Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Dynamics Simulation of the Complex PBP-2x with Drug Cefuroxime to Explore the Drug Resistance Mechanism of Streptococcus suis R61

Drug resistance of Streptococcus suis strains is a worldwide problem for both humans and pigs. Previous studies have noted that penicillin-binding protein (PBPs) mutation is one important cause of β-lactam antibiotic resistance. In this study, we used the molecular dynamics (MD) method to study the interaction differences between cefuroxime (CES) and PBP2x within two newly sequenced Streptococcus suis: drug-sensitive strain A7, and drug-resistant strain R61. The MM-PBSA results proved that the drug bound much more tightly to PBP2x in A7 (PBP2x-A7) than to PBP2x in R61 (PBP2x-R61). This is consistent with the evidently different resistances of the two strains to cefuroxime. Hydrogen bond analysis indicated that PBP2x-A7 preferred to bind to cefuroxime rather than to PBP2x-R61. Three stable hydrogen bonds were formed by the drug and PBP2x-A7, while only one unstable bond existed between the drug and PBP2x-R61. Further, we found that the Gln569, Tyr594, and Gly596 residues were the key mutant residues contributing directly to the different binding by pair wise energy decomposition comparison. By investigating the binding mode of the drug, we found that mutant residues Ala320, Gln553, and Thr595 indirectly affected the final phenomenon by topological conformation alteration. Above all, our results revealed some details about the specific interaction between the two PBP2x proteins and the drug cefuroxime. To some degree, this explained the drug resistance mechanism of Streptococcus suis and as a result could be helpful for further drug design or improvement.
Interactive Visualization of Hyperspectral Images of Historical Documents

This paper presents an interactive visualization tool to study and analyze hyperspectral images (HSI) of historical documents. This work is part of a collaborative effort with the Nationaal Archief of the Netherlands (NAN) and Art Innovation, a manufacturer of hyperspectral imaging hardware designed for old and fragile documents. The NAN is actively capturing HSI of historical documents for use in a variety of tasks related to the analysis and management of archival collections, from ink and paper analysis to monitoring the effects of environmental aging. To assist their work, we have developed a comprehensive visualization tool that offers an assortment of visualization and analysis methods, including interactive spectral selection, spectral similarity analysis, time-varying data analysis and visualization, and selective spectral band fusion. This paper describes our visualization software and how it is used to facilitate the tasks needed by our collaborators. Evaluation feedback from our collaborators on how this tool benefits their work is included.
Discussion of “ Liquidity , Moral Hazard , and Interbank Market Collapse ”

Financial intermediaries, such as banks, perform many roles: they screen risks, evaluate and fund worthy entrepreneurs, pool risks, monitor borrowers, refinance projects, and—when confronted with the default in their loans—they perform a valuable role in loss discovery and assessing whether the bankrupt concern is economically viable or not. All these activities, which constitute the actions of a bank in what concerns the asset side of its balance sheet, need to be funded, and much depends on how the bank structures its liabilities to obtain these funds, whether with time deposits, shortor long-term debt, equity, or other more novel forms of short-term financing such as commercial paper or repo transactions. Independently of the particular liability structure adopted by financial intermediaries, it typically involves some form of maturity transformation. For instance, bank deposits, which are available on demand, are transformed into longer-maturity loans to finance projects. Maturity mismatch is almost inherent in the intermediation business. A liquidity shock for banks occurs whenever at some interim stage additional funds are needed to bridge the maturity mismatch between assets and liabilities. Given the nature of the bank’s balance sheet, there are two potential sources of liquidity problems. First, it may be that projects that were funded at some past date need to be refinanced in some contingency and that failure to provide additional funds may result in some loss or even the wasteful liquidation of those projects. Alternatively, it may be that liabilities are coming due before the proceeds of the investments are realized and that funds need to be produced to meet those liabilities; a bank run is the classic example of the latter. Of course, both things can happen simultaneously: projects on the asset side of the bank’s balance sheet
Individual Differences in Addition Strategy Choice: A Psychometric Evaluation

The strategy choice model (SCM) is a highly influential theory of human problem-solving. One strength of this theory is the allowance for both item and person variance to contribute to problem-solving outcomes, but this central tenet of the model has not been empirically tested. Explanatory item response theory (EIRT) provides an ideal approach to testing this core feature of SCM, as it allows for simultaneous estimation of both item and person effects on problem-solving outcomes. We used EIRT to test and confirm this central tenet of the SCM for adolescents’ (n = 376) solving of addition problems. The approach also allowed us to identify the strategy choices of adolescents who still struggle with basic arithmetic. The synthesis of SCM theory and EIRT modeling has implications for more fully investigating the sources of individual differences in students’ problem solving, and for identifying problem-solving patterns associated with poor academic achievement.
A better regulation is required in viral hepatitis smartphone applications.

