bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Use of miRNA-derived SSR Markers to Study Genetic Diversity, Population Structure and Characterization of Genotypes for Heat Tolerance Breeding in Bread Wheat (Triticum aestivumL.)
Authors: Tyagi Sandhya , Kumar Anuj , Gautam Tinku , Pandey Renu , Mir Reyazul Rouf 
Published: March 2020

AbstractWheat is one of the most important cereal crop in the world. Heat stress is an important abiotic stress limiting wheat production and productivity in the world including south-east Asia. The importance of miRNAs in gene expression under various biotic and abiotic stresses is well documented. Molecular markers, especially SSR markers, plays an important role for the success in molecular plant breeding programs. The discovery of SSRs from non-coding regions has been a challenging task. Therefore, development of novel miRNA-based SSRs from the conserved portions of the genome will prove useful for the study of genetic diversity of heat-responsive miRNA-genes in wheat. In the present study, efforts are made to mine SSR markers from 96 members of heat-responsive miRNA-genes of wheat followed by their validation using 37 contrasting (heat tolerance/susceptible) wheat genotypes. Among a set of 13 miRNA-SSRs used,7 SSRs were found polymorphic. Among these polymorphic SSR markers, three found to be very informative SSRs (HT-169j, HT-160a and HT-160b) and could largely discriminate heat tolerant genotypes from the heat susceptible ones. Further analysis based on Polymorphism Information Content (PIC) revealed that miRNA genes were more diverse in susceptible genotypes compared to tolerant genotypes. Ours is the first report that the genic/miRNA markers could be successfully used to study wheat diversity, population structure and characterization of trait specific germplasm. The important and useful miRNA-based SSRs, therefore, would serve as best markers in the marker-assisted breeding programs aimed at enhancing heat tolerance of Indian wheat.
Spatial analysis of American Eel (Anguilla rostrata), fish passage and land use in Chesapeake Bay tributaries
Authors: Walker Nicholas J. , Prasad V. , de Mutsert K. , Dolloff C.A. , Aguirre A.A. 
Published: March 2020

AbstractCatadromous eels are found in more habitats than any other fish and are capable of inhabiting marine, brackish and freshwater environments. In this study we used the American Eel (Anguilla rostrata) as a bioindicator organism to create a novel method of using spatial analysis to study species conservation over landscape scales. We built a model of the subwatersheds of the Chesapeake Bay using a Digital Elevation Model (DEM) and overlaid eel density data (> 1 million eels sampled), dam density data and land use in ArcGIS. Dam construction in the study area peaked between 1955 and 1975, possibly as a result of flood control measures. Effects of land use were localized and most pronounced in areas around Baltimore, Maryland, Washington, D.C. and Richmond, Virginia, USA. Results indicate the Potomac and Rappahannock rivers appear to be areas of lesser concern while the upper James and York rivers are ideal for follow-up studies, since these area rank poorly in both eel density and barriers to fish passage. Because these rivers have high eel density downstream, the dams appear to be the limiting factor. Sampling methods have been inconsistent over time, making it is difficult to determine where eel densities are low vs. the area having had little sampling effort. This is partially resolved with catch per sampling event (CPSE), which appears to show a relationship between eels sampled and the number caught per sample. Potential strategies for improving watersheds include dam removal, fish passage and habitat restoration.
The Neuroprotective Beta Amyloid Hexapeptide Core Reverses Deficits in Synaptic Plasticity in the 5×FAD APP/PS1 Mouse Model
Authors: Forest Kelly H. , Taketa Ruth , Arora Komal , Todorovic Cedomir , Nichols Robert A. 
Published: March 2020

