bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exogenously applied ABA induced changes in physio-biochemical attributes in selected rice varieties under osmotic stress
Authors: Dash Goutam Kumar , Geda Chaitanya Kumar , Sahoo Soumya Kumar , Baig Mirza Jaynul , Swain Padmini 
Published: May 2020

AbstractDrought is the most catastrophic abiotic stress that affect plant growth and development. Plant initiates alterations at physiological, biochemical and molecular levels to combat deleterious effects of drought in which abscisic acid, play a pivotal role. The present investigation was conducted to investigate how abscisic acid modulates different biochemical traits under osmotic stress. Twenty-one days old seedlings were exposed to osmotic stress, exogenously applied abscisic acid and the combination of both osmotic stress and abscisic acid to study the influence of abscisic acid on biochemical traits under moisture stress. The results reveals that abscisic acid has no influence on leaf water potential, however, it has active role in increasing osmolytes like proline. Δ1-pyrroline-5-carboxylate reductase and proline dehydrogenase remained unresponsiveness to ABA that indicates ABA-independent regulation of these two enzymes but the activity of Δ1-pyrroline-5-carboxylate synthesase and Ornithine-δ-aminotransferase was enhanced (3 fold) in response to abscisic acid. Antioxidative enzymes increased (catalase-2.5 fold; peroxidase-3 fold and SOD-6 fold) in response to abscisic acid and osmotic stress, gave an insight of the regulation of these traits under the influence of abscisic acid. Aldehyde oxidase remained unresponsive to abscisic acid but showed enhanced expression when both abscisic acid and osmotic stress was applied suggest its ABA-independent regulation. The information provided here has significance in understanding the regulation of different catabolite that play important role in drought tolerance and can be implemented for the development of drought-tolerant varieties.
A rapid urban biodiversity blitz using aquatic environmental DNA
Authors: Hupało Kamil , Majaneva Markus , Czachur Molly Victoria , Sire Lucas , Marquina Daniel , Lijtmaer Darío A. , Ivanov Vladislav , Leidenberger Sonja , Čiampor Fedor , Čiamporová-Zaťovičová Zuzana , Mendes Izabela S. , Desiderato Andrea , Topstad Lasse , Meganck Kenny , Hariz Z. A. Danial , Kjærstad Gaute , Lin Xiao-Long , Price Benjamin , Stevens Mark , Ekrem Torbjørn , Deiner Kristy 
Published: May 2020

AbstractBackgroundAs global biodiversity declines, there’s an increasing need to create an educated and engaged society. Having people from all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we test whether sampling eDNA and metabarcoding can be used for rapid urban biodiversity surveys for educational purposes.Materials & MethodsWe sampled 2×1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine and brackish habitats. DNA was extracted, amplified in triplicate for the COI gene and sequenced. The obtained data were analysed on the novel mBRAVE platform, an online open access software and computing resource.ResultsThe water samples were collected in two days by two people and the lab analysis was completed in five days by one person. Overall, we detected the presence of 501 taxa identified as belonging to 435 species, representing 90 orders and 18 phyla. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota.DiscussionOur results match expected patterns of biodiversity in the landscape and show that with minimal sampling effort, hundreds of species can be detected. Thus, using eDNA analysis of water is promising for rapid biodiversity surveys, and it is likely that more detailed results could be obtained by optimising field and lab methods for particular groups of interest. We recommend that rapid eDNA surveys, with openly available services and softwares, can be used to raise awareness in the importance of biodiversity.
SS3D: Sequence similarity in 3D for comparison of protein families
Authors: Lima Igor , Cino Elio A. 
Published: May 2020

