nils-herrmann/clean_scirepeval huggingface dataset:
Nonlinear relationship between biodiversity and human population density: evidence from Southeast Asia

The geographical distribution of terrestrial vertebrate biodiversity was assessed in Southeast Asia, an area characterized by highly heterogeneous human population densities (HPDs). We tested the hypothesis that recent (between 1990 and 2000) population increases may result in increased threats to biodiversity. GIS data were compiled from the International Union for the Conservation of Nature, BirdLife, and the Socioeconomic Data and Applications Center. Polygon data sets were transformed into rasters with different resolutions from 2.5$$'$$′ to 1$$^{\circ }.$$∘. Relationships between species diversity were assessed globally and separately for terrestrial vertebrates (mammals, birds, reptiles, and amphibians) and for five countries (Cambodia, Laos, Myanmar, Thailand, and Vietnam). The number of species within a 20 km$$^{2}$$2-cell varied greatly and reached a maximum of 801. The species-rich cells ($$>700$$>700 species) were located in a single, almost continuous area across Myanmar, Thailand, Vietnam, and South China. The relationship between vertebrate biodiversity and population density showed that biodiversity increased with HPD until around 10 persons km$$^{-2},$$-2, then decreased until around 200 persons km$$^{-2}$$-2 where it stabilized. This relationship was mediated by land cover and protection status with significant interactions between these variables and with population density. The areas with moderately increasing populations between 1990 and 2000 were those with the highest overall diversity (median 607) whereas those with decreasing populations were those with the lowest diversity (median 479). Our results suggest that population pressure on biodiversity has increased between 1990 and 2000 and this is a relatively widespread phenomenon. The presence of a continuous area of high vertebrate biodiversity calls for international action at a regional scale involving China, Laos, Myanmar, Thailand, and Vietnam.

Field of study: Environmental science
BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts

Most of somatic mutations in cancer occur outside of gene coding regions. These mutations may disrupt the gene regulation by affecting protein-DNA interaction. A study of these disruptions is important in understanding tumorigenesis. However, current computational tools process DNA sequence variants individually, when predicting the effect on protein-DNA binding. Thus, it is a daunting task to identify functional regulatory disturbances among thousands of mutations in a patient. Previously, we have reported and validated a pipeline for identifying functional non-coding somatic mutations in cancer patient cohorts, by integrating diverse information such as gene expression, spatial distribution of the mutations, and a biophysical model for estimating protein binding affinity. Here, we present a new user-friendly Python package BayesPI-BAR2 based on the proposed pipeline for integrative whole-genome sequence analysis. This may be the first prediction package that considers information from both multiple mutations and multiple patients. It is evaluated in follicular lymphoma and skin cancer patients, by focusing on sequence variants in gene promoter regions. BayesPI-BAR2 is a useful tool for predicting functional non-coding mutations in whole genome sequencing data: it allows identification of novel transcription factors (TFs) whose binding is altered by non-coding mutations in cancer. BayesPI-BAR2 program can analyze multiple datasets of genome-wide mutations at once and generate concise, easily interpretable reports for potentially affected gene regulatory sites. The package is freely available at

Field of study: Biology
The Theory of Decision Procedures for Distributions with Monotone Likelihood Ratio

