nils-herrmann/clean_scirepeval huggingface dataset:
Null diffusion based enrichment for metabolomics data
Venue: PloS one
Year: 2017

Metabolomics experiments identify metabolites whose abundance varies as the conditions under study change. Pathway enrichment tools help in the identification of key metabolic processes and in building a plausible biological explanation for these variations. Although several methods are available for pathway enrichment using experimental evidence, metabolomics does not yet have a comprehensive overview in a network layout at multiple molecular levels. We propose a novel pathway enrichment procedure for analysing summary metabolomics data based on sub network analysis in a graph representation of a reference database. Relevant entries are extracted from the database according to statistical measures over a null diffusive process that accounts for network topology and pathway crosstalk. Entries are reported as a sub pathway network, including not only pathways, but also modules, enzymes, reactions and possibly other compound candidates for further analyses. This provides a richer biological context, suitable for generating new study hypotheses and potential enzymatic targets. Using this method, we report results from cells depleted for an uncharacterised mitochondrial gene using GC and LC MS data and employing KEGG as a knowledge base. Partial validation is provided with NMR based tracking of 13C glucose labelling of these cells.
Assessment of Plant Growth Promoting and Abiotic Stress Tolerance Properties of Wheat Endophytic Fungi
Venue: BioMed research international
Year: 2019

The aims of the present work were to isolate and characterize fungal endophytic communities associated with healthy wheat (Triticum aestivum L. plants, collected from the North China. Segregated endophytes were screened for their PGP traits, abiotic stresses (heavy metals, salinity, drought, and temperature) and antibiotic sensitivity. A total of 16 endophytic fungi were isolated using the culture dependent approach from different tissue parts of wheat plants. Based upon their internal transcribed spacer (ITS) rDNA gene sequencing, 15 out of 16 isolates were selected for further analysis. In the contemporary investigation, a number of the tested endophytes exhibited fairly good 1 aminocyclopropane 1 carboxylic acid deaminase (ACCD) (0.03+ 0.011 to 1.43+ 0.01 umol a KB mg 1 protein hr 1) indole acetic acid (IAA) (1.125+ 0.04 to36.12+ 0.004ugml 1) and phosphate solubilizing index (PSI) (2.08+ 0.03to5.16+ 0.36) activities. More than 30% isolates gave positive result for siderophore and ammonia tests, whereas all exhibited catalase activity but only 2 (582PDA1 and 582PDA11) produced hydrogen cyanide. Trichoderma strains showed salt, heavy metals, and drought tolerance at high levels and also exhibited resistance to all the tested antibiotics. Strain 582PDA4 was found to be the most temperature (55degC) tolerant isolate. The findings of this study indicated that the microbial endophytes isolated from wheat plants possessing a crucial function to improve plant growth could be utilized as biofertilizers or bioagents to establish a sustainable crop production system.
Author s personal copy PERFORMING HERITAGE RETHINKING AUTHENTICITY IN TOURISM
Year: 2012

This paper explores how the dongba as the ritual practitioner perceives his authenticity during the marriage ceremony in the Naxi Wedding Courtyard in Lijiang, China. Through the dongba's life story, the paper indicates that, the power of his making judgment is not entirely related to the toured objects, socially constructed reality or the existential feeling, but also has to do with what happens in between. The ritual performance, integrated with the external world, gives rise to the performative experience of the authenticity and offers a deep understanding of the link between memory, habitus and embodied practice. The dynamic process of 'becoming' authentic weaves the interaction between the individual agency and the reality.
Vanadium compounds induced damage of human umbilical vein endothelial cells and the protective effect of berberine
Venue: BioMetals
Year: 2019

