nils-herrmann/clean_scirepeval huggingface dataset:
Removing Batch Effects from Longitudinal Gene Expression Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data
Venue: PloS one

Technical variation plays an important role in microarray based gene expression studies, and batch effects explain a large proportion of this noise. It is therefore mandatory to eliminate technical variation while maintaining biological variability. Several strategies have been proposed for the removal of batch effects, although they have not been evaluated in large scale longitudinal gene expression data. In this study, we aimed at identifying a suitable method for batch effect removal in a large study of microarray based longitudinal gene expression. Monocytic gene expression was measured in 1092 participants of the Gutenberg Health Study at baseline and 5 year follow up. Replicates of selected samples were measured at both time points to identify technical variability. Deming regression, Passing Bablok regression, linear mixed models, non linear models as well as ReplicateRUV and ComBat were applied to eliminate batch effects between replicates. In a second step, quantile normalization prior to batch effect correction was performed for each method. Technical variation between batches was evaluated by principal component analysis. Associations between body mass index and transcriptomes were calculated before and after batch removal. Results from association analyses were compared to evaluate maintenance of biological variability. Quantile normalization, separately performed in each batch, combined with ComBat successfully reduced batch effects and maintained biological variability. ReplicateRUV performed perfectly in the replicate data subset of the study, but failed when applied to all samples. All other methods did not substantially reduce batch effects in the replicate data subset. Quantile normalization plus ComBat appears to be a valuable approach for batch correction in longitudinal gene expression data.
Lexico do discurso religioso: um estudo comparado

Este trabalho se insere nos estudos de Lexicologia e tem como fonte teorica a Semantica Estrutural, com enfase na Teoria do Campo Lexical, de Trier (GEERAERTS, 2010) a Lexicologia Social, de Matore (1973) e, como fonte metodologica, a Linguistica de Corpus, de Sardinha (2004) Nos estudos do lexico, a realidade social tem se mostrado uma importante aliada. Lexico e realidade caminham juntos, sendo um o reflexo do outro. Dentre os aspectos sociais que atuam sobre o lexico esta a religiosidade. Os falantes religiosos possuem um lexico especifico, e a manutencao desse lexico esta diretamente relacionada a manutencao da crenca. O objetivo deste trabalho, portanto, foi analisar o lexico do discurso religioso de falantes de tres religioes diferentes e compara lo, a fim de verificar se as diferencas sociais, expressas nas diferencas doutrinarias, sao refletidas no lexico. Para tanto, foi feito um levantamento tanto da parte social quanto do discurso religioso de cada igreja. Para a parte social, pesquisaram se a historia das igrejas, sua organizacao eclesiologica e sua base doutrinaria. Para a parte de dados, foram coletados sermoes das igrejas, seguindo os pressupostos da Linguistica de Corpus, ate se atingir um total de 250 mil palavras para cada uma, formando um corpus de 750 mil palavras. Com a ajuda do programa AntConc, foi criada uma lista das 150 lexias mais frequentes de cada igreja, da qual se extrairam os lemas mais frequentes. Foram produzidas, a partir dos lemas e o suporte do programa CMapTools, redes semanticas e campos lexicos como uma proposta de descricao da organizacao mental do lexico do discurso religioso. Esses dados foram analisados com base nas doutrinas e comparados, a fim de se averiguar o que as igrejas tem em comum e o que e exclusivo. Feito isso, estabeleceu se uma comparacao com outras descricoes de lexico religioso dos secs. XIII, XV, XVI e XX. Como resultados da analise, comprovou se a hipotese inicial de que falantes de igrejas diferentes falam de forma diferente, pois verificou se que o lexico dos falantes religiosos reproduz as doutrinas das igrejas. Assim, os falantes falaram de forma diferente naquilo que foi doutrinariamente diferente e de forma igual naquilo que foi doutrinariamente igual.
Responses of bacterial community and functional marker genes of nitrogen cycling to biochar, compost and combined amendments in soil
Venue: Applied Microbiology and Biotechnology

