Miracle-dz/UniFAR-FTUs huggingface dataset:
CcpA and LacD.1 Affect Temporal Regulation of Streptococcus pyogenes Virulence Genes

ABSTRACT Production of H2O2 follows a growth phase-dependent pattern that mimics that of many virulence factors of Streptococcus pyogenes. To gain greater insight into mechanisms coupling virulence factor expression to growth phase, we investigated the molecular basis for H2O2 generation and its regulation. Deletion of the gene encoding lactate oxidase (lctO) or culture in the presence of glucose eliminated H2O2 production, implicating carbohydrate regulation of lctO as a key element of growth phase control. In examining known carbohydrate-responsive regulators, deletion of the gene encoding CcpA but not that encoding LacD.1 resulted in both derepression and an uncoupling of lctO transcription from its growth phase pattern. Expanding this analysis to additional virulence factors demonstrated both negative (cfa, encoding CAMP factor) and positive (speB, encoding a cysteine protease) regulation by CcpA and that CcpA mutants were highly cytotoxic for cultured macrophages. This latter property resulted from enhanced transcription of the streptolysin S biogenesis operon. Examination of CcpA-promoter interactions using a DNA pull-down assay mimicking physiological conditions showed direct binding to the promoters of lctO and speB but not those of sagA. CcpA but not LacD.1 mutants were attenuated in a murine model of soft-tissue infection, and analysis of gene expression in infected tissue indicated that CcpA mutants had altered expression of lctO, cfa, and speB but not the indirectly regulated sagA gene. Taken together, these data show that CcpA regulates virulence genes via at least three distinct mechanisms and that disruption of growth phase regulation alters transcriptional patterns in infected tissues.
Synthetic Generation of Radio Maps for Device-Free Passive Localization

In this paper, we present the design, implementation, and evaluation of a system that automatically constructs accurate radio maps for device-free WLAN localization systems. The system is capable of generating deterministic and probabilistic radio maps for localization systems. Our system uses 3D ray tracing enhanced with the uniform theory of diffraction (UTD) to model the electric field behavior and the human shadowing effect. We present our system architecture and describe the details of its different components. We also propose an optional module, location-0 correction, that can significantly enhances the system accuracy and reduces its dependence on the 3D model details by using just one signal strength sample. Our experiments in a real testbed show that the predicted signal strength differs from the measurements by a maximum average absolute error of $2.77$ dB achieving a maximum localization error of $3.13$m and $2.84$m for both the deterministic and probabilistic radio maps, respectively. In addition, the results show that our system is not sensitive to the 3D model details.
Monoclonal antibodies against simian virus 40 T antigens: evidence for distinct sublcasses of large T antigen and for similarities among nonviral T antigens

We have isolated three clones of hybrid cells which synthesize antibodies specific for determinants on simian virus 40 (SV40) T antigens. Mouse myeloma NS1 cells were fused with spleen cells from mice that had been immunized with SV40-transformed mouse cells. Hybrid cells were selected in HAT medium and cloned in soft agar. We used an enzyme-linked immunosorbent assay for detection and quantification of mouse antibodies against SV40 T antigens. Monoclonal antibodies from 3 of the 24 clones that scored as positive in the enzyme-linked immunosorbent assay were verified by immunoprecipitation to be specific for SV40 T antigens. Two clones (7 and 412) produced antibodies that recognized denaturation-sensitive antigenic determinants unique to large T antigen. Antibodies from clone 7 appeared to have a low affinity for large T antigen. Antibodies from clone 412 had a higher affinity for large T antigen but did not recognize a subclass of large T antigen that was recognized by tumor serum. Antibodies of the third clone, clone 122, recognized a denaturation-stable antigenic determinant of the 53,000-dalton mouse nonviral T antigen in SV40-transformed cells. Antibodies from clone 122 also recognized similar (51,000- to 56,000-dalton) nonviral T antigens in SV40-transormed or lytically infected cells from five mammalian species and in four uninfected mouse lines. From these observations, we have concluded that (i) the 94,000-dalton SV40 large T antigen may exist as immunologically distinguishable subclasses, and (ii) the nonviral T antigens of five mammalian species share at least one antigenic determinant.
Global features selection for dynamic signature verification

In this paper we collect 1210 global features of dynamics signature. All features are collected from previous research and we also add global features from FRESH framework. The purpose is to select relevant features from those features set. For doing that, we compute the importance score of each features using two methods: Information Gain Ratio and Correlation. Then each features will be ranked based on its score. After that, we divide 1210 features into 10, 20, 30, and so on until all 1210 features set are used in ascending order of the rank. Then, each features set is validated with Random Forrest, SVM, and Naïve Bayes classifier using 10 folds cross validation. The experiment was conducted in SVC2004 dataset task 1. The result show that, 120 first features from correlation method is the most relevant features. And therefore, those 120 global features is a good candidate for dynamic signature verification and will be used for the next research using dataset collected from mobile device.
Graphene and its derivatives as biomedical materials: future prospects and challenges