This study was conducted to investigate the damage caused by vanadium compounds and to explore the protective effects of berberine (BBR) in human umbilical vein endothelial cells (HUVECs) BBR is a biologically active small molecule found in Coptis rhizome, a remedy used in traditional Chinese medicine to treat diabetes. BBR has also been shown to lower blood glucose in diabetic patients. MTT assay was performed to observe the influence of bis(acetylacetonato) oxidovanadium [VO(acac)2] or sodium metavanadate (NaVO3) and BBR on viability of HUVECs. The monolayer permeability of the HUVECs was assessed by measuring the transendothelial electrical resistance (TER) The endothelial nitric oxide synthase (eNOS) activity was detected by ELISA. Flow cytometry was performed to detect the generation of reactive oxygen species (ROS) The results showed that the viability of HUVECs was decreased by treatment with vanadium compounds 50 400 mM in a concentration dependent manner, while 0.01 1 mM BBR effectively protected HUVECs from the inhibitory effects of vanadium compounds on cell viability. Also 100 and 200 mM VO(acac)2 induced high permeability and decreased eNOS activity in HUVECs. While 0.01 1 mM BBR showed no improvement in the permeability, and failed to reverse the VO(acac)2 induced changes of eNOS activity, but BBR treatment increased the eNOS activity in control cells. The addition of 200 mM VO(acac)2 significantly induced ROS generation in HUVECs, while 0.01 or 0.1 mM BBR reversed the change of ROS. In summary, BBR has protective effects in HUVECs damage induced by vanadium compounds, which is not mediated by eNOS, but related to reduced intracellular ROS.
The Impact of Workplace Mentors on the Moral Disengagement of Business Student Proteges
Year: 2019

Educators and practitioners often raise the question of whether business schools sufficiently prepare students to stay morally engaged when faced with ethical dilemmas in the workforce. Specifically, they criticize the theoretical nature of traditional in class exercises for inhibiting students' moral development. We investigate the impact working business mentors have on business student moral disengagement. We collected three waves of data from an 8 month formal mentoring program that matched business students with working mentors from the business community. We found that student protege moral disengagement decreased during the mentoring program as a function of mentor ethical leadership skills, moral identity internalization, and moral awareness. Consequently, we recommend that mentoring programs pay close attention to these mentor characteristics to elevate business student moral reasoning and avoid unintended negative consequences. To guide mentoring programs in this endeavor, we provide specific recommendations for structuring a training program that focuses on improving mentor critical thinking, moral awareness, and ethical leadership.
Pengaruh Doping Palladium (Pd) Terhadap Lapisan TiO2 dengan Metoda LPD untuk Applikasi Fotoanoda Sel Surya DSSC
Year: 2020

Lapisan TiO 2 yang didoping Pd dengan metode deposisi fase cair (Liquid Phase Deposition, LPD) telah dilakukan. Adapun tujuan sintesis lapisan tersebut adalah untuk mendapatkan lapisan yang terdiri dari nanoplate yang akan diaplikasikan untuk fotoanoda sel surya. Sebagai larutan prekursor digunakan 0,5 M (NH 4 2 TiF 6 dengan variasi doping Pd adalah 0; 6.25; 12.50; 25,00 dan 50,00 mM. Penumbuhan lapisan dilakukan pada suhu 900degC selama 9 jam. Didapatkan berturut turut energi gap adalah 3,20, 3,25, 3,18, 3,16, dan 3,10 eV. Karakterisasi FESEM menunjukkan bahwa lapisan yang dihasilkan terdiri dari partikel berbentuk nanoplate yang tersebar merata di permukaan substrat ITO. Luas nanoplate yang dihasilkan di bawah 100 mm 2 dengan ketebalan beberapa nanameter. Karakterisasi I V menunjukkan bahwa lapisan TiO 2 yang didoping oleh Pd sangat berpotensi sebagai photoanode untuk elektroda sel surya DSSC (Dye Sensitized Solar Cell) Kata kunci:TiO 2 Pd, DSSC, LPD, fotoanoda
Quantifying the Prosecutorial Preauthorization Intake System and the Costs of 'No Action' Cases
Year: 2020