Biochar and compost are seen as two attractive waste management options and are used for soil amendment and pollution remediation. The interaction between biochar and composting may improve the potential benefits of biochar and compost. We investigated soil physicochemical properties, bacterial community, bacterial 16S rRNA, and functional marker genes of nitrogen cycling of the soil remedied with nothing (S) compost (SC) biochar (SB) a mixture of compost and biochar (SBC) composted biochar (SBced) and a composted mixture of biochar and biomass (SBCing) The results were that all amendments (1) increased the bacterial community richness (except SB) and SBCing showed the greatest efficiency; (2) increased the bacterial community diversity (SBCing SBC SC SBced SB S) and (3) changed the gene copy numbers of 16S rRNA, nirK, nirS, and nosZ genes of bacteria, ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) All amendments (except SB) could increase the gene copy number of 16S rRNA, and SBCing had the greatest efficiency. The changes of soil bacterial community richness and diversity and the gene copy numbers of 16S rRNA, nirK, nirS, nosZ, AOA, and AOB would affect carbon and nitrogen cycling of the ecosystem and also implied that BCing had the greatest efficiency on soil amendment.
Global biogeography of microbial nitrogen cycling traits in soil
Venue: Proceedings of the National Academy of Sciences

Microorganisms drive much of the Earth's nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N cycling specialists or generalists. For instance, taxa within the Deltaproteobacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils.
Patterns and Controls on Nitrogen Cycling of Biological Soil Crusts

In low nutrient environments with few vascular plant symbiotic N fixers, biocrusts play an important role in ecosystem N cycling. A large number of studies across a wide range of biomes clearly confirm that not only the presence of biocrusts but biocrust community composition strongly influences N fixation activity, with N fixation increasing with level of development (cyanobacterial lichen biocrusts dark cyanobacterial biocrust (e.g. Nostoc spp. and Collema spp. light Microcoleus dominated biocrust) Nitrogen fixation by biocrusts results in N release to the soil in a variety of N forms (inorganic and organic N) thus elevating soil inorganic N pools in the top few millimeters of soil. The influence of N release on the bulk soil at greater soil depths is less clear, with biocrusts either elevating or having no influence on bulk soil inorganic N pools. The fate of N fixed and released by biocrusts, and whether this N is retained in the ecosystem in either soils or plants, determines ecosystem N balance over longer time scales, and results on the influence of biocrusts are mixed. Whereas we have multiple studies that examine a single compartment of N budgets, we lack studies that simultaneously address N inputs, losses, and soil and plant pools, thus precluding the construction of definitive N balances. One of the most consistent impact biocrusts have on ecosystem N is reducing N loss via wind and water erosion, with such losses consistently decreasing with increasing biocrust development.
Moderation role of attitude on the relationship between participation in competitive sports and academic performance of student athletes in Saudi Arabia

This study aims to investigate how the attitude of undergraduate student athletes moderates the relationship between competitive sports participation (CSP) and academic performance (AP) In this study, a type of attitudes was taken into consideration namely academic performance attitude (APT)  A total of 102 undergraduate student athletes from 3 academic institutions in the Eastern Region of Kingdom of Saudi Arabia (KSA) were selected as subjects. Instruments used were Survey of Study Habits Attitudes (SSHA) by Brown and Holtzman, to obtain the data on APT. The instrument was back translated to the Arabic language in order to improve its comprehensiveness. Data on sports participation and academic performance were obtained by directly enquire the participants about their grade point average (GPA) and the frequency of their CSP in a self developed questionnaire.  The results showed that APT significantly alters the effect of CSP on AP, because the b value of the effect of CSP on AP was greater than the b value of the effect of CSP and APT on AP. Because b value shows the strength of the influence, it can be concluded that the actual strength of the CSP is not as strong as when it is combined with APT. In other words, APT moderates the influence of CSP on AP.  The moderation effect occurs due to the regulation of Saudi Universities Sports Federation (SUSF) that only student athletes with required academic scores can participate in competitive sports. Without such a regulation, APT might not be correlated to the AP because some students might pay more focus on CSP and less on AP. It can be concluded that the regulation helped student athletes in KSA to improve their AP without sacrificing their CSP and vice versa.
Indian husbands' support of their wives' upward mobility in corporate South Africa: Wives' perspectives

Spousal support is a crucial area to explore, particularly due to the increased prevalence of dual career couples in South Africa and the dynamics facing them.  The main objective of this study was to explore Indian wives' perceptions regarding the support they receive from their husbands and the impact that such support has on their career progression.  The limited qualitative research available globally on the subject and the dearth of research that focuses on Indian professional females in the South African context motivated the study. Research design, approach and method: A qualitative research approach was followed, and the data were collected through in depth, life story interviews. Purposeful and snowball sampling methods yielded a sample of nine Indian female managers who were in dual career marriages.  Spouses are essential sources of support for Indian professional women. The findings revealed that there are various marital and socio cultural dynamics that impact on the spousal support received by these women, which ultimately influences their career advancement.  The findings provided valuable information regarding the marital challenges that Indian women face in their career progression. The awareness of such dynamics can assist management in devising strategies to accommodate and retain the unique talent that Indian women have to offer.  The study contributes to the evolving body of knowledge on dual career couples by focusing on an under researched, but essential aspect of the dual career arrangement.
One sided Dynamic Undersampling No Propagation Neural Networks for imbalance problem
Venue: Eng. Appl. Artif. Intell.

