bluuebunny/crossref_metadata_2025_split huggingface dataset:
When no answer is better than a wrong answer: a causal perspective on batch effects
Authors: Bridgeford Eric W. , Powell Michael , Kiar Gregory , Noble Stephanie , Chung Jaewon , Panda Sambit , Lawrence Ross , Xu Ting , Milham Michael , Caffo Brian , Vogelstein Joshua T. 
Published: September 2021

AbstractBatch effects, undesirable sources of variability across multiple experiments, present significant challenges for scientific and clinical discoveries. Batch effects can (i) produce spurious signals and/or (ii) obscure genuine signals, contributing to the ongoing reproducibility crisis. Because batch effects are typically modeled as classical statistical effects, they often cannot differentiate between sources of variability due to confounding biases, which may lead them to erroneously conclude batch effects are present (or not). We formalize batch effects as causal effects, and introduce algorithms leveraging causal machinery, to address these concerns. Simulations illustrate that when non-causal methods provide the wrong answer, our methods either produce more accurate answers or “no answer”, meaning they assert the data are an inadequate to confidently conclude on the presence of a batch effect. Applying our causal methods to 27 neuroimaging datasets yields qualitatively similar results: in situations where it is unclear whether batch effects are present, non-causal methods confidently identify (or fail to identify) batch effects, whereas our causal methods assert that it is unclear whether there are batch effects or not. In instances where batch effects should be discernable, our techniques produce different results from prior art, each of which produce results more qualitatively similar to not applying any batch effect correction to the data at all. This work therefore provides a causal framework for understanding the potential capabilities and limitations of analysis of multi-site data.
Sex Chromosome Heteromorphism and the Fast-X Effect in Poeciliids
Authors: Darolti Iulia , Fong Lydia J. M. , Sandkam Benjamin A. , Metzger David C. H. , Mank Judith E. 
Published: September 2021

AbstractAccelerated rates of sequence evolution on the X chromosome compared to autosomes, known as Fast-X evolution, have been observed in a range of heteromorphic sex chromosomes. However, it remains unclear how early in the process of sex chromosome differentiation the Fast-X effect becomes detectible. Recently, we uncovered an extreme variation in sex chromosome heteromorphism across Poeciliid fish species. The common guppy,Poecilia reticulata, Endler’s guppy,P. wingei, swamp guppy,P. picta, and para guppy,P. parae, appear to share the same XY system and exhibit a remarkable range of heteromorphism. This sex chromosome system is absent in recent outgroups. We combined analyses of sequence divergence and polymorphism data across Poeciliids to investigate X chromosome evolution as a function of hemizygosity and reveal the causes for Fast-X effects. Consistent with the extent of Y degeneration in each species, we detect higher rates of divergence on the X relative to autosomes, a signal of Fast-X evolution, inP. pictaandP. parae, while no change in the rate of evolution of X-linked relative to autosomal genes inP. reticulata. InP. wingei, the species with intermediate sex chromosome differentiation, we see an increase in the rate of nonsynonymous substitutions on the older stratum of divergence only. We also use our comparative approach to test different models for the origin of the sex chromosomes in this clade. Taken together, our study reveals an important role of hemizygosity in Fast-X and suggests a single, recent origin of the sex chromosome system in this clade.
Single-cell perturbation dissects transcription factor control of progression speed and trajectory choice in early T-cell development
Authors: Zhou Wen , Gao Fan , Romero-Wolf Maile , Jo Suin , Rothenberg Ellen V. 
Published: September 2021

AbstractIn early T-cell development, single cells dynamically shift expression of multiple transcription factors (TFs) during transition from multipotentiality to T-lineage commitment, but the functional roles of many TFs have been obscure. Here, synchronizedin vitrodifferentiation systems, scRNA-seq with batch indexing, and controlled gene-disruption strategies have unraveled single-cell impacts of perturbing individual TFs at two stages in early T-cell development. Single-cell CRISPR perturbation revealed that early-acting TFs Bcl11a, Erg, Spi1 (PU.1), Gata3, and Tcf7 (TCF1) each play individualized roles promoting or retarding T-lineage progression and suppressing alternative trajectories, collectively determining population dynamics and path topologies. Later, during T-lineage commitment, cells prevented from expressing TF Bcl11b ‘realized’ this abnormality not with a developmental block, but by shifting into a divergent path via bZIP and Sox TF activation as well as E protein antagonism, finally exiting the T-lineage trajectory. These TFs thus exert a network of impacts to control progression kinetics, trajectories, and differentiation outcomes of early pro-T cells.
Properties of Photosystem II lacking the PsbJ subunit
Authors: Boussac Alain , Sellés Julien , Hamon Marion , Sugiura Miwa 
Published: September 2021

