Miracle-dz/UniFAR-FTUs huggingface dataset:
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

MOTIVATION Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. RESULTS Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. AVAILABILITY GROMACS is an open source and free software available from http://www.gromacs. org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Enabling static analysis for partial java programs

Software engineering tools often deal with the source code of programs retrieved from the web or source code repositories. Typically, these tools only have access to a subset of a program's source code (one file or a subset of files) which makes it difficult to build a complete and typed intermediate representation (IR). Indeed, for incomplete object-oriented programs, it is not always possible to completely disambiguate the syntactic constructs and to recover the declared type of certain expressions because the declaration of many types and class members are not accessible. We present a framework that performs partial type inference and uses heuristics to recover the declared type of expressions and resolve ambiguities in partial Java programs. Our framework produces a complete and typed IR suitable for further static analysis. We have implemented this framework and used it in an empirical study on four large open source systems which shows that our system recovers most declared types with a low error rate, even when only one class is accessible.
Type sharing constraints and undecidability

Abstract Let ${\cal A}$ be a set of modules and parameterized modules including type sharing constraint specifications. We prove that determining the set of the effective modules described by ${\cal A}$ is undecidable. As a consequence, type sharing constraints are proved to be not always avoidable by constructive transformations.
Concerns of Seventh-Graders about Their Transition to Junior High School

A critical ingredient for understanding the experiences that students undergo in the transition from elementary school to junior high school is the changing perceptions of the students themselves. To this end, students completed a Concerns Questionnaire during the fifth week of seventh grade where they responded to a list of potential transition concerns by indicating the degree of their concern both when they first entered junior high school and at the present time. Results showed that most students did not have great concerns about items listed. Given this low absolute level of concerns, students perceived even lower total concerns levels after five weeks in junior high. Also, students reported relatively more concerns about academic work than the social aspects of junior high school. Comparisons suggested that the independent variables of student sex, participation style, and previous classroom organization were important, but consistent patterns were not found.
Graphical assessment of internal and external calibration of logistic regression models by using loess smoothers

Predicting the probability of the occurrence of a binary outcome or condition is important in biomedical research. While assessing discrimination is an essential issue in developing and validating binary prediction models, less attention has been paid to methods for assessing model calibration. Calibration refers to the degree of agreement between observed and predicted probabilities and is often assessed by testing for lack‐of‐fit. The objective of our study was to examine the ability of graphical methods to assess the calibration of logistic regression models. We examined lack of internal calibration, which was related to misspecification of the logistic regression model, and external calibration, which was related to an overfit model or to shrinkage of the linear predictor. We conducted an extensive set of Monte Carlo simulations with a locally weighted least squares regression smoother (i.e., the loess algorithm) to examine the ability of graphical methods to assess model calibration. We found that loess‐based methods were able to provide evidence of moderate departures from linearity and indicate omission of a moderately strong interaction. Misspecification of the link function was harder to detect. Visual patterns were clearer with higher sample sizes, higher incidence of the outcome, or higher discrimination. Loess‐based methods were also able to identify the lack of calibration in external validation samples when an overfit regression model had been used. In conclusion, loess‐based smoothing methods are adequate tools to graphically assess calibration and merit wider application. © 2013 The Authors. Statistics in Medicine published by John Wiley & Sons, Ltd
Do Insects Have Emotions? Some Insights from Bumble Bees

While our conceptual understanding of emotions is largely based on human subjective experiences, research in comparative cognition has shown growing interest in the existence and identification of “emotion-like” states in non-human animals. There is still ongoing debate about the nature of emotions in animals (especially invertebrates), and certainly their existence and the existence of certain expressive behaviors displaying internal emotional states raise a number of exciting and challenging questions. Interestingly, at least superficially, insects (bees and flies) seem to fulfill the basic requirements of emotional behavior. Yet, recent works go a step further by adopting terminologies and interpretational frameworks that could have been considered as crude anthropocentrism and that now seem acceptable in the scientific literature on invertebrate behavior and cognition. This change in paradigm requires, therefore, that the question of emotions in invertebrates is reconsidered from a cautious perspective and with parsimonious explanations. Here we review and discuss this controversial topic based on the recent finding that bumblebees experience positive emotions while experiencing unexpected sucrose rewards, but also incorporating a broader survey of recent literature in which similar claims have been done for other invertebrates. We maintain that caution is warranted before attributing emotion-like states to honey bees and bumble bees as some experimental caveats may undermine definitive conclusions. We suggest that interpreting many of these findings in terms of motivational drives may be less anthropocentrically biased and more cautious, at least until more careful experiments warrant the use of an emotion-related terminology.
Bit Allocation for Variable Bitrate Video