Graphene and its derivatives possess some intriguing properties, which generates tremendous interests in various fields, including biomedicine. The biomedical applications of graphene-based nanomaterials have attracted great interests over the last decade, and several groups have started working on this field around the globe. Because of the excellent biocompatibility, solubility and selectivity, graphene and its derivatives have shown great potential as biosensing and bio-imaging materials. Also, due to some unique physico-chemical properties of graphene and its derivatives, such as large surface area, high purity, good bio-functionalizability, easy solubility, high drug loading capacity, capability of easy cell membrane penetration, etc., graphene-based nanomaterials become promising candidates for bio-delivery carriers. Besides, graphene and its derivatives have also shown interesting applications in the fields of cell-culture, cell-growth and tissue engineering. In this article, a comprehensive review on the applications of graphene and its derivatives as biomedical materials has been presented. The unique properties of graphene and its derivatives (such as graphene oxide, reduced graphene oxide, graphane, graphone, graphyne, graphdiyne, fluorographene and their doped versions) have been discussed, followed by discussions on the recent efforts on the applications of graphene and its derivatives in biosensing, bio-imaging, drug delivery and therapy, cell culture, tissue engineering and cell growth. Also, the challenges involved in the use of graphene and its derivatives as biomedical materials are discussed briefly, followed by the future perspectives of the use of graphene-based nanomaterials in bio-applications. The review will provide an outlook to the applications of graphene and its derivatives, and may open up new horizons to inspire broader interests across various disciplines.
Social Relatedness and Physical Health Are More Strongly Related in Older Than Younger Adults: Findings from the Korean Adult Longitudinal Study

Previous research indicates that social relatedness is beneficial to physical health; however, findings on the relative strength of the relationship between these variables have been inconsistent. The present study employed cross-sectional survey (Study 1) and a daily diary survey (Study 2) to examine the link between social relatedness and physical health by age. Using a representative sample of Korean adults (N = 371) aged from 20 to 69, Study 1 examines the link between social relatedness (loneliness, perceived social support) and physical health (physical symptoms, chronic health conditions) using age as a moderator. The results show that participants' age moderates the association between social relatedness and physical health. Study 2 (N = 384) further corroborated the findings from Study 1 by showing that when controlling for the physical symptoms experienced prior to the daily diary reports, the level of loneliness experienced over a 13-day period exacerbates the age differences in the physical symptoms. The present study thus provides converging evidence that social relatedness plays a significant role in physical health, particularly in the older population.
Dental microwear textural analysis as an analytical tool to depict individual traits and reconstruct the diet of a primate.

OBJECTIVES Dental microwear is a promising tool to reconstruct animals' diet because it reflects the interplay between the enamel surface and the food items recently consumed. This study examines the sources of inter-individual variations in dietary habits in a free-ranging population of mandrills (Mandrillus sphinx) using a combination of feeding monitoring and in vivo dental microwear textural analysis (DMTA). METHODS We investigated the impact of seasonality and individual traits on four DMTA parameters. In parallel, we further studied the influence of the physical properties of the food items consumed on these four parameters, using three proxies (mechanical properties, estimates of phytolith and external grit contents). RESULTS We found that seasonality, age, and sex all impact DMTA parameters but those results differ depending on the facet analyzed (crushing vs. shearing facets). Three DMTA parameters (anisotropy, complexity, and heterogeneity of complexity) appear sensitive to seasonal variations and anisotropy also differs between the sexes while textural fill volume tends to vary with age. Moreover, the physical properties of the food items consumed vary seasonally and also differ depending on individual sex and age. CONCLUSION Considering the interplay between the tested variables and both dental microwear and diet, we reaffirm that food physical properties play a major role in microwear variations. These results suggest that DMTA parameters may provide valuable hints for paleoecological reconstruction using fragmentary fossil dental remains.
Texture Analysis and Machine Learning for Detecting Myocardial Infarction in Noncontrast Low-Dose Computed Tomography: Unveiling the Invisible