AbstractHomologous proteins are often compared by pairwise sequence alignment, and structure superposition if the atomic coordinates are available. Unification of sequence and structure data is an important task in structural biology. Here, we present Sequence Similarity 3D (SS3D), a new method for integrating sequence and structure information for comparison of homologous proteins. SS3D quantifies the spatial similarity of residues within a given radius of homologous through-space contacts. The spatial alignments are scored using native BLOSUM and PAM substitution matrices. This work details the SS3D approach and demonstrates its utility through case studies comparing members of several protein families: GPCR, p53, kelch, SUMO, and SARS coronavirus spike protein. We show that SS3D can more clearly highlight biologically important regions of similarity and dissimilarity compared to pairwise sequence alignments or structure superposition alone. SS3D is written in C++, and is available with a manual and tutorial athttps://github.com/0x462e41/SS3D/.
Activating an adaptive immune response from a hydrogel scaffold imparts regenerative wound healing
Authors: Griffin Donald R. , Archang Maani M. , Kuan Chen H. , Weaver Westbrook M. , Weinstein Jason S. , Feng An Chieh , Ruccia Amber , Sideris Elias , Ragkousis Vasileios , Koh Jaekyung , Plikus Maksim V. , Di Carlo Dino , Segura Tatiana , Scumpia Philip O. 
Published: May 2020

AbstractBiomaterial scaffolds represent a promising approach for material-based tissue regeneration. We previously developed microporous annealed particle (MAP) hydrogels - a flowable, microparticle-based hydrogel in which neighboring hydrogel particles are linkedin situto form a porous scaffold that accelerates wound healing. To promote more extensive tissue ingrowth before scaffold degradation, we aimed to slow scaffold degradation by switching the chirality of the crosslinking peptides from L-peptides to D-peptides. Unexpectedly, despite showing the predicted slower enzymatic degradationin vitro, D-peptide crosslinked MAP hydrogel (D-MAP) hastened material degradationin vivoand imparted significant tissue regeneration to healed cutaneous wounds, including increased tensile strength and hair neogenesis. By themselves, D-chiral peptides were poor activators of macrophage innate immune signalingin vivo, but MAP particles elicit IL-33 type 2 myeloid cell recruitment which is amplifiedin vivoin the presence of D-peptides. Remarkably, D-MAP elicited significant antigen-specific immunity against the D-chiral peptides, and an intact adaptive immune system was required for the hydrogel-induced skin regeneration. These findings demonstrate that the generation of an adaptive immune response from a biomaterial is sufficient to induce cutaneous regenerative healing despite faster scaffold degradation.
Movement-related changes in pallidocortical synchrony differentiate action execution and observation in humans
Authors: Cross Katy A. , Malekmohammadi Mahsa , Choi Jeong Woo , Pouratian Nader 
Published: May 2020

AbstractSuppression of local and network alpha (8-12 Hz) and beta (12-35 Hz) oscillations in the human basal ganglia-thalamocortical (BGTC) circuit is a prominent feature of movement. Local alpha/beta power, cross-region beta phase coupling, and phase-amplitude coupling (PAC) have all been shown to be suppressed during movement in multiple nodes of the BGTC. However, the specificity of these various movement-related changes to actual movement execution remains poorly understood. To differentiate signals that are specifically related to movement execution, we compared changes in globus pallidus internus (GPi) and motor cortical local oscillatory activity and coupling (cross-region phase coupling and local PAC) during movement execution and movement observation in 12 patients with Parkinson disease undergoing deep brain stimulator implantation. We hypothesized that network coupling is more directly related to movement execution than local power changes, given the putative role of pathological network coupling in movement disorders such as Parkinson disease. We observed suppression of alpha/beta power during action observation and execution in the globus pallidus and motor cortex during both action execution and action observation. In contrast, pallidocortical coherence and GPi and motor cortical alpha/beta-gamma PAC were significantly suppressed only during action execution. Our results demonstrate a functional dissociation within the BG-cortical network during action execution and observation in which suppression of BG-cortical functional connectivity and local phase amplitude coupling are features specifically of overt movement, suggesting a particularly important role in motor execution. This has implications for identification and use of intracranial signals for closed loop brain stimulation therapies.
Integrate Heterogeneous NGS and TGS Data to Boost Genome-free Transcriptome Research
Authors: Qin Yangmei , Lin Zhe , Shi Dan , Zhong Mindong , An Te , Chen Linshan , Wang Yiquan , Lin Fan , Li Guang , Ji Zhi-Liang 
Published: May 2020

