Miracle-dz/UniFAR-FTUs huggingface dataset:
GrainSpotter: a fast and robust polycrystalline indexing algorithm

A new approach for indexing multigrain diffraction data is presented. It is based on the use of a monochromatic beam simultaneously illuminating all grains. By operating in sub-volumes of Rodrigues space, a powerful vertex-finding algorithm can be applied, with a running time that is compatible with online analysis. The resulting program, GrainSpotter, is sufficiently fast to enable online analysis during synchrotron sessions. The program applies outlier rejection schemes, leading to more robust and accurate data. By simulations it is shown that several thousand grains can be retrieved. A new method to derive partial symmetries, called pseudo-twins, is introduced. Uniquely, GrainSpotter includes an analysis of pseudo-twins, which is shown to be critical to avoid erroneous grains resulting from the indexing.
Medical Students’ Knowledge of Fertility Awareness-Based Methods of Family Planning

Objective Traditional medical school curricula have not addressed fertility awareness-based methods (FABMs) of family planning. The objective of this study was to assess (1) 3-year medical students’ knowledge of FABMs of family planning, (2) their confidence in utilizing that knowledge in patient care, and (3) to implement focused education on FABMs to improve knowledge and confidence. Methods Third-year medical students at one institution in the United States were given a 10-question assessment at the beginning of their OB-GYN rotation. Two lectures about FABMs and their clinical applications were given during the rotation. Students were given the same questions at the end of the rotation. Each questionnaire consisted of eight questions to assess a student’s knowledge of FABMs and two questions to assess the student’s confidence in sharing and utilizing that information in a clinical setting. McNemar’s test was used to analyze the data. Results Two hundred seventy-seven students completed a pretest questionnaire and 196 students completed the posttest questionnaire. Medical knowledge improved from an initial test score of 38.99% to final test score of 53.57% (p < 0.05). Confidence in sharing FABM information with patients (0 = very uncomfortable; 5 = very comfortable) improved from 1.51 to 3.00 (p < 0.05). Confidence in utilizing FABM to diagnose and treat gynecologic/reproductive problems (0 = not very confident and 5 = very confident) improved from 1.01 to 3.15 (p < 0.05). Conclusion Medical schools may not include FABMs in OB-GYN curriculum; however, to patients, these methods remain a sought after and valid form of family planning. This study shows that brief, focused education can increase medical students’ knowledge of and confidence with FABMs of family planning.
CCG supertagging with bidirectional long short-term memory networks*

Abstract Neural Network-based approaches have recently produced good performances in Natural language tasks, such as Supertagging. In the supertagging task, a Supertag (Lexical category) is assigned to each word in an input sequence. Combinatory Categorial Grammar Supertagging is a more challenging problem than various sequence-tagging problems, such as part-of-speech (POS) tagging and named entity recognition due to the large number of the lexical categories. Specifically, simple Recurrent Neural Network (RNN) has shown to significantly outperform the previous state-of-the-art feed-forward neural networks. On the other hand, it is well known that Recurrent Networks fail to learn long dependencies. In this paper, we introduce a new neural network architecture based on backward and Bidirectional Long Short-Term Memory (BLSTM) Networks that has the ability to memorize information for long dependencies and benefit from both past and future information. State-of-the-art methods focus on previous information, whereas BLSTM has access to information in both previous and future directions. Our main findings are that bidirectional networks outperform unidirectional ones, and Long Short-Term Memory (LSTM) networks are more precise and successful than both unidirectional and bidirectional standard RNNs. Experiment results reveal the effectiveness of our proposed method on both in-domain and out-of-domain datasets. Experiments show improvements about (1.2 per cent) over standard RNN.
Crystal structure of 3,5-dimethoxy-2-[5-(naphthalen-1-yl)-4,5-dihydro-1H-pyrazol-3-yl]phenol

In the title compound, C21H20N2O3, the planes of the benzene ring and the naphthalene ring system are inclined to one another by 70.95°, and by 4.99 (6) and 75.93 (5)°, respectively, to the mean plane of the pyrazoline ring. The latter has an envelope conformation with the methine (CH) C atom as the flap. There is an intramolecular O—H⋯N hydrogen bond that forms an S(6) ring motif. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, forming chains along [100]. The chains are linked via C—H⋯N hydrogen bonds, forming sheets parallel to the ab plane. The sheets are linked by a series of N—H⋯π and C—H⋯π interactions forming a three-dimensional structure.
Modeling for Optimization of Hybrid Dynamic Networks ∗