In this paper we propose a special bit allocation method which can be used in most rate control algorithms in variable rate video applications. In real-time video communication applications, we need a constant short-term average bitrate, while in variable bitrate applications such as streaming and local recording applications, a constant long-term average bitrate is sufficient and more short-term variation in bitrate is acceptable. In comparison with constant bitrate video, a variable bitrate video can provide better visual quality and coding efficiency for compressed video sequences. Furthermore, while more variation in bitrate is possible we have additional degrees of freedom to control the encoding parameters. We propose a special bit allocation algorithm to take advantage of this freedom in variable bitrate video. We introduce a new type of frame namely SPP frame (SPecial P frame) that can be used in combination with I, P, B and other types of frames in different encoders including H.263, MPEG-4 and H.264/AVC encoders. We propose a simple method to implement the SPP frames independently of the rate control algorithm. The experimental results show that the SPP frames can considerably increase the total average quality of variable rate encoded video
Dynamic pattern formation leads to 1/f noise in neural populations.

We present a generic model that generates long-range (power-law) temporal correlations, 1/f noise, and fractal signals in the activity of neural populations. The model consists of a two-dimensional sheet of pulse coupled nonlinear oscillators (neurons) driven by spatially and temporally uncorrelated external noise. The system spontaneously breaks the translational symmetry, generating a metastable quasihexagonal pattern of high activity clusters. Fluctuations in the spatial pattern cause these clusters to diffuse. The macroscopic dynamics (diffusion of clusters) translate into 1/f power spectra and fractal (power-law) pulse distributions on the microscopic scale of a single unit.
Shortest-Weight Paths in Random Regular Graphs

Consider a random regular graph with degree $d$ and of size $n$. Assign to each edge an independent and identically distributed exponential random variable with mean one. In this paper we establish a precise asymptotic expression for the maximum number of edges on the shortest-weight paths between a fixed vertex and all the other vertices, as well as between any pair of vertices. Namely, for any fixed $d \geq 3$, we show that the longest of these shortest-weight paths has about $\widehat{\alpha} \log n$ edges, where $\widehat{\alpha} $ is the unique solution of the equation $\alpha \log\big(\frac{d-2}{d-1}\alpha\big) - \alpha = \frac{d-3}{d-2}$ for $\alpha > \frac{d-1}{d-2}$.
A Multilevel Examination of the Drivers of Firm Multinationality

Significant research has been devoted to studying the factors that affect firm multinationality. In this study, the authors organize the vast multinationality literature by levels of analysis using a multilevel framework based on the interaction paradigm and conduct a meta-analysis that aggregates the empirical findings from 154 independent samples reported in 145 studies. The cumulative evidence provides strong support for the upper echelons theory that emphasizes the central importance of executives’ characteristics as major determinants of firm multinationality. Moreover, the results indicate that the accumulation of the international experience embedded in human and relational capital is the most significant firm-level factor that affects firm multinationality. The meta-analytic results also reveal that the measurement and sample characteristics of original studies explain the inconsistent findings pertaining to the effects of firm size, firm age, and top management team size on multinationality. On the basis of the meta-analytic findings, several directions for future research are provided.
Effects of nicotine on blood flow and delayed neuronal death following intermittent transient ischemia in rat hippocampus.