AbstractAlzheimer’s disease (AD) is the most common cause of dementia in the aging population. Evidence implicates elevated soluble oligomeric Aβ as one of the primary triggers during the prodromic phase leading to AD, effected largely via hyperphosphorylation of the microtubule-associated protein tau. At low, physiological levels (pM-nM), however, oligomeric Aβ has been found to regulate synaptic plasticity as a neuromodulator. Through mutational analysis, we found a core hexapeptide sequence within the N-terminal domain of Aβ (N-Aβcore) accounting for its physiological activity, and subsequently found that the N-Aβcore peptide is neuroprotective. Here, we characterized the neuroprotective potential of the N-Aβcore against dysfunction of synaptic plasticity assessed inex vivohippocampal slices from 5×FAD APP/PS1 mice, specifically hippocampal long-term potentiation (LTP) and long-term depression (LTD). The N-Aβcore was shown to reverse impairment in synaptic plasticity in hippocampal slices from 5×FAD APP/PS1 model mice, both for LTP and LTD. The reversal by the N-Aβcore correlated with alleviation of downregulation of hippocampal AMPA-type glutamate receptors in preparations from 5×FAD mice. The action of the N-Aβcore depended upon a critical di-histidine sequence and involved the PI3 kinase pathway via mTOR. Together, the present findings indicate that the non-toxic N-Aβcore hexapeptide is not only neuroprotective at the cellular level but is able to reverse synaptic dysfunction in AD-like models, specifically alterations in synaptic plasticity.
Quantitative Properties of the Creation and Activation of a Cell-Intrinsic Engram
Authors: Gallistel C.R. , Johansson Fredrik , Jirenhed Dan-Anders , Rasmussen Anders , Ricci Matthew , Hesslow Germund 
Published: March 2020

AbstractThe conditional pause in the spontaneous firing of the cerebellar Purkinje, which determines the timing of the conditional eyeblink response, is mediated by a cell-intrinsic engram (Johansson, et al. 2014) that encodes the interstimulus interval. Our trial-by-trial analysis of the pause parameters reveals that it consists of a single unusually long interspike interval, whose onset and offset latencies are stochastically independent scalar functions of the interstimulus interval. The coefficients of variation are comparable to those observed in the timing of the overt conditional eyeblink. The onsets of the long interspike interval are step changes; there is no prior build-up of inhibition. A single spike volley in the parallel fiber input triggers the read-out of the engram into the long interspike interval; subsequent volleys have no effect on the pause. The high spontaneous firing rate on which the one-interval firing pause supervenes is markedly non-stationary (Fano factors >> 1).
pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods
Authors: Behdenna Abdelkader , Colange Maximilien , Haziza Julien , Gema Aryo , Appé Guillaume , Azencott Chloé-Agathe , Nordor Akpéli 
Published: March 2020

AbstractBackgroundVariability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical biases, called batch effects, in, respectively, microarray and RNA-Seq expression data.ResultsIn this technical note, we present a new Python implementation of ComBat and ComBat-Seq. While the mathematical framework is strictly the same, we show here that our implementations: (i) have similar results in terms of batch effects correction; (ii) are as fast or faster than the original implementations in R and; (iii) offer new tools for the bioinformatics community to participate in its development. pyComBat is implemented in the Python language and is distributed under GPL-3.0 (https://www.gnu.org/licenses/gpl-3.0.en.html) license as a module of the inmoose package. Source code is available athttps://github.com/epigenelabs/inmooseand Python package athttps://pypi.org/project/inmoose.ConclusionsWe present a new Python implementation of state-of-the-art tools ComBat and ComBat-Seq for the correction of batch effects in microarray and RNA-Seq data. This new implementation, based on the same mathematical frameworks as ComBat and ComBat-Seq, offers similar power for batch effect correction, at reduced computational cost.Contactakpeli@epigenelabs.com
A Robust Method for Collecting X-ray Diffraction Data from Protein Crystals across Physiological Temperatures
Authors: Doukov Tzanko , Herschlag Daniel , Yabukarski Filip 
Published: March 2020

AbstractTraditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Further, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that is directly related to biological function. The next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperatures and was addressed herein. This approach provides complete diffraction datasets with total collection times as short as ~5 sec from single protein crystals, dramatically increasing the amount of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293–363 K for proteinase K, thaumatin, and lysozyme crystals. Our analyses indicate that the diffraction data is of high-quality and do not suffer from excessive dehydration or damage.
Meta-analysis of diets used inDrosophilamicrobiome research and introduction of theDrosophilaDietary Composition Calculator (DDCC)
Authors: Lesperance Danielle N.A. , Broderick Nichole A. 
Published: March 2020

AbstractWhile the term standard diet is commonly used in studies usingDrosophila melanogaster, more often than not these diets are anything but standard, making it difficult to contextualize results in the broader scope of the field. This is especially evident in microbiome studies, despite diet having a pivotal role in microbiome composition and resulting host-microbe interactions. Here, we performed a meta-analysis of diets used in fly microbiome research and provide a web-based tool for researchers to determine the nutritional content of diets of interest. Our goal is for these community resources to aid in contextualizing both past and future microbiome studies (with utility to other fields as well) to better understand how individual lab diets can contribute to observed phenotypes.
The landscape of longevity across phylogeny
Authors: Podolskiy Dmitriy I. , Avanesov Andrei , Tyshkovskiy Alexander , Porter Emily , Petrascheck Michael , Kaeberlein Matt , Gladyshev Vadim N. 
Published: March 2020

AbstractLifespan of model organisms can be extended by genetic, dietary and pharmacological interventions, but these effects may be negated by other factors. To understand robustness of longevity interventions within and across species, we analyzed age-dependent mortality of yeast, fruit flies, nematodes and mice subjected to thousands of genetic, pharmacological or dietary interventions, and applied the principles learned to other organisms. Across phylogeny, the accessible space of lifespan distribution functions, the “landscape of longevity”, has a distinct structure of a fiber bundle, with individual fibers given by Strehler-Mildvan degeneracy manifolds. Within species, most interventions perturb parameters of survival curves along particular degeneracy manifolds. Transitions across manifolds are difficult to achieve, but they may lead to robust lifespan-modulating effects. Analyses of intraspecific degeneracy manifolds revealed soft bounds on achievable longevity. For humans, this bound is ∼138 years.
TiTUS: Sampling and Summarizing Transmission Trees with Multi-strain Infections
Authors: Sashittal Palash , El-Kebir Mohammed 
Published: March 2020

AbstractMotivationThe combination of genomic and epidemiological data hold the potential to enable accurate pathogen transmission history inference. However, the inference of outbreak transmission histories remains challenging due to various factors such as within-host pathogen diversity and multi-strain infections. Current computational methods ignore within-host diversity and/or multi-strain infections, often failing to accurately infer the transmission history. Thus, there is a need for efficient computational methods for transmission tree inference that accommodate the complexities of real data.ResultsWe formulate the Direct Transmission Inference (DTI) problem for inferring transmission trees that support multi-strain infections given a timed phylogeny and additional epidemiological data. We establish hardness for the decision and counting version of the DTI problem. We introduce TiTUS, a method that uses SATISFIABILITY to almost uniformly sample from the space of transmission trees. We introduce criteria that prioritizes parsimonious transmission trees that we subsequently summarize using a novel consensus tree approach. We demonstrate TiTUS’s ability to accurately reconstruct transmission trees on simulated data as well as a documented HIV transmission chain.Availabilityhttps://github.com/elkebir-group/TiTUSContactmelkebir@illinois.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Nitrogen starvation and stationary phase lipophagy have distinct molecular mechanisms
Authors: Kumar Ravinder , Rahman Muhammad Arifur , Nazarko Taras Y. 
Published: March 2020