Objectives The aim of this study was to test whether texture analysis and machine learning enable the detection of myocardial infarction (MI) on non–contrast-enhanced low radiation dose cardiac computed tomography (CCT) images. Materials and Methods In this institutional review board–approved retrospective study, we included non–contrast-enhanced electrocardiography-gated low radiation dose CCT image data (effective dose, 0.5 mSv) acquired for the purpose of calcium scoring of 27 patients with acute MI (9 female patients; mean age, 60 ± 12 years), 30 patients with chronic MI (8 female patients; mean age, 68 ± 13 years), and in 30 subjects (9 female patients; mean age, 44 ± 6 years) without cardiac abnormality, hereafter termed controls. Texture analysis of the left ventricle was performed using free-hand regions of interest, and texture features were classified twice (Model I: controls versus acute MI versus chronic MI; Model II: controls versus acute and chronic MI). For both classifications, 6 commonly used machine learning classifiers were used: decision tree C4.5 (J48), k-nearest neighbors, locally weighted learning, RandomForest, sequential minimal optimization, and an artificial neural network employing deep learning. In addition, 2 blinded, independent readers visually assessed noncontrast CCT images for the presence or absence of MI. Results In Model I, best classification results were obtained using the k-nearest neighbors classifier (sensitivity, 69%; specificity, 85%; false-positive rate, 0.15). In Model II, the best classification results were found with the locally weighted learning classification (sensitivity, 86%; specificity, 81%; false-positive rate, 0.19) with an area under the curve from receiver operating characteristics analysis of 0.78. In comparison, both readers were not able to identify MI in any of the noncontrast, low radiation dose CCT images. Conclusions This study indicates the ability of texture analysis and machine learning in detecting MI on noncontrast low radiation dose CCT images being not visible for the radiologists' eye.
Compound heterozygous CASQ2 mutations and long‐term course of catecholaminergic polymorphic ventricular tachycardia

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a potentially lethal inherited cardiac disorder characterized by episodic ventricular tachycardia during adrenergic stimulation. It is associated with significant morbidity and mortality. Knowledge of the underlying genetic cause, pathogenesis, and the natural history of the disease remains incomplete. Approximately 50% of CPVT cases are caused by dominant mutations in the cardiac ryanodine receptor (RYR2) gene, <5% of cases are accounted for by recessive mutations in cardiac calsequestrin (CASQ2) or Triadin (TRDN).
L2S: Transforming Natural Language Questions into SQL Queries

The reliability of a question answering system is bounded by the availability of resources and linguistic tools. In this paper, we introduce a hybrid approach to transforming natural language questions into structured queries. It alleviates the lack of experts in domain observation and the deficient performance of linguistic tools. Specifically, we exploit the semantic information for mapping natural language terminologies to structured query and bipartite graph model for the matching phase. Experimental results on the Vietnam national university entrance exam dataset and the Geoqueries880 dataset achieve accuracies of 91.14% and 87.55%, respectively.
Current use of linux in spacecraft flight software

Spacecraft on-board computers are responsible for controlling the spacecraft platform, payloads, or other on-board devices. Their mission-specific software allows communication with ground or other on-board computers. Traditionally, on-board software has been written close to the hardware in assembly language, Ada, C, or C++, with or without a real-time operating system (RTOS) [1]. As the spacecraft computer hardware capabilities are increasing, spacecraft software is becoming larger and more complex, handling more tasks from payload data processing to landing a first stage of a launch vehicle on an ocean-going barge. Spacecraft will still continue to include very small embedded systems that can be developed without operating systems (OS), but some systems will also have large software bases, requiring efficient software development processes and reuse of existing software modules. The last decade has seen increasing use of Linux in spacecraft on-board software. This article presents common features of spacecraft on-board computers and software and discusses potential benefits and drawbacks of on-board Linux use. The focus of this article is on spacecraft on-board avionics software, that is, spacecraft- controlling code that flies into orbit with the spacecraft. Other types of computers are not included in this analysis; for example, many laptops on the International Space Station run Linux [2].
Is HLA matching relevant in pancreas transplantation?: A registry analysis

Abstract. The International Pancreas Transplant Registry data base was analyzed for the effect of HLA and mismatching on pancreas survival rate. Typing data was available for both donor and recipient at the A, B and DR loci in 524 of 855 cadaver cases reported since 1982 and in 37 related cases. For cadaver cases, the 1‐year functional survival rates for grafts mismatched at3 (N= 163) versus4 (N= 361) A, B and DR antigens were 49% versus 39% (P= 0.121); for technically successful (TS) cases the rates were 66% (N= 123) versus 54% (N= 257) (P= 0.038). An effect was seen at A, B and DR loci, but the differences were not significant when considered separately. The analysis of TS related donor transplants showed a 1‐year graft survival rate of 89% for HLA mismatched donors (N= 11) and of 80% for HLA identical donors (N= 11). The survival rate of the latter is significantly higher (P= 0.046) than that of the TS cadaver donor transplants (59% at 1 year, N= 361). The data suggest that the results of pancreas transplantation will be improved by minimizing HLA mismatches. However, a reanalysis with a more complete data base is needed before firm conclusions can be drawn.
Patients with chronic bipolar disorder exhibit widespread increases in extracellular free water

Bipolar disorder (BP) is a debilitating psychiatric disease that is not well understood. Previous diffusion magnetic resonance imaging (dMRI) studies of BP patients found prominent microstructural white matter (WM) abnormalities of reduced fractional anisotropy (FA). Because FA is a nonspecific measure, relating these abnormalities to a specific pathology is difficult. Here, dMRI specificity was increased by free water (FW) imaging, which allows identification of changes in extracellular space (FW) from neuronal tissue (fractional anisotropy of tissue [FA‐t]). Previous studies identified increased FW in early schizophrenia (SZ) stages which was replaced by widespread decreased FA‐t in chronic stages. This is the first analysis utilizing this method to compare BP patients and controls.
Cytoplasmic 3′ poly(A) addition induces 5′ cap ribose methylation: implications for translational control of maternal mRNA.

