nils-herrmann/clean_scirepeval huggingface dataset:
A Novel Method to Detect Functional microRNA Regulatory Modules by Bicliques Merging
Venue: IEEE/ACM Transactions on Computational Biology and Bioinformatics

MicroRNAs (miRNAs) are post transcriptional regulators that repress the expression of their targets. They are known to work cooperatively with genes and play important roles in numerous cellular processes. Identification of miRNA regulatory modules (MRMs) would aid deciphering the combinatorial effects derived from the many to many regulatory relationships in complex cellular systems. Here, we develop an effective method called BiCliques Merging (BCM) to predict MRMs based on bicliques merging. By integrating the miRNA/mRNA expression profiles from The Cancer Genome Atlas (TCGA) with the computational target predictions, we construct a weighted miRNA regulatory network for module discovery. The maximal bicliques detected in the network are statistically evaluated and filtered accordingly. We then employed a greedy based strategy to iteratively merge the remaining bicliques according to their overlaps together with edge weights and the gene gene interactions. Comparing with existing methods on two cancer datasets from TCGA, we showed that the modules identified by our method are more densely connected and functionally enriched. Moreover, our predicted modules are more enriched for miRNA families and the miRNA mRNA pairs within the modules are more negatively correlated. Finally, several potential prognostic modules are revealed by Kaplan Meier survival analysis and breast cancer subtype analysis.
Close correlation of copy number aberrations detected by next generation sequencing with results from routine cytogenetics in acute myeloid leukemia
Venue: Genes, chromosomes cancer

High throughput sequencing approaches, including the analysis of exomes or gene panels, are widely used and established to detect tumor specific sequence variants such as point mutations or small insertions/deletions. Beyond single nucleotide resolution, sequencing data also contain information on changes in sequence coverage between samples and thus allow the detection of somatic copy number alterations (CNAs) representing gain or loss of genomic material in tumor cells arising from aneuploidy, amplifications, or deletions. To test the feasibility of CNA detection in sequencing data we analyzed the exomes of 25 paired leukemia/remission samples from acute myeloid leukemia (AML) patients with well defined chromosomal aberrations, detected by conventional chromosomal analysis and/or molecular cytogenetics assays. Thereby, we were able to confirm chromosomal aberrations including trisomies, monosomies, and partial chromosomal deletions in 20 out of 25 samples. Comparison of CNA detection using exome, custom gene panel, and SNP array analysis showed equivalent results in five patients with variable clone size. Gene panel analysis of AML samples without matched germline control samples resulted in confirmation of cytogenetic findings in 18 out of 22 cases. In all cases with discordant findings, small clone size <33% was limiting for CNA detection. We detected CNAs consistent with cytogenetics in 83% of AML samples including highly correlated clone size estimation (R 0.85) while six out of 65 cytogenetically normal AML samples exhibited CNAs apparently missed by routine cytogenetics. Overall, our results show that high throughput targeted sequencing data can be reliably used to detect copy number changes in the dominant AML clone.
In Ovo Sexing of Domestic Chicken Eggs by Raman Spectroscopy.
Venue: Analytical chemistry

Male birds of egg laying hen strains have no commercial value and are culled immediately after hatching, raising concerns for animal welfare. Existing experimental methods for in ovo sexing require taking samples and are applicable after embryos' sexual differentiation. We demonstrate that Raman spectroscopy enables contactless in ovo sex determination of the domestic chicken (Gallus gallus f. dom. already at day 3.5 of egg incubation. A sexing accuracy of 90% was obtained by analyzing the spectra of blood circulating in the extraembryonic vessels. The measurement is damage free and barely affects the hatching rate. Sex recognition is achieved before the onset of sensitivity. Therefore, Raman spectroscopy provides an alternative to the culling of 1 day old male chicks in laying hen production.
Modeling scour depth downstream of grade control structures using data driven and empirical approaches