AbstractIt is a long-term challenge to undertake reliable transcriptomic research under different circumstances of genome availability. Here, we newly developed a genome-free computational method to aid accurate transcriptome assembly, using the amphioxus as the example. Via integrating ten next generation sequencing (NGS) transcriptome datasets and one third-generation sequencing (TGS) dataset, we built a sequence library of non-redundant expressed transcripts for the amphioxus. The library consisted of overall 91,915 distinct transcripts, 51,549 protein-coding transcripts, and 16,923 novel extragenic transcripts. This substantially improved current amphioxus genome annotation by expanding the distinct gene number from 21,954 to 38,777. We consolidated the library significantly outperformed the genome, as well asde novomethod, in transcriptome assembly from multiple aspects. For convenience, we curated the Integrative Transcript Library database of the amphioxus (http://www.bio-add.org/InTrans/). In summary, this work provides a practical solution for most organisms to alleviate the heavy dependence on good quality genome in transcriptome research. It also ensures the amphioxus transcriptome research grounding on reliable data.
The role of sodium thiocyanate supplementation during dextran sodium sulphate-stimulated experimental colitis
Authors: Liu Yuyang (Anna) , Burton Thomas , Rayner Benjamin Saul , Gabriel Patrick San , Shi Han , Kazzi Mary El , Wang XiaoSuo , Dennis Joanne M , Ahmad Gulfam , Witting Paul Kenneth , Chami Belal 
Published: May 2020

AbstractUlcerative colitis is a condition characterised by the infiltration of leukocytes into the gastrointestinal wall. Leukocyte-MPO catalyses hypochlorous acid (HOCl) and hypothiocyanous acid (HOSCN) formation from chloride (Cl-) and thiocyanous (SCN-) anions, respectively. While HOCl indiscriminately oxidises biomolecules, HOSCN primarily targets low-molecular weight protein thiols. Oxidative damage mediated by HOSCN may be reversible, potentially decreasing MPO-associated host tissue destruction. This study investigated the effect of SCN-supplementation in a model of acute colitis. Female mice were supplemented dextran sodium sulphate (DSS, 3% w/v) in the presence of 10 mM Cl-or SCN-in drinking waterad libitum, or with salts (NaCl and NaSCN only) or water only (controls). Behavioural studies showed mice tolerated NaSCN and NaCl-treated water with water-seeking frequency. Ion-exchange chromatography showed increased fecal and plasma SCN-levels in thiocyanate supplemented mice; plasma SCN-reached similar fold-increase for smokers. Overall there was no difference in weight loss and clinical score, mucin levels, crypt integrity and extent of cellular infiltration between DSS/SCN-and DSS/Cl-groups. Neutrophil recruitment remained unchanged in DSS-treated mice, as assessed by fecal calprotectin levels. Total thiol and tyrosine phosphatase activity remained unchanged between DSS/Cl-and DSS/SCN-groups, however, colonic tissue showed a trend in decreased 3-chlorotyrosine (1.5-fold reduction,p<0.051) and marked increase in colonic GCLC, the rate-limiting enzyme in glutathione synthesis. These data suggest that SCN-administration can modulate MPO activity towards a HOSCN-specific pathway, however, this does not alter the development of colitis within a DSS murine model.HighlightsSodium thiocyanate (SCN-) supplementation increased plasma and fecal SCN-level.Thiocyanate supplementation diverted HOCl-mediated oxidative damage in mice colon.Thiocyanate supplementation stimulated thiol synthesis in the DSS colitis model.Thiocyanate provides no protection in an acute experimental model of UC.
Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase)
Authors: Leino Lyydia , Tall Tuomas , Helander Marjo , Saloniemi Irma , Saikkonen Kari , Ruuskanen Suvi , Puigbò Pere 
Published: May 2020

