Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display

Neisseria gonorrhoeae is one of the most prevalent sexually transmitted diseases worldwide with more than 100 million new infections per year. A lack of intense research over the last decades and increasing resistances to the recommended antibiotics call for a better understanding of gonococcal infection, fast diagnostics and therapeutic measures against N. gonorrhoeae. Therefore, the aim of this work was to identify novel immunogenic proteins as a first step to advance those unresolved problems. For the identification of immunogenic proteins, pHORF oligopeptide phage display libraries of the entire N. gonorrhoeae genome were constructed. Several immunogenic oligopeptides were identified using polyclonal rabbit antibodies against N. gonorrhoeae. Corresponding full-length proteins of the identified oligopeptides were expressed and their immunogenic character was verified by ELISA. The immunogenic character of six proteins was identified for the first time. Additional 13 proteins were verified as immunogenic proteins in N. gonorrhoeae.
How Strong Do Global Commodity Prices Influence Domestic Food Prices? A Global Price Transmission Analysis

This paper analyzes the transmission from global commodity to domestic food prices for a large set of countries. First, a theoretical model is developed to explain price transmission for different trade regimes. Drawing from the competitive storage model under rational expectations, it is shown that domestic prices can respond instantaneously to global prices even if no trade takes place but future trade is expected. Using a global database on food prices, we construct national and international grain price indices. With an autoregressive distributed lag model, we empirically detect countries in which food prices are influenced by global commodity prices, including futures prices. Mapping transmission elasticities with the size of the population below the poverty line which spends typically a large share of its income on food, we are able to estimate the size of vulnerable population. Our empirical analysis reveals that 90 percent of the global poor (income below 1.25$/day) live in countries where domestic food prices respond to international prices - but the extent of transmission varies substantially. For 360 million poor people, international prices transmit to their country at rates of 30 percent or higher within three months.
The Value of Corporate Votes and Control Benefits: A Cross-Country Analysis

This paper measures corporate control benefits - the value that dominant vote-holders expropriate from a controlled company to the detriment of other shareholders. Control benefits are extracted from the total value of the votes in the control block, based on a baseline control contest model in the case of a dual-class firm. The study is based on a sample of 661 dual-class firms in 18 countries, using data for 1997. The determinants of control benefits are then explored in a consistent fashion across countries. We use measures of the general strictness of the legal environment, an index of takeover regulations, and a measure of power-concentrating Corporate Charter provisions, the probability of a control contest, and costs of holding the control block. We control for differences in the security value of the share classes, e.g. differences in dividend payments and liquidity. The value of control, or equivalently the total value of votes in the control block, ranges from about 0% in Denmark to 50% of firm market value in Mexico. Legal environment variables explain 75% of the cross-country variation in the value of control benefits.
How do different components of Effortful Control contribute to children’s mathematics achievement?

This work sought to investigate the specific contribution of two different components of Effortful Control (EC) -attentional focusing (AF) and inhibitory control- to children’s mathematics achievement. The sample was composed of 142 children aged 9–12 year-old. EC components were measured through the Temperament in Middle Childhood Questionnaire (TMCQ; parent’s report); math achievement was measured via teacher’s report and through the standard Woodcock–Johnson test. Additionally, the contribution of other cognitive and socio-emotional processes was taken into account. Our results showed that only AF significantly contributed to the variance of children’s mathematics achievement; interestingly, mediational models showed that the relationship between effortful attentional self-regulation and mathematics achievement was mediated by academic peer popularity, as well as by intelligence and study skills. Results are discussed in the light of the current theories on the role of children’s self-regulation abilities in the context of school.
Reasoning about inconsistencies in natural language requirements

The use of logic in identifying and analyzing inconsistency in requirements from multiple stakeholders has been found to be effective in a number of studies. Nonmonotonic logic is a theoretically well-founded formalism that is especially suited for supporting the evolution of requirements. However, direct use of logic for expressing requirements and discussing them with stakeholders poses serious usability problems, since in most cases stakeholders cannot be expected to be fluent with formal logic. In this article, we explore the integration of natural language parsing techniques with default reasoning to overcome these difficulties. We also propose a method for automatically discovering inconsistencies in the requirements from multiple stakeholders, using both theorem-proving and model-checking techniques, and show how to deal with them in a formal manner. These techniques were implemented and tested in a prototype tool called CARL. The effectiveness of the techniques and of the tool are illustrated by a classic example involving conflicting requirements from multiple stakeholders.
Evidence for Large-Scale Structure at z ≈ 2.4 from Lyα Imaging