AbstractIn yeast, the selective autophagy of intracellular lipid droplets (LDs) or lipophagy can be induced by either nitrogen (N) starvation or carbon limitation (e.g. in the stationary (S) phase). We developed the yeast,Komagataella phaffii(formerlyPichia pastoris), as a new lipophagy model and compared the N-starvation and S-phase lipophagy in over 30 autophagy-related mutants using the Erg6-GFP processing assay. Surprisingly, two lipophagy pathways had hardly overlapping stringent molecular requirements. While the N-starvation lipophagy strictly depended on the core autophagic machinery (Atg1-Atg9, Atg18 and Vps15), vacuole fusion machinery (Vam7 and Ypt7) and vacuolar proteolysis (proteinases A and B), only Atg6 and proteinases A and B were essential for the S-phase lipophagy. The rest of the proteins were only partially required in the S-phase. Moreover, we isolated theprl1(for positive regulator of lipophagy 1) mutant affected in the S-phase lipophagy but not N-starvation lipophagy. Theprl1defect was at a stage of delivery of the LDs from the cytoplasm to the vacuole further supporting mechanistically different nature of the two lipophagy pathways. Taken together, our results suggest that N-starvation and S-phase lipophagy have distinct molecular mechanisms.
Technical Report: Targeted Proteomic Analysis Reveals Enrichment of Atypical Ubiquitin Chains in Contractile Murine Tissues
Authors: Heunis Tiaan , Lamoliatte Frederic , Marín-Rubio José Luis , Dannora Abeer , Trost Matthias 
Published: March 2020

SummaryUbiquitylation is an elaborate post-translational modification involved in all biological processes. Its pleotropic effect is driven by the ability to form complex polyubiquitin chain architectures that can influence biological functions. In this study, we optimised sample preparation and chromatographic separation of Ubiquitin peptides for Absolute Quantification by Parallel Reaction Monitoring (Ub-AQUA-PRM). Using this refined Ub-AQUA-PRM assay, we were able to quantify all ubiquitin chain types in 10-minute LC-MS/MS runs. We used this method to determine the ubiquitin chain-linkage composition in murine bone marrow-derived macrophages and different mouse tissues. We could show tissue-specific differences in ubiquitin levels in murine tissues, with polyubiquitin chain types contributing a small proportion to the total pool of ubiquitin. Interestingly, we observed enrichment of atypical (K33) ubiquitin chains in heart and muscle. Our approach enabled high-throughput screening of ubiquitin chain-linkage composition in different murine tissues and highlighted a possible role for atypical ubiquitylation in contractile tissues.
An assessment into mechanical properties and microstructural behavior of TIG welded Ti-6Al-4V titanium alloy
Authors: Dewangan Saurabh , Mohapatra Suraj Kumar , Sharma Abhishek 
Published: March 2020

PurposeTitanium (Ti) alloys are in high demand in manufacturing industries all over the world. The property like high strength to weight ratio makes Ti alloys highly recommended for aerospace industries. Ti alloys possess good weldability, and therefore, they were extensively investigated with regard to strength and metallurgical properties of welded joint. This study aims to deal with the analysis of strength and microstructural changes in Ti-6Al-4V (Grade 5) alloy after tungsten inert gas (TIG) welding.Design/methodology/approachTwo pair of Ti alloy plates were welded in two different voltages, i.e. 24 and 28 V, with keeping the current constant, i.e. 80 A It was a random selection of current and voltage values to check the performance of welded material. Both the welded plates were undergone through some mechanical property analysis like impact test, tensile test and hardness test. In addition, the microstructure of the welded joints was also analyzed.FindingsIt was found that hardness and tensile properties gets improved with an increment in voltage, but this effect was reverse for impact toughness. A good corroboration between microstructure and mechanical properties, such as tensile strength, hardness and toughness, was reported in this work. Heat distribution in both the welded plates was simulated through ANSYS software to check the temperature contour in the plates.Originality/valueA good corroboration between microstructure and mechanical properties, such as tensile strength, hardness and toughness, was reported in this study.
Health, well-being and education
Authors: Dadaczynski Kevin , Jensen Bjarne Bruun , Viig Nina Grieg , Sormunen Marjorita , von Seelen Jesper , Kuchma Vladislav , Vilaça Teresa 
Published: March 2020

