Miracle-dz/UniFAR-FTUs huggingface dataset:
$^1$S$_0$ Neutron Pairing vs Observations of Cooling Neutron Stars

As shown recently by Kaminker et al. (2001), current observations of thermal emission of isolated middle-aged neutron stars (NSs) can be explained by cooling of NSs of different masses with the cores composed of neutrons, protons and electrons, assuming rather strong superfluidity (SF) of protons, weak triplet-state SF of neutrons and neglecting singlet-state SF of neutrons. We show that this explanation remains correct in the presence of singlet-state SF of neutrons in the NS crust and outermost core but under stringent constraints on the density profile of the SF critical temperature $T_{\rm cns}(\rho)$. In order to explain observations of (young and hot) RX J0822--43 and (old and warm) PSR 1055--52 and RX J1856--3754 as cooling not too massive NSs, the maximum $T_{\rm cns}^{\rm max}$ should be rather high ($\ga 5 \times 10^9$ K) and the decrease of $T_{\rm cns}(\rho)$ outside the maximum should be sharp. These results place important constraints on the models of nucleon SF in dense matter.
The HIV Care Continuum: Changes over Time in Retention in Care and Viral Suppression

Background The HIV care continuum (diagnosis, linkage to care, retention in care, receipt of antiretroviral therapy (ART), viral suppression) has been used to identify opportunities for improving the delivery of HIV care. Continuum steps are typically calculated in a conditional manner, with the number of persons completing the prior step serving as the base population for the next step. This approach may underestimate the prevalence of viral suppression by excluding patients who are suppressed but do not meet standard definitions of retention in care. Understanding how retention in care and viral suppression interact and change over time may improve our ability to intervene on these steps in the continuum. Methods We followed 17,140 patients at 11 U.S. HIV clinics between 2010-2012. For each calendar year, patients were classified into one of five categories: (1) retained/suppressed, (2) retained/not-suppressed, (3) not-retained/suppressed, (4) not-retained/not-suppressed, and (5) lost to follow-up (for calendar years 2011 and 2012 only). Retained individuals were those completing ≥2 HIV medical visits separated by ≥90 days in the year. Persons not retained completed ≥1 HIV medical visit during the year, but did not meet the retention definition. Persons lost to follow-up had no HIV medical visits in the year. HIV viral suppression was defined as HIV-1 RNA ≤200 copies/mL at the last measure in the year. Multinomial logistic regression was used to determine the probability of patients’ transitioning between retention/suppression categories from 2010 to 2011 and 2010 to 2012, adjusting for age, sex, race/ethnicity, HIV risk factor, insurance status, CD4 count, and use of ART. Results Overall, 65.8% of patients were retained/suppressed, 17.4% retained/not-suppressed, 10.0% not-retained/suppressed, and 6.8% not-retained/not-suppressed in 2010. 59.5% of patients maintained the same status in 2011 (kappa=0.458) and 53.3% maintained the same status in 2012 (kappa=0.437). Conclusions Not counting patients not-retained/suppressed as virally suppressed, as is commonly done in the HIV care continuum, underestimated the proportion suppressed by 13%. Applying the care continuum in a longitudinal manner will enhance its utility.
Lichens of Gujarat state, India with special reference to coastal habitats

The present communication reports 39 lichen species from Gujarat state, belonging to 23 genera and 13 families. The lichens were collected mostly from 10 coastal districts of the state. A total of 21 species are new additions to the lichen mycota of Gujarat while 11 partially identified species are expected to be new to science. The paper emphasizes the uniqueness of coastal habitats in terms of interesting lichen mycota.
Prothrombotic Effects of Fibronectin Isoforms Containing the EDA Domain