In connection with the ordinary testing problem,  showed that for the composite testing problem of the one-sided type for the special case of the exponential family of distributions, an admissible minimax procedure must be of the form: choose action 1 (accept the hypothesis) if x xo . If x = xo, randomization may be required. Sobel [21 and Chernoff obtained partial results for the same class of distributions when the set of decisions is finite. This paper unifies, extends, and strengthens these results and treats of a wide variety of stati stical decision problems for which the densities have a monotone likelihood ratio' In Section 1 the fundamental definition and preliminaries are introduced. In particular, the conditions imposed on the loss functions and the densities are delimited and some simple properties of these quantities are developed. In Section 2 we establish some of the basic lemmas. Noteworthy are Lemmas 1 and 2 which express the variation of sign diminishing properties of the densities which possess a monotone likelihood ratio. The essential completeness of the set of all monotone strategies (see Section 3 for the definition) in the class of all statistical procedures is demonstrated in Section 3 for the case of a finite number of actions. Section 4 deals with the problem of determining the form of all Bayes strategies for the statistician. The important problem of admissibility is studied in detail in Section 5. In the next section a study of the Bayes strategies for nature is made for the case of two actions. In Section 7 the complete class theory is carried through for the case of an infinite number of actions. This is accomplished by employing an argument involving a limiting procedure from the case of finite actions as treated in Section 3. The eighth section presents an analysis of the nature of the Bayes strategies for the case of an infinite number of actions. The final

Field of study: Mathematics
Research Framework of Human Resource Development Based on Competency about Knowledge Enterprise

Former studies of competency focus on individuals, regarding individuals as primary units of understanding enterprise performance. Beginning from the competency, this paper constructs a systematic research framework for knowledge enterprise. The framework is based on the theory of human capital, theory of knowledge management, theory of team role, and the theory of organizational learning, taking enterprise strategy as the core, chiefly studying the development of competency of individuals, teams, and organizations in knowledge enterprises. Its ultimate objective is to improve the performance of individuals, teams, and organizations.

Field of study: Business
Internality vs Externality and Personal Adjustment: A Factor Analytic Study

This study compared three tests to determine the degree to which they might be measuring a single construct: Rotter's Internal-External Reinforcement Scale, Rest's adaptation of Kohlberg's test of moral development, and selected scales from Shostrom's Personal Orientation Inventory. All three scales were expected to show positive relationships with a measure of personal adjustment, the Tennessee Self-concept Scale. Numerous significant correlations were found among these instruments, suggesting some commonality in the personality dimensions being measured. There were enough differences to suggest continued refinement and to mitigate against substitution of one test for another without loss of information.

Field of study: Psychology
Warmer or cooler late Holocene marine palaeoenvironments?: interpreting southeast Australian and Brazilian sea-level changes using fixed biological indicators and their δ18O composition

Relic inter-tidal assemblages of sessile organisms, which are referred to as fixed biological indicators (FBIs), are shown to be useful proxies for late Holocene climatic and environmental changes as well as direct indicators of short term fluctuations in sea-level. A detailed comparison of change in the inter-tidal assemblages of two Southern Hemisphere sites at comparable latitudes (Port Hacking, New South Wales, south–east Australia and the Laguna-Imbituba region of southern Brazil) indicates periods of marked similarities in the timing and nature of changes at ∼5200, ∼3800 cal. years BP and differences after ∼2400 cal. years BP. There is sufficient concurrence of cooling phases and falling sea-levels to strongly suggest that in some cases global rather than regional forcing factors are at work. The value of inter-tidal organisms as indicators of changed environments is developed by identifying the past and present distributions of the common marker species: tubeworms, barnacles and mussels. The δ 18 O content of these extant specimens at Port Hacking confirmed changes in ocean water temperature and associated sea-level behaviour corresponding to invasion or extinction of temperature-sensitive species. A similar pattern is repeated, although in a less marked fashion, in the Laguna-Imbituba region of southern Brazil.

Field of study: Environmental science, Geography
Optimization of microwave-assisted extraction of polysaccharides from bamboo leaves by response surface analysis

The extraction of polysaccharides from Neosinocalamus affinins was studied in this paper.Ac-cording to the single factor experiment,three levels of the factors(extraction temperature,time and the ratio of liquid-to-solid) were selected for the Box-Behnken factorial design to establish a quadric regression equation for describing the yield of polysaccharides.By response surface analysis,the optimal extraction conditions were obtained as follows: extraction power of 600 W,extraction temperature of 124℃,extraction time of 44 min and liquid-to-solid ratio of 41:1,under which the experimental yield(0.45%) of polysaccharides accounts for 98.68% of the theoretically predicted value of 0.456% with one-time extraction.

