Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibody Evasion by a Gammaherpesvirus O-Glycan Shield

All gammaherpesviruses encode a major glycoprotein homologous to the Epstein-Barr virus gp350. These glycoproteins are often involved in cell binding, and some provide neutralization targets. However, the capacity of gammaherpesviruses for long-term transmission from immune hosts implies that in vivo neutralization is incomplete. In this study, we used Bovine Herpesvirus 4 (BoHV-4) to determine how its gp350 homolog - gp180 - contributes to virus replication and neutralization. A lack of gp180 had no impact on the establishment and maintenance of BoHV-4 latency, but markedly sensitized virions to neutralization by immune sera. Antibody had greater access to gB, gH and gL on gp180-deficient virions, including neutralization epitopes. Gp180 appears to be highly O-glycosylated, and removing O-linked glycans from virions also sensitized them to neutralization. It therefore appeared that gp180 provides part of a glycan shield for otherwise vulnerable viral epitopes. Interestingly, this O-glycan shield could be exploited for neutralization by lectins and carbohydrate-specific antibody. The conservation of O-glycosylation sites in all gp350 homologs suggests that this is a general evasion mechanism that may also provide a therapeutic target.
Administration of a Histone Deacetylase Inhibitor into the Basolateral Amygdala Enhances Memory Consolidation, Delays Extinction, and Increases Hippocampal BDNF Levels

Gene expression related to the formation and modification of memories is regulated epigenetically by chromatin remodeling through histone acetylation. Memory formation and extinction can be enhanced by treatment with inhibitors of histone deacetylases (HDACs). The basolateral amygdala (BLA) is a brain area critically involved in regulating memory for inhibitory avoidance (IA). However, previous studies have not examined the effects of HDAC inhibition in the amygdala on memory for IA. Here we show that infusion of an HDAC inhibitor (HDACi), trichostatin A (TSA), into the BLA, enhanced consolidation of IA memory in rats when given at 1.5, 3, or 6 h posttraining, but not when the drug was infused immediately after training. In addition, intra-BLA administration of TSA immediately after retrieval delayed extinction learning. Moreover, we show that intra-BLA TSA in rats given IA training increased the levels of brain-derived neurotrophic factor in the dorsal hippocampus, but not in the BLA itself. These findings reveal novel aspects of the regulation of fear memory by epigenetic mechanisms in the amygdala.
Towards an Inferential Lexicon of Event Selecting Predicates for French

We present a manually constructed seed lexicon encoding the inferential profiles of French event selecting predicates across different uses. The inferential profile (Karttunen, 1971a) of a verb is designed to capture the inferences triggered by the use of this verb in context. It reflects the influence of the clause-embedding verb on the factuality of the event described by the embedded clause. The resource developed provides evidence for the following three hypotheses: (i) French implicative verbs have an aspect dependent profile (their inferential profile varies with outer aspect), while factive verbs have an aspect independent profile (they keep the same inferential profile with both imperfective and perfective aspect); (ii) implicativity decreases with imperfective aspect: the inferences triggered by French implicative verbs combined with perfective aspect are often weakened when the same verbs are combined with imperfective aspect; (iii) implicativity decreases with an animate (deep) subject: the inferences triggered by a verb which is implicative with an inanimate subject are weakened when the same verb is used with an animate subject. The resource additionally shows that verbs with different inferential profiles display clearly distinct sub-categorisation patterns. In particular, verbs that have both factive and implicative readings are shown to prefer infinitival clauses in their implicative reading, and tensed clauses in their factive reading.
Relationship between patient income level and mitral valve repair utilization.