Objective—Fibronectin (FN) plays an important role in the formation of stable arterial thrombi at the site of vascular injury. FN containing Extra Domain A (EDA+FN) is absent from normal plasma, but elevated plasma levels of EDA+FN are found in several pathological conditions. We hypothesized that EDA+FN plays a special role in thrombosis. Methods and Results—We used mouse strains constitutively including (EDA+/+) or excluding (EDA−/−) the EDA domain in all tissues and plasma. Using a flow chamber and the ferric-chloride injury model we found that EDA+FN accelerates thrombosis both in vitro and in vivo at arterial shear rates. In EDA+/+ mice thrombi (>30 &mgr;m) grew faster when compared with EDAWT/WT (6.6±0.2 minutes versus 8.3±0.6 minutes, P<0.05) and the mean vessel occlusion time was shorter (9.9±0.4 minutes versus 14.6±1.7 minutes, P<0.05). However, the presence of EDA+FN affected neither single platelet adhesion to subendothelium nor thrombosis in veins. In addition, the mortality rate of EDA+/+ mice after collagen/epinephrine infusion was twice that of EDAWT/WT or EDA−/− mice. Conclusions—Our findings reveal that EDA+FN has prothrombotic activity, and its presence in plasma may worsen pathological conditions in which this form is elevated.
Mechanisms of Resistance to Imatinib and Second-Generation Tyrosine Inhibitors in Chronic Myeloid Leukemia

Targeted therapy in the form of selective tyrosine kinase inhibitors (TKI) has transformed the approach to management of chronic myeloid leukemia (CML) and dramatically improved patient outcome to the extent that imatinib is currently accepted as the first-line agent for nearly all patients presenting with CML, regardless of the phase of the disease. Impressive clinical responses are obtained in the majority of patients in chronic phase; however, not all patients experience an optimal response to imatinib, and furthermore, the clinical response in a number of patients will not be sustained. The process by which the leukemic cells prove resistant to TKIs and the restoration of BCR-ABL1 signal transduction from previous inhibition has initiated the pursuit for the causal mechanisms of resistance and strategies by which to surmount resistance to therapeutic intervention. ABL kinase domain mutations have been extensively implicated in the pathogenesis of TKI resistance, however, it is increasingly evident that the presence of mutations does not explain all cases of resistance and does not account for the failure of TKIs to eliminate minimal residual disease in patients who respond optimally. The focus of exploring TKI resistance has expanded to include the mechanism by which the drug is delivered to its target and the impact of drug influx and efflux proteins on TKI bioavailability. The limitations of imatinib have inspired the development of second generation TKIs in order to overcome the effect of resistance to this primary therapy. (Clin Cancer Res 2009;15(24):7519–27)
Analysis of Range and Position Comparison Methods as a Means to Provide GPS Integrity in the User Receiver

Integrity is the ability of a system to let its users know whether the system is operating out of its specified performance limits. This paper analyzes two receiver-based methods for assuring the integrity of Global Positioning System (GPS) signals-in-space. These methods are called the range comparison method and the position comparison method. Equations relating unknown satellite range errors to the quantity measured in each method are analyzed. The equations reveal important characteristics of the methods, including their mathematical equivalence. The performance of the two methods is derived in terms of satellite range errors. Numerical results are then obtained for the performance of the methods, alone and in combination with monitoring of the receiver clock bias estimate.
IL-27, a novel anti-HIV cytokine, activates multiple interferon-inducible genes in macrophages