Surging interest in hybrid dynamic systems is bringing together a diverse set of solution methods and application domains. The study of combined continuous-discrete systems is complicated by the existence of numerous representational frameworks, each specialized for various application domains and algorithms. For optimization, mixed-integer programming (MIP) is the standard modeling language. Although MIP provides powerful solution methods, its modeling capabilities are severely limited. We provide a richer modeling language, incorporating modular hybrid automata and logic models. These novel constructs are linked to existing solution methods by defining transformations which automatically generate MIPs. Results are provided on a supply network example. The system is represented in the proposed framework and then transformed using the general procedure. Models in the new framework are several times smaller, more intuitive, easier to modify, extensible, and amenable to different algorithms. The net result is an improved modeling language tied to existing optimization algorithms.
Enhanced Antiviral T Cell Function in the Absence of B7-H1 Is Insufficient To Prevent Persistence but Exacerbates Axonal Bystander Damage during Viral Encephalomyelitis

The T cell inhibitory ligand B7-H1 hinders T cell-mediated virus control, but also ameliorates clinical disease during autoimmune and virus-induced CNS disease. In mice infected with gliatropic demyelinating coronavirus, B7-H1 expression on oligodendroglia delays virus control, but also dampens clinical disease. To define the mechanisms by which B7-H1 alters pathogenic outcome, virus-infected B7-H1–deficient (B7-H1−/−) mice were analyzed for altered peripheral and CNS immune responses. B7-H1 deficiency did not affect peripheral T or B cell activation or alter the magnitude or composition of CNS-infiltrating cells. However, higher levels of IFN-γ mRNA in CNS-infiltrating virus-specific CD8 T cells as well as CD4 T cells contributed to elevated IFN-γ protein in the B7-H1−/− CNS. Increased effector function at the single-cell level was also evident by elevated granzyme B expression specifically in virus-specific CNS CD8 T cells. Although enhanced T cell activity accelerated virus control, 50% of mice succumbed to infection. Despite enhanced clinical recovery, surviving B7-H1−/− mice still harbored persisting viral mRNA, albeit at reduced levels compared with wild-type mice. B7-H1−/− mice exhibited extensive loss of axonal integrity, although demyelination, a hallmark of virus-induced tissue damage, was not increased. The results suggest that B7-H1 hinders viral control in B7-H1 expressing glia cells, but does not mediate resistance to CD8 T cell-mediated cytolysis. These data are the first, to our knowledge, to demonstrate that B7-H1–mediated protection from viral-induced immune pathology associated with encephalomyelitis resides in limiting T cell-mediated axonal bystander damage rather than direct elimination of infected myelinating cells.
Defects influenced by the Jahn-Teller effect as the sources of flicker noise in GaAs based devices

In order to determine the origin of 1/ƒ noise in devices made on the basis of GaAs the model of bistable defects is developed. The origin and the structure of multistable point defects (bistable in the simplest case) in GaAs are researched. It is suggested that the mechanism of spatial and charge multistability of the defects could be linked with the influence of the Jahn-Teller effect. The DX center and the complex of defects containing the vacancy VGa are analyzed as an example of multistable defects. The carried out research demonstrates that one of the possible sources of the 1/ƒ noise in GaAs based devices could be defects subjected to the Jahn-Teller effect.
Proposta de melhorias a um algoritmo para agrupamento de padrões via Colônia de Formigas

