Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Clone Information on the Performance of Developers Fixing Cloned Bugs

Duplicated source code -- clones -- is known to occur frequently in software systems and bears the risk of inconsistent updates of the code. The impact of clones has been investigated mostly by retrospective analysis of software systems. Only little effort has been spent to investigate human interaction when dealing with clones. A previous study by Chatterji and colleagues found that cloned defects are removed significantly more accurately when clone information is provided to the programmers. We conducted a controlled experiment to extend the previous study on the use of clone information by investigating the effect of clone information on the performance of developers in common bug-fixing tasks. The experiment shows that developers are quite capable to compensate missing clone information through testing to provide correct solutions. Clone information does help to detect cloned defects faster, although developers may exploit semantic code relations such as inheritance to uncover cloned defects only slightly slower if they do not have clone information. If cloned defects lurk in semantically unrelated places however, clone information helps to find them faster at statistical significance. Developers without clone information needed 17 minutes longer on average or 140% more time in relative terms to complete the task successfully.
Delineation and Modelling of a Nucleolar Retention Signal in the Coronavirus Nucleocapsid Protein

Unlike nuclear localization signals, there is no obvious consensus sequence for the targeting of proteins to the nucleolus. The nucleolus is a dynamic subnuclear structure which is crucial to the normal operation of the eukaryotic cell. Studying nucleolar trafficking signals is problematic as many nucleolar retention signals (NoRSs) are part of classical nuclear localization signals (NLSs). In addition, there is no known consensus signal with which to inform a study. The avian infectious bronchitis virus (IBV), coronavirus nucleocapsid (N) protein, localizes to the cytoplasm and the nucleolus. Mutagenesis was used to delineate a novel eight amino acid motif that was necessary and sufficient for nucleolar retention of N protein and colocalize with nucleolin and fibrillarin. Additionally, a classical nuclear export signal (NES) functioned to direct N protein to the cytoplasm. Comparison of the coronavirus NoRSs with known cellular and other viral NoRSs revealed that these motifs have conserved arginine residues. Molecular modelling, using the solution structure of severe acute respiratory (SARS) coronavirus N‐protein, revealed that this motif is available for interaction with cellular factors which may mediate nucleolar localization. We hypothesise that the N‐protein uses these signals to traffic to and from the nucleolus and the cytoplasm.
Local Interpretable Model-Agnostic Explanations for Music Content Analysis

The interpretability of a machine learning model is essential for gaining insight into model behaviour. While some machine learning models (e.g., decision trees) are transparent, the majority of models used today are still black-boxes. Recent work in machine learning aims to analyse these models by explaining the basis of their decisions. In this work, we extend one such technique, called local interpretable model-agnostic explanations, to music content analysis. We propose three versions of explanations: one version is based on temporal segmentation, and the other two are based on frequency and time-frequency segmentation. These explanations provide meaningful ways to understand the factors that influence the classification of specific input data. We apply our proposed methods to three singing voice detection systems: the first two are designed using decision tree and random forest classifiers, respectively; the third system is based on convolutional neural network. The explanations we generate provide insights into the model behaviour. We use these insights to demonstrate that despite achieving 71.4% classification accuracy, the decision tree model fails to generalise. We also demonstrate that the model-agnostic explanations for the neural network model agree in many cases with the model-dependent saliency maps. The experimental code and results are available online. 1
Additional benefit of combined therapy with melatonin and apoptotic adipose‐derived mesenchymal stem cell against sepsis‐induced kidney injury