Imbalanced problem occurs when the size of one class, i.e. the minority class, is much lower than that of the other classes, i.e. the majority classes. Conventional data level methods are employed as the preprocessing approaches to balance the datasets before the classifier learning. Since the balanced data remains unchanged during the learning process, one pre deleted sample would never be used to train the classifier, which may result in information loss. To solve this problem, this work presents an One sided Dynamic Undersampling (ODU) technique which adopts all samples in the training process, and dynamically determines whether a majority sample should be used for the classifier learning. Thus, ODU can dynamically undersample the majority class to balance the dataset. To validate the effectiveness of ODU, we integrate it into No Propagation neural networks to propose an ODU No Propagation Neural Networks (ODUNPNN) ODUNPNN takes all training samples into consideration, and dynamically undersamples majority class after each iteration, i.e. ODUNPNN integrates undersampling approach into the classifier learning process. Experimental results on both synthetic and real world imbalance datasets demonstrate that ODUNPNN outperforms the NPNN based algorithms, and results in comparative performance compared with LASVM AL, EasyEnsemble, and DyS on real world imbalance datasets. The contributions of this paper are: (1) ODUNPNN integrates undersampling approach into the classifier learning process. (2) ODUNPNN dynamically balances training data in each iteration. (3) ODU technique can be integrated into other classification learning machines.
A Swarm Intelligence Approach in Undersampling Majority Class
Venue: ANTS Conference

Over the years, machine learning has been facing the issue of imbalance dataset. It occurs when the number of instances in one class significantly outnumbers the instances in the other class. This study investigates a new approach for balancing the dataset using a swarm intelligence technique, Stochastic Diffusion Search (SDS) to undersample the majority class on a direct marketing dataset. The outcome of the novel application of this swarm intelligence algorithm demonstrates promising results which encourage the possibility of undersampling a majority class by removing redundant data whist protecting the useful data in the dataset. This paper details the behaviour of the proposed algorithm in dealing with this problem and investigates the results which are contrasted against other techniques.
Path ensembles and a tradeoff between communication efficiency and resilience in the human connectome
Venue: Brain Structure and Function

Computational analysis of communication efficiency of brain networks often relies on graph theoretic measures based on the shortest paths between network nodes. Here, we explore a communication scheme that relaxes the assumption that information travels exclusively through optimally short paths. The scheme assumes that communication between a pair of brain regions may take place through a path ensemble comprising the k shortest paths between those regions. To explore this approach, we map path ensembles in a set of anatomical brain networks derived from diffusion imaging and tractography. We show that while considering optimally short paths excludes a significant fraction of network connections from participating in communication, considering k shortest path ensembles allows all connections in the network to contribute. Path ensembles enable us to assess the resilience of communication pathways between brain regions, by measuring the number of alternative, disjoint paths within the ensemble, and to compare generalized measures of path length and betweenness centrality to those that result when considering only the single shortest path between node pairs. Furthermore, we find a significant correlation, indicative of a trade off, between communication efficiency and resilience of communication pathways in structural brain networks. Finally, we use k shortest path ensembles to demonstrate hemispherical lateralization of efficiency and resilience.
Effects of Communication Efficiency and Exit Capacity on Fundamental Diagrams for Pedestrian Motion in an Obscure Tunnel A Particle System Approach
Venue: Multiscale Model. Simul.

Fundamental diagrams describing the relation between pedestrians' speed and density are key points in understanding pedestrian dynamics. Experimental data evidence the onset of complex behaviors in which the velocity decreases with the density, and different logistic regimes are identified. This paper addresses the issue of pedestrian transport and of fundamental diagrams for a scenario involving the motion of pedestrians escaping from an obscure tunnel. We capture the effects of communication efficiency and exit capacity by means of two thresholds controlling the rate at which particles (walkers, pedestrians) move on the lattice. Using a particle system model, we show that in the absence of limitation in communication among pedestrians, we reproduce with good accuracy the standard fundamental diagrams, whose basic behaviors can be interpreted in terms of exit capacity limitation. When the effect of limited communication ability is considered, then interesting nonintuitive phenomena occur. In particular, we shed light on the loss of monotonicity of the typical speed density curves, revealing the existence of a pedestrian density optimizing the escape. We study both the discrete particle dynamics and the corresponding hydrodynamic limit (a porous medium equation and a transport (continuity) equation) We also point out the dependence of the effective transport coefficients on the two thresholds the essence of the microstructure information.
Estimation of Age by Pulp Tooth Area Ratio Using Three Computer Aided Software's