BACKGROUND The superiority of mitral valve (MV) repair is well established with respect to long-term survival, preservation of ventricular function, and valve-related complications. The relationship between patient income level and the selection of MV procedure (repair versus replacement) has not been studied. METHODS The 2005 to 2007 Nationwide Inpatient Sample database was searched for patients ≥ 30 years old with MV repair or replacement; patients with ischemic and congenital MV disease were excluded. Patients were stratified into quartiles according to income level (quartile 1, lowest; quartile 4, highest). We used univariate and multivariate models to compare patients with respect to baseline characteristics, selection of MV procedure, and hospital mortality. RESULTS The preoperative profiles of the income quartiles differed significantly, with more risk factors occurring in the lower income quartiles. Unadjusted hospital mortality decreased with increasing income quartile. The percentage of patients receiving MV repair increased with increasing income (35.6%, 39.6%, 48.2%, and 55.8% for quartiles 1, 2, 3, and 4, respectively; P = .0001). Following adjustment for age, race, sex, urban residency, admission status, primary payer, Charlson comorbidity index, and hospital location and teaching status, the income quartiles had similar hospital death rates, whereas the highly significant relationship between valve repair and income level persisted (P = .0008). CONCLUSIONS Significant disparity exists among patients in the different income quartiles with respect to the likelihood of receiving MV repair. MV repair is performed less frequently in patients with lower incomes, even after adjustment for differences in baseline characteristics. The higher unadjusted mortality rate for less affluent patients appears mostly related to their worse preoperative profiles.
Tools in Mining Software Repositories

Mining software repositories (MSR) is an important area of research. An international workshop on MSR has been established under the umbrella of international conference on software engineering (ICSE) in year 2004. The quality papers received and presented in the workshop has led to initiate full-fledged conference which purely focuses on issues related to mining software engineering data since 2007. This paper is the result of reviewing all the papers published in the proceedings of the conferences on Mining Software Repositories (MSR) and in other related conference/journals. We have analyzed the papers that contained experimental analysis of software projects related to data mining in software engineering. We have identified the data sets, techniques and tools used/ developed/ proposed in these papers. More than half of the papers are involved in the task accomplished by building or using the data mining tools to mine the software engineering data. It is apparent from the results obtained by analyzing these papers that MSR authors process the raw data which in general publicly available. We categorizes different tools used in MSR on the basis of newly developed, traditional data mining tools, prototype developed and scripts. We have shown the type of mining task that has been performed by using these tools along with the datasets used in these studies.
Development and Evaluation of Automatic Punctuation for French and English Speech-to-Text

Automatic punctuation of speech is important to make speechto-text output more readable and to facilitate downstream language processing. This paper describes the development of an automatic punctuation system for French and English. The punctuation model uses both textual information and acoustic (prosodic) information and is based on adaptive boosting. The system is evaluated on a challenging speech corpus under real-application conditions using output from a state-of-the-art speech-to-text system and automatic audio segmentation and speaker diarization. Unlike previous work, automatic punctuation is scored on two independent manual references. Comparisons are made for the two languages and the performance of the automatic system is compared with inter-annotator agreement.
The Housing Market Impacts of Constraining Second Home Investments

We investigate how political backlash against wealthy second home investors in high-amenity places - tourist areas or superstar cities - affects local residents. We develop a general equilibrium model and exploit a quasi-natural experiment -the 'Swiss Second Home Initiative' (SHI) -to test the key predictions of the model. Consistent with theory, we find that the SHI, which banned the construction of new second homes in desirable tourist locations, lowered transaction prices of primary homes in affected areas by around 12 percent but did not adversely affect prices of second homes. Our findings suggest that the negative effect on local economies dominated positive amenity-preservation effects. We conclude that constraining second home investments may reinforce rather than reduce wealth inequality.
Nutrient digestion in the large intestine as influenced by forage to concentrate ratio and forage physical form.