The history of large-scale structure depends on cosmological parameters and on how merging unfolds among both galaxies and groups. There has been recent evidence for clustering among Lyα emitters, Lyman-break galaxies, and Lyman absorbers. We present deep, wide-field medium-band imaging in redshifted Lyα of fields surrounding regions selected to have HST detections of faint Lyα emitters, over a range of surface densities, to characterize the large-scale environment. The radio galaxy 53W002 was previously found, using HST, to be part of a rich grouping at z = 2.39, including ≈5 spectroscopically confirmed, compact, lower luminosity star-forming objects. Our new data show this to be part of a larger structure traced by bright active nuclei, all contained within a projected span of 6. ′8 (3.2 Mpc). Of the 14 candidate emitters, six have been spectroscopically confirmed as active nuclei in the range z = 2.390 ± 0.008. Various statistical tests give a significance of 95%–99% for the reality of this structure on the sky. Our data thus strengthen the evidence for clustering at these redshifts. The grouping around 53W002 is more extended than a relaxed King model, at the 90% confidence level. This may be evidence either for a configuration that has yet to decouple fully from the Hubble expansion or for multiple subgroupings that will themselves at some point form a more compact, relaxed structure. The redshift range for measured members is comparable to the Hubble flow across the structure, which may imply that the structure is seen near turnaround and suggests that its mass cannot be derived from the velocity dispersion. We surveyed two additional 14′ fields at z = 2.4, each centered on an HST WFPC2 field that has been searched for faint Lyα emitters, as well as on three contiguous fields near 53W002 for objects at z ∼ 2.55. Only a single emitter consistent with showing Lyα at z ≈ 2.4 appears in these fields, to a somewhat brighter flux limit, while a total of six candidate emitters appear in the three fields at z ∼ 2.6. Comparison with the (deeper but narrower) WFPC2 surveys suggests that the surface-density contrast from field to field is larger for brighter objects. From this survey alone, groupings such as the 53W002 "cluster" must have an area-covering fraction less than 0.04 in this redshift range. Three of the active galactic nuclei in the structure at z = 2.4 show extended emission-line structure, with equivalent widths suggesting in situ photoionization as far as 50 kpc from the nuclei. Such objects may populate deep surveys as diffuse Lyα-emission clouds when their cores are sufficiently obscured.
Redundant Hydrogen Peroxide Scavengers Contribute to Salmonella Virulence and Oxidative Stress Resistance

ABSTRACT Salmonella enterica serovar Typhimurium is an intracellular pathogen that can survive and replicate within macrophages. One of the host defense mechanisms that Salmonella encounters during infection is the production of reactive oxygen species by the phagocyte NADPH oxidase. Among them, hydrogen peroxide (H2O2) can diffuse across bacterial membranes and damage biomolecules. Genome analysis allowed us to identify five genes encoding H2O2 degrading enzymes: three catalases (KatE, KatG, and KatN) and two alkyl hydroperoxide reductases (AhpC and TsaA). Inactivation of the five cognate structural genes yielded the HpxF− mutant, which exhibited a high sensitivity to exogenous H2O2 and a severe survival defect within macrophages. When the phagocyte NADPH oxidase was inhibited, its proliferation index increased 3.7-fold. Moreover, the overexpression of katG or tsaA in the HpxF− background was sufficient to confer a proliferation index similar to that of the wild type in macrophages and a resistance to millimolar H2O2 in rich medium. The HpxF− mutant also showed an attenuated virulence in a mouse model. These data indicate that Salmonella catalases and alkyl hydroperoxide reductases are required to degrade H2O2 and contribute to the virulence. This enzymatic redundancy highlights the evolutionary strategies developed by bacterial pathogens to survive within hostile environments.
Identification and characterization of a mouse cell mutant defective in the intracellular transport of glycoproteins

We have isolated a mutant line of mouse L cells, termed gro29, in which the growth of herpes simplex virus (HSV) and vesicular stomatitis virus (VSV) is defective. The block occurs late in the infectious cycle of both viruses. We demonstrate that HSV and VSV enter gro29 cells normally, negotiate the early stages of infection, yet are impaired at a late stage of virus maturation. During VSV infection of the mutant cell line, intracellular transport of its glycoprotein (G protein) is slowed. Pulse-chase experiments showed that oligosaccharide processing is impeded, and immunofluorescence localization revealed an accumulation of G protein in a juxtanuclear region that contains the Golgi complex. We conclude that export of newly made glycoproteins is defective in gro29 cells, and speculate that this defect may reflect a lesion in the glycoprotein transport apparatus.
Determinants of Bank Interest Margins in Central and Eastern Europe