In most jurisdictions, a police officer arrests and books a defendant, then files the criminal complaint before a judge. The judge sets bail, and if necessary, appoints defense counsel for the accused. Inadequate cases are later dropped often weeks or months later by prosecutors. This happens only after extensive investigation and usually not before the accused spent several nights in detention. In 1973, Harris County, Texas developed a solution to this inefficiency: prosecutors receive a phone call from the police officer at the moment of arrest. The officer explains the circumstances of the arrest, and the prosecutor evaluates whether it meets the required elements of the crime. If satisfied, the prosecutor grants authorization, and only then does the police officer file. We quantify the efficacy of this unique pre authorization intake system, comparing arrests filed in Harris County, TX, Miami Dade County, FL, and dozens of counties in New Mexico. We find that a pre authorization intake system would save a municipality like Miami, FL, many millions of dollars annually.
Deprivation matters: understanding associations between neighbourhood deprivation, unhealthy food outlets, unhealthy dietary behaviours and child body size using structural equation modelling
Venue: Journal of Epidemiology Community Health
Year: 2020

Children residing in neighbourhoods of high deprivation are more likely to have poorer health, including excess body size. While the availability of unhealthy food outlets are increasingly considered important for excess child body size, less is known about how neighbourhood deprivation, unhealthy food outlets and unhealthy dietary behaviours are interlinked.  This study involves children aged 8 13 years (n=1029) and resided in Auckland, New Zealand. Unhealthy dietary behaviours (frequency of consumption of unhealthy snacks and drinks) and food purchasing behaviour on the route to and from school were self reported. Height and waist circumference were measured to calculate waist to height ratio (WtHR) Geographic Information Systems mapped neighbourhood deprivation and unhealthy food outlets within individual, child specific neighbourhood buffer boundaries (800 m around the home and school) Associations between neighbourhood deprivation (calculated using the New Zealand Index of Deprivation 2013) unhealthy food outlets, unhealthy dietary behaviours and WtHR were investigated using structural equation modelling in Mplus V.8.0. Age, sex and ethnicity were included as covariates, and clustering was accounted for at the school level.  Structural equation models showed that unhealthy food outlets were unrelated to unhealthy dietary behaviours (estimate 0.029, p=0.416) and excess body size (estimate 0.038, p=0.400) However, greater neighbourhood deprivation and poorer dietary behaviours (estimate 0.134, p=0.001) were associated with greater WtHR (estimate 0.169, p<0.001)  Excess child body size is associated with neighbourhood deprivation and unhealthy dietary behaviours but not unhealthy outlet density or location of these outlets near home and school.
Genome Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds
Venue: Genes
Year: 2019

Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs) homozygosity by descent (HBD) and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair wise genetic differentiation (FST) among the populations is 9.60% and the inter and intra population molecular variations are 9.68% and 89.6% respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross population extended haplotype homozygosity (XP EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.
Mengoptimalkan Penggunaan Model Inquiri Learning Upaya Meningkatkan Aktivitas Dan Hasil Belajar Pendidikan Agama Hindu Peserta Didik Kelas IV Semester Satu Tahun Pelajaran 2019/2020 Di SD Negeri 34 Cakranegara
Year: 2020