Field of study: Agricultural and Food sciences
Development and test of solar Rankine cycle heating and cooling systems

Well-designed solar-powered Rankine-cycle systems can be used to drastically reduce building heating and cooling energy requirements while meeting all comfort operational requirements. A turbocompressor system using a common refrigerant, R11, and advanced aerodynamic and mechanical design features can efficiently provide heating and cooling at efficiency levels equal to or above those of current systems. Equipment costs, i.e., collector, storage, and heat pump, as well as installation costs are currently too high for widespread solar application. However, as energy costs continue to escalate and equipment cost is reduced due to increased production, solar cooling and heating will become competitive and gain acceptance. The Southwest will probably lead the way to solar energy utilization.

Field of study: Engineering
Establishment of a patient-derived Wilms' tumor xenograft model: a promising tool for individualized cancer therapy.

Lack of appropriate approaches that reliably predict response of Wilms' tumor (WT) to anticancer agents remains a major deficiency in clinical practice of individualized cancer therapy. The aim of this study was to establish a patient-derived tumor tissue (PDTT) xenograft model of WT for individualized chemotherapeutic regimen selection in accordance with the patient's tumor nature.



Tumor specimens of a primary WT were orthotopically implanted into three nude mice, and after 4 weeks xenografts were harvested for serial heterotopic transplantation in 20 nude mice that were divided into three experimental groups and one control group. In vitro and in vivo chemosensitivity to doxorubicin, actinomycin-D, and vincristine were evaluated. Hematoxylin and eosin (H&E) staining and immunohistochemical examination with desmin, vimentin, myogenin, and neuron-specific enolase (NSE) were also applied to determine histological stability of the xenograft during serial transplantation compared with the original tumor tissue.



The xenograft model was successfully established. Histopathologic characteristics of the xenograft tumors were similar to the patient's tumor. Early passage of the PDTT showed a similar chemosensitivity pattern to the original tumor tissue.



PDTT xenograft of WT provides an appropriate model for individualized cancer therapeutic regimen selection by means of its biological stability compared with original patient's tumor.

Field of study: Medicine
Respiration-Related Artifacts in EDA Recordings: Introducing a Standardized Method to Overcome Multiple Interpretations

When electrodermal activity (EDA) recordings are controlled for artifacts, i.e., electrodermal reactions [EDRs] elicited by breathing irregularities, several problems arise. For example, respiration is difficult to evaluate because there are no clear-cut criteria for its values, e.g., wave form, depth. Furthermore, respiration and EDA are rather complexly intertwined, and there is no established or standardized method for evaluation. Especially when subjects are not stimulated, i.e., when nonspecific EDRs are taken, EDR recordings elicited by irregular breathing may overestimate the subject's arousal and bias any given research question. Moreover, incidences of concurrent consecutive EDRs and changes in respiratory activity may encourage multicausal interpretation due to both signals' having a common central causation. To circumvent such problems, we developed a method which provides rule-based guidelines to identify potential artifacts. Two experiments (N = 14 and N = 12) were conducted to test the accuracy of the judgments of three independent raters. The reliability coefficients for the number of electrodermal reactions and the sum of their amplitudes yielded satisfactory coefficients of convergence for each individual experiment (.87 and .82 in Exp. 1 vs .94 and .95 in Exp. 2) as well as for the two experiments combined (.92 and .91).

