Miracle-dz/UniFAR-FTUs huggingface dataset:
The use of neutrophil to lymphocyte ratio as a predictor for clinical outcomes in spontaneous intracerebral hemorrhage

Objective Neutrophil to lymphocyte ratio (NLR) is used as an independent predictor for clinical outcomes in cancers, cardiovascular disorders and ischemic stroke. The prognostic role of NLR in spontaneous intracerebral hemorrhage (sICH) is still controversial. The aim of this report is to conduct a meta-analysis to evaluate the prognostic significance NLR in patients with sICH. Materials and Methods All related articles were searched on PubMed, EMBASE, Cochrane Central Register of Controlled Trials followed the PRISMA flow diagram. The quality of eligible studies were evaluated and the related data were extracted by two reviewers independently. The end points included the mortality and poor outcomes and subgroup analyses were performed. Results Five studies with 1944 subjects were included and had acceptable quality. The high NLR had a higher risk of in-hospital mortality (OR: 0.97; 95% CI: 0.94–0.99, p = 0.02) and 90-day mortality (OR: 2.43; 95% CI: 1.01–5.83, p = 0.047); without association with the poor outcomes (OR: 1.17; 95% CI: 0.93–1.47, p = 0.18). After subgroup analyses, the high NLR correlated with an increased 90-day mortality in the high cut-off group (OR: 1.56; 95% CI: 1.15–2.13, p = 0.005). The high NLR additionally predicts poor outcomes in smaller hematoma group (OR: 1.16; 95% CI: 1.01–1.32, p = 0.04) and the high cut-off group (OR: 2.20; 95% CI: 1.54–3.14, p < 0.001). Conclusions The high NLR was significantly associated with in-hospital and 90-day mortality in patients with sICH. The NLR with cut-off of 7.5 had statistically significant potential for predicting mortality and poor outcomes, regardless of country, time of laboratory test and hematoma volumes.
Corner Points Detection for Vertebral Mobility Analysis

In this paper we introduce a new segmentation approach used to detect the location and the orientation of the cervical vertebrae in medical x-ray images. A first pre-processing step consists on determining a global polygonal region for each vertebra. After this, we propose a new approach of vertebra localization by extracting the anterior faces of vertebra contours. This approach is based on automatic corner points of interest detection using the Harris operator. A specific goal of the proposed application is to create an efficient semi-automated method of identifying the overall angle of curvature of the spine and the angles between vertebrae.
A Research Framework for Software-Fault Localization Tools

Once a program run exposes a bug, the programmers' first task is fault localization: identifying the portions of code they need to change to correct the bug. Help for this task takes the form of fault-localization tools, which vary from static code analyzers to debuggers. This dissertation develops a research framework for fault-localization tools that require only a set of runs, some of which fail, to produce their output. The first part of the framework is an architecture for fault-localization tools. The architecture prescribes five phases: data collection for each run, data abstraction for each run, modeling of sets of runs to produce models of correct and failing runs, contrasting the two models, and finally mapping the difference back to source code. This architecture also describes a number of existing tools. The second part of the framework provides an evaluation method for fault-localization tools, based on the effort an ideal user must invest to interpret a tool's results. This effort is measured as the proportion of code that lies between the report and the faulty locations on a graph representing the structure of source locations. The dissertation presents and evaluates a number of fault-localization tools developed within this framework that are built around program profiles and collections of dynamically discovered invariants. Notable contributions include the nearest neighbor idea, where failing runs are compared with their most similar successful run, and the discrete comparison and differencing of program profiles based on permutation distances. The combination of these two contributions achieved the best results of the tools we developed, as computed by the evaluation method. Finally, this dissertation presents and quantifies elided events, a cause for caution in the interpretation of program profile data. The problem is that the execution of a part of code may have no effect on the run's correctness. As a result, code that should be suspicious is considered safe, with adverse effects for debugging.
Purification and characterization of a tetrachloro-p-hydroquinone reductive dehalogenase from a Flavobacterium sp