AIM To describe the characteristics and content of the available viral hepatitis mobile applications, as well as assess the level of participation of medical professionals in their development. METHODS A descriptive observational study was carried out in September 2013. We searched smartphone apps specifically relating to the viral hepatitis for using a keyword search with the following terms; «hepatitis», «hepatology», «hbv» and «hcv» in the Google Play Store (Android) and the Apple App Store (iOS). Data recorded included: name, platform, category, cost, user star rating, number of downloads, date the app was updated by the developer and target audience. We analysed the content of the applications, and these were then categorised based on the viral hepatitis type into three groups. We conducted an analysis in which we specifically examined the authorship in order to assess the prevalence of health professional participation in their development. RESULTS A total of 33 apps were included (from 232 that were identified), among which there were 10 duplicates. Most of these apps were uploaded under the medical category. Three had ratings less than 3.9 stars (out of 5). Only 6 apps had exceeded 1000 downloads. A total of 12 apps were aimed at health professionals, while 4 focused on patients (7 for both of them). The participation of health professionals in the development of apps was 56.6%. CONCLUSIONS Viral hepatitis apps are available for both professionals and patients; however, much of the information contained within them is often not validated. They should be certificated.
Embedding values in the South African curriculum: by design or default?

This article explores the way in which values education is incorporated in the Life Orientation (LO) curriculum of the Senior Phase (Grades 7–9) i in South Africa. Researchers agree that in the light of the current need to regenerate morals and re-norm the nation, values are critical. From the moment they are born, children learn by observing adults; they mimic what they see, and repeat the words they utter. Parents and teachers have the greatest influence on a child’s upbringing and therefore have a responsibility to teach them about the core values that help them become well-rounded citizens. Theoretically, the study on which this article is based was located in the literature on approaches to implementing values education. The study employed a qualitative perspective, with a descriptive case study design. Participants include purposively selected school principals, school governing body (SGB) members, and LO teachers. The data was collected using semi-structured interviews and analysed using inductive thematic analysis. The analysis revealed that the values in the school LO curriculum were incorporated eclectically through explicit, implicit and critical approaches. On the basis of these findings, it is recommended that the school community sustain an eclectic approach to values education that covers learners’ holistic experiences. Keywords: embedding values; Life Orientation; Senior Phase; values education
Improving Neural Machine Translation Models with Monolingual Data

Neural Machine Translation (NMT) has obtained state-of-the art performance for several language pairs, while only using parallel data for training. Target-side monolingual data plays an important role in boosting fluency for phrase-based statistical machine translation, and we investigate the use of monolingual data for NMT. In contrast to previous work, which combines NMT models with separately trained language models, we note that encoder-decoder NMT architectures already have the capacity to learn the same information as a language model, and we explore strategies to train with monolingual data without changing the neural network architecture. By pairing monolingual training data with an automatic back-translation, we can treat it as additional parallel training data, and we obtain substantial improvements on the WMT 15 task English German (+2.8-3.7 BLEU), and for the low-resourced IWSLT 14 task Turkish->English (+2.1-3.4 BLEU), obtaining new state-of-the-art results. We also show that fine-tuning on in-domain monolingual and parallel data gives substantial improvements for the IWSLT 15 task English->German.
Illness among schoolchildren during influenza season: effect on school absenteeism, parental absenteeism from work, and secondary illness in families.

BACKGROUND High attack rates of Influenzavirus among school-aged children tend to be expected to cause significant disruption of usual activities at school and at home. OBJECTIVE To quantify the effect of influenza season on illness episodes, school absenteeism, medication use, parental absenteeism from work, and the occurrence of secondary illness in families among a cohort of children enrolled in an elementary school during the 2000-2001 influenza season. DESIGN Prospective survey study. SETTING Kindergarten through eighth grade elementary school in Seattle, Wash. PATIENTS OR OTHER PARTICIPANTS All children enrolled in the school were eligible for the study. Study participants were 313 children in 216 families. MAIN OUTCOME MEASURES The primary outcome measure was missed school days. Secondary outcomes measures included total illness episodes, febrile illness episodes, medication usage, physician visits, parental workdays missed, and secondary illnesses among family members of children in the study cohort. Differences between the rates of study events among participants when influenza was circulating and the event rates during the winter season when influenza was not circulating were used to calculate influenza-attributable excess events. RESULTS Total illness episodes, febrile illness episodes, analgesic use, school absenteeism, parental industrial absenteeism, and secondary illness among family members were significantly higher during influenza season compared with the noninfluenza winter season. For every 100 children followed up for this influenza season, which included 37 school days, an excess 28 illness episodes and 63 missed school days occurred. Similarly, for every 100 children followed up, influenza accounted for an estimated 20 days of work missed by the parents and 22 secondary illness episodes among family members. CONCLUSION Influenza season has significant adverse effects on the quality of life of school-aged children and their families.
Volume of the set of unistochastic matrices of order 3 and the mean Jarlskog invariant

