bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of feedlot performance, carcass characteristics, carcass retail cut distribution, Warner-Bratzler shear force, and fatty acid composition of purebred Jersey and crossbred Jersey steers
Authors: Jaborek Jerad R , Zerby Henry N , Moeller Steven J , Fluharty Francis L , Relling Alejandro E 
Published: July 2019

AbstractFeedlot performance, carcass yield, fatty acid composition, and tenderness of crossbred Jersey steers compared with purebred Jersey steers was investigated. Purebred Jersey (n = 21) and crossbred Jersey steers sired by Angus (n = 9), SimAngus (n = 10), and Red Wagyu (n = 15) bulls were assessed. Adjusted to a common initial body weight (BW), crossbred Jersey steers had a greater rate of BW gain (P ≤ 0.01) compared with purebred Jersey steers. Angus sired steers had a greater daily dry matter intake (P ≤ 0.01) compared with Wagyu and Jersey sired steers, whereas SimAngus sired steers had a greater daily dry matter intake compared with Jersey sired steers. Wagyu sired steers were more feed efficient (P ≤ 0.03) compared with Jersey sired steers. Even with a greater (P ≤ 0.01) number of days on feed, off-test BW of purebred Jersey steers was less (P ≤ 0.01) compared with crossbred Jersey steers. Adjusted to a common hot carcass weight, Angus sired steers had a greater backfat thickness (P ≤ 0.01) compared with steers from the other sire breeds. Kidney fat percentage (P ≤ 0.01) was greatest for Jersey sired steers, with SimAngus and Wagyu sired steers being intermediate, and the lowest for Angus sired steers. Carcasses from Angus and Wagyu sired steers had a greater marbling score (P ≤ 0.03) compared with carcasses from Jersey sired steers. Carcasses from Wagyu sired steers had a greater (P ≤ 0.01) total red meat yield compared with Angus and Jersey sired steers, whereas SimAngus sired steers had a greater total red meat yield compared with Jersey sired steers. Carcasses from Angus sired steers tended (P = 0.07) to have a greater percentage of fat trim compared with Wagyu sired steer carcasses. There were no sire breed differences (P = 0.38) for the percentage of total bone from the carcasses. Tenderness, measured by Warner-Bratzler shear force (WBSF), was improved (P ≤ 0.01) with 14 d of postmortem aging compared with 7 d. Wagyu and SimAngus sired steers produced steaks with a lesser (P ≤ 0.01) WBSF compared with steaks from Angus and Jersey sired steers. Steaks from Angus sired steers tended (P = 0.10) to have a greater percentage of total lipid and had a greater (P ≤ 0.05) percentage of 16:0 compared with steaks from Jersey sired steers. Overall, crossbred Jersey steers improved economically relevant production parameters of feedlot performance, carcass quality, carcass yield, and instrumental predictors of eating quality compared with purebred Jersey steers.
Misclassification of a whole genome sequence reference defined by the Human Microbiome Project: a detrimental carryover effect to microbiome studies
Authors: Bandoy DJ Darwin R. , Huang B Carol , Weimer Bart C. 
Published: July 2019

AbstractTaxonomic classification is an essential step in the analysis of microbiome data that depends on a reference database of whole genome sequences. Taxonomic classifiers are built on established reference species, such as the Human Microbiome Project database, that is growing rapidly. While constructing a population wide pangenome of the bacterium Hungatella, we discovered that the Human Microbiome Project reference species Hungatella hathewayi (WAL 18680) was significantly different to other members of this genus. Specifically, the reference lacked the core genome as compared to the other members. Further analysis, using average nucleotide identity (ANI) and 16s rRNA comparisons, indicated that WAL18680 was misclassified as Hungatella. The error in classification is being amplified in the taxonomic classifiers and will have a compounding effect as microbiome analyses are done, resulting in inaccurate assignment of community members and will lead to fallacious conclusions and possibly treatment. As automated genome homology assessment expands for microbiome analysis, outbreak detection, and public health reliance on whole genomes increases this issue will likely occur at an increasing rate. These observations highlight the need for developing reference free methods for epidemiological investigation using whole genome sequences and the criticality of accurate reference databases.
A Single-Cell Immune Atlas of Triple Negative Breast Cancer Reveals Novel Immune Cell Subsets
Authors: Qiu Si , Hong Ruoxi , Zhuang Zhenkun , Li Yuan , Zhu Linnan , Lin Xinxin , Zheng Qiufan , Liu Shang , Zhang Kai , Huang Mengxian , Lee Kaping , Lu Qianyi , Xia Wen , Xu Fei , Wang Xi , Tang Jun , Xiao Xiangsheng , Wei Weidong , Yuan Zhongyu , Shi Yanxia , Hou Yong , Zhang Xiuqing , Wang Jian , Yang Huanming , Zhan Qimin , Li Bo , Wang Shusen 
Published: July 2019