Objective: IL-27 is a novel anti-HIV cytokine that inhibits HIV-1 replication in both CD4 T cells and monocyte-derived macrophages (MDM) as IFN-α does. To elucidate the mechanism of the antiviral activity, we compared the activity and the gene expression profile of IL-27-treated cells with that of IFN-α-treated cells. Methods: CD4 T cells and monocytes were isolated from peripheral blood mononuclear cells of healthy donors. CD4 T cells were stimulated with phytohemagglutinin, and MDM were induced from monocytes using macrophage-colony stimulating factor. HIV-1 replication was monitored by p24 antigen capture assay. The gene expression profiles were analysed using DNA microarray analysis. The increase in the expression of IFN-inducible genes (IFIG) was confirmed by the Quantigene plex assay. Results: Both cytokines preferentially inhibited HIV-1 replication in MDM compared with CD4 T cells. Quantitative real time polymerase chain reaction, enzyme-linked immunosorbent assay and neutralization assay using anti-IFN indicated that IFN-α, IFN-β and IFN-γ had no significant impact on IL-27-mediated HIV inhibition. DNA microarray analysis illustrated that IFN-α induced 33 and 18 IFIG in MDM and CD4 T cells, respectively. IL-27 induced 28 IFIG in MDM and five IFIG in CD4 T cells. The quantitative assay confirmed that IL-27 activated genes of RNA-dependent kinase, oligoadenylate synthetase, myxovirus protein, and apolipoprotein B messenger RNA-editing enzyme-catalytic polypeptide-like 3G. Conclusion: IL-27 differentially regulates the gene expression between CD4 T cells and MDM. IL-27 significantly induces antiviral genes in MDM as does IFN-α, suggesting that IL-27 inhibits HIV replication in MDM via mechanism(s) similar to that of IFN-α.
The sbcDC Locus Mediates Repression of Type 5 Capsule Production as Part of the SOS Response in Staphylococcus aureus

ABSTRACT Most strains of Staphylococcus aureus produce one type of capsular polysaccharide that belongs to either type 5 or type 8. The production of these capsules has been shown to be regulated by various regulators. Here we report that the sbcD and sbcC genes are involved in the repression of type 5 capsule production. Chromosomal deletions in the sbcDC genes resulted in increased capsule promoter activity, capsule gene transcripts, and capsule production. The survival rates of the sbcDC deletion mutant were reduced upon UV irradiation compared to those for the wild-type strain Newman, suggesting that the genes are involved in DNA repair in S. aureus. The two genes were organized as an operon and were expressed very early in the exponential growth phase. A subinhibitory concentration of ciprofloxacin or mitomycin C induced sbcDC transcription but repressed the capsule promoter activity, suggesting that the sbcDC genes and the capsule genes are part of the SOS regulon. By reporter gene fusion and Northern blotting, we found that sbcDC regulated capsule by downregulating arl and mgr. Further genetic studies indicate that sbcDC functions upstream of arl and mgr in capsule regulation. Collectively, our results indicate that sbcDC, upon the SOS response, represses type 5 capsule production through an arl-mgr pathway. To our knowledge, this is the first demonstration that an SbcDC homolog was involved in transcriptional regulation.
Clinical performance indicators: intolerance for variety?

PURPOSE The performance of NHS U.K. hospitals is under continuous scrutiny as they are constantly under pressure to perform well. A recent document published by an independent body has recommended a host of clinical indicators to assess non-financial performance of hospitals. This study aims to critically analyse the performance of a single U.K. hospital against several of these recommended indicators. DESIGN/METHODOLOGY/APPROACH Data presented to the Hospital Trust Board for 12 months were used for this study. Previous years' data were used wherever available. FINDINGS Based on data analysis, this hospital's performance is extremely difficult to calculate. The indicators use complex ratios and due to lack of standardisation, the hospital performance could be interpreted as better, worse or indifferent. RESEARCH LIMITATIONS/IMPLICATIONS This study analyses most of the recommended indicators. Literature review did not reveal a similar analysis of another hospital against these indicators which precludes comparison. PRACTICAL IMPLICATIONS This study highlights the difficulty in comparing the performance of hospitals due to the inherent lack of consistency. Therefore it is apparent that any reward-rebuke system linked to performance should interpret the data with caution. It is therefore suggested that easy to control single value activities and standardised routine activities could be used to measure hospital performance. Alternatively, the hospital could compare with its own statistics from previous years. ORIGINALITY/VALUE Literature acknowledges the difficulties in measuring clinical performance. This paper elucidates these difficulties applied to the NHS and suggests alternatives.
Unraveling Biochemical Pathways Affected by Mitochondrial Dysfunctions Using Metabolomic Approaches