A bistochastic matrix B of size N is called unistochastic if there exists a unitary U such that Bij=|Uij|2 for i,j=1,…,N. The set U3 of all unistochastic matrices of order N=3 forms a proper subset of the Birkhoff polytope, which contains all bistochastic (doubly stochastic) matrices. We compute the volume of the set U3 with respect to the flat (Lebesgue) measure and analytically evaluate the mean entropy of an unistochastic matrix of this order. We also analyze the Jarlskog invariant J, defined for any unitary matrix of order three, and derive its probability distribution for the ensemble of matrices distributed with respect to the Haar measure on U(3) and for the ensemble which generates the flat measure on the set of unistochastic matrices. For both measures the probability of finding |J| smaller than the value observed for the Cabbibo–Kobayashi–Maskawa matrix, which describes the violation of the CP parity, is shown to be small. Similar statistical reasoning may also be applied to the Maki–Nakagawa–Sa.
Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.
Effect of Lemon Juice on the Egg Shell Quality of Layers Subjected to Heat Stress

Heat stress is an effective factor on immune responses, body weight, egg production and egg quality of chickens. The major effect of heat stress is due to decreased food intake and alteration in acid-base balance. During the recent years, efforts to improve laying performance at high temperatures have been relatively successful. Supplementation of the diet or drinking water with special nutrient has been proposed as a means to reduce the effects of heat on the layer hens. There is scantly information about the effects of natural compounds on the heat-stressed hens. In this regard, the aim of the present study was to determine the effect of lemon juice on egg shell quality in layers subjected to hot climate. 50-week-old commercial layer chickens were divided into 2 equal treatment groups of 2400 birds each. Each treatment has three replicates. The experimental groups were fed as follows: in the control and test groups (groups A and B), birds were fed a standard diet. In the test group (group B), 5 ml/L of lemon juice was added to the drinking water for 30 days. At the end of each week, eggs with broken and fragile shell were recorded. Our results showed that the addition of lemon juice in drinking water was significantly reduced eggs with broken and fragile shells during heat stress (P<0.05). Based on findings, it is concluded that lemon juice can be considered as a natural supplement to alleviate heat stress in laying hens under hot climate.
Tiludronate concentrations and cytologic findings in synovial fluid after intravenous regional limb perfusion with tiludronate in horses

Anecdotal accounts of tiludronate administration via intravenous regional limb perfusion (IVRLP) exist despite a lack of information regarding safety for synovial structures in the perfused area. The objective of this study was to determine whether tiludronate concentrations in synovial structures after IVRLP with low dose (0.5 mg, LDT) or high dose (50 mg, HDT) tiludronate remain below a value demonstrated in vitro to be safe for articular cartilage (<19,000 ng/ml), and to determine effects of tiludronate on synovial fluid cytology variables compared to saline perfused control limbs. Using a randomized controlled experimental study design, horses received IVRLP with LDT (n = 6) or HDT (n = 6) in one forelimb and IVRLP with saline in the contralateral limb. Synovial fluid cytology variables and tiludronate concentrations were evaluated in navicular bursae (NB), and distal interphalangeal (DIP) and metacarpophalangeal (MCP) joints one week before and 30–45 min after IVRLP, and in DIP and MCP joints 24 h after IVRLP. Data were analyzed with 2-way rmANOVA (p < 0.05). Highest measured synovial fluid tiludronate concentrations occurred 30–45 min post-perfusion. Mean tiludronate concentrations were lower in LDT limbs (MCP = 39.6 ± 14.3 ng/ml, DIP = 118.1 ± 66.6 ng/ml, NB = 82.1 ± 30.2 ng/ml) than in HDT limbs (MCP = 3,745.1 ± 1,536.6 ng/ml, DIP = 16,274.0 ± 5,460.2 ng/ml, NB = 6,049.3 ± 1,931.7 ng/ml). Tiludronate concentration was >19,000 ng/ml in DIP joints of two HDT limbs. Tiludronate was measurable only in synovial fluid from HDT limbs 24 h post-perfusion. There were no differences in synovial fluid cytology variables between control and treated limbs. Conclusions. In some horses, IVRLP with HDT may result in synovial fluid concentrations of tiludronate that may have adverse effects on articular cartilage, based on in vitro data. IVRLP with LDT is unlikely to promote articular cartilage degradation. Further studies to determine a safe and effective dose for IVRLP with tiludronate are needed.
Absolute dimensions of eclipsing binaries. XXVI. - Setting a new standard: Masses, radii, and abundances for the F-type systems AD Bootis, VZ Hydrae, and WZ Ophiuchi