Métodos inspirados em formigas são uma grande promessa para problemas de agrupamento. No algoritmo de Agrupamento baseado em Formigas, proposto por Deneubourg et al. (1991), os padrões são espalhados em uma grade e a cada formiga é atribuído um padrão. As formigas são responsáveis por carregar, transportar e descarregar os padrões na grade. Após a convergência do algoritmo, a recuperação dos grupos é feita, usando-se as posições dos padrões na grade. O objetivo do presente artigo é propor melhorias a este algoritmo, doravante denominado de algoritmo proposto, avaliando o seu desempenho comparativamente ao Método de Ward, aos Mapas de Kohonen Unidimensionais e ao algoritmo ACAM (Ant-based Clustering Algorithm Modified), proposto por Boryczka (2009). No algoritmo proposto, as principais modificações foram: a introdução de uma comparação da probabilidade de descarregar um padrão na posição escolhida aleatoriamente, com a probabilidade de deixar este padrão em sua posição atual; a introdução de uma avaliação da probabilidade de uma posição vizinha, quando a decisão de descarregar um padrão for positiva e a célula em que o padrão deveria ser descarregado estiver ocupada; e a substituição do padrão carregado por uma formiga, caso este padrão não seja descarregado em 100 iterações consecutivas. Para a avaliação do desempenho do algoritmo proposto, foram utilizadas três bases de dados reais e públicas (ÍRIS, WINE e PIMA Indians Diabetes). Os resultados mostraram que houve superioridade no desempenho do algoritmo proposto, em relação ao ACAM para duas das três bases de dados e igualdade, em relação aos outros dois métodos. Palavras-chave: Mineração de Dados; Metaheurística; Agrupamento Baseado em Formigas.
Source of gross-alpha radioactivity anomalies in recharge wells, central Florida phosphate district. Final report

The central Florida phosphate industry utilizes recharge wells to mitigate withdrawals of water from the Florida aquifer and to dewater the surficial aquifer prior to mining. From a water-management point of view, these wells are efficient and serve a vital function. Recent monitoring of the radiation environment in these wells, however, casts doubts on the safety of the wells. While most of the wells conform to state and federal standards for radium, gross-alpha radiation frequently exceeds standards. The purpose of the study was to determine the radionuclide(s) responsible for the high gross-alpha radiation and to identify a method for sampling of the recharge wells that would standardize data across the phosphate district. It was found that excess gross alpha is primarily due to polonium-210. Since gross alpha and polonium-210 measurements are quite sensitive to methods of sample collections, preservation and analyses, standard procedures for sample processing are presented in the report.
Analysis of Unstructured Kinetic Modeling for a Sulfate- Reducing Process Using Desulfobivrio alaskensis 6SR

RESUMEN En este articulo se presenta un analisis cinetico de un proceso sulfato reductor tomando como caso de estudio a la cepa Desulfovibrio alaskensis 6SR. Este analisis considero cinco modelos cineticos no estructurados de tipo inhibicion por producto, ademas se propone una expresion de ley de potencias para la produccion del exopolisacarido (EPS) que se genera durante la fase de maxima produccion de sulfuro de hidrogeno y conlleva a una condicion de estres. Cada modelo considero las variables de estado de consumo de sulfato y lactato, produccion de sulfuro de hidrogeno, acetato y biomasa. Los modelos considerados fueron validados por comparacion con los datos experimentales generados obteniendose coeficientes de correlacion satisfactorios. El resultado de las simulaciones sugirio que el modelo de Levenspiel es la mejor representacion matematica del crecimiento bacteriano y del proceso sulfato reductor al combinarse con el modelo de la ley de potencias para el EPS. Los parametros cineticos obtenidos fueron una µmax = 0.36 1/h, KS = 6559 mg/l, P* = 610 mg/l y n = 0.89, con un indice de correlacion de R 2 = 0.96. El analisis cinetico del proceso sulfato reductor permite dar una mayor aproximacion de este tipo de crecimiento anaerobio para explorar su comportamiento bajodiferentes condiciones de operacion segun el interes biotecnologico deseado. Palabras clave: Sulfato reduccion, modelos no estructurados, inhibicion, cinetica.
Joint iterative decoding for LDPC-coded multi-relay cooperation with receive multi-antenna in the destination

This study proposes an low density party check (LDPC)-coded multi-relay cooperation with receive multi-antenna in the destination over a Rayleigh-fading channel, where maximal ratio combining and belief propagation algorithm (BP)-based joint iterative decoding based on the introduced multi-layer Tanner graph are effectively designed to detect and decode the corrupted received sequence at the destination. The overall code rate from the destination is derived mathematically in relation to all the constituent LDPC codes employed by source and multiple relays. Theoretical analysis and numerical simulation show that the proposed approach can well combine diversity and coding gains, which consequently result in significant advantage over the conventional cooperations under the same conditions.
Exercise training and impaired glucose tolerance in obese humans