Mitochondrial dysfunction(s) (MDs) can be defined as alterations in the mitochondria, including mitochondrial uncoupling, mitochondrial depolarization, inhibition of the mitochondrial respiratory chain, mitochondrial network fragmentation, mitochondrial or nuclear DNA mutations and the mitochondrial accumulation of protein aggregates. All these MDs are known to alter the capacity of ATP production and are observed in several pathological states/diseases, including cancer, obesity, muscle and neurological disorders. The induction of MDs can also alter the secretion of several metabolites, reactive oxygen species production and modify several cell-signalling pathways to resolve the mitochondrial dysfunction or ultimately trigger cell death. Many metabolites, such as fatty acids and derived compounds, could be secreted into the blood stream by cells suffering from mitochondrial alterations. In this review, we summarize how a mitochondrial uncoupling can modify metabolites, the signalling pathways and transcription factors involved in this process. We describe how to identify the causes or consequences of mitochondrial dysfunction using metabolomics (liquid and gas chromatography associated with mass spectrometry analysis, NMR spectroscopy) in the obesity and insulin resistance thematic.
Differences in Ankle Range of Motion before and after Exercise in 2 Tape Conditions

Background Athletic tape has been used on the ankle to decrease range of motion and to prevent injuries. Results from previous research found that with physical exercise athletic tape loses some of its restricting properties; recently, a new self-adherent taping product was developed that may restrict range of motion regardless of exercise. Hypothesis Self-adherent tape will maintain ankle range of motion restriction more than traditional white cloth tape both before and after activity. Study Design Controlled laboratory study. Methods Twenty volunteers participated in testing procedures on 3 separate days, 1 for each taping condition (self-adherent, white cloth, and no tape). The participant's ankle range of motion was measured with an electrogoniometer before application of the tape, immediately after application of the tape, and after 30 minutes of physical exercise. Range of motion was measured in 2 planes of motion: inversion to eversion and dorsiflexion to plantar flexion. Results White cloth tape and self-adherent tape both restricted inversion to eversion range of motion immediately after application, but with 30 minutes of exercise only the self-adherent tape maintained the decreased range of motion. For dorsiflexion to plantar flexion range of motion, the white tape and self-adherent tape both significantly decreased range of motion immediately after application and after the exercise protocol. Conclusions and Clinical Relevance The self-adherent tape maintained range of motion restriction both before and after exercise. Conversely, the white cloth tape lost some of its restrictive properties after 30 minutes of exercise.
Interleukin-2 receptors in experimental Chagas' disease

Mammals infected with the protozoan parasite Trypanosoma cruzi develop suppressed cellular and humoral immune responses. This immunosuppression has been correlated with reduced T-cell responses involving deficient interleukin-2 (IL-2) production and is apparently mediated primarily by suppressor macrophages. Various forms of immunosuppression in other systems have been associated with increased levels of soluble IL-2 receptors (sIL-2R), and in the present study levels of sIL-2R in the sera of T. cruzi-infected mice during the course of infection were examined in enzyme-linked immunosorbent assays. It was found that serum levels of sIL-2R were elevated only during the third week of acute infection, a time of intense immunosuppression. In addition, IL-2R on the surface of T cells were examined by flow cytometric analyses to determine whether there is an alteration in the number of IL-2R-positive cells and whether there is a change in expression of these receptors as infection progresses. The results revealed no significant change in the percentage of cells expressing IL-2R, nor did T cells become suppressed in their ability to express IL-2R in response to concanavalin A during the course of infection.
Structure Based Annotation of Helicobacter pylori Strain 26695 Proteome