Digestion in the large intestine was investigated in four growing steers fitted with duodenal and ileal cannulas. Diets assigned within a 4 x 4 Latin square were: 20% long alfalfa hay and 80% grain; 15% pelleted alfalfa, 5% hay, and 80% grain; 80% hay and 20% grain; and 60% pellets, 20% hay, and 20% grain. Intake of DM was not affected by diet. Organic matter digestion in the large intestine averaged 9, 3, 1, and -4% of total tract digestion for the 20% hay, 20% pellet, 80% hay, and 80% pellet diets, respectively, with significant increases due to high grain diets and long hay. Digestion of CP in the large intestine as a percentage of total tract digestion was unaffected by diet but averaged 3, -1, . 3, and -6% for the respective diets. Percentage of total tract starch digestion occurring in the large intestine increased with grain feeding and averaged 6, 3, 1, and 1%, respectively. Digestion of ADF and NDF in the large intestine as a percentage of total tract was unaffected by diet; however, the respective means were 16 and 15, 7 and 7, 5 and 15, and 1 and 1%. In a second trail the same animals were fed a more typical dairy cow diet consisting of 50% grain, 25% corn silage, and 25% long alfalfa hay for a single 18-d period. Digestion in the large intestine accounted for 2.1, . 2, 3.6, and 6.4% of total tract digestion of organic matter, starch, ADF, and NDF, respectively; however, feed intake was not as great as in the first trail. Although conditions of these studies differed from those commonly experienced by lactating cows, the underlying principals should apply. The large intestine would be expected to make an even greater contribution to total tract digestion in lactating cows consuming proportionally more DM.
The heat shock protein Gp96 links innate and specific immunity

Among other heat shock proteins (HSPs), the ER-resident chaperone Gp96 has been described as a potent tumour vaccine in animal models. A growing list of data underlines that Gp96 triggers both arms of pathogen defence--innate and specific immunity--in a synergistic and most efficient way: It enables specific immune responses by transferring immunogenic peptides that have been acquired in the ER to the MHC class I pathway of antigen presenting cells (APCs). For this, two important features of Gp96 are required. First, its ability to bind immunogenic peptides. Secondly, its acquisition by specialized antigen presenting cells capable of inducing cellular immune responses. Due to specific receptors on the surface of APCs, this uptake from the extracellular space occurs very efficiently and rapidly. Serving the innate branch of immunity, Gp96 unspecifically activates APCs, which then provide a pro-inflammatory cytokine milieu and co-stimulation to cytotoxic T cells. Thus, Gp96 uses all resources of the immune system to trigger cytotoxic T cell responses against associated peptides.
Local-Global principles for certain images of Galois representations

Let $K$ be a number field and let $E/K$ be an elliptic curve whose mod $\ell$ Galois representation locally has image contained in a group $G$, up to conjugacy. We classify the possible images for the global Galois representation in the case where $G$ is a Cartan subgroup or the normalizer of a Cartan subgroup. When $K = \mathbf{Q}$, we deduce a counterexample to the local-global principle in the case where $G$ is the normalizer of a split Cartan and $\ell = 13$. In particular, there are at least three elliptic curves (up to twist) over $\mathbf{Q}$ whose mod $13$ image of Galois is locally contained in the normalizer of a split Cartan, but whose global image is not.
EVALUATION OF PHYTOCHEMICAL CONSTITUENTS AND ANTIMICROBIAL ACTIVITY OF SILVER NANOPARTICLE SYNTHESIZED IPOMOEA NIL AGAINST SELECTED PATHOGENS

ABSTRACT Objective: The objective of this study is to investigate a simple and feasible approach for the production of silver nanoparticles (AgNPs) by using leaf extract of Ipmoea nil and to evaluate its antibacterial activity. Methods: The AgNPs synthesized was characterized by a change in color and the absorption peaks by ultraviolet-visible spectroscopy. The phyto compounds responsible for the reduction and capping of silver ions was known from Fourier transform infrared spectra and phytochemical analysis. The antibacterial effects of prepared aqueous AgNPs were detected against five types of pathogenic bacteria, including Gram-negative and Grampositive bacteria (Escherichia coli, Salmonella, Bacillius, Proteus, and Klebsilla pneumonia) using agar well diffusion method. Results: A peak absorption value between 400 and 450 nm and the color change of the extract from yellowish to red wine were corresponds to the plasmon absorbance of AgNPs. On the other hand, aqueous extract of I. nil mediated AgNPs found to be effective against tested microorganisms (Salmonella, Bacillus, and Proteus) with inhibition zone in the range of 10-13 mm (20 μl and 10 μl) except E. coli and K. pneumonia. Furthermore, aqueous extract of I. nil leaves had no ability to suppress the growth of the tested microorganisms in the concentration of 10 μl. The control also produced similar inhibition zones like AgNPs. Conclusions: Our findings indicated that green synthesized AgNPs mediated by I. nil leaf extract had an efficient anti-bactericidal activity against the bacterial species tested. Hence, further studies are needed to highlight its mechanism and application as an antibacterial agent. Keywords: Ipomoea nil, Silver nanoparticles, Antibacterial activity, Bacteria.
Secure and private proofs for location-based activity summaries in urban areas