A cholinergic neural vasodilative response in the cerebral cortex and hippocampus, independent of metabolic vasodilation, was recently demonstrated by activating the nicotinic acetylcholine receptors (nAChRs) via activation of cholinergic neurons originating in the nucleus basalis of Meynert and septal complex in the basal forebrain and projecting to the cortex and hippocampus (see reviews by Sato A and Sato Y: Neurosci Res 14: 242--274, 1992; Sato A and Sato Y: Alzheimer Dis Assoc Disord 9: 28--38, 1995). In the present study, we aimed to examine whether an increase in regional blood flow in the hippocampus (Hpc-BF) following stimulation of the nAChRs by i.v. injection of nicotine could improve the delayed death of the hippocampal neurons following transient ischemia in rats. Hpc-BF was measured by using a laser Doppler flowmeter. During intermittent (every 2 min) transient occlusion for a total of 6 min of bilateral carotid arteries besides permanent ligation of bilateral vertebral arteries, Hpc-BF decreased to about 16% of the preocclusion level, and 5 or 7 d later, after the occlusion, delayed neuronal death occurred in approximately 70% of the CA1 hippocampal neurons. Hpc-BF was increased dose-dependently by injection of nicotine (30--100 microg/kg, i.v.), independent of mean arterial pressure. Nicotine (30--100 microg/kg) administered 5 min before occlusion slightly but significantly attenuated the occlusion-induced decrease in Hpc-BF. The delayed death of the CA1 hippocampal neurons occurring after transient occlusion was attenuated by pretreatment with nicotine (30--100 microg/kg) to approximately 50% of the total neurons. The results indicate that nAChR stimulation-induced increases in Hpc-BF can protect against ischemia-induced delayed death of hippocampal neurons.
Who Plans (Not) to Study Abroad? An Examination of U.S. Student Intent

With the number of American students studying abroad increasing each year and the expected passage of a federal law that would increase and diversify study abroad participation and locations, U.S. colleges and universities likely will have to make changes related to curriculum, faculty involvement, institutional leadership, programming, and resources (both financial and human) to meet the mandate. Therefore, it is imperative that colleges and universities understand how the characteristics and backgrounds of their students influence intent to study abroad. This study examined factors that may affect U.S. student participation in study abroad, including parental income and education, gender, race, intended major, attitudes about other cultures, and distance of college from home. Data were collected from a large, public northeastern university in the United States that participated in the 2007 Cooperative Institutional Research Program (CIRP) survey, which provides information about incoming students’ backgrounds, academic and career expectations, personal goals, and opinions on a wide range of political and social issues. The results indicate that being female, attending school more than 100 miles from home, and expressing an interest in improving one’s understanding of other cultures and countries have a positive influence on American students’ intent to study abroad. Planning to pursue a master’s degree or higher, living with family while attending school and majoring in engineering and professional areas such as architecture and medicine negatively affect U.S. student intent to study abroad.
Continued Stabilization of the Nuclear Higher-Order Structure of Post-Mitotic Neurons In Vivo

Background Cellular terminal differentiation (TD) correlates with a permanent exit from the cell cycle and so TD cells become stably post-mitotic. However, TD cells express the molecular machinery necessary for cell proliferation that can be reactivated by experimental manipulation, yet it has not been reported the stable proliferation of any type of reactivated TD cells. Neurons become post-mitotic after leaving the ventricular zone. When neurons are forced to reenter the cell cycle they invariably undergo cell death. Wider evidence indicates that the post-mitotic state cannot solely depend on gene products acting in trans, otherwise mutations in the corresponding genes may lead to reentry and completion of the cell cycle in TD cells, but this has not been observed. In the interphase, nuclear DNA of metazoan cells is organized in supercoiled loops anchored to a nuclear nuclear matrix (NM). The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS). We have previously compared the NHOS of aged rat hepatocytes with that of early post-mitotic rat neurons and our results indicated that a very stable NHOS is a common feature of both senescent and post-mitotic cells in vivo. Principal Findings In the present work we compared the NHOS in rat neurons from different post-natal ages. Our results show that the trend towards further stabilization of the NHOS in neurons continues throughout post-natal life. This phenomenon occurs in absence of overt changes in the post-mitotic state and transcriptional activity of neurons, suggesting that it is independent of functional constraints. Conclusions Apparently the continued stabilization of the NHOS as a function of time is basically determined by thermodynamic and structural constraints. We discuss how the resulting highly stable NHOS of neurons may be the structural, non-genetic basis of their permanent and irreversible post-mitotic state.
A novel 115-kD peripheral membrane protein is required for intercisternal transport in the Golgi stack