Local scour occurs in the immediate vicinity of structures as a result of impinging a bed with a high velocity flow. Prediction of scour depth has an important role in control structures management and water resource engineering issues, so a study into new heuristic expressions governing it is necessary. The present study aims to investigate different methods capabilities to estimate scour depth downstream of grade control structures using field measurements from the literature. Accordingly, data driven based feed forward neural network and gene expression programming techniques were selected for the investigation. Additionally, the optimum data driven based scour depth models were compared with the corresponding physical empirical based formulas. Three data categories corresponding to (a) scouring downstream of a ski jump bucket, (b) sharp crested weir, and (c) inclined slope controlled structure (as grade control structures) were applied as reference patterns for developing and validating the applied models. A sensitivity analysis was also performed to identify the most influential parameters on scouring. The obtained results indicated that the applied methods have promising performance in estimating the scour depth downstream of spillways and control structures. Nevertheless, the applied data driven approaches show higher accuracy than the corresponding traditional formulas.
Functional community ecology meets restoration ecology: Assessing the restoration success of alluvial floodplain meadows with functional traits

Species rich grasslands are highly endangered habitats in Central Europe. To halt their ongoing loss, many sites have become subjects of restoration efforts. Traditionally, restoration success is measured using target species or by comparing similarity in species composition. Here, we suggest to additionally use functional community composition to assess restoration success as functional traits might offer mechanistic insights into restoration processes. In a 5 year restoration experiment, we annually evaluated the responses of (i) floristic composition and species diversity, (ii) number and cover of target species, (iii) functional identity and (iv) functional diversity to four different methods of assisted recolonization through species introduction: hay transfer and application of threshing material from a local provenance, combined with and without addition of regional seed mixtures of target species, as well as to a control treatment. Across all treatments, floristic composition, species diversity, and number and cover of target species approached the values of reference sites. In the last observation year, Shannon diversity was still lower in all treatment plots than in the reference plots, while the number of target forb species had reached or exceeded the reference levels. We demonstrated that the community was also restored functionally in many aspects, but not in all studied traits. Calculated community weighted means (CWMs) specific leaf area (SLA) and leaf dry matter content (LDMC) in experimental plots did not differ significantly from the reference plots, thereby indicating that productivity of restored sites had reached target values. In contrast, CWMs of strategy types and pollination modes revealed significant differences, showing that biotic interactions among plant species and with other trophic levels have not yet been fully restored. However, almost all CWMs showed a trajectory towards the reference, thus giving a positive prospect for the future development. With respect to functional diversity (FD) we found steadily increasing FD values for almost all traits analysed. Synthesis and applications. We demonstrated that all applied restoration measures were appropriate to achieve the restoration aim in terms of species composition of a given community and the establishment of target species. With respect to many functional traits, the restored meadows were already as functional as communities from the reference sites. Hence, including functional criteria did not only corroborate traditional criteria of restoration success but also allowed identifying those floodplain meadow's functions that can be quickly and less quickly restored.
Some Thoughts on Toilets, Transgenders, and the LGBT 'Community'

The North Carolina legislature passed a law that prohibits transgender individuals from using certain public toilets. The legislation has been controversial. Some entertainers have stated they will not hold concerts in North Carolina until the law is repealed. Some corporations have been critical of the law, and at least one corporation has decided not to open a facility in North Carolina because of the law. This article examines the issue of the use of public toilets by transgenders and applies logic and ethical theory to arrive at a resolution of the problem that does not involve the violation of anyone's rights.
A Pilot Study to Assess Emotional Distress and Quality of Life among Transgenders in South India

Transgenders face several social disadvantages in the Indian cultural context, and often live on the fringe of the society. Presence of adverse life circumstances predisposes them to have psychological morbidity. In the absence of previous systematic evidence, this pilot study aimed to assess emotional distress and quality of life among transgenders attending a clinic in south India.  This hospital based cross sectional study assessed transgenders attending a specialized multi speciality clinic. Participants were assessed for relevant demographic and clinical information. Anxiety and depression were assessed using Hospital Anxiety and Depression Scale (HADS) while General Health Questionnaire (GHQ) was used to assess for general emotional distress. WHOQOL Bref was used to assess quality of life.  The pilot study included 15 transgenders with a median age of 30 years. All the participants had experienced sexual abuse in childhood, and 11/15 (73.3% had a lifetime suicide attempt. The median HADS anxiety, HADS depression and GHQ scores were 9, 14 and 8 respectively. About 66.7% of the sample had significant anxiety symptoms while 100% had significant depressive symptoms as per HADS cut off. The quality of life scores were particularly low for the 'social' domain.  Transgenders experience considerable emotional distress and have poor social quality of life. Medical professionals need to be sensitive to the health care needs of transgenders to improve their psychological wellbeing.
A Comparative Evaluation of Unsupervised Anomaly Detection Algorithms for Multivariate Data
Venue: PloS one