ABSTRACTTriple-negative breast cancer (TNBC) represents the most aggressive breast cancer subtype, which recently attracts great interest for immune therapeutic development. In this context, in-depth understanding of TNBC immune landscape is highly demanded. Here we report single-cell RNA sequencing results of 9683 tumor-infiltrated immune cells isolated from 14 treatment naïve TNBC tumors, where 22 immune cell subsets, including T cells, macrophages, B cells, and DCs have been characterized. We identify a new T cell subset, CD8+CXCL8+ naïve T cell, which associates with poor survival. A novel immune cell subset comprised of TCR+ macrophages, is found to be widely distributed in TNBC tumors. Further analyses reveal an up-regulation of molecules associated with TCR signaling and cytotoxicity in these immune cells, indicating TCR signaling activation. Altogether, our study provides a valuable resource to understand the immune ecosystem of TNBC. The novel immune cell subsets reported herein might be functionally important in cancer immunity.SIGNIFICANCEThis work demonstrates a single-cell transcriptome atlas of immune cells in treatment naïve TNBC tumors, revealing novel immune cell subsets. This study provides a valuable resource to understand the immune ecosystem of TNBC, which will be helpful for the immunotherapeutic strategy design of TNBC.
Spin∞ an improved miniaturized spinning bioreactor for the generation of human cerebral organoids from pluripotent stem cells
Authors: Romero-Morales Alejandra I. , O’Grady Brian J. , Balotin Kylie M. , Bellan Leon M. , Lippmann Ethan S. , Gama Vivian 
Published: July 2019

AbstractThree-dimensional (3D) brain organoids derived from human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs), have become a powerful system to study early development events and to model human disease. Cerebral organoids are generally produced in static culture or in a culture vessel with active mixing, and the two most widely used systems for mixing are a large spinning flask and a miniaturized multi-well spinning bioreactor (also known as Spin Omega (SpinΩ)). The SpinΩ provides a system that is amenable to drug testing, has increased throughput and reproducibility, and utilizes less culture media. However, technical limitations of this system include poor stability of select components and an elevated risk of contamination due to the inability to sterilize the device preassembled. Here, we report a new design of the miniaturized bioreactor system, which we term Spin∞ that overcomes these concerns to permit long-term experiments.
Assessing neurophysiological changes associated with combined transcranial direct current stimulation and cognitive emotional training for treatment-resistant depression
Authors: Nikolin Stevan , Martin Donel , Loo Colleen K. , Iacoviello Brian M. , Boonstra Tjeerd W. 
Published: July 2019

ABSTRACTTranscranial direct current stimulation (tDCS), a form of non-invasive brain stimulation, is a promising treatment for depression. Recent research suggests that tDCS efficacy can be augmented using concurrent cognitive emotional training (CET). However, the neurophysiological changes associated with this combined intervention remain to be elucidated. We therefore examined the effects of tDCS combined with CET using electroencephalography (EEG). A total of 20 participants with treatment resistant depression took part in this open-label study and received 18 sessions over 6 weeks of tDCS and concurrent CET. Resting-state and task-related EEG during a 3-back working memory task were aquired at baseline and immediately following the treatment course. Results showed an improvement in mood and working memory accuracy, but not response time, following the intervention. We did not find significant effects of the intervention on resting-state power spectral density (frontal theta and alpha asymmetry), time-frequency power (alpha event-related desynchronization and theta event-related synchronisation), or event-related potentials (P2 and P3 components). We therefore identified little evidence of neurophysiological changes associated with treatment using tDCS and concurrent CET, despite significant improvements in mood and near transfer effects of cognitive training to working memory accuracy. Further research incorporating a sham controlled group may be necessary to identify the neurophysiological effects of the intervention.
Functionally Distinct Subgroups of Oligodendrocyte Precursor Cells Integrate Neural Activity and Execute Myelin Formation
Authors: Hoche Tobias , Marisca Roberta , Agirre Eneritz , Hoodless Laura Jane , Barkey Wenke , Auer Franziska , Castelo-Branco Gonçalo , Czopka Tim 
Published: July 2019