Activity-based social networks, where people upload and share information about their location-based activities (e.g., the routes of their activities), are increasingly popular. Such systems, however, raise privacy and security issues: The service providers know the exact locations of their users; the users can report fake location information in order to, for example, unduly brag about their performance. In this paper, we propose a secure privacy-preserving system for reporting location-based activity summaries (e.g., the total distance covered and the elevation gain). Our solution is based on a combination of cryptographic techniques and geometric algorithms, and it relies on existing Wi-Fi access-point networks deployed in urban areas. We evaluate our solution by using real data sets from the FON community networks and from the Garmin Connect activity-based social network, and we show that it can achieve tight (up to a median accuracy of 76%) verifiable lower-bounds of the distance covered and of the elevation gain, while protecting the location privacy of the users with respect to both the social network operator and the access-point network operator(s).
Pressure-controlled, inverse ratio ventilation that avoids air trapping in the adult respiratory distress syndrome.

OBJECTIVES To investigate physiologic and outcome data in patients switched from volume-cycled conventional ratio ventilation to pressure-controlled inverse ratio ventilation that did not produce air trapping and intrinsic positive end-expiratory pressure (PEEP). SETTING Medical intensive care unit. DESIGN Retrospective analysis of crossover data and outcome. PATIENTS Fourteen patients with the adult respiratory distress syndrome who were receiving mechanical ventilation with volume-cycled, conventional ratio ventilation followed by pressure-controlled, inverse ratio ventilation. INTERVENTIONS Our approach to pressure-controlled, inverse ratio ventilation was to use tidal volumes and applied PEEP values comparable to those volumes and values used on volume-cycled, conventional ratio ventilation, use inspiratory times to increase mean airway pressure instead of additional applied PEEP, and avoid air trapping (intrinsic PEEP). MEASUREMENTS AND MAIN RESULTS With this approach, there was a reduction in peak airway pressure from 53 +/- 8.5 (SD) to 40 +/- 5.9 cm H2O (p < .01), and an increase in mean airway pressure from 20 +/- 3.9 to 30 +/- 5.2 cm H2O (p < .01). Tidal volume, mean inflation pressure, and compliance did not change. Oxygenation (PaO2) improved from 57 +/- 11.3 torr (7.6 +/- 1.5 kPa) to 94 +/- 40.2 torr (12.5 +/- 5.4 kPa) (p = .01) but the oxygenation index (mean airway pressure x FIO2 x 100/PaO2) did not change significantly (25.9 +/- 10.3 to 27.2 +/- 12.2). There was no significant change in PaCO2 or pH even though delivered minute ventilation decreased from 17.4 +/- 4.3 to 14.8 +/- 5.8 L/min (p = .02). Cardiac index slightly decreased, but hemodynamic values were otherwise stable. Only three of the 14 study patients survived. CONCLUSIONS These data demonstrate that oxygenation is primarily a function of mean airway pressure, and that longer inspiratory times can be used as an alternative to applied PEEP to increase this oxygenation. If no air trapping develops, lung inflation pressures and delivered volumes remain constant with this approach. Because the technique was used only in patients refractory to conventional techniques, the poor outcome is not surprising.
Cardiac-Specific IGF-1 Expression Attenuates Dilated Cardiomyopathy in Tropomodulin-Overexpressing Transgenic Mice