We have used an in vitro Golgi protein transport assay dependent on high molecular weight (greater than 100 kD) cytosolic and/or peripheral membrane proteins to study the requirements for transport from the cis- to the medial-compartment. Fractionation of this system indicates that, besides the NEM-sensitive fusion protein (NSF) and the soluble NSF attachment protein (SNAP), at least three high molecular weight protein fractions from bovine liver cytosol are required. The activity from one of these fractions was purified using an assay that included the second and third fractions in a crude state. The result is a protein of 115-kD subunit molecular mass, which we term p115. Immunodepletion of the 115- kD protein from a purified preparation with mAbs removes activity. Peptide sequence analysis of tryptic peptides indicates that p115 is a "novel" protein that has not been described previously. Gel filtration and sedimentation analysis indicate that, in its native state, p115 is a nonglobular homo-oligomer. p115 is present on purified Golgi membranes and can be extracted with high salt concentration or alkaline pH, indicating that it is peripherally associated with the membrane. Indirect immunofluorescence indicates that p115 is associated with the Golgi apparatus in situ.
Predicting scorpion sting incidence in an endemic region using climatological variables

Abstract Scorpionism is a public health problem in several regions of the world. The highest mortality, with over 1000 deaths per year, has been reported in Mexico. We analysed the significance of climatological variables to predict the incidence of scorpion stings in humans in the state of Colima (Mexico) for the years 2000–2001. The pluvial precipitation (mm), the evaporation (mm), and the mean, maximum, and minimum temperatures (°C) were obtained from local meteorological offices. There are approximately 3 stings/year per 1000 people in municipalities of Colima and Villa de Alvarez and about 18–30 stings/year per 1000 people in the rest of the municipalities. There is very little rain and there are few stings in the winter when the minimum temperature is below about 16°C. The number of scorpion stings is independent of the actual rainfall when this is above 30 mm/month. Using multiple linear regression, we used a backward model selection procedure to estimate that the minimum temperature is correlated with scorpion sting incidence with a statistically significance of 95%. We briefly discuss the application of predictive models of scorpion sting incidence in the appropriate allocation of antivenom serum in hospital clinics.
Learning where to search using visual attention

One of the central tasks for a household robot is searching for specific objects. It does not only require localizing the target object but also identifying promising search locations in the scene if the target is not immediately visible. As computation time and hardware resources are usually limited in robotics, it is desirable to avoid expensive visual processing steps that are exhaustively applied over the entire image. The human visual system can quickly select those image locations that have to be processed in detail for a given task. This allows us to cope with huge amounts of information and to efficiently deploy the limited capacities of our visual system. In this paper, we therefore propose to use human fixation data to train a top-down saliency model that predicts relevant image locations when searching for specific objects. We show that the learned model can successfully prune bounding box proposals without rejecting the ground truth object locations. In this aspect, the proposed model outperforms a model that is trained only on the ground truth segmentations of the target object instead of fixation data.
Gene transfer in astrocytes: Comparison between different delivering methods and expression of the HIV‐1 protein Nef

To identify a good system to introduce foreign genes into normal and tumoral astrocytes, we studied the efficiency of two chemical methods, calcium phosphate precipitation and lipofection, and of a viral‐mediated transfer by a vector derived from the highly attenuated modified vaccinia virus Ankara (MVA). Using the β‐galactosidase (β‐gal) gene (lacZ) as reporter, we searched for optimal experimental conditions to obtain an efficient gene transfer into human embryonic and neonatal rat astrocytes and into a human astrocytoma cell line (U373 MG). The β‐gal protein production was evaluated by cytochemical staining and enzymatic activity assay. Among chemical methods, lipofection was the most efficient system to transfect astrocytes in providing up to 60% of β‐gal‐positive cells in all the cell types analyzed. MVA infection also proved to be an efficient system to introduce heterologous genes into human embryonic astrocytes that appeared 80–100% positive 48–96 hr after an infection at a multiplicity of 1–10. In contrast, only a limited infection was observed with rat astrocytes, human astrocytoma cells, and human leptomeningeal cells. A recombinant MVA vector expressing the human immunodeficiency virus‐1 (HIV‐1) regulatory protein Nef was used to transfect human embryonic astrocytes, and the resulting Nef expression was compared with that detected after lipofection in the same cells. By Western blot analysis, Nef expression was observed in human astrocytes 24–96 hr after infection and was similar to that present in stably HIV‐1–infected astrocytoma cells. Lipofection resulted in lower Nef expression. In spite of these promising results, the negative effects of MVA infection on cell viability and the possibility that a productive infection occurs in human embryonic astrocytes limit the use of this vector for gene delivery in developmentally immature human glial cells. J. Neurosci. Res. 55:569–577, 1999. © 1999 Wiley‐Liss, Inc.