Context. Accurate mass, radius, and abundance determinations from binaries provide important information on stellar evolution, fundamental to central fields in modern astrophysics and cosmology. Aims. We aim to determine absolute dimensions and abundances for the three F-type main-sequence detached eclipsing binaries ADBoo, VZHya, and WZOph and to perform a detailed comparison with results from recent stellar evolutionary models. Methods. uvby light curves and uvbyβ standard photometry were obtained with the Stromgren Automatic Telescope at ESO, La Silla, radial velocity observations at CfA facilities, and supplementary high-resolution spectra with ESO’s FEROS spectrograph. State-ofthe-art methods were applied for the analyses: the EBOP andWilson-Devinney binary models, two-dimensional cross-correlation and disentangling, and the VWA abundance analysis tool. Results. Masses and radii that are precise to 0.5–0.7% and 0.4–0.9%, respectively, have been established for the components, which span the ranges of 1.1 to 1.4 M and 1.1 to 1.6 R. The [Fe/H] abundances are from –0.27 to +0.10, with uncertainties between 0.07 and 0.15 dex. We find indications of a slight α-element overabundance of [α/Fe] ∼ +0.1 for WZOph. The secondary component of ADBoo and both components of WZOph appear to be slightly active. Yale-Yonsai and Victoria-Regina evolutionary models fit the components of ADBoo and VZHya almost equally well, assuming coeval formation, at ages of about 1.75/1.50 Gyr (ADBoo) and 1.25/1.00 Gyr (VZHya). BaSTI models, however, predict somewhat different ages for the primary and secondary components. For WZOph, the models from all three grids are significantly hotter than observed. A low He content, decreased envelope convection coupled with surface activity, and/or higher interstellar absorption would remove the discrepancy, but its cause has not been definitively identified. Conclusions. We have demonstrated the power of testing and comparing recent stellar evolutionary models using eclipsing binaries, provided their abundances are known. The strongest limitations and challenges are set by Teff and interstellar absorption determinations, and by their effects on and correlation with abundance results.
The Characteristics of Incidental Pituitary Microadenomas in 120 Korean Forensic Autopsy Cases

To investigate the characteristics of incidental pituitary microadenomas, we examined 120 pituitary glands from Korean forensic autopsy cases, from which eight tumors were identified (incidence 6.7%). The average age of the affected subjects was 50 yr (range: 33-96 yr) with a female predominance. The maximum diameters of the tumors ranged from 0.4 to 5.4 mm (mean: 2.8 mm). Immunohistochemical analysis of pituitary hormones revealed three growth hormone-secreting adenomas, one prolactin-producing adenoma, one gonadotropin-producing adenoma, one plurihormonal adenoma, and two null cell adenomas. MIB-1 staining for Ki-67 antigen showed no positive expression. The microvessel density (MVD) of the pituitary microadenomas ranged from 2.3 to 11.6% (mean: 5.3%) and was significantly lower than that of nonneoplastic pituitary glands (11.9-20.1%, mean: 14.8%). Our study provides reference data on incidental pituitary microadenomas in the Korean population.
Statistical properties of high-lying chaotic eigenstates

We study the statistical properties of the high-lying chaotic eigenstates (200000 and above) which are deep within the semiclassical regime. The system we are analysing is the billiard system inside the region defined by the quadratic (complex) conformal map of the unit disk as introduced by Robnik (1983). We are using Heller's method of plane-wave decomposition of the numerical eigenfunctions, and perform extensive statistical analysis with the following conclusions: (i) the local average probability density is in excellent agreement with the microcanonical assumption and all statistical properties are also in excellent agreement with the Gaussian random model; (ii) the autocorrelation function is found to be strongly direction dependent and only after averaging over all directions agrees well with Berry's (1977) prediction; (iii) although the scars of unstable classical periodic orbits (in such an ergodic regime) are expected to exist, so far we have not found any (around the 200000th state) other than a scar-like feature resembling the whispering-gallery modes.