SummaryRecent reports revealed heterogeneity of oligodendrocyte precursor cells (OPCs). It remains unclear if heterogeneity reflects different types of cells with distinct functions, or rather transiently acquired states of cells with the same function. By integrating lineage formation of individual OPC clones, single-cell transcriptomics, calcium imaging and manipulation of neural activity, we show that OPCs in the zebrafish spinal cord can be divided into two functionally distinct entities. One subgroup forms elaborate networks of processes and exhibits a high degree of calcium signalling, but infrequently differentiates, despite contact to permissive axons. Instead, these OPCs divide in an activity and calcium dependent manner to produce another subgroup with higher process motility and less calcium signaling, which readily differentiates. Our data show that OPC subgroups are functionally diverse in responding to neurons and reveal that activity regulates proliferation of a subset of OPCs that is distinct from the cells that generate differentiated oligodendrocytes.
Muscarinic modulation of spike-timing dependent plasticity at recurrent layer 2/3 synapses in mouse auditory cortex
Authors: Rao Deepti , Kratz Megan B. , Manis Paul B. 
Published: July 2019

AbstractCholinergic systems contribute to the refinement of auditory cortical receptive fields by activating muscarinic acetylcholine receptors (mAChRs). However, the specific cellular and synaptic mechanisms underlying acetylcholine’s effects on cortical circuits are not fully understood. In this study, we investigate the effects of muscarinic receptor modulation on spike-timing dependent plasticity (STDP) at synapses onto layer 2/3 pyramidal neurons in mouse auditory cortex (AC). Synapses onto layer 2/3 pyramidal neurons exhibit a STDP rule for pairing of postsynaptic spike bursts with single presynaptic stimuli. Pre-before-post pairing at +10 ms results in a timing-dependent long-term potentiation (tLTP), whereas pre-before-post pairing at +50 ms intervals, and post-before-pre pairing at -10 to -20 ms produce a timing-dependent long-term depression. We also characterize how mAChR activation affects plasticity at these synapses, focusing on the induction of tLTP. During pre-before-post pairing at +10 ms, mAChR activation by either carbachol or oxotremorine-M suppresses tLTP. mAChR activation also reduces the NMDA-receptor dependent synaptically evoked increase in calcium in dendrites, apparently without affecting presynaptic transmitter release. Pharmacological experiments suggest that M1 and M3 receptors are not involved in the mAChR-mediated suppression of tLTP. Taken together, these results suggest activating mAChRs in layer 2/3 intracortical circuits can modify the circuit dynamics of AC by depressing tLTP mediated by NMDA receptors, and depressing calcium influx at excitatory synapses onto layer 2/3 pyramidal cells.
Metagenomic analysis of virus diversity and relative abundance in a eutrophic freshwater harbour
Authors: Palermo Christine N. , Fulthorpe Roberta R. , Saati Rosemary , Short Steven M. 
Published: July 2019

ABSTRACTAquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize particle-associated virus communities seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus families Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Diverse Mimiviridae contigs were detected in the samples, but the two sites contained distinct Mimiviridae communities. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Caudovirales were present at low abundances in most samples, contrasting other studies of freshwater environments. Similarly, Phycodnaviridae abundances were surprisingly low in all samples despite the harbour’s capacity to support high algal biomass during the summer and autumn months, suggesting that Mimiviridae are the dominant algae-infecting viruses in this system. Overall, our findings provided insights into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales.
Genetically encoded nanostructures enable acoustic manipulation of engineered cells
Authors: Wu Di , Baresch Diego , Cook Colin , Malounda Dina , Maresca David , Abundo Maria Paulene , Mittelstein David Reza , Shapiro Mikhail G. 
Published: July 2019