To test the hypothesis that early interventional treatment with insulin-like growth factor-1 (IGF-1) alleviates subsequent development of dilated cardiomyopathy, cardiac-specific IGF-1 expression was introduced by selective cross-breeding into a transgenic mouse model of heart failure that displays phenotypic characteristics of severe dilation. Hemodynamic, structural, and cellular parameters of the heart were compared between nontransgenic, tropomodulin-overexpressing cardiomyopathic, and the hybrid tropomodulin/IGF-1-overexpressing mice. Beneficial effects of IGF-1 were apparent by multiple indices of cardiac structure and function, including normalization of heart mass, anatomy, hemodynamics, and apoptosis. IGF-1 expression also acted as a proliferative stimulus as evidenced by calculated increases in myocyte number as well as expression of Ki67, a nuclear marker of cellular replication. Cellular analyses revealed that IGF-1 inhibited characteristic cardiomyocyte elongation in dilated hearts and restored calcium dynamics comparable to that observed in normal cells. Collectively, these results provide novel information regarding the ability of IGF-1 to inhibit progression of cardiomyopathic disease in a defined model system and suggest that heart failure may benefit from early interventional IGF-1 treatment.
Estimating software maintenance effort: a neural network approach

Software maintenance forms an essential component of software development. Its planning includes estimation of maintenance effort, duration, personnel and costs. Adequate information regarding size, complexity and maintainability is however often unavailable. In the present work, a Neural Network (NN) based effort estimator is developed using Matlab. A feed forward back- propagation NN employing Bayesian regularization training is selected and trained for one dataset. Various categories of software maintenance cost drivers and their effect on maintenance effort have been analyzed using different combinations of number of hidden layers and hidden neurons etc. The NN is able to successfully model the maintenance effort as the obtained results are well within the previously published error limits
Using the health action process approach to predict and improve health outcomes in individuals with type 2 diabetes mellitus

Background The purpose of this study was to explore the predictive utility of the Health Action Process Approach (HAPA) and test a HAPA-based healthy eating intervention, in adults with type 2 diabetes mellitus. Materials and methods The study employed a prospective, randomized, controlled trial design. The 4-month intervention consisted of self-guided HAPA-based workbooks in addition to two telephone calls to assist participants with the program implementation, and was compared to “treatment as usual”. Participants (n=87) completed health measures (diet, body mass index [BMI], waist circumference, blood pressure, blood glucose levels, lipid levels, and diabetes distress) and HAPA measures prior to the intervention and again upon completion 4 months later. Results The overall HAPA model predicted BMI, although only risk awareness and recovery self-efficacy were significant independent contributors. Risk awareness, intentions, and self-efficacy were also independent predictors of health outcomes; however, the HAPA did not predict healthy eating. No significant time × condition interaction effects were found for diet or any HAPA outcome measures. Conclusion Despite the success of HAPA in predicting health outcomes for those with type 2 diabetes mellitus, the intervention was unsuccessful in changing healthy eating or any of the other measured variables, and alternative low-cost health interventions for those with type 2 diabetes mellitus should be explored.
Translational research on sustained attention and attentional control in rats, healthy humans and patients with Schizophrenia

Attentional deficits are often studied in schizophrenia, yet treatments to alleviate these impairments remain undeveloped. In part, this gap between basic and clinical research stems from a lack of tasks validated for translational research. The current work develops the distractor condition sustained attention task (dSAT), an attentional control paradigm traditionally used in rats to investigate the cholinergic system’s role in attention, for cross-species, translational research by adapting it for use in humans. In the basic sustained attention task (SAT), subjects report the presence or absence of a brief, centrally-presented signal of varying duration. In the distractor condition (dSAT), a visual distractor evokes top-down control mechanisms in order to stabilize performance. The current work demonstrates that rats and healthy, young human adults have qualitatively similar patterns of performance on the SAT and dSAT, including decreased attentional performance during distraction. Neuroimaging in young human adults shows that this decreased attentional performance is correlated with increased activation of right middle frontal gyrus (MFG). The sensitivity of right MFG to the attentional effort demands in the dSAT is of interest because this region is implicated as a site of disruption in patients with schizophrenia (Minzenberg et al., 2009). To investigate the dSAT’s sensitivity to attentional deficits in schizophrenia, stable, medicated schizophrenic outpatients and healthy controls were tested on the dSAT. Healthy children were also tested to compare the patients to a group with similar overall accuracy levels. While