Estimation of age in an individual whether living or dead has received a considerable attention in forensic science. Recently, the dental maturation system has gained impetus as a valuable index for age estimation, as teeth are more resistant to most peri and post mortem changes. Radiological age estimation using teeth rely on developmental stages of teeth especially in children while in adults; the continuous deposition of secondary dentin throughout life is depicted by reduction in pulp area. Through this paper we bring across a radiological study to estimate the age of an individual via 3 computer aided software's on maxillary central incisor. 30 periapical radiographs of individual aged 12 to 30 years were taken using radiovisiography (RVG) Radiographic images were processed using the software; data was statistically analyzed to compare the age. There was no statistical significant difference in age calculated by Adobe Photoshop and Auto CAD, Adobe Photoshop p=0.432 and Auto CAD p=0.004; though there was significant statistical difference in age calculated by Image J, p<0.001. It was concluded that pulp/tooth area ratios of maxillary central incisor are reliable for estimation of age and AutoCAD gave the most accurate results.
Patient activation and guideline concordant pharmacological treatment after bone density testing: the PAADRN randomized controlled trial
Venue: Osteoporosis International

SummaryPatients often do not know or understand their bone density test results, and pharmacological treatment rates are low. In a clinical trial of 7749 patients, we used a tailored patient activation result letter accompanied by a bone health brochure to improve appropriate pharmacological treatment. Treatment rates, however, did not improve.IntroductionPatients often do not know or understand their dual energy x ray absorptiometry (DXA) test results, which may lead to suboptimal care. We tested whether usual care augmented by a tailored patient activation DXA result letter accompanied by an educational brochure would improve guideline concordant pharmacological treatment compared to usual care only.MethodsWe conducted a randomized, controlled, double blinded, pragmatic clinical trial at three health care centers in the USA. We randomized 7749 patients =50 years old and presenting for DXA between February 2012 and August 2014. The primary clinical endpoint at 12 and 52 weeks post DXA was receiving guideline concordant pharmacological treatment. We also examined four of the steps along the pathway from DXA testing to that clinical endpoint, including (1) receiving and (2) understanding their DXA results and (3) having subsequent contact with their provider and (4) discussing their results and options.ResultsMean age was 66.6 years, 83.8 were women, and 75.3 were non Hispanic whites. Intention to treat analyses revealed that guideline concordant pharmacological treatment was not improved at either 12 weeks (65.1 vs. 64.3 p 0.506) or 52 weeks (65.2 vs. 63.8 p 0.250) post DXA, even though patients in the intervention group were more likely (all p 0.001) to recall receiving their DXA results letter at 12 weeks, correctly identify their results at 12 and 52 weeks, have contact with their provider at 52 weeks, and have discussed their results with their provider at 12 and 52 weeks. tailored DXA result letter and educational brochure failed to improve guideline concordant care in patients who received DXA.
Paper Tigers, Hidden Dragons: Firms and the Political Economy of China's Technological Development

China presents us with a conundrum. How has a developing country with a spectacularly inefficient financial system, coupled with asset destroying state owned firms, managed to create a number of vibrant high tech firms? China's domestic financial system fails most private firms by neglecting to give them sufficient support to pursue technological upgrading, even while smothering state favoured firms by providing them with too much support. Due to their foreign financing, multinational corporations suffer from neither insufficient funds nor soft budget constraints, but they are insufficiently committed to China's development. Hybrid firms that combine ethnic Chinese management and foreign financing are the hidden dragons driving China's technological development. They avoid the maladies of China's domestic financial system while remaining committed to enhancing China's domestic technological capabilities. In sad contrast, China's domestic firms are technological paper tigers. State efforts to build local innovation clusters and create national champions have not managed to transform these firms into drivers of technological development. These findings upend fundamental debates about China's political economy. Rather than a choice between state capitalism and building domestic market institutions, China has fostered state capitalism even while tolerating the importing of foreign market institutions. While the book's findings suggest that China's state and domestic market institutions are ineffective, the hybrids promise an alternative way to avoid the middle income trap. By documenting how variation in China's institutional terrain impacts technological development, the book also provides much needed nuance to widespread yet mutually irreconcilable claims that China is either an emerging innovation power or a technological backwater. Looking beyond China, hybrid led development has implications for new alternative economic development models and new ways to conceptualize contemporary capitalism that go beyond current domestic institution centric approaches.