ABSTRACTThe ability to mechanically manipulate and control the spatial arrangement of biological materials is a critical capability in biomedicine and synthetic biology. Ultrasound has the ability to manipulate objects with high spatial and temporal precision via acoustic radiation force, but has not been used to directly control biomolecules or genetically defined cells. Here, we show that gas vesicles (GVs), a unique class of genetically encoded gas-filled protein nanostructures, can be directly manipulated and patterned by ultrasound and enable acoustic control of genetically engineered GV-expressing cells. Due to their differential density and compressibility relative to water, GVs experience sufficient acoustic radiation force to allow these biomolecules to be moved with acoustic standing waves, as demonstrated within microfluidic devices. Engineered variants of GVs differing in their mechanical properties enable multiplexed actuation and act as sensors of acoustic pressure. Furthermore, when expressed inside genetically engineered bacterial cells, GVs enable these cells to be selectively manipulated with sound waves, allowing patterning, focal trapping and translation with acoustic fields. This work establishes the first genetically encoded nanomaterial compatible with acoustic manipulation, enabling molecular and cellular control in a broad range of contexts.
Modeling the Role of Hypoxia in Glioblastoma Growth and Recurrence Patterns
Authors: Curtin Lee , Hawkins-Daarud Andrea , Porter Alyx B. , Owen Markus R. , van der Zee Kristoffer G. , Swanson Kristin R. 
Published: July 2019

AbstractA typical feature of glioblastoma (GBM) growth is local recurrence after surgery. However, some GBMs recur distally. It has been noted that GBM patients with perioperative ischemia are more likely to have distal recurrence and that GBM cells migrate faster under hypoxic conditions. We apply the Proliferation Invasion Hypoxia Necrosis Angiogenesis (PIHNA) model to examine the effect of faster hypoxic cell migration on simulated GBM growth. Results suggest that a highly migratory hypoxic cell population drives the growth of the whole tumor and leads to distant recurrence, as do higher normoxic tumor cell migration and low cellular proliferation rates.
Protocols for all-atom reconstruction and high-resolution refinement of protein-peptide complex structures
Authors: Badaczewska-Dawid Aleksandra , Khramushin Alisa , Kolinski Andrzej , Schueler-Furman Ora , Kmiecik Sebastian 
Published: July 2019

SummaryStructural characterizations of protein-peptide complexes may require further improvements. These may include reconstruction of missing atoms and/or structure optimization leading to higher accuracy models. In this work, we describe a workflow that generates accurate structural models of peptide-protein complexes starting from protein-peptide models in C-alpha representation generated using CABS-dock molecular docking. First, protein-peptide models are reconstructed from their C-alpha traces to all-atom representation using MODELLER. Next, they are refined using RosettaFlexPepDock. The described workflow allows for reliable all-atom reconstruction of CABS-dock models and their further improvement to high-resolution models.
Evaluation of longitudinal time-lapsedin vivomicro-CT for monitoring fracture healing in mouse femur defect models
Authors: Wehrle Esther , Tourolle né Betts Duncan C , Kuhn Gisela A , Scheuren Ariane C , Hofmann Sandra , Müller Ralph 
Published: July 2019