Field of study: Psychology
Hidden Markov Models and Disease Mapping

We present new methodology to extend hidden Markov models to the spatial domain, and use this class of models to analyze spatial heterogeneity of count data on a rare phenomenon. This situation occurs commonly in many domains of application, particularly in disease mapping. We assume that the counts follow a Poisson model at the lowest level of the hierarchy, and introduce a finite-mixture model for the Poisson rates at the next level. The novelty lies in the model for allocation to the mixture components, which follows a spatially correlated process, the Potts model, and in treating the number of components of the spatial mixture as unknown. Inference is performed in a Bayesian framework using reversible jump Markov chain Monte Carlo. The model introduced can be viewed as a Bayesian semiparametric approach to specifying flexible spatial distribution in hierarchical models. Performance of the model and comparison with an alternative well-known Markov random field specification for the Poisson rates are demonstrated on synthetic datasets. We show that our allocation model avoids the problem of oversmoothing in cases where the underlying rates exhibit discontinuities, while giving equally good results in cases of smooth gradient-like or highly autocorrelated rates. The methodology is illustrated on an epidemiologic application to data on a rare cancer in France.

Field of study: Mathematics
Rapoport's rule: an explanation or a byproduct of the latitudinal gradient in species richness?

A recent explanation of the declining species richness gradient with increasing latitude away from the tropics implicated broad scale habitat variability, an associated range expansion, and a resulting increase in niche breadth. The niche breadth in turn was thought to affect richness by competition and rescue effect. While all three factors appear to be correlated, neither the postulated nor alternative causal mechanisms have been tested. We conduct such a test using a system which has all the attributes of the large scale pattern but which, in contrast to continental scale observations, allows for estimation or control of crucial variables such as taxonomic composition, habitat heterogeneity, habitat variability, exact species distribution, and local richness. Specifically, we test the alternative that the correlation between the geographical range of species and local diversity is a function of differential species survival and link this phenomenon to habitat variability. We use 40 species of aquatic invertebrates inhabiting a landscape of 49 miniature rock pools on the coast of Jamaica. The system we examined exhibits a gradient of increasing richness with decreasing habitat variability, analogous to the broad scale latitudinal pattern. Furthermore, species with broader ecological ranges are also broadly distributed. Superficially, this appears to be in agreement with the older explanations but two facts suggest different causes. First, there is no evidence of a ‘rescue effect’ maintaining high richness in many habitats despite their proximity to species sources. Second, ecologically broad species coexist with habitat specialists without reducing richness in jointly occupied habitats.

Field of study: Environmental science
New algorithm for integration between wireless microwave sensor network and radar for improved rainfall measurement and mapping

One of the main challenges for meteorological and hydrological modelling is accurate rainfall measurement and mapping across time and space. To date, the most effective methods for large-scale rainfall estimates are radar, satellites, and, more recently, received signal level (RSL) measurements derived from commercial microwave networks (CMNs). While these methods provide improved spatial resolution over traditional rain gauges, they have their limitations as well. For example, wireless CMNs, which are comprised of microwave links (ML), are dependant upon existing infrastructure and the ML' arbitrary distribution in space. Radar, on the other hand, is known in its limitation for accurately estimating rainfall in urban regions, clutter areas and distant locations. In this paper the pros and cons of the radar and ML methods are considered in order to develop a new algorithm for improving rainfall measurement and mapping, which is based on data fusion of the different sources. The integration is based on an optimal weighted average of the two data sets, taking into account location, number of links, rainfall intensity and time step. Our results indicate that, by using the proposed new method, we not only generate more accurate 2-D rainfall reconstructions, compared with actual rain intensities in space, but also the reconstructed maps are extended to the maximum coverage area. By inspecting three significant rain events, we show that our method outperforms CMNs or the radar alone in rain rate estimation, almost uniformly, both for instantaneous spatial measurements, as well as in calculating total accumulated rainfall. These new improved 2-D rainfall maps, as well as the accurate rainfall measurements over large areas at sub-hourly timescales, will allow for improved understanding, initialization, and calibration of hydrological and meteorological models mainly necessary for water resource management and planning.