Tetrachloro-p-hydroquinone (TeCH) is the first intermediate in pentachlorophenol (PCP) degradation by Flavobacterium sp. strain ATCC 39723. We previously purified a PCP hydroxylase that oxidized PCP to TeCH. Subsequently, we identified the reductive dehalogenation of TeCH to 2,3,6-trichloro-p-hydroquinone and then to 2,6-dichloro-p-hydroquinone in a cell extract with the reduced form of glutathione as the reducing agent under anaerobic conditions. Here we report the purification of a TeCH reductive dehalogenase that reductively dehalogenated TeCH to trichlorohydroquinone and then to dichlorohydroquinone. The enzyme was purified by protamine sulfate treatment, ammonium sulfate fractionation, and phenyl-agarose, anion-exchange, and gel filtration column chromatographies. As determined by gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses, the protein has a molecular weight of about 30,000; nondenaturing polyacrylamide gel electrophoresis analysis suggests that the native enzyme exists as a dimer. The enzyme used glutathione but not NADPH, NADH, dithiothreitol, or ascorbic acid as the reducing agent. The optimal pH was close to neutral.
Housing Demand and Community Choice: An Empirical Analysis

Housing demand reflects the household's simultaneous choice of neighborhood, whether to own or rent the dwelling, and the quantity of housing services demanded. Existing literature emphasizes the final two factors, but overlooks the choice of community. This paper develops an econometric model that incorporates all three components, and then estimates this model using a sample of households in Tampa, Florida. Incorporating community choice increases the price elasticity of demand and reduces the differential between white and comparable nonwhite households. The results are robust to the inclusion of permanent income and taxes.
III / Winter 2008 ADVANCES IN KNOWLEDGE DISCOVERY IN DATABASES

The Knowledge Discovery in Databases and Data Mining field proposes the development of methods and techniques for assigning useful meanings for data stored in databases. It gathers researches from many study fields like machine learning, pattern recognition, databases, statistics, artificial intelligence, knowledge acquisition for expert systems, data visualization and grids. While Data Mining represents a set of specific algorithms of finding useful meanings in stored data, Knowledge Discovery in Databases represents the overall process of finding knowledge and includes the Data Mining as one step among others such as selection, pre–processing, transformation and interpretation of mined data. This paper aims to point the most important steps that were made in the Knowledge Discovery in Databases field of study and to show how the overall process of discovering can be improved in the future.
The ASTRAL compendium for protein structure and sequence analysis

The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. The SPACI scores included in the system summarize the overall characteristics of a protein structure. A structural alignments database indicates residue equivalencies in superimposed protein domain structures. The PDB sequence-map files provide a linkage between the amino acid sequence of the molecule studied (SEQRES records in a database entry) and the sequence of the atoms experimentally observed in the structure (ATOM records). These maps are combined with information in the SCOPdatabase to provide sequences of protein domains. Selected subsets of the domain database, with varying degrees of similarity measured in several different ways, are also available. ASTRALmay be accessed at http://astral.stanford. edu/
A distributed polylogarithmic time algorithm for self-stabilizing skip graphs

Peer-to-peer systems rely on scalable overlay networks that enable efficient routing between its members. Hypercubic topologies facilitate such operations while each node only needs to connect to a small number of other nodes. In contrast to static communication networks, peer-to-peer networks allow nodes to adapt their neighbor set over time in order to react to join and leave events and failures. This paper shows how to maintain such networks in a robust manner. Concretely, we present a distributed and self-stabilizing algorithm that constructs a (variant of the) skip graph in polylogarithmic time from any initial state in which the overlay network is still weakly connected. This is an exponential improvement compared to previously known self-stabilizing algorithms for overlay networks. In addition, individual joins and leaves are handled locally and require little work.
Generating folding sequences from crease patterns of flat-foldable origami