Banks’ interest margins are among the most important indicators of the cost of financial intermediation. This paper investigates the determinants of banks’ interest margins in Central and Eastern Europe (CEE). Given the run-up to EU entry and EU membership itself, dynamics in the banking sector in CEE have developed rather differently than in other emerging market economies. We document that, in contrast to the literature, foreign ownership has a positive effect on interest margins, whereas state ownership proves to be irrelevant. Banks’ pricing of loans and deposits, however, is risk-adjusted in CEE – we detect positive risk premia for both interest and credit risk. However, our data provide some evidence for moral hazard behavior. Moreover, the decreasing interest margins in the region during the first half of the current decade seem to be caused by a decrease in operating costs as well as an increase of efficiency levels and rapid financial deepening.
Notes on Noise Contrastive Estimation and Negative Sampling

Estimating the parameters of probabilistic models of language such as maxent models and probabilistic neural models is computationally difficult since it involves evaluating partition functions by summing over an entire vocabulary, which may be millions of word types in size. Two closely related strategies---noise contrastive estimation (Mnih and Teh, 2012; Mnih and Kavukcuoglu, 2013; Vaswani et al., 2013) and negative sampling (Mikolov et al., 2012; Goldberg and Levy, 2014)---have emerged as popular solutions to this computational problem, but some confusion remains as to which is more appropriate and when. This document explicates their relationships to each other and to other estimation techniques. The analysis shows that, although they are superficially similar, NCE is a general parameter estimation technique that is asymptotically unbiased, while negative sampling is best understood as a family of binary classification models that are useful for learning word representations but not as a general-purpose estimator.
Not All Scientists pay to be Scientists

A growing body of research on firms’ “open science” strategies rests on the notion that scientists have a strong preference for publishing and that firms are able to extract a wage discount if they allow scientists to publish. Drawing on a survey of 1,400 life scientists about to enter the job market, we suggest an alternative view. First, we show significant heterogeneity in the price scientists assign to the opportunity to publish in firms, and those scientists who seek industry careers have particularly low preferences for publishing. Thus, many job applicants are not willing to accept lower wages for jobs that let them publish and firms pursuing open science strategies may instead have to pay publishing incentives that fulfill both sorting and incentive functions. Second, we show that scientists with higher ability have a higher price of publishing but also expect to be paid higher wages regardless of the publishing regime. Thus, they are not cheaper to hire than other scientists if allowed to publish, but they are more expensive if publishing is restricted. Finally, we show that scientists publish not simply for “peer recognition” but also for more specific reasons, including the opportunity to advance science or to move to higher-paying jobs. Different reasons predict what price a scientist assigns to the opportunity to publish and may also have very different implications for the sustainability of competitive advantages derived from open science strategies.
Improving integrated care: modelling the performance of an online community of practice

Introduction This article aims to confirm the following core hypothesis: a Community of Practice's use of a Web 2.0 platform for communication between primary and hospital care leads to improved primary care and fewer hospital referrals. This core hypothesis will be corroborated by testing a further five partial hypotheses that complete the main hypothesis being estimated. Methods An ad-hoc questionnaire was designed and sent to a sample group of 357 professionals from the Badalona-Sant Adrià de Besòs Primary Care Service in Catalonia, Spain, which includes nine primary care centres and three specialist care centres. The study sample was formed by 159 respondents. The partial least squares methodology was used to estimate the model of the causal relationship and the proposed hypotheses. Results It was found that when healthcare staff used social networks and information and communication technologies professionally, and the more contact hours they have with patients, the more a Web 2.0 platform was likely to be used for communication between primary and hospital care professionals. Such use led to improved primary care and fewer hospital referrals according to the opinions of health professionals on its use. Conclusions The research suggests that the efficiency of medical practice is explained by the intensity of Web 2.0 platform use for communication between primary and specialist care professionals. Public policies promoting the use of information and communication technologies in communities of practice should go beyond the technological dimension and consider other professional, organisational and social determinants.
Dynamical evolution of rotating stellar systems – III. The effect of the mass spectrum

We have studied the dynamical evolution of rotating star clusters with mass spectrum using a Fokker-Planck code. As the simplest multimass model, we first investigated two-component clusters. Rotation is found to accelerate the dynamical evolution through the transfer of angular momentum outward, as well as from high masses to low masses. However, the degree of acceleration depends sensitively on the assumed initial mass function since dynamical friction, which generates mass segregation, also tends to accelerate the evolution, and the combined effect of both is not linear or multiplicative. As long as dynamical friction dominates in the competition with angular momentum exchange, the heavy masses lose random energy and angular momentum and sink towards the centre, but their remaining angular momentum is sufficient to speed them up rotationally. This is gravo-gyro instability. As a consequence, we find that the high-mass stars in the central parts rotate faster than low-mass stars. This leads to the suppression of mass segregation compared with the non-rotating clusters. From the study of multicomponent models, we observe similar trends to the two-component models in almost all aspects. The mass function changes less drastically for clusters with rotation. Unlike non-rotating clusters, the mass function depends on R and z. Our models are the only ones that can predict mass function and other quantities to be compared with new observations.
Mapping a viral phylogeny onto outbreak trees to improve host transmission inference