AbstractPhotosystem II (PSII), the oxygen-evolving enzyme, consists of 17 trans-membrane and 3 extrinsic membrane proteins. Other subunits bind to PSII during assembly, like Psb27, Psb28, Tsl0063. The presence of Psb27 has been proposed (Zabret et al. 2021; Huang et al. 2021; Xiao et al. 2021) to prevent the binding of PsbJ, a single transmembrane α-helix close to the quinone QB binding site. Consequently, a PSII rid of Psb27, Psb28 and Tsl0034 prior to the binding of PsbJ would logically correspond to an assembly intermediate. The present work describes experiments aiming at further characterizing such a ΔPsbJ-PSII, purified from the thermophilic Thermosynechococcus elongatus, by means of MALDI-TOF spectroscopy, Thermoluminescence, EPR spectroscopy and UV-visible time-resolved spectroscopy. In the purified ΔPsbJ-PSII, an active Mn4CaO5 cluster is present in 60-70 % of the centers. In these centers, although the forward electron transfer seems not affected, the Em of the QB/QB- couple increases by ≥ 120 mV thus disfavoring the electron coming back on QA. The increase of the energy gap between QA/QA- and QB/QB- could contribute in a protection against the charge recombination between the donor side and QB-, identified at the origin of photoinhibition under low light (Keren et al. 1997), and possibly during the slow photoactivation process.
Highly specific chimeric DNA-RNA guided genome editing with enhanced CRISPR-Cas12a system
Authors: Kim Hanseop , Lee Wi-jae , Kim Chan Hyoung , Oh Yeounsun , Gwon Lee Wha , Lee Hyomin , Song WooJeung , Hur Junho K. , Lim Kyung-Seob , Jeong Kang Jin , Nam Ki-Hoan , Won Young-Suk , Lee Youngjeon , Kim Young-Hyun , Huh Jae-Won , Jun Bong-Hyun , Lee Dong-Seok , Lee Seung Hwan 
Published: September 2021

AbstractThe clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a system is composed of a Cas12a effector that acts as a deoxyribonucleic acid (DNA)-cleaving endonuclease and a crispr ribonucleic acid (crRNA) that guides the effector to the target DNA. It is considered a key molecule for inducing target-specific gene editing in various living systems. Here, we improved the efficiency and specificity of the CRISPR-Cas12a system through protein and crRNA engineering. In particular, to optimize the CRISPR-Cas12a system at the molecular level, we used a chimeric DNA-RNA guide chemically similar to crRNA to maximize target sequence specificity. Compared to the wild type (wt)-Cas12a system, when using enhanced Cas12a system (en-Cas12a), the efficiency and target specificity improved on average by 7.41 and 7.60 times respectively. In our study, when the chimeric DNA-RNA guided en-Cas12a effector was used, the gene editing efficiency and accuracy were simultaneously increased. These findings could contribute to highly accurate genome editing, such as human gene therapy, in the near future.
CluSem: Accurate Clustering-based Ensemble Method to Predict Motor Imagery Tasks from Multi-channel EEG Data
Authors: Miah Md. Ochiuddin , Muhammod Rafsanjani , Al Mamun Khondaker Abdullah , Farid Dewan Md. , Kumar Shiu , Sharma Alok , Dehzangi Abdollah 
Published: September 2021

