reference interval (RI), and to compare from a clinical perspective, GSP/GA with glycated Hb (glyHb) results. Methods: Validation studies followed the CLSI guidelines and included precision, linearity, interferences, concordance of results with glyHb, and RI calculation. GSP was analyzed on representative samples with previously ordered HbA1c and albumin from the Dyna LIFE DX laboratory. Samples from patients with bisalbuminemia, hemoglobinopathies, and multiple myeloma were also included. Results: Within-run and total imprecision was <3.0% at both levels of control, analytical sensitivity was 5.31 μmol/L, and linearity was verified from 10 to 1150 μmol/L (total allowable error of 5%). Clinical concordance between %GA and glyHb was substantial (n = 175, R2 = .91, kappa = .78, P = .167). GSP RI was 160 to 340 μmol/L or if expressed as %GA 10.5 to 17.5%. Conclusion: Analytical performance of the Diazyme GSP assay on the Siemens ADVIA 1800 is acceptable for clinical use. The RI obtained was higher than that suggested by the manufacturer.
A critical realist rationale for using a combination of quantitative and qualitative methods

Although using a combination of quantitative and qualitative approaches is widely advocated, there is considerable scope for confusion due to the complex ontological and epistemological issues that need to be resolved. This paper examines some of the issues that may arise when the methods are combined. Three distinct standpoints with regard to using mixed method approaches are highlighted: a methodological purist position, a pragmatic standpoint and an anti-conflationist position. It is suggest that an anti-conflationist approach that is underpinned by the philosophy of critical realism is compatible with all three of the purposes of methodological triangulation identified by Risjord and his co-authors (Risjord et al., 2001, 2002) and that adopting a critical realist perspective may circumvent many of the problems that are associated with paradigm ‘switching’. The case for adopting a critical realist framework is illustrated by a case study, in which a combination of quantitative and qualitative methods was used to explore how and why gatekeeping decisions emerge at the interface between primary care and community mental health teams.
Visual Eyes: A Quantitative Analysis of the Photoreceptor Layer in Deep-Sea Sharks

The marine environment presents unique visual challenges for a range of organisms, particularly those dwelling at great depths, where sunlight may either be absent or drop to very low levels. Under these environmental conditions, the visual system must maximise light absorption in order to enhance the detection of prey, predators and potential mates. Using stereological analysis of retinal wholemounts, the distribution and number of photoreceptors (rods) was determined for 5 deep-sea shark species from a range of depths (46-1,500 m). All species possessed areas of increased photoreceptor density (with peaks between 41,000 and 82,000 rods/mm2) within discrete regions of the retina. The total number of rods in the photoreceptor layer also varied between 17 × 106 and 63 × 106. It is evident that increasing sensitivity of the retina is an important adaptation to life in the deep sea. The location of discrete areas of high cell density within the photoreceptor layer of the retina corresponds to discrete areas of the visual field that are sampled at a higher intensity, hence increasing sensitivity. The location of these areas of increased sensitivity differed between the species of this study. The disparity of areas of increased sensitivity seen between species is thought to reflect distinctive predator avoidance and prey capture strategies. This study reveals that the visual demands of deep-sea sharks vary interspecifically and that sampling of each species' visual field is not solely determined by its habitat.
Program obfuscation: a quantitative approach

Despite the recent advances in the theory underlying obfuscation, there still is a need to evaluate the quality of practical obfuscating transformations more quickly and easily. This paper presents the first steps toward a comprehensive evaluation suite consisting of a number of deobfuscating transformations and complexity metrics that can be readily applied on existing and future transformations in the domain of binary obfuscation. In particular, a framework based on software complexity metrics measuring four program properties: code, control flow, data and data flow is suggested. A number of well-known obfuscating and deobfuscating transformations are evaluated based upon their impact on a set of complexity metrics. This enables us to quantitatively evaluate the potency of the (de)obfuscating transformations.
A general invariance principle for nonlinear time-varying systems and its applications

A general invariance principle is proposed from the output-to-state viewpoint for a class of nonlinear time-varying systems. This is achieved by the construction of a simple and intuitive criterion using integral inequality involving the output function and modified detectability conditions. The well-known "LaSalle invariance principle" is shown to be deduced from the proposed approach when a Lyapunov function is given to the applied systems. A similar criterion, the so-called "integral invariance principle", was proposed by Byrnes and Martin (1995) for nonlinear time-invariant systems. However, in general, these two approaches cannot be applied to time-varying systems directly. The proposed scheme can be viewed as an extension of the integral invariance principle for time-invariant systems to time-varying systems. Such extension is non-trivial and can be used in various research areas, such as adaptive control, tracking control and the control of driftless systems. Applications to the global tracking control of four-wheeled mobile robots are given to demonstrate the feasibility and validity of the proposed approach.
The Role of Market Orientation and Learning Orientation in Improving Innovativeness and Performance of Small and Medium Enterprises

The purpose of study is to describe contradiction relationship between market orientation toward organizational performance and to provide a quantitative analysis, in which learning orientation, market orientation, entrepreneurial orientation, and innovativeness function as the key success factors in technology-intensive firms. The authors formulate a structural equation model to examine the relationship among these constructs. A structural equation model was designed to examine the relationship. To test the model, the authors conducted covariance structural analyses of data collected from 150 small medium enterprises in Banyumas Regency. The central finding is that learning orientation plays a mediating role in the relationship between market orientation and innovativeness. The results indicate that innovativeness has effect on business performance. Market orientation can strengthen learning orientation and innovativeness. In the small medium enterprises, the market information obtained from customers and competitors helps firms to keep an eye on the market. For better competitive advantages and business performance, firms must have learning capabilities and employees’ identity with organizational mission. The findings indicate that firms should strengthen their learning orientation and innovativeness to improve business performance.
Homotypic cluster formation of dendritic cells, a close correlate of their state of maturation. Defects in the biobreeding diabetes‐prone rat

Aggregation of dendritic cells (DCs) in homotypic clusters has been described in vivo in lymph and skin, and here we report studies on homotypic clustering of rat splenic (s) DCs in vitro. Wistar rat sDCs readily formed homotypic clusters in culture, which increased in number and size over time (with a peak att = 3 h). Keeping the cells at higher densities or treatment with anti‐CD43 induced more and larger homotypic clusters. After such enhanced clustering the DCs had increased their T cell stimulating capabilities in syngeneic mixed lymphocyte reaction, and had a higher expression of CD80 and CD86 (signs of maturation). Ag transfer from bovine serum albumin‐fluorescein isothiocyanate‐pulsed to unpulsed DCs was observed during clustering. Here we also show that sDCs of the biobreeding diabetes‐prone (BB‐DP) rat, a model of autoimmune diabetes/thyroiditis, formed fewer and smaller clusters than Wistar sDCs, and that DC‐DC clustering resulted in only a modest maturation of the cells (as determined in syn MLR and by phenotyping). Anti‐CD43 completely restored the clustering defect BB‐DP DCs in vitro, yet T cell‐stimulating capability was only restored to a limited extent. Ag transfer in BB‐DP DC clusters was similar.