AbstractLongitudinalin vivomicro-computed tomography (micro-CT) is of interest to non-invasively capture the healing process of individual animals in preclinical fracture healing studies. However, it is not known whether longitudinal imaging itself has an impact on callus formation and remodeling. In this study, a scan group received weekly micro-CT measurements (week 0-6), whereas controls were only scanned post-operatively and at week 5 and 6. Registration of consecutive scans using a branching scheme (bridged vs. unbridged defect) combined with a two-threshold approach enabled assessment of localized bone turnover and mineralization kinetics relevant for monitoring callus remodeling. Weekly micro-CT application did not significantly change any of the assessed callus parameters in the defect and periosteal volumes. This was supported by histomorphometry showing only small amounts of cartilage residuals in both groups, indicating progression towards the end of the healing period. Also, immunohistochemical staining of Sclerostin, previously associated with mediating adverse radiation effects on bone, did not reveal differences between groups.The established longitudinalin vivomicro-CT-based approach allows monitoring of healing phases in mouse femur defect models without significant effects of anesthesia, handling and radiation on callus properties. Therefore, this study supports application of longitudinalin vivomicro-CT for healing-phase-specific monitoring of fracture repair in mice.
Determining Temporal Stability in Dominance Hierarchies
Authors: Vilette C. , Bonnell T.R. , Henzi S.P. , Barrett L 
Published: July 2019

AbstractThe importance of social hierarchies has led to the development of many techniques for inferring social ranks, leaving researchers with an overwhelming array of options to choose from. Many of our research questions involve longitudinal analyses, so we were interested in a method that would provide reliable ranks across time. But how does one determine which method performs best?We attempt to answer this question by using a training-testing procedure to compare 13 different approaches for calculating dominance hierarchies (seven methods, plus 6 analytical variants of these). We assess each method’s performance, its efficiency, and the extent to which the calculated ranks obtained from the training dataset accurately predict the outcome of observed aggression in the testing dataset.We found that all methods tested performed well, despite some differences in inferred rank order. With respect to the need for a “burn-in” period to enable reliable ranks to be calculated, again, all methods were efficient and able to infer reliable ranks from the very start of the study period (i.e., with little to no burn-in period). Using a common 6-month burn-in period to aid comparison, we found that all methods could predict aggressive outcomes accurately for the subsequent 10 months. Beyond this 10-month threshold, accuracy in prediction decreased as the testing dataset increased in length. The decay was rather shallow, however, indicating overall rank stability during this period.In general, a training-testing approach allows researchers to determine the most appropriate method for their dataset, given sampling effort, the frequency of agonistic interactions, the steepness of the hierarchy, and the nature of the research question being asked. Put simply, we did not find a single best method, but our approach offers researchers a valuable tool for identifying the method that will work best for them.HighlightsAll ranking methods tested performed well at predicting future aggressive outcomes, despite some differences in inferred rank order.All ranking methods appear to be efficient in inferring reliable ranks from the very start (i.e., with little to no burn-in period), but all showed improvement as the burn-in period increased.Using a common 6-month burn-in period, we found that all methods could predict aggressive outcomes accurately for the subsequent 10 months. Beyond this threshold, accuracy in prediction decreased as the testing dataset increased in length.Switching to a data-driven approach to assign k-values, via the training/validation/testing procedure, resulted in a marked improvement in performance in the modified Elo-rating method.
Multivariable regulation of gene expression plasticity in metazoans
Authors: Xiao Long , Zhao Zhiguang , He Fei , Du Zhuo 
Published: July 2019

ABSTRACTAn important capacity of genes is the rapid change of expression levels to cope with environment, known as expression plasticity. Elucidating the genomic mechanisms determining expression plasticity is critical for understanding the molecular basis of phenotypic plasticity, fitness, and adaptation. In this study, we systematically quantified genome-wide gene expression plasticity in four metazoan species by integrating changes of expression levels under a large number of genetic and environmental conditions. From this, we demonstrated that expression plasticity measures a distinct feature of gene expression that is orthogonal to other well-studies features including gene expression potential and tissue specificity/broadness. Expression plasticity is conserved across species with important physiological implications. The magnitude of expression plasticity is highly correlated with gene function and genes with high plasticity are implicated in disease susceptibility. Genome-wide analysis identified many conserved promoter cis-elements, trans-acting factors (such as CFCF), and gene body histone modifications (H3K36me3, H3K79me2, and H4K20me1) that are significantly associated with expression plasticity. Analysis of expression changes in perturbation experiments further validated a causal role of specific transcription factors and histone modifications. Collectively, this work reveals general properties, physiological implications, and multivariable regulation of gene expression plasticity in metazoans, extending the mechanistic understanding of gene regulation.