ABSTRACTGlyphosate is the most common broad-spectrum herbicide. It targets the key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), which synthesizes three essential aromatic amino acids (phenylalanine, tyrosine and tryptophan) in plants. Because the shikimate pathway is also found in many prokaryotes and fungi, the widespread use of glyphosate may have unsuspected impacts on the diversity and composition of microbial communities, including the human gut microbiome. Here, we introduce the first bioinformatics method to assess the potential sensitivity of organisms to glyphosate based on the type of EPSPS enzyme. We have precomputed a dataset of EPSPS sequences from thousands of species that will be an invaluable resource to advancing the research field. This novel methodology can classify sequences from >90% of eukaryotes and >80% of prokaryotes. A conservative estimate from our results shows that 54% of species in the core human gut microbiome are sensitive to glyphosate.
The Homo-Edit Distance Problem
Authors: Brand Maren , Tran Nguyen Khoa , Spohr Philipp , Schrinner Sven , Klau Gunnar W. 
Published: May 2020

AbstractWe consider the homo-edit distance problem, which is the minimum number of homo-deletions or homo-insertions to convert one string into another. A homo-insertion is the insertion of a string of equal characters into another string, while a homo-deletion is the inverse operation. We show how to compute the homo-edit distance of two strings in polynomial time: We first demonstrate that the problem is equivalent to computing a common subsequence of the two input strings with a minimum number of homo-deletions and then present a dynamic programming solution for the reformulated problem.2012 ACM Subject ClassificationApplied computing → Bioinformatics; Applied computing → Molecular sequence analysis; Theory of computation → Dynamic programming
Patterns of microbiome variation among infrapopulations of permanent bloodsucking parasites
Authors: Doña Jorge , Herrera Stephany Virrueta , Nyman Tommi , Kunnasranta Mervi , Johnson Kevin P. 
Published: May 2020

AbstractWhile interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louseEchinophthirius horridussampled from individual Saimaa ringed sealsPusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.
Optimizing the Electric Field Strength in Multiple Targets for Multichannel Transcranial Electric Stimulation
Authors: Saturnino Guilherme B. , Madsen Kristoffer H. , Thielscher Axel 
Published: May 2020

AbstractObjectiveMost approaches to optimize the electric field pattern generated by multichannel Transcranial Electric Stimulation (TES) require the definition of a preferred direction of the electric field in the target region(s). However, this requires knowledge about how the neural effects depend on the field direction, which is not always available. Thus, it can be preferential to optimize the field strength in the target(s), irrespective of the field direction. However, this results in a more complex optimization problem.ApproachWe introduce and validate a novel optimization algorithm that maximizes focality while controlling the electric field strength in the target to maintain a defined value. It obeys the safety constraints, allows limiting the number of active electrodes and allows also for multi-target optimization.Main ResultsThe optimization algorithm outperformed naïve search approaches in both quality of the solution and computational efficiency. Using the amygdala as test case, we show that it allows for reaching a reasonable trade-off between focality and field strength in the target. In contrast, simply maximizing the field strength in the target results in far more extended fields. In addition, by maintaining the pre-defined field strengths in the targets, the new algorithm allows for a balanced stimulation of two or more regions.SignificanceThe novel algorithm can be used to automatically obtain individualized, optimal montages for targeting regions without the need to define preferential directions. It will automatically select the field direction that achieves the desired field strength in the target(s) with the most focal stimulation pattern.
Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing
Authors: Parker Matthew T. , Knop Katarzyna , Barton Geoffrey J. , Simpson Gordon G. 
Published: May 2020

AbstractTranscription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the true complexity of processing. However, the relatively high error rates of long-read sequencing technologies can reduce the accuracy of intron identification. Here we apply alignment metrics and machine-learning-derived sequence information to filter spurious splice junctions from long read alignments and use the remaining junctions to guide realignment in a two-pass approach. This method, available in the software package 2passtools (https://github.com/bartongroup/2passtools), improves the accuracy of spliced alignment and transcriptome assembly for species both with and without existing high-quality annotations.
The efficacy of a virtual reality exposure therapy treatment for fear of flying: A retrospective study
Authors: Gottlieb Amihai , Doniger Glen M. , Hussein Yara , Noy Shlomo , Plotnik Meir 
Published: May 2020