Penelitian ini bertujuan untuk mengetahui efektifitas penerapan pendekatan Saintifik model Pembelajaran Inquiri dalam upaya meningkatkan Aktivitas dan hasil belajar Pendidikan Agama Hindu Peserta didik Kelas IV SD Negeri 34 Cakranegara. Manfaat penelitian ini adalah mendorong peserta didik untuk mengembangkan ketrampilan belajar dalam kelompok (kognitif) dan bersosiolisasi dengan teman dalam proses pembelajaran di kelas senyatanya. Dan bagi guru meningkatkan pengembangan pendekatan dan model pembelajaran dengan penerapan saintifik Model Pembelajaran Inquiri dalam pembelajaran kerja kelompok (kooperatif) Penelitian ini dilaksanakan dua siklus, masing masing siklus kegiatannya adalah; perencanaan, pelaksanaan, observasi dan refleksi. Hasil akhir tindakan pada siklus II menunjukkan bahwa hasil observasi guru pada pertemuan kedua memperoleh skor rata rata (4,43) dan hasil observasi Peserta didik pertemuan kedua mencapai skor rata rata (4,63) Sedangkan hasil belajar Peserta didik mencapai nilai rata rata (80,89) artinya indikator keberhasilan 4,0) dan hasil belajar 75,00) telah terlampaui. Karena indikator keberhasilan telah terbukti penelitian dinyatakan berhasil dan dihentikan pada siklus II.
Which Social Psychological Models Explain Rangers' Participation in Rangeland Management Cooperatives? An Application of Path Analysis
Venue: Rangeland Ecology Management
Year: 2018

The highly centralized management of rangelands in northwest Iran has caused their degradation. Rangeland Management Cooperatives (RMCs) have been taken into account by the Iranian researchers and practitioners as the best mode of managing and tackling these resources. In this regard, stakeholders' participation (i.e. the rangers) in such institutions is a substantial issue because without their close collaboration, any management scheme is likely to fail or succeed partially. Therefore, this study investigates the rangers' participation in RMCs using the theory triangulation method. We developed the main research question: how the explanatory variables, extracted from the social psychological models, influence rangers' participation in RMCs. A sample of 200 rangers participated in the survey method, of which we received 179 completed self reported questionnaires. The reliability of the questionnaire was calculated using the Confirmatory Factor Analysis and Kuder Richardson 21, the metrics that measure the consistency of items in indicator variables with the interval and binary scales, respectively. The results of path analysis unveil that job satisfaction and progressivism have a direct effect on participation, and the improved economic conditions of industries developed by the RMCs, good intrarelation, fatalism, progressivism, optimism, and cost benefit indirectly influence participation via job satisfaction. On the basis of these results, it is concluded that to increase rangers' participation in RMCs, which is a key factor in preventing the degradation of rangelands, RMCs' officials need to improve the local industries benefiting from the rangelands and upgrade intracommunication skills via training. It is also suggested that all rangers, even those with fatalistic beliefs, need to be included in RMCs' participatory activities. Finally, it is needed to assess progressivist rangers' needs, promote optimism, and visualize the economic, social, and conservation benefits of the participation in RMCs.
Electrodeposition of organic inorganic tri halide perovskites solar cell
Year: 2018

Perovskite (CH3NH3PbI3) semiconductor materials are promising high performance light energy absorber for solar cell application. However, the power conversion efficiency of perovskite solar cell is severely affected by the surface quality of the deposited thin film. Spin coating is a low cost and widely used deposition technique for perovskite solar cell. Notably, film deposited by spin coating evolves surface hydroxide and defeats from uncontrolled precipitation and inter diffusion reaction. Alternatively, vapor deposition (VD) method produces uniform thin film but requires precise control of complex thermodynamic parameters which makes the technique unsuitable for large scale production. Most deposition techniques for perovskite require tedious surface optimization to improve the surface quality of deposits. Optimization of perovskite surface is necessary to significantly improve device structure and electrical output. In this review, electrodeposition of perovskite solar cell is demonstrated as a scalable and reproducible technique to fabricate uniform and smooth thin film surface that circumvents the need for high vacuum environment. Electrodeposition is achieved at low temperatures, supports precise control and optimization of deposits for efficient charge transfer.
Impact of phosphate solubilizing fungi on the soil nutrient status and yield mungbean (Vigna radiate L) crop
Year: 2014