Abstract Individuals with impaired glucose tolerance (IGT) are at greater risk of developing diabetes than in normoglycaemia. The aim of this study was to examine the effects of 12-weeks exercise training in obese humans with IGT. Eleven participants (6 males and 5 females; 49±9 years; mean Body Mass Index (BMI) 32.4 kg · m−2), completed a 12-week brisk walking intervention (30 min per day, five days a week (d · wk−1), at 65% of age-predicted maximal heart rate (HRmax). Anthropometric measurements, dietary intake, pulse wave velocity (PWV, to determine arterial stiffness) and blood pressure (BP) were examined at baseline and post intervention. Fasting blood glucose, glycosylated haemoglobin, insulin, blood lipids, indices of oxidative stress and inflammation (lipid hydroperoxides; superoxide dismutase; multimeric adiponectin concentration and high-sensitivity C-reactive protein) were also determined. Post intervention, PWV (9.08±1.27 m · s−1 vs. 8.39±1.21 m · s−1), systolic BP (145.4±14.5 vs. 135.8±14.9 mmHg), triglycerides (1.52±0.53 mmol . L−1 vs. 1.31±0.54 mmol . L−1), lipid hydroperoxides (1.20±0.47 μM · L−1 vs. 0.79±0.32 μM · L−1) and anthropometric measures decreased significantly (P < 0.05). Moderate intensity exercise training improves upper limb vascular function in obese humans with IGT, possibly by improving triglyceride metabolism, which may subsequently reduce oxidative stress. These changes were independent of multimeric adiponectin modification and alterations in other blood biomarkers.
Vitamin E supplementation and in vivo immune response in healthy elderly subjects. A randomized controlled trial.

OBJECTIVE To determine whether long-term supplementation with vitamin E enhances in vivo, clinically relevant measures of cell-mediated immunity in healthy elderly subjects. DESIGN Randomized, double-blind, placebo-controlled intervention study. SETTING AND PARTICIPANTS A total of 88 free-living, healthy subjects at least 65 years of age. INTERVENTION Subjects were randomly assigned to a placebo group or to groups consuming 60, 200, or 800 mg/d of vitamin E for 235 days. MAIN OUTCOME MEASURES Delayed-type hypersensitivity skin response (DTH); antibody response to hepatitis B, tetanus and diphtheria, and pneumococcal vaccines; and autoantibodies to DNA and thyroglobulin were assessed before and after supplementation. RESULTS Supplementation with vitamin E for 4 months improved certain clinically relevant indexes of cell-mediated immunity in healthy elderly. Subjects consuming 200 mg/d of vitamin E had a 65% increase in DTH and a 6-fold increase in antibody titer to hepatitis B compared with placebo (17% and 3-fold, respectively), 60-mg/d (41% and 3-fold, respectively), and 800-mg/d (49% and 2.5-fold, respectively) groups. The 200-mg/d group also had a significant increase in antibody titer to tetanus vaccine. Subjects in the upper tertile of serum alpha-tocopherol (vitamin E) concentration (>48.4 micromol/L [2.08 mg/dL]) after supplementation had higher antibody response to hepatitis B and DTH. Vitamin E supplementation had no effect on antibody titer to diphtheria and did not affect immunoglobulin levels or levels of T and B cells. No significant effect of vitamin E supplementation on autoantibody levels was observed. CONCLUSIONS Our results indicate that a level of vitamin E greater than currently recommended enhances certain clinically relevant in vivo indexes of T-cell-mediated function in healthy elderly persons. No adverse effects were observed with vitamin E supplementation.
Ionic Strength Sensing in Living Cells

Knowledge of the ionic strength in cells is required to understand the in vivo biochemistry of the charged biomacromolecules. Here, we present the first sensors to determine the ionic strength in living cells, by designing protein probes based on Förster resonance energy transfer (FRET). These probes allow observation of spatiotemporal changes in the ionic strength on the single-cell level.
Endothelial‐rich microenvironment supports growth and branching morphogenesis of prostate epithelial cells

Development of epithelial organs depends on interaction between the epithelium and the underlying mesenchyme including the vasculature. The aim of this study was to explore the morphogenic effect of endothelial cells on prostate epithelial cell lines in 3D culture and to establish an in vitro model for prostate branching morphogenesis.
Derivation, Characterization, and Differentiation of Human Embryonic Stem Cells