During the early development of many animal species, the expression of new genetic information is governed by selective translation of stored maternal mRNAs. In many cases, this translational activation requires cytoplasmic poly(A) elongation. However, how this modification at the 3′ end of an mRNA stimulates translation from the 5′ end is unknown. Here we show that cytoplasmic polyadenylation stimulates cap ribose methylation during progesterone‐induced oocyte maturation in Xenopus laevis. Translational recruitment of a chimeric reporter mRNA that is controlled by cytoplasmic polyadenylation coincides temporally with cap ribose methylation during this period. In addition, the inhibition of cap ribose methylation by S‐isobutyladenosine significantly reduces translational activation of a reporter mRNA without affecting the increase of general protein synthesis or polyadenylation during maturation. These results provide evidence for a functional interaction between the termini of an mRNA molecule and suggest that 2′‐O‐ribose cap methylation mediates the translational recruitment of maternal mRNA.
Fatigue and cardiorespiratory function following abdominal surgery

Subjective feelings of fatigue were assessed before operation and 10, 20 and 30 days after uncomplicated elective abdominal surgery in 16 otherwise healthy patients, using a constructed fatigue scale model. In addition, all patients had an orthostatic stress test performed at the same times. Six of the patients also underwent a bicycle ergometer test measuring heart rate and oxygen consumption. Subjective feelings of fatigue were increased (P<0.01) at all three postoperative observations, and only 5 of 16 patients returned to their preoperative level. The increased subjective feeling of fatigue correlated positively (Rs = 0.53, P<0.001) with the increased pulse rate seen during orthostatic stress after operation. Heart rate was about 5 per cent higher (n.s.) after operation when bicycling at the same work loads, while oxygen consumption decreased by about 2 per cent (P<0.01) at all three postoperative bicycle tests. It is concluded that even elective uncomplicated abdominal surgery is followed by a pronounced feeling of fatigue, which may persist 1 month after surgery in about one‐third of patients. The fatigue scale model seems applicable for future studies on the pathogenesis and treatment of the postoperative fatigue syndrome.
Gone with the Headwinds: Global Productivity

Productivity growthâthe key driver of living standardsâfell sharply following the global financial crisis and has remained sluggish since, adding to a slowdown already in train before. Building on new research, this note finds that the productivity slowdown reflects both crisis legacies and structural headwinds. In advanced economies, the global financial crisis has led to âproductivity hysteresisââpersistent productivity losses from a seemingly temporary shock. Behind this are balance sheet vulnerabilities, protracted weak demand and elevated uncertainty, which jointly triggered an adverse feedback loop of weak investment, weak productivity and bleak income prospects. Structural headwindsâalready blowing before the crisisâinclude a waning ICT boom and slowing technology diffusion, partly reflecting an aging workforce, slowing global trade and weaker human capital accumulation. Reviving productivity growth requires addressing remaining crisis legacies in the short run while pressing ahead with structural reforms to tackle longer-term headwinds.
Tactile discrimination of grating orientation: fMRI activation patterns

Grating orientation discrimination is employed widely to test tactile spatial acuity. We used functional magnetic resonance imaging (fMRI) to investigate the neural circuitry underlying performance of this task. Two studies were carried out. In the first study, an extensive set of parietal and frontal cortical areas was activated during covert task performance, relative to a rest baseline. The active regions included the postcentral sulcus bilaterally and foci in the left parietal operculum, left anterior intraparietal sulcus, and bilateral premotor and prefrontal cortex. The second study examined selective recruitment of cortical areas during discrimination of grating orientation (a task with a macrospatial component) compared to discrimination of grating spacing (a purely microspatial task). The foci activated on this contrast were in the left anterior intraparietal sulcus, right postcentral sulcus and gyrus, left parieto‐occipital cortex, bilateral frontal eye fields, and bilateral ventral premotor cortex. These findings not only confirm and extend previous studies of the neural processing underlying grating orientation discrimination, but also demonstrate that a distributed network of putatively multisensory areas is involved. Hum Brain Mapp, 2005. © 2005 Wiley‐Liss, Inc.