AbstractBackgroundThe classification of motor imagery electroencephalogram (MI-EEG) is a pivotal task in the biosignal classification process in the brain-computer interface (BCI) applications. Currently, this bio-engineering-based technology is being employed by researchers in various fields to develop cuttingedge applications. The classification of real-time MI-EEG signals is the most challenging task in these applications. The prediction performance of the existing classification methods is still limited due to the high dimensionality and dynamic behaviors of the real-time EEG data.Proposed MethodTo enhance the classification performance of real-time BCI applications, this paper presents a new clustering-based ensemble technique called CluSem to mitigate this problem. We also develop a new brain game called CluGame using this method to evaluate the classification performance of real-time motor imagery movements. In this game, real-time EEG signal classification and prediction tabulation through animated balls are controlled via threads. By playing this game, users can control the movements of the balls via the brain signals of motor imagery movements without using any traditional input devices.ResultsOur results demonstrate that CluSem is able to improve the classification accuracy between 5% and 15% compared to the existing methods on our collected as well as the publicly available EEG datasets. The source codes used to implement CluSem and CluGame are publicly available at https://github.com/MdOchiuddinMiah/MI-BCI_ML.
Pilot identification of the Live-1/Prox-1 expressing lymphatic vessels and lymphatic elements in the unaffected and affected human brain
Authors: Semyachkina-Glushkovskaya O. , Fedosov I. , Navolokin N. , Shirokov A. , Maslyakova G. , Bucharskaya A. , Blokhina I. , Terskov A. , Khorovodov A. , Postnov D. , Kurths J. 
Published: September 2021

AbstractWe report here a pilot identification of the presence of the lumenized Lyve-1/Prox-1-expressing vessels with distinct walls composed of a single endothelial layer in the unaffected brain and with intraventricular hemorrhages. These lymphatic vessels (LVs) have valves and an undulating shape in the distal region that is the classical characteristic of lymphatic precollectors. Furthermore, we identified Lyve-1/Prox-1-expressing lymphatic elements in the enlarged perivascular spaces. These pioneering results might be a revolutionary step in our understanding of anatomy and physiology of the cerebral lymphatics and stimulate a reassessment of basic assumptions in the aetiology of brain diseases associated with lymphatic dysfunction. The discovery of the cerebral LVs is a crucial step in the development of breakthrough technologies of modulations of lymphatic removing of toxins and blood from the brain.One Sentence SummaryLyve1/Prox1-expressing lymphatic vessels and elements in the unaffected and affected human brain.
Hippocampal astroglial hypertrophy in mice subjected to early life maternal deprivation
Authors: Nandi Arnab , Virmani Garima , Marathe Swananda 
Published: September 2021

AbstractEarly-life stress (ELS), including chronic deprivation of maternal care, exerts persistent life-long effects on animal physiology and behavior, and is associated with several neurodevelopmental disorders. Long-lasting changes in neuronal plasticity and electrophysiology are documented extensively in the animal models of ELS. However, the role of astroglia in the lasting effects of ELS remains elusive. Astrocytes are intricately involved in the regulation of synaptic physiology and behavior. Moreover, astrocytes play a major role in the innate and adaptive immune responses in the central nervous system (CNS). The role of immune responses and neuroinflammation in the altered brain development and persistent adverse effects of ELS are beginning to be explored. Innate immune response in the CNS is characterized by a phenomenon called astrogliosis, a process in which astrocytes undergo hypertrophy, along with changes in gene expression and function. While the immune activation and neuroinflammatory changes concomitant with ELS, or in juveniles and young adults have been reported, it is unclear whether mice subjected to ELS exhibit astrogliosis-like alterations well into late-adulthood. Here, we subjected mice to maternal separation from postnatal day 2 to day 22 and performed comprehensive morphometric analysis of hippocampal astrocytes during late-adulthood. We found that the astrocytes in the stratum radiatum region of the CA1 hippocampal subfield from maternally separated mice exhibit significant hypertrophy as late as 8 months of age, revealing the crucial changes in astrocytes that manifest long after the cessation of ELS. This study highlights the persistence of neuroinflammatory changes in mice exposed to ELS.
Continuous tracking of gravistimulated roots in a chambered coverslip by confocal microscopy allows first glimpse on mechanoadaptation of cell files during curvature initiation
Authors: Retzer Katarzyna 
Published: September 2021

AbstractMechanical responses of individual cells to plant internal and external stimuli modulate organ movement and ensure plant survival as sessile organism in a constantly changing environment. The root is a complex, three-dimensional object, which continuously modifies its growth path. Autonomous and paratonic root movements are both orchestrated by different signaling pathways, whereby auxin modulated directional growth adaptations, including gravitropic response, were already subject of manifold studies. But we still know very little about how cells adapt upon gravitropic stimulus to initiate curvature establishment, which is required