This study tested whether combined therapy with melatonin and apoptotic adipose‐derived mesenchymal stem cells (A‐ADMSCs) offered additional benefit in ameliorating sepsis‐induced acute kidney injury. Adult male Sprague–Dawley rats (n = 65) were randomized equally into five groups: Sham controls (SC), sepsis induced by cecal‐ligation and puncture (CLP), CLP‐melatonin, CLP‐A‐ADMSC, and CLP‐melatonin‐A‐ADMSC. Circulating TNF‐α level at post‐CLP 6 hr was highest in CLP and lowest in SC groups, higher in CLP‐melatonin than in CLP‐A‐ADMSC and CLP‐melatonin‐A‐ADMSC groups (all P < 0.001). Immune reactivity as reflected in the number of splenic helper‐, cytoxic‐, and regulatory‐T cells at post‐CLP 72 hr exhibited the same pattern as that of circulating TNF‐α among all groups (P < 0.001). The histological scoring of kidney injury and the number of F4/80+ and CD14+ cells in kidney were highest in CLP and lowest in SC groups, higher in CLP‐melatonin than in CLP‐A‐ADMSC and CLP‐melatonin‐A‐ADMSC groups, and higher in CLP‐A‐ADMSC than in CLP‐melatonin‐A‐ADMSC groups (all P < 0.001). Changes in protein expressions of inflammatory (RANTES, TNF‐1α, NF‐κB, MMP‐9, MIP‐1, IL‐1β), apoptotic (cleaved caspase 3 and PARP, mitochondrial Bax), fibrotic (Smad3, TGF‐β) markers, reactive‐oxygen‐species (NOX‐1, NOX‐2), and oxidative stress displayed a pattern identical to that of kidney injury score among the five groups (all P < 0.001). Expressions of antioxidants (GR+, GPx+, HO‐1, NQO‐1+) were lowest in SC group and highest in CLP‐melatonin‐A‐ADMSC group, lower in CLP than in CLP‐melatonin and CLP‐A‐ADMSC groups, and lower in CLP‐melatonin‐ than in CLP‐A‐ADMSC‐tretaed animals (all P < 0.001). In conclusion, combined treatment with melatonin and A‐ADMSC was superior to A‐ADMSC alone in protecting the kidneys from sepsis‐induced injury.
Reference Resolution in Situated Dialogue with Learned Semantics

Understanding situated dialogue requires identifying referents in the environment to which the dialogue participants refer. This reference resolution problem, often in a complex environment with high ambiguity, is very challenging. We propose an approach that addresses those challenges by combining learned semantic structure of referring expressions with dialogue history into a ranking-based model. We evaluate the new technique on a corpus of human-human tutorial dialogues for computer programming. The experimental re-sults show a substantial performance improvement over two recent state-of-the-art approaches. The proposed work makes a stride toward automated dialogue in complex problem-solving environments.
Prevalence and patterns of presentation of genetic disorders in a pediatric emergency department.

OBJECTIVES To determine the prevalence and patterns of presentation of previously diagnosed and of suspected genetic disorders among pediatric emergency department (ED) visits to a hospital that serves an inner-city population. PATIENTS AND METHODS A retrospective review of 15,258 pediatric (<18 years old) ED visits at Lincoln Medical and Mental Health Center was undertaken for visits that occurred between October 1998 and February 1999. Suspected genetic disorders, classified into chromosomal, single gene, multifactorial, and other syndromic categories, were recorded. RESULTS Of 15,258 visits reviewed, 2839 visits (18.6%) were by patients who had known or suspected genetic disorders. Previously diagnosed genetic disorders were documented in 80 visits (2.8%). Of these, 69 visits (86.2%) were related to single gene disorders, 3 (3.8%) to chromosomal disorders, 6 (7.5%) to multifactorial disorders, and 2 (2.5%) to disorders in the "other" category. Of these 80 visits, 59 (74%) were associated with sickle cell disease. The remaining 2759 visits (97.2%) were associated with complaints or diagnoses that suggested the possibility of an underlying genetic disorder requiring further evaluation and diagnostic work-up. CONCLUSIONS Pediatric patients with known or suspected genetic disorders are frequently treated in EDs. Awareness of underlying genetic disorders facilitates diagnostic evaluation, treatment planning, and referral to a genetics clinic for counseling.
Acute and Chronic Toxicity of Thioacteamide and Alterations in Blood Cell Indices in Rats