The derivation of human embryonic stem (hES) cells establishes a new avenue to approach many issues in human biology and medicine for the first time. To meet the increased demand for characterized hES cell lines, we present the derivation and characterization of six hES cell lines. In addition to the previously described immunosurgery procedure, we were able to propagate the inner cell mass and establish hES cell lines from pronase‐treated and hatched blastocysts. The cell lines were extensively characterized by expression analysis of markers characteristic for undifferentiated and differentiated hES cells, karyotyping, telomerase activity measurement, and pluripotency assays in vitro and in vivo. Whereas three of the cell lines expressed all the characteristics of undifferentiated pluripotent hES cells, one cell line carried a chromosome 13 trisomy while maintaining an undifferentiated pluripotent state, and two cell lines, one of which carried a triploid karyotype, exhibited limited pluripotency in vivo. Furthermore, we clonally derived one cell line, which could be propagated in an undifferentiated pluripotent state.
Do Animals Feel Pain?

In an oft-quoted passage from The Principles of Morals and Legislation (1789), Jeremy Bentham addresses the issue of our treatment of animals with the following words: ‘the question is not, Can they reason? nor, can they talk? but, Can they suffer? ’ The point is well taken, for surely if animals suffer, they are legitimate objects of our moral concern. It is curious therefore, given the current interest in the moral status of animals, that Bentham's question has been assumed to be merely rhetorical. No-one has seriously examined the claim, central to arguments for animal liberation and animal rights, that animals actually feel pain. Peter Singer's Animal Liberation is perhaps typical in this regard. His treatment of the issue covers a scant seven pages, after which he summarily announces that ‘there are no good reasons, scientific or philosophical, for denying that animals feel pain’. In this paper I shall suggest that the issue of animal pain is not so easily dispensed with, and that the evidence brought forward to demonstrate that animals feel pain is far from conclusive.
Reporter Mutation Studies Show That Nicotinic Acetylcholine Receptor (nAChR) α5 Subunits and/or Variants Modulate Function of α6*-nAChR*

Background: We asked how partner subunits influence α6*-nicotinic receptor (nAChR) function. Results: We found several, novel ways to manipulate effects of α5 subunits on α6*-nAChR function. Conclusion: Extracellular domains in α6 and cytoplasmic/transmembrane domains in α6/α3/α5/β3 subunits have unexpected influences on α6*-nAChR function. Significance: We found factors that influence assembly and function of α6*-nAChRs, which play important roles in mood, reward, and nicotine dependence. To further the understanding of functional α6α5*-nicotinic acetylcholine receptors (nAChR; the asterisk (*) indicates known or possible presence of other subunits), we have heterologously expressed in oocytes different, mouse or human, nAChR subunit combinations. Coexpression with wild-type α5 subunits or chimeric α5/β3 subunits (in which the human α5 subunit N-terminal, extracellular domain is linked to the remaining domains of the human β3 subunit) almost completely abolishes the very small amount of function seen for α6β4*-nAChR and does not induce function of α6β2*-nAChR. Coexpression with human α5V9′S subunits bearing a valine 290 to serine mutation in the 9′ position of the second transmembrane domain does not rescue the function of α6β4*-nAChR or induce function of α6β2*-nAChR. However, coexpression with mutant chimeric α5/β3V9′S subunits has a gain-of-function effect (higher functional expression and agonist sensitivity and spontaneous opening inhibited by mecamylamine) on α6β4*-nAChR. Moreover, N143D + M145V mutations in the α6 subunit N-terminal domain enable α5/β3V9′S subunits to have a gain-of-function effect on α6β2*-nAChR. nAChR containing chimeric α6/α3 subunits plus either β2 or β4 subunits have some function that is modulated in the presence of α5 or α5/β3 subunits. Coexpression with α5/β3V9′S subunits has a gain-of-function effect more pronounced than that in the presence of α5V9′S subunits. Gain-of-function effects are dependent, sometimes subtly, on the nature and apparently the extracellular, cytoplasmic, and/or transmembrane domain topology of partner subunits. These studies yield insight into assembly of functional α6α5*-nAChR and provide tools for development of α6*-nAChR-selective ligands that could be important in the treatment of nicotine dependence, and perhaps other neurological diseases.