PurposeThe purpose of this paper is to introduce the official statement of the Fifth European Conference on Health-Promoting Schools.Design/methodology/approachThe Fifth European Conference on Health-Promoting Schools was held on 20–22 November 2019 in Moscow, Russian Federation, with over 450 participants from 40 countries. A writing group was established to prepare a draft version of the statement before the conference. On the basis of an online and offline feedback process, the opinions of the participants were collected during the conference and included in the finalisation of the statement.FindingsThe final conference statement comprises six thematic categories (values and principles; environment, climate and health; schools as part of the wider community; non-communicable diseases (NCDs); evidence base; and digital media), with a total of 23 recommendations and calls for action.Originality/valueThe recommendations and calls for action reflect current challenges for Health Promoting Schools in Europe. They are addressed to all actors in governmental, non-governmental and other organisations at international, national and regional levels involved in health promotion in schools and are to be applied for the further development of the concept.
The path of teachers' learning through lesson and learning studies
Authors: Wood Keith 
Published: March 2020

PurposeThe purpose of this article is to discern and discuss dimensions of variation opened by the articles in the issue 9(2) of the International Journal of Lesson and Learning Studies (IJLLS).Design/methodology/approachThe approach draws on the path of teachers learning through lesson and learning studies presented as a pattern of variation forming a temporal sequence.FindingsAttention is drawn to the importance of being explicit about the theory of learning informing lesson and learning studies and how its implementation leads to teacher learning.Originality/valueThe depiction of the path of learning through lesson and learning studies is original.
Theoretical explanation, understanding and prediction in management studies
Authors: Styhre Alexander 
Published: March 2020

Purpose
The purpose of this paper is to question whether the management studies is rigorous and/or relevant is a recurrent debate in the discipline. There is reason to believe that this dichotomy is simplistic as relevance is a consequence of rigor (defined in a variety of ways in the literature), whereas the epistemic value of rigor must per se be examined in more detail.

Design/methodology/approach
Drawing on the study of the analytical philosophy of Donald Davidson, rigor is here conceptualized as the capacity to examine how intersubjective meaning is constituted on the basis of the semantics of the everyday language.

Findings
In Davidson’s pragmatist view, individual beliefs are established through communication, and beliefs generate preferences and “pro-attitudes” that result in social action. Using Ian Hacking’s term undoing as a critique of a proposition or idea as being no contender for truth (or some other quality) at all, the paper questions the proposition that scientific rigor can be operationalized as the use of data collection and analysis methods developed in other and more authoritative disciplines, e.g. economics. On the contrary, to make accurate descriptions of beliefs, preferences and actions on the basis of the use of everyday language is the mark of scientific rigor in management studies.

Originality/value
The paper addresses the question of how rigorous research in management studies is essentially a matter of explanation, and that explanation, in turn, demands a more elaborate theory of action. The paper also introduces the work of Donald Davidson as an important figure when theorizing action.
Deviation from the direction of motion across gaits in a hexapodal robot
Authors: Niu Zijie , Zhan Aiwen , Cui Yongjie 
Published: March 2020

Purpose
The purpose of this study is to test a chassis robot on rugged road cargo handling.

Design/methodology/approach
Attitude solution of D-H series robot gyroscope speed and acceleration sensor.

Findings
In identical experimental environments, hexapodal robots experience smaller deviations when using a four-footed propulsive gait from a typical three-footed gait for forward motion; for the same distance but at different speeds, the deviation basically keeps itself within the same range when the robot advances forward with four-foot propulsive gait; because the foot slide in the three-footed gait sometimes experiences frictions, the robot exhibits a large gap in directional deviations in different courses during motion; for motion using a four-footed propulsive gait, there are minor directional deviations of hexapodal robots resulting from experimental errors, which can be reduced through optimizing mechanical structures.

Originality/value
Planning different gaits can solve problems existing in some typical gaits. This article has put forward a gait planning method for hexapodal robots moving forward with diverse gaits as a redundant multifreedom structure. Subsequent research can combine a multiparallel-legged structure to analyze kinematics, optimize the robot’s mechanical structure and carry out in-depth research of hexapod robot gaits.