AbstractBackgroundFear of flying (FoF) is an anxiety disorder classified as a phobia. Its prevalence is estimated at 10–40% in the industrialized world, and it is accompanied by severe economic, social, vocational and emotional consequences. In recent years, virtual reality-based exposure therapy (VRET) for FoF has been introduced. One such FoF-VRET is offered as a paid clinical service at the Center of Advanced Technologies in Rehabilitation (CATR), Sheba Medical Center, Israel. Positive long-term efficacy of FoF-VRET has been found in several studies. However, these studies are limited by relatively small, non-representative samples and a lack of comparative pre/post functional efficacy outcome measures.MethodsTo address these limitations, we conducted a retrospective survey of self-referred individuals treated with FoF-VRET at CATR over the previous four years. The aim of the present study was to evaluate the efficacy of our FoF-VRET in this representative real-world sample. Of 274 individuals who received the treatment, 214 met inclusion/criteria, and 103 agreed to participate. The survey focused mainly on collecting information regarding flight activity before and after treatment. The primary outcome measures were: (1) number of flights per month (FpM); (2) number of flight hours per month (FHpM). For each participant, these outcomes were computed for the post-treatment period (≥6 months after FoF-VRET) and the corresponding pre-treatment period.ResultsFpM (mean±SD) increased from .05±.07 to .16±.07 flights (p<.0001). FHpM rose from.22±.41 to .80±.86 hours per month (p<.0001).ConclusionsThese results are indicative of FoF-VRET treatment efficacy. Future studies should evaluate long-term maintenance of the treatment effect and thus identify the optimal frequency for delivery of periodic booster treatments.
Mitochondrial dysfunction in skeletal muscle of fukutin deficient mice is resistant to exercise- and AICAR-induced rescue
Authors: Southern W. Michael , Nichenko Anna S. , Qualls Anita E. , Portman Kensey , Gidon Ariel , Beedle Aaron , Call Jarrod A. 
Published: May 2020

AbstractDisruptions in the dystrophin-glycoprotein complex (DGC) are clearly the primary basis underlying various forms of muscular dystrophies and dystroglycanopathies, but the cellular consequences of DGC disruption are still being investigated. Mitochondrial abnormalities are becoming an apparent consequence and contributor to dystrophy disease pathology. Herein, we demonstrate that muscle-specific deletion of the fukutin gene [Myf5/fktn-KO mice (KO)], a model of secondary dystroglycanopathy, results in ~30% lower muscle strength (P<0.001) and 16% lower mitochondrial function (P=0.002) compared to healthy littermate controls (LM). We also observed ~80% lower PGC-1α signaling (P=0.004), a primary transcription factor for mitochondrial biogenesis, in KO mice that likely contributes to the mitochondrial defects. PGC-1α is post-translationally regulated via phosphorylation by AMPK. Treatment with the AMPK agonist AICAR (5-aminoimidazole-4-carboxamide ribonucleotide) failed to rescue mitochondrial deficits in KO mice (P=0.458) but did have beneficial (~30% greater) effects on recovery of muscle contractility following injury in both LM and KO mice compared to saline treatment (P=0.006). The beneficial effects of AMPK stimulation via AICAR on muscle function may be partially explained by AMPK’s other role of regulating skeletal muscle autophagy, a cellular process critical for clearance of damaged and/or dysfunctional organelles. Two primary conclusions can be drawn from this data, 1) fukutin deletion produces intrinsic muscular metabolic defects that likely contribute to dystroglycanopathy disease pathology, and 2) AICAR treatment accelerates recovery of muscle function following injury suggesting AMPK signaling as a possible target for therapeutic strategies.