The most common form to convey origami is through origami diagrams, which are step-by-step sequences, composed of figures that represent the state of the folded paper, in combination with lines and arrows indicating the position of the folds and the movement of the paper (Figure 1b). With the development of modern techniques of origami design, the range of achievable shapes have increased drastically and the crease pattern (the pattern of creases left on the paper after folding an origami model) has gained importance as an efficient method of documenting origami [Lang 2012]. However, the disadvantage of crease patterns is that it is difficult to use them to re-create the design, since crease patterns show only where each crease must be made and not folding instructions.
A Test of Objectification Theory: The Effect of the Male Gaze on Appearance Concerns in College Women

This study extends the research on objectification theory by examining the effect of anticipating a male or female gaze on appearance-related concerns in 105 female undergraduates. Gaze anticipation was manipulated by having participants believe they would be interacting with a man or woman before completing several self-report measures. Results demonstrated that anticipating a male gaze produced significantly greater body shame and social physique anxiety than anticipating a female gaze, while no differences were observed for dietary intent. Discussion centers on the pervasiveness of the experience of self-objectification and the implications of these findings for future research.
Respiratory syncytial virus infection in inbred mice

Respiratory syncytial virus infected the nose and lungs of each of 20 strains of inbred mice, with viral titers varying 100-fold from least permissive to most permissive strains. Viral titers appeared to be under genetic control, but did not correlate with the H-2 haplotype.
The Language of Bioscience: Facts, Speculations, and Statements In Between

We explore the use of speculative language in MEDLINE abstracts. Results from a manual annotation experiment suggest that the notion of speculative sentence can be reliably annotated by humans. In addition, an experiment with automated methods also suggest that reliable automated methods might also be developed. Distributional observations are also presented as well as a discussion of possible uses for a system that can recognize speculative language.
DESASTRES NATURAIS: PERDAS E REAÇÕES PSICOLÓGICAS DE VÍTIMAS DE ENCHENTE EM TERESINA-PI

The Natural disasters have been gaining prominence in the news worldwide. In Brazil, this situation has caused intense concern, given the serious consequences of this type of event. Attentive to the national scenery, committed socially, the psychologists argue this thematic, seeking to systematize interventions to offer emotional support to disaster victims. In Teresina, the flood of 2009 inundated several places of city, bringing damages for the neighborhoods most affected. According to this situation, this study aimed to investigate the losses experienced and the consequent psychological reactions of the flood victims, 2009. It was proposed also point the subjective mechanisms create by the community members for treatment of the crisis, of its consequences losses. The emerging contents suggest greater attention to the mental health of people affected by disasters, as well as the need for more research in the area to support the interventions in this context.
Possible Introgression of B Chromosomes between Bee Species (Genus Partamona)

The origin of supernumerary (B) chromosomes is still a debated topic, with intra- and interspecific origins being the most plausible options. In the bee Partamona helleri, a sequence-characterized amplified region (SCAR) marker being specific to B chromosomes suggested the possibility of interspecific origin. Here, we search for this marker in 3 close relative species and perform DNA sequence comparison between species. The SCAR sequence does not show homology with other sequences in the databases, but does contain an open reading frame with sequence homology with a reverse transcriptase. Dot-blot hybridization using the SCAR marker as a probe confirmed that it is present in B-carrying, but not B-lacking larvae of P. helleri, and indicated its presence in adult individuals of P. cupira and P. criptica. Additionally, PCR amplification of the SCAR marker was successful on genomic DNA obtained from P. helleri and P. rustica larvae carrying B chromosomes, and on genomic DNA obtained from adult individuals of P. cupira, P. criptica and P. rustica. Finally, a comparison of the DNA sequence of the SCAR markers amplified from these 4 species showed very few nucleotide differences between the species. The complete association between B chromosome and SCAR presence and the scarce divergence observed for this DNA sequence between the 4 species analyzed suggest the possibility that this B chromosome has recently been transferred between species through several episodes of interspecific hybridization.
Ascophyllum nodosum Seaweed Extract Alleviates Drought Stress in Arabidopsis by Affecting Photosynthetic Performance and Related Gene Expression