Background: Thioacetamide (TAA) has been used extensively in the development of suitable animal models of acute and chronic liver injury employing various doses, times and routes of its administration, particularly in drinking water due to its resemblance with human liver fibrosis and cirrhosis. The aim of this study was to investigate and compare hematological alteration during the acute and chronic liver inflammation. Methods: Acute Liver inflammation was induced in Wistar rats via intraperitoneal injection of thioacetamide and the animals were sacrificed 12 h after the TAA administration. Induction of chronic liver inflammation was performed by continuous administration of TAA in the drinking water (200 mg/L) during 18 weeks of experiment. After that all animals were sacrificed and Blood samples were collected for further analysis. Results: Single intra peritoneal injection of TAA (300 mg/kg B.W.) induced an acute condition with hematological changes including leukocytosis with marked neutrophilia (P = 0.0429), lymphopenia, thrombocytosis as well as increased hemoglobin concentration (P 0.05) and decline of erythrocytic count (P = 0.0009). Eighteen weeks of uninterrupted supply of TAA (200 mg/L) in drinking water lead to chronic inflammation and the hematological alterations were leucopenia (P = 0.0197) accompanied with neutropenia and thrombocytopenia. Increase in RBCs (P = 0.0073) and Hb contents was also observed with a decline of red cell indices. Conclusion: Taken together these findings we can conclude that the animals respond differently under acute and chronic inflammatory condition with TAA administration. Leukocytosis with marked neutrophilia, thrombocytosis as well as increased hemoglobin concentration and decline of erythrocytic count were observed in acute while leucopenia accompanied with neutropenia and thrombocytopenia and increase in RBCs, Hb and Hct was also observed with a decline of other red cell indices during chronic phase.
Learning Deep Representations of Appearance and Motion for Anomalous Event Detection

We present a novel unsupervised deep learning framework for anomalous event detection in complex video scenes. While most existing works merely use hand-crafted appearance and motion features, we propose Appearance and Motion DeepNet (AMDN) which utilizes deep neural networks to automatically learn feature representations. To exploit the complementary information of both appearance and motion patterns, we introduce a novel double fusion framework, combining both the benefits of traditional early fusion and late fusion strategies. Specifically, stacked denoising autoencoders are proposed to separately learn both appearance and motion features as well as a joint representation (early fusion). Based on the learned representations, multiple one-class SVM models are used to predict the anomaly scores of each input, which are then integrated with a late fusion strategy for final anomaly detection. We evaluate the proposed method on two publicly available video surveillance datasets, showing competitive performance with respect to state of the art approaches.
Clustering Voices in The Waste Land

T.S. Eliot’s modernist poem The Waste Land is often interpreted as collection of voices which appear multiple times throughout the text. Here, we investigate whether we can automatically cluster existing segmentations of the text into coherent, expert-identified characters. We show that clustering The Waste Land is a fairly difficult task, though we can do much better than random baselines, particularly if we begin with a good initial segmentation.
A rapid in vivo screen for pancreatic ductal adenocarcinoma therapeutics

ABSTRACT Pancreatic ductal adenocarcinoma (PDA) is the fourth leading cause of cancer-related deaths in the United States, and is projected to be second by 2025. It has the worst survival rate among all major cancers. Two pressing needs for extending life expectancy of affected individuals are the development of new approaches to identify improved therapeutics, addressed herein, and the identification of early markers. PDA advances through a complex series of intercellular and physiological interactions that drive cancer progression in response to organ stress, organ failure, malnutrition, and infiltrating immune and stromal cells. Candidate drugs identified in organ culture or cell-based screens must be validated in preclinical models such as KIC (p48Cre;LSL-KrasG12D;Cdkn2af/f) mice, a genetically engineered model of PDA in which large aggressive tumors develop by 4 weeks of age. We report a rapid, systematic and robust in vivo screen for effective drug combinations to treat Kras-dependent PDA. Kras mutations occur early in tumor progression in over 90% of human PDA cases. Protein kinase and G-protein coupled receptor (GPCR) signaling activates Kras. Regulators of G-protein signaling (RGS) proteins are coincidence detectors that can be induced by multiple inputs to feedback-regulate GPCR signaling. We crossed Rgs16::GFP bacterial artificial chromosome (BAC) transgenic mice with KIC mice and show that the Rgs16::GFP transgene is a KrasG12D-dependent marker of all stages of PDA, and increases proportionally to tumor burden in KIC mice. RNA sequencing (RNA-Seq) analysis of cultured primary PDA cells reveals characteristics of embryonic progenitors of pancreatic ducts and endocrine cells, and extraordinarily high expression of the receptor tyrosine kinase Axl, an emerging cancer drug target. In proof-of-principle drug screens, we find that weanling KIC mice with PDA treated for 2 weeks with gemcitabine (with or without Abraxane) plus inhibitors of Axl signaling (warfarin and BGB324) have fewer tumor initiation sites and reduced tumor size compared with the standard-of-care treatment. Rgs16::GFP is therefore an in vivo reporter of PDA progression and sensitivity to new chemotherapeutic drug regimens such as Axl-targeted agents. This screening strategy can potentially be applied to identify improved therapeutics for other cancers. Editor's choice - Drug Discovery Collection: The study describes a rapid in vivo screen for novel strategies to treat pancreatic ductal adenocarcinoma (PDA).
The nature of late-type spiral galaxies: structural parameters, optical and near-infrared colour profiles and dust extinction