Anomaly detection is the process of identifying unexpected items or events in datasets, which differ from the norm. In contrast to standard classification tasks, anomaly detection is often applied on unlabeled data, taking only the internal structure of the dataset into account. This challenge is known as unsupervised anomaly detection and is addressed in many practical applications, for example in network intrusion detection, fraud detection as well as in the life science and medical domain. Dozens of algorithms have been proposed in this area, but unfortunately the research community still lacks a comparative universal evaluation as well as common publicly available datasets. These shortcomings are addressed in this study, where 19 different unsupervised anomaly detection algorithms are evaluated on 10 different datasets from multiple application domains. By publishing the source code and the datasets, this paper aims to be a new well funded basis for unsupervised anomaly detection research. Additionally, this evaluation reveals the strengths and weaknesses of the different approaches for the first time. Besides the anomaly detection performance, computational effort, the impact of parameter settings as well as the global/local anomaly detection behavior is outlined. As a conclusion, we give an advise on algorithm selection for typical real world tasks.
Writing Integrative Literature Reviews

This article presents the integrative review of literature as a distinctive form of research that uses existing literature to create new knowledge. As an expansion and update of a previously published article on this topic, it reviews the growing body of literature on how to write literature reviews. The article identifies the main components of the integrative literature review, provides examples of visual representations for use in literature reviews, and describes how to write literature reviews that are integrative, definitive, and provocative. The article concludes by discussing the role of the integrative literature review in assessing future directions for policy and practice and in catalyzing further research.
Novel mutations in IBA57 are associated with leukodystrophy and variable clinical phenotypes
Venue: Journal of Neurology

Defects of the Fe/S cluster biosynthesis represent a subgroup of diseases affecting the mitochondrial energy metabolism. In the last years, mutations in four genes (NFU1, BOLA3, ISCA2 and IBA57) have been related to a new group of multiple mitochondrial dysfunction syndromes characterized by lactic acidosis, hyperglycinemia, multiple defects of the respiratory chain complexes, and impairment of four lipoic acid dependent enzymes: a ketoglutarate dehydrogenase complex, pyruvic dehydrogenase, branched chain a keto acid dehydrogenase complex and the H protein of the glycine cleavage system. Few patients have been reported with mutations in IBA57 and with variable clinical phenotype. Herein, we describe four unrelated patients carrying novel mutations in IBA57. All patients presented with combined or isolated defect of complex I and II. Clinical features varied widely, ranging from fatal infantile onset of the disease to acute and severe psychomotor regression after the first year of life. Brain MRI was characterized by cavitating leukodystrophy. The identified mutations were never reported previously and all had a dramatic effect on IBA57 stability. Our study contributes to expand the array of the genotypic variation of IBA57 and delineates the leukodystrophic pattern of IBA57 deficient patients.
Early History of the Fields of Practice of Training and Development and Organization Development

The Problem While the time and place of the birth of the Academy of Human Resource Development are documented, the field of human resource development (HRD) has historical roots that began decades earlier with the emergence of training and development and organization development as fields of practice.  This article addresses the early history of training and development and organization development, and begins with the influence of World War II on work related education and training and ends in the mid 1990s. It traces the origins of the field up to, but not including, the founding of the Academy of Human Resource Development in 1994. The historical development of training and development and organization development is shown to be a confluence of historical events and the intellectual contributions of seminal thinkers. The Stakeholders Stakeholders for this article are researchers, practitioners, and others interested in the history of training and development and organization development.
Writing Integrative Reviews of the Literature: Methods and Purposes
Venue: Int. J. Adult Vocat. Educ. Technol.

This article discusses the integrative review of the literature as a distinctive form of research that uses existing literature to create new knowledge. As an expansion and update of a previously published article on this topic, it acknowledges the growth and appeal of this form of research to scholars, it identifies the main components of the integrative literature review, and summarizes guidelines for organizing and writing integrative literature reviews. Not addressed elsewhere in the literature, this article describes five reasons and purposes for writing literature reviews and discusses these purposes in relation to the methods for writing literature reviews. The article concludes that aligning the integrative literature review's methods with its purpose provides unity and coherence to the review.
The Persistence of Working Poor Families in a Changing U.S. Job Market