Drought represents one of the most relevant abiotic stress affecting growth and yield of crop plants. In order to improve the agricultural productivity within the limited water and land resources, it is mandatory to increase crop yields in presence of unfavorable environmental stresses. The use of biostimulants, often containing seaweed extracts, represents one of the options for farmers willing to alleviate abiotic stress consequences on crops. In this work, we investigated the responses of Arabidopsis plants treated with an extract from the brown alga Ascophyllum nodosum (ANE), under drought stress conditions, demonstrating that ANE positively influences Arabidopsis survival. Pre-treatment with ANE induced a partial stomatal closure, associated with changes in the expression levels of genes involved in ABA-responsive and antioxidant system pathways. The pre-activation of these pathways results in a stronger ability of ANE-treated plants to maintain a better photosynthetic performance compared to untreated plants throughout the dehydration period, combined with a higher capacity to dissipate the excess of energy as heat in the reaction centers of photosystem II. Our results suggest that drought stressed plants treated with ANE are able to maintain a strong stomatal control and relatively higher values of both water use efficiency (WUE) and mesophyll conductance during the last phase of dehydration. Simultaneously, the activation of a pre-induced antioxidant defense system, in combination with a more efficient energy dissipation mechanism, prevents irreversible damages to the photosynthetic apparatus. In conclusion, pre-treatment with ANE is effective to acclimate plants to the incoming stress, promoting an increased WUE and dehydration tolerance.
Endocytosis as a Biological Response in Receptor Pharmacology: Evaluation by Fluorescence Microscopy

The activation of G-protein coupled receptors by agonist compounds results in diverse biological responses in cells, such as the endocytosis process consisting in the translocation of receptors from the plasma membrane to the cytoplasm within internalizing vesicles or endosomes. In order to functionally evaluate endocytosis events resulted from pharmacological responses, we have developed an image analysis method –the Q-Endosomes algorithm– that specifically discriminates the fluorescent signal originated at endosomes from that one observed at the plasma membrane in images obtained from living cells by fluorescence microscopy. Mu opioid (MOP) receptor tagged at the carboxy-terminus with yellow fluorescent protein (YFP) and permanently expressed in HEK293 cells was used as experimental model to validate this methodology. Time-course experiments performed with several agonists resulted in different sigmoid curves depending on the drug used to initiate MOP receptor endocytosis. Thus, endocytosis resulting from the simultaneous activation of co-expressed MOP and serotonin 5-HT2C receptors by morphine plus serotonin was significantly different, in kinetics as well as in maximal response parameters, from the one caused by DAMGO, sufentanyl or methadone. Therefore, this analytical tool permits the pharmacological characterization of receptor endocytosis in living cells with functional and temporal resolution.
Evaluating the effectiveness of visual summaries for web search

With ever-increasing amounts of information on the World Wide Web, an effective interface for displaying search results is required. Recent studies have developed various novel approaches for visual summaries, aiming to improve the effectiveness of search results. In this study we evaluate the effectiveness of four types of visual summary: thumbnails, salient images, visual snippets and visual tags. Fifty participants carried out five informational topics using five different interfaces. The results show that visual summaries significantly impact on the behavior of users, but not on their performance when predicting the relevance of answer resources. Users spend significantly less time looking at the textual components of summaries with the visual summary interfaces. Comparing the performance of users in predicting the relevance of answer pages with a text interface versus visual interfaces suggests that the tested visual summaries can mislead users to select non relevant items on informational search topics.
Expression of CCR2 in Both Resident and Bone Marrow-Derived Microglia Plays a Critical Role in Neuropathic Pain