Background Developing methods to reconstruct transmission histories for viral outbreaks could provide critical information to support locating sources of disease transmission. Phylogenetic methods used to measure the degree of relatedness among sequenced viral samples have proven useful in identifying potential outbreak sources. The complex nature of infectious disease, however, makes it difficult to assign a rigorously defined quantitative confidence value assessing the likelihood of a true direct transmission event using genetic data alone. Results A new method is presented to calculate a confidence value assessing the likelihood of a transmission event using both phylogenetic inference and limited knowledge of incubation and infectious duration times. The method is applied to simulations of a foot and mouth disease (FMD) outbreak to demonstrate how the combination of both phylogenetic and epidemiology data can be used to strengthen the assessment of the likelihood of direct transmission over methods using just phylogenetic data or infection timing data alone. The method is applied to a previous FMD outbreak to identify areas where over confidence in previously inferred direct transmission may exist. Conclusion Combining knowledge from viral evolution and epidemiology within a single integrated transmission inference framework is an important approach to assess the potential likelihood of transmission events and makes clear how specific features of a virus’ spread through the course of an outbreak will directly determine the potential for confidence in inferred host transmission links.
Alternative translation of human fibroblast growth factor 2 mRNA occurs by internal entry of ribosomes

Alternative initiations of translation of the human fibroblast growth factor 2 (FGF-2) mRNA, at three CUG start codons and one AUG start codon, result in the synthesis of four isoforms of FGF-2. This process has important consequences on the fate of FGF-2: the CUG-initiated products are nuclear and their constitutive expression is able to induce cell immortalization, whereas the AUG-initiated product, mostly cytoplasmic, can generate cell transformation. Thus, the different isoforms probably have distinct targets in the cell. We show here that translation initiation of the FGF-2 mRNA breaks the rule of the cap-dependent ribosome scanning mechanism. First, translation of the FGF-2 mRNA was shown to be cap independent in vitro. This cap-independent translation required a sequence located between nucleotides (nt) 192 and 256 from the 5' end of the 318-nt-long 5' untranslated region. Second, expression of bicistronic vectors in COS-7 cells indicated that the FGF-2 mRNA is translated through a process of internal ribosome entry mediated by the mRNA leader sequence. By introducing additional AUG codons into the RNA leader sequence, we localized an internal ribosome entry site to between nt 154 and 318 of the 5' untranslated region, just upstream of the first CUG. The presence of an internal ribosome entry site in the FGF-2 mRNA suggests that the process of internal translation initiation, by controlling the expression of a growth factor, could have a crucial role in the control of cell proliferation and differentiation.
Awareness, perceptions and beliefs about physiotherapy held by physicians working in Saudi Arabia: a cross-sectional study

[Purpose] Over the years physiotherapy has been recognized as a popular mode of treatment that decreases the disability and dependency rate of patients. However, there is still a need for its recognition in multidisciplinary health care structures. If a physician were well aware of how a physical therapist could help with treatment if patients and prevent complications, hospital patient load could be decreased to a greater extent. The aim of this study was to study the awareness, perception and beliefs of physicians working in Saudi Arabia about physiotherapy. [Subjects and Methods] Three hundred fifteen members of the Saudi Commission for Health Specialties (SCFHS) with different specialties, nationalities, designation, and work experience, working in various hospitals in 5 regions of Saudi Arabia were invited to participate in this study. A 22-item questionnaire was used for data collection including sections on physicians’ demographics, educational levels and knowledge about physiotherapy. [Results] After applying the inclusion and exclusion criteria, data from 280 respondents was used for analysis. Seventy-five percent of respondents reported to having some knowledge of physiotherapy, and 11% of them referred patients to physiotherapy departments regularly, while 14% referred patients occasionally. To the best of our knowledge, this is first study performed in Saudi Arabia to evaluate awareness of physicians about the physiotherapy profession. [Conclusion] The results of this study highlight the need to organize various workshops and lectures about the effectiveness of physiotherapy in various diseases for physicians, on a regular basis, to update them with evidence-based treatment. It is the responsibility of physical therapists to raise the perceptions of other healthcare professionals about their profession.