This article explores the persistence of working poor families in the United States families that live on the threshold of poverty despite at least one family member working full time. The persistence of poverty in the United States has been exacerbated by recent changes in the job market that have altered the composition and availability of jobs due to technological unemployment, the polarization of jobs, declining job quality, and stagnation in job growth. The relationships between the persistence of working poor families and these changes in the job market are examined. The article concludes with a review of human resource development (HRD) research on poverty and the working poor, and a discussion of the implications of the persistence of working poor families for HRD research and practice.
Family Incomes Fall While Admission Requirements Rise: Implications for Community Colleges

Median family incomes in the United States are falling while admissions requirements for community colleges are rising. The purpose of this paper was to call attention to the predicament faced by low income and academically underprepared students aspiring to complete community college programs in this environment and the implications for community college leaders. Average family incomes in the U.S. have fallen for the third year in a row, with poverty at 15.1% and 46.5 million people living in poverty conditions. Rising income inequality between the wealthy and the poor contributes to the persistence of working poor families in the U.S. Reversing the trend of increasing income inequality and reducing the poverty rate are difficult. However, education has always been a way in which upward mobility for the disadvantaged can get started. Community colleges in particular have a strong tradition of serving low income and academically underprepared students. But community colleges are now struggling to maintain their tradition of open access in the push for academic and fiscal accountability. Some colleges are shifting to serve better prepared students. What effects are these changes having on the types of students and programs at community colleges? We examined this issue and the implications for community college leaders.
LYRM7 mutations cause a multifocal cavitating leukoencephalopathy with distinct MRI appearance.
Venue: Brain a journal of neurology

This study focused on the molecular characterization of patients with leukoencephalopathy associated with a specific biochemical defect of mitochondrial respiratory chain complex III, and explores the impact of a distinct magnetic resonance imaging pattern of leukoencephalopathy to detect biallelic mutations in LYRM7 in patients with biochemically unclassified leukoencephalopathy. 'Targeted resequencing' of a custom panel including genes coding for mitochondrial proteins was performed in patients with complex III deficiency without a molecular genetic diagnosis. Based on brain magnetic resonance imaging findings in these patients, we selected additional patients from a database of unclassified leukoencephalopathies who were scanned for mutations in LYRM7 by Sanger sequencing. Targeted sequencing revealed homozygous mutations in LYRM7, encoding mitochondrial LYR motif containing protein 7, in four patients from three unrelated families who had a leukoencephalopathy and complex III deficiency. Two subjects harboured previously unreported variants predicted to be damaging, while two siblings carried an already reported pathogenic homozygous missense change. Sanger sequencing performed in the second cohort of patients revealed LYRM7 mutations in three additional patients, who were selected on the basis of the magnetic resonance imaging pattern. All patients had a consistent magnetic resonance imaging pattern of progressive signal abnormalities with multifocal small cavitations in the periventricular and deep cerebral white matter. Early motor development was delayed in half of the patients. All patients but one presented with subacute neurological deterioration in infancy or childhood, preceded by a febrile infection, and most patients had repeated episodes of subacute encephalopathy with motor regression, irritability and stupor or coma resulting in major handicap or death. LYRM7 protein was strongly reduced in available samples from patients; decreased complex III holocomplex was observed in fibroblasts from a patient carrying a splice site variant; functional studies in yeast confirmed the pathogenicity of two novel mutations. Mutations in LYRM7 were previously found in a single patient with a severe form of infantile onset encephalopathy. We provide new molecular, clinical, and neuroimaging data allowing us to characterize more accurately the molecular spectrum of LYRM7 mutations highlighting that a distinct and recognizable magnetic resonance imaging pattern is related to mutations in this gene. Inter and intrafamilial variability exists and we observed one patient who was asymptomatic by the age of 6 years.
We Knew It All Along! Using Cognitive Science to Explain How Andragogy Works.

This paper aims to link recent findings in cognitive neuroscience to better understand how andragogically informed instructional practices impact cognition and learning.  The research questions guiding the study is in what ways can the recent findings in cognitive neuroscience help to inform adult education theory, including andragogy in particular, to deepen our understanding of how andragogical instructional principles and practices can improve learning? We adopted Torraco's (2005) integrative literature review approach of providing enough details regarding the selection of the literature and the identification and verification of emerged themes of main ideas.  The core assumptions of andragogy (self direction, prior experience, readiness to learn and immediacy of application) have a connection to the neural networks related to memory and cognition.  First, this study provides fundamental foundations for combining cognit.