The availability of complete genome sequences of H. pylori 26695 has provided a wealth of information enabling us to carry out in silico studies to identify new molecular targets for pharmaceutical treatment. In order to construe the structural and functional information of complete proteome, use of computational methods are more relevant since these methods are reliable and provide a solution to the time consuming and expensive experimental methods. Out of 1590 predicted protein coding genes in H. pylori, experimentally determined structures are available for only 145 proteins in the PDB. In the absence of experimental structures, computational studies on the three dimensional (3D) structural organization would help in deciphering the protein fold, structure and active site. Functional annotation of each protein was carried out based on structural fold and binding site based ligand association. Most of these proteins are uncharacterized in this proteome and through our annotation pipeline we were able to annotate most of them. We could assign structural folds to 464 uncharacterized proteins from an initial list of 557 sequences. Of the 1195 known structural folds present in the SCOP database, 411 (34% of all known folds) are observed in the whole H. pylori 26695 proteome, with greater inclination for domains belonging to α/β class (36.63%). Top folds include P-loop containing nucleoside triphosphate hydrolases (22.6%), TIM barrel (16.7%), transmembrane helix hairpin (16.05%), alpha-alpha superhelix (11.1%) and S-adenosyl-L-methionine-dependent methyltransferases (10.7%).
Dynamic organization of multi-agent systems

Many models of organizations for multi-agent systems have been proposed so far. However the complexity implied by the design of social organizations in a given multi-agent system is often not mentioned. Too little has been said about rules that must be applied to build the architecture of acquaintances between agents. Moreover, tools for managing the dynamic evolution of organizations are seldom provided in current framework propositions.In this paper we discuss self-adaptation of organizations in multi-agent systems according to the dynamic of interactions between agents. Starting from a default organization, the architecture of acquaintances evolves autonomously depending on messages flow in order to improve the global behaviour of the system. We propose three principles that can be applied to adapt the organization: "have a good address book", "share knowledge", "recruit new able collaborators". These principles have been applied in our multi-agent platform called MAGIQUE.
Multi-layered approach for recovering links between bug reports and fixes

The links between the bug reports in an issue-tracking system and the corresponding fixing changes in a version repository are not often recorded by developers. Such linking information is crucial for research in mining software repositories in measuring software defects and maintenance efforts. However, the state-of-the-art bug-to-fix link recovery approaches still rely much on textual matching between bug reports and commit/change logs and cannot handle well the cases where their contents are not textually similar. This paper introduces MLink, a multi-layered approach that takes into account not only textual features but also source code features of the changed code corresponding to the commit logs. It is also capable of learning the association relations between the terms in bug reports and the names of entities/components in the changed source code of the commits from the established bug-to-fix links, and uses them for link recovery between the reports and commits that do not share much similar texts. Our empirical evaluation on real-world projects shows that MLink can improve the state-of-the-art bug-to-fix link recovery methods by 11--18%, 13--17%, and 8--17% in F-score, recall, and precision, respectively.
Fast-yet-accurate PVT simulation by combined direct and iterative methods

The operations and performances of deep-submicron integrated circuits are affected significantly by the variations of process parameters, power supply voltages and operating temperatures. Circuit simulation for all the combinations of process-voltage-temperature (PVT) conditions, known as PVT simulation, is emerging as a must not only for analog and RF circuit designs, but also for the designs of digital library cells and critical paths. With the number of PVT conditions in the range of hundreds and even thousands, existing solution of invoking a simulator repeatedly for all these PVT conditions is becoming extremely time consuming. This paper presents a new simulation approach capable of simulating hundreds and thousands PVT corners with the computational cost comparable to or even less than that of a few corner simulations, yet with the same simulation accuracy and robustness. The proposed approach is based on the combination of the LU-factorization based direct method and Krylov subspace based iterative methods to explore the common characteristics shared by a circuit under all PVT corners. The key novelty is a systematic method that uses as few LU based direct solving as possible for underlying linearized systems, and then solves the rest of linearized systems across the entire PVT linear system space using Krylov subspace based iterative methods with preconditioners computed from those LU factors.