Neuropathic pain resulting from damage to or dysfunction of peripheral nerves is not well understood and difficult to treat. Although CNS hyperexcitability is a critical component, recent findings challenge the neuron-centric view of neuropathic pain etiology and pathology. Indeed, glial cells were shown to play an active role in the initiation and maintenance of pain hypersensitivity. However, the origins of these cells and the triggers that induce their activation have yet to be elucidated. Here we show that, after peripheral nerve injury induced by a partial ligation on the sciatic nerve, in addition to activation of microglia resident to the CNS, hematogenous macrophage/monocyte infiltrate the spinal cord, proliferate, and differentiate into microglia. Signaling from chemokine monocyte chemoattractant protein-1 (MCP-1, CCL2) to its receptor CCR2 is critical in the spinal microglial activation. Indeed, intrathecal injection of MCP-1 caused activation of microglia in wild-type but not in CCR2-deficient mice. Furthermore, treatment with an MCP-1 neutralizing antibody prevented bone marrow-derived microglia (BMDM) infiltration into the spinal cord after nerve injury. In addition, using selective knock-out of CCR2 in resident microglia or BMDM, we found that, although total CCR2 knock-out mice did not develop microglial activation or mechanical allodynia, CCR2 expression in either resident microglia or BMDM is sufficient for the development of mechanical allodynia. Thus, to effectively relieve neuropathic pain, both CNS resident microglia and blood-borne macrophages need to be targeted. These findings also open the door for a novel therapeutic strategy: to take advantage of the natural ability of bone marrow-derived cells to infiltrate selectively affected CNS regions by using these cells as vehicle for targeted drug delivery to inhibit hypersensitivity and chronic pain.
Draft Genome Sequence of Clostridium sporogenes Strain UC9000 Isolated from Raw Milk

ABSTRACT Clostridium sporogenes is a causative agent of food spoilage and is often used as the nontoxigenic surrogate for Clostridium botulinum. Here, we described the draft genome sequence and annotation of C. sporogenes strain UC9000 isolated from raw milk.
How Theories Represent

An account of scientific representation in terms of partial structures and partial morphisms is further developed. It is argued that the account addresses a variety of difficulties and challenges that have recently been raised against such formal accounts of representation. This allows some useful parallels between representation in science and art to be drawn, particularly with regard to apparently inconsistent representations. These parallels suggest that a unitary account of scientific and artistic representation is possible, and our article can be viewed as laying the groundwork for such an account—although, as we shall acknowledge, significant differences exist between these two forms of representation. 1 Introduction 2 Partial Structures View 3 An Example: Representation and Analogy in Superconductivity 4 Representation and Isomorphism in Art 5 Inconsistent Representations 6 Reduction and Disentangling: Callendar and Cohen and Contessa 7 From Art to Science 8 Challenges to the Formal Account 8.1 Necessity 8.2 Sufficiency 8.3 Logic 8.4 Mechanism 8.5 Style 8.6 Misrepresentation 8.7 Ontology 9 The Formal Account Defended 9.1 Preamble: ‘informational’ versus ‘functional’ accounts 9.2 Necessity 9.3 Logic and sufficiency 9.4 Mechanism 9.5 Style 9.6 Misrepresentation 9.7 Ontology 10 Conclusion 1 Introduction 2 Partial Structures View 3 An Example: Representation and Analogy in Superconductivity 4 Representation and Isomorphism in Art 5 Inconsistent Representations 6 Reduction and Disentangling: Callendar and Cohen and Contessa 7 From Art to Science 8 Challenges to the Formal Account 8.1 Necessity 8.2 Sufficiency 8.3 Logic 8.4 Mechanism 8.5 Style 8.6 Misrepresentation 8.7 Ontology 8.1 Necessity 8.2 Sufficiency 8.3 Logic 8.4 Mechanism 8.5 Style 8.6 Misrepresentation 8.7 Ontology 9 The Formal Account Defended 9.1 Preamble: ‘informational’ versus ‘functional’ accounts 9.2 Necessity 9.3 Logic and sufficiency 9.4 Mechanism 9.5 Style 9.6 Misrepresentation 9.7 Ontology 9.1 Preamble: ‘informational’ versus ‘functional’ accounts 9.2 Necessity 9.3 Logic and sufficiency 9.4 Mechanism 9.5 Style 9.6 Misrepresentation 9.7 Ontology 10 Conclusion