We analyse V-and H-band surface photometry of a sample of 18 Sb-Sd galaxies. Combining high-resolution Hubble Space Telescope (HST) images with ground-based near-infrared observations, we extract photometric profiles, which cover the whole disc and provide the highest possible resolution. This is the first photometric study of late-type spirals for which the stellar kinematics have been measured. For 10 out of the 18 galaxies, HST data in both F160W (H) and F606W (V) are available, and, for those, we present colour maps and radial colour profiles at the resolution of the HST. Colours vary significantly from galaxy to galaxy, but tend to be highly homogeneous within each galaxy, with smooth and flat colour profiles. Some of the colour maps show jumps in the inner regions, likely due to dust. We determine extinction maps in an almost model-independent way using the V-H colour map and the SAURON Mgb absorption line map of Ganda et al. The maps show that AV ranges from 0 to 2 mag, in the centre from 0 to 1.5 mag, in agreement with the models of Tuffs et al. We describe the surface brightness profiles as the superposition of an exponential disc and a Sersic bulge. The bulges are small (0.1-2.5 kpc), and show a shape parameter n ranging from approximate to 0.7 to 3, with a mean value smaller than two: well below the value for the classical de Vaucouleurs bulges. Most galaxies (16 out of 18) show a central light excess above the Sersic fit to the bulge, which can be interpreted as a nuclear cluster, as shown by previous studies. We provide zero-order estimates for the magnitude of these components. We discuss the correlations among the structural galaxy parameters and with other relevant quantities, such as Hubble type and stellar velocity dispersion. We compare these results with a recent paper by Graham & Worley, who present a summary of most of the NIR surface photometry of spirals in the literature. For both early-and late-type spirals, bulge luminosity strongly correlates with central velocity dispersion; at constant velocity dispersion, later type bulges are larger and less dense, and have lower Sersic n-values.
Current State of Psychiatry in Saudi Arabia

Background: In 1983, an article and accompanying editorial was published on the state of psychiatry in the Kingdom of Saudi Arabia (KSA), which was described as “a mental health system in statu nascendi. ” Methods: We provide a 30-year update on advances in mental health care in KSA. Data are reported from a wide range of sources, including the 2007 Saudi Arabian Mental and Social Health Atlas, which compares services in KSA with the rest of the world. Results: We examine how the current mental health system operates in KSA, including recent changes in mental healthcare policy and development of a national mental healthcare plan. Discussed are current needs based on the prevalence and recognition of mental disorders; availability of services and providers (psychiatrists, psychiatric nurses, psychologists, and social workers); education and training in psychiatry; developments in consultation-liaison, addictions, child-adolescent, and geriatric psychiatry; and progress in mental health research. Conclusions: Mental healthcare in Saudi Arabia has come a long way in a very short time, despite cultural, religious, social, and political challenges, although there still remain areas where improvement is needed. The development of psychiatry in KSA serves as a model for countries in the Middle East and around the world.
Aldose Reductase Protects Against Early Atherosclerotic Lesion Formation in Apolipoprotein E–Null Mice