To enhance the availability of P and other macro and micro nutrients from the fertile calciorthent soil, phosphorus solublizing fungi (PSF) were isolated from the rhizoshere of the agricultural/ horticultural crops. The P solublizing potential of PSF was tested under in vitro and in viv o conditions. Penicillium citrinum isolate6 exhibited the maximum and constant P solublization potential throughout the incubation period in the presence of TCP (Tri calcium phosphate) in Pikovskaya's medium. On the basis laboratory experiment, three fungi Aspergillus niger isolate 2, Aspergillus niger isolate 3 and Penicilliun citrinum isolate 6) were selected for pot experiments, to test their efficacy on nutrient availability as well as on growth promotion of mungbean crop. Stimulatory effect of Aspergillus niger isolate 3, Aspergillus niger isolate 2 Aspergillus niger isolate 3 and Aspergillus niger isolate 2+ Penicillium citrinum isolate 6 was recorded on N, P and K availability in soil, respectively. Combination of Aspergillus niger isolates with PSB significantly enhanced the Mn availability. While Aspergillus nige r isolate 2 inoculation exhibited pronounced effect on Zn and Cu availability. Most of the biometric parameters were increased with the inoculation of fungal combination. The result indicates that the effective strains of Aspergillus and Penicillium can be used for nutrient availability and crop production in calcium rich soil.
Transthyretin Stabilization by AG10 in Symptomatic Transthyretin Amyloid Cardiomyopathy.
Venue: Journal of the American College of Cardiology
Year: 2019

Transthyretin (TTR) amyloidosis (ATTR) is an under diagnosed disease caused by destabilization of TTR due to pathogenic mutations or aging. Both pathogenic and protective mutations illuminate mechanisms of disease and potential interventions. AG10 is a selective, oral TTR stabilizer under development for ATTR cardiomyopathy (ATTR CM) that mimics a protective TTR mutation.  This randomized, double blind, placebo controlled study evaluated safety, tolerability, pharmacokinetics and pharmacodynamics of AG10 in ATTR CM patients with symptomatic, chronic heart failure.  Class II III subjects (n 49, mutant or wild type) were randomized 1:1:1 to AG10 400mg, 800mg or placebo bid for 28 days. Safety and tolerability were assessed by clinical and laboratory criteria. AG10 plasma levels were measured. TTR stability was assessed by changes in serum TTR and two established ex vivo assays (Fluorescent Probe Exclusion [FPE] and Western blot) RESULTS AG10 treatment was well tolerated, achieved target plasma concentrations and demonstrated near complete stabilization of TTR. TTR stabilization was more complete and less variable at the higher dose with stabilization by FPE of 92 10% (mean+ SD) at trough and 96 9% at peak (both p<10 12 vs placebo) Average serum TTR increased by 36 21% and 51 38% at 400 mg and 800 mg respectively (both p<0.0001 vs placebo) Baseline serum TTR in treated subjects was below normal in 80% of mutant and 33% of wild type subjects. AG10 treatment restored serum TTR to the normal range in all subjects.  AG10 has the potential to be a safe and effective treatment for patients with ATTR CM. A Phase 3 trial is planned.
An empirical study of just in time defect prediction using cross project models
Venue: MSR 2014
Year: 2014

Prior research suggests that predicting defect inducing changes, i.e. Just In Time (JIT) defect prediction is a more practical alternative to traditional defect prediction techniques, providing immediate feedback while design decisions are still fresh in the minds of developers. Unfortunately, similar to traditional defect prediction models, JIT models require a large amount of training data, which is not available when projects are in initial development phases. To address this flaw in traditional defect prediction, prior work has proposed cross project models, i.e. models learned from older projects with sufficient history. However, cross project models have not yet been explored in the context of JIT prediction. Therefore, in this study, we empirically evaluate the performance of JIT cross project models. Through a case study on 11 open source projects, we find that in a JIT cross project context: (1) high performance within project models rarely perform well; (2) models trained on projects that have similar correlations between predictor and dependent variables often perform well; and (3) ensemble learning techniques that leverage historical data from several other projects (e.g. voting experts) often perform well. Our findings empirically confirm that JIT cross project models learned using other projects are a viable solution for projects with little historical data. However, JIT cross project models perform best when the data used to learn them is carefully selected.