Field of study: Environmental science
Parts-per-trillion LC-MS(Q) analysis of herbicides and transformation products in surface water

The goal of this study was to develop a robust method of analyzing surface water samples for S-triazine herbicides, chloroacetanilide herbicides, and their transformation products (TPs) using solid-phase extraction (SPE) followed by liquid chromatograph-mass spectrometry (LC-MS) with electrospray ionization (ESI) by in-source collision-induced dissociation (ISCID) capability of an orthogonal electrospray ionization probe on a single quadrupole LC-MS system. The method developed here met the goals of the study and yielded estimated method detection limits (EMDLs) averaging 0.3 ± 0.1 ng L−1 for S-triazines and their TPs and 0.7 ± 0.4 ng L−1 for chloroacetanilides and TPs. Spiked filtered river water yielded SPE recoveries ranging from 94.2 % ± 4.8 % for S-triazines and TPs after eliminating three compounds with less that 65 % recovery from analysis and 95.9 % ± 19 % for chloroacetanilides and their TPs. The method was field-tested with filtered water samples collected from four sites over a four-month period. Detectible values of S-triazines and TPs ranged from 0.3 to 1540 ng L−1 with a mean of 79.3 and a median of 19.4 ng L−1. Detectible values for chloroacetanilides and TPs ranged from 0.31 to 3780 ng L−1 with a mean of 252 and a median of 25.6 ng L−1. An additional goal was to determine if the method was useful for microbial degradation studies using native bacterial communities. The bacteria transformed atrazine (2-chloro-4-ethylamino-6-isopropylamino-S-triazine) solely into 2-hydroxy atrazine (2-hydroxy-4-ethylamino-6-isopropylamino-S-triazine) with concentrations of 78.4, 63.3 and 32.5 ng L−1 after 12 days of incubation compared with 6.3 and 7.1 ng L−1 for control dark and control sunlight respectively.

Field of study: Agricultural and Food sciences
MAD data collection - current trends.

The multiwavelength anomalous dispersion (MAD) method of protein structure determination is becoming a routine technique in protein crystallography. The increased number of wavelength-tuneable synchrotron beamlines capable of performing challenging MAD experiments, coupled with the widespread availability of charge-coupled device (CCD) based X-ray detectors with fast read-out times have brought MAD structure determination to a new exciting level. Ultrafast MAD data collection is now possible and, with the widespread use of selenium in the form of selenomethionine for phase determination, the method is growing in popularity. Recent developments in crystallographic software are complementing the above advances, paving the way for rapid protein structure determination. An overview of a typical MAD experiment is described, with emphasis on the rates and quality of data acquisition now achievable at third-generation synchrotron sources.

Field of study: Chemistry
Reserpine increases proenkephalin mRNA content in rat corpus striatum.

Single sc of reserpine increased the proenkephalin mRNA in rat corpus striatum dose-dependently at 24 h after injection. Reserpine did not change the proenkephalin mRNA in the basal hypothalamus, pituitary, adrenal and spleen or the proopiomelanocortin mRNA in the basal hypothalamus, pituitary, adrenal and spleen. The mechanism for reserpine to increase proenkephalin mRNA in the striatum is most likely via the removal of a tonic trans-synaptic dopaminergic inhibition on the enkephalinergic neurones.

Field of study: Biology, Chemistry, Medicine
Cut off frequency and transit time analysis of lightly doped drain (LDD) MOSFETs

Analytical model for the transconductance, cut off frequency, transit time and fringing capacitance of LDD MOSFETs is presented with a simple approach. The analysis is carried out considering the LDD device as a conventional MOSFET with a series resistance [Z.-H. Liu et al., Threshold voltage model for submicrometer MOSFETs.  ] and a simple closed form expressions for cut off frequency and transit time is obtained. The total gate capacitance, i.e. the geometric and fringing capacitance, is calculated for both LDD and non-LDD devices and lower fringing capacitance is reported in LDD devices. Lower cut-off frequencies and higher transit time are reported in LDD devices for the same channel length.

Field of study: Engineering