Rationale: Atherosclerotic lesion formation is associated with the accumulation of oxidized lipids. Products of lipid oxidation, particularly aldehydes, stimulate cytokine production and enhance monocyte adhesion; however, their contribution to atherosclerotic lesion formation remains unclear. Objective: To test the hypothesis that inhibition of aldehyde removal by aldose reductase (AR), which metabolizes both free and phospholipid aldehydes, exacerbates atherosclerotic lesion formation. Methods and Results: In atherosclerotic lesions of apolipoprotein (apo)E-null mice, AR protein was located in macrophage-rich regions and its abundance increased with lesion progression. Treatment of apoE-null mice with AR inhibitors sorbinil or tolrestat increased early lesion formation but did not affect the formation of advanced lesions. Early lesions of AR−/−/apoE−/− mice maintained on high-fat diet were significantly larger when compared with age-matched AR+/+/apoE−/− mice. The increase in lesion area attributable to deletion of the AR gene was seen in both male and female mice. Pharmacological inhibition or genetic ablation of AR also increased the lesion formation in male mice made diabetic by streptozotocin treatment. Lesions in AR−/−/apoE−/− mice exhibited increased collagen and macrophage content and a decrease in smooth muscle cells. AR−/−/apoE−/− mice displayed a greater accumulation of the AR substrate 4-hydroxy trans-2-nonenal (HNE) in the plasma and protein-HNE adducts in arterial lesions than AR+/+/apoE−/− mice. Conclusions: These observations indicate that AR is upregulated in atherosclerotic lesions and it protects against early stages of atherogenesis by removing toxic aldehydes generated in oxidized lipids.
What is a “Health Disparity”?

With the launch of Healthy People 2010 in January 2000, the Department of Health and Human Services (DHHS) committed the nation to an overarching goal, to “eliminate health disparities. ” Like the preceding Healthy People 2000 initiative, Healthy People 2010 outlines a comprehensive disease prevention and health promotion agenda. Although this goal has met with considerable support throughout the nation, upon further examination, it is clear that the term “health disparity” has been used with a number of very different meanings. Since the scope of the eliminating disparities goal for the DHHS Imitative to Eliminate Racial and Ethnic Disparities in Health is narrower than that of Healthy People 2010, discussion of the two goals in the same context can lead to confusion.
On compressing massive streaming graphs with Quadtrees

Social networks are constantly changing as new members join, existing members leave, and `followers' or `friends' are formed and disappear. The model that captures this constantly changing graph is the streaming graph model. Given a massive graph data stream wherein the number of nodes is in the order of millions and the number of edges is the tens of millions, we propose a simple algorithm to compress this graph without having read in the entire graph into the main memory. Our algorithm uses the quadtree data structure that is implicitly constructed to produce the compressed graph output. As a result of this implicit construction, our algorithm allows for node and edge additions/deletions that directly modifies the output compressed graph. We further develop algorithms to solve edge queries (is there any between two nodes? ) and node queries (for a given node, list all its neighbors) that directly operates on the compressed graph. We have performed extensive empirical evaluations of our algorithms using publicly available, large social networks such as LiveJournal, Pokec, Twitter, and others. Our empirical evaluation is based on several parameters including time to compress, memory required by the compression algorithm, size of compressed graph, and time and memory size required to execute queries. We have also presented extensions to the compression algorithm that we have developed.
Security Scheme for Distributed DoS in Mobile Ad Hoc Networks

In Mobile Ad Hoc Networks (MANET), various types of Denial of Service Attacks (DoS) are possible because of the inherent limitations of its routing protocols. Considering the Ad Hoc On Demand Vector (AODV) routing protocol as the base protocol it is possible to find a suitable solution to over-come the attack of initiating / forwarding fake Route Requests (RREQs) that lead to hogging of network resources and hence denial of service to genuine nodes. In this paper, a proactive scheme is proposed that could prevent a specific kind of DoS attack and identify the misbehaving node. Since the proposed scheme is distributed in nature it has the capability to prevent Distributed DoS (DDoS) as well. The performance of the proposed algorithm in a series of simulations reveal that the proposed scheme provides a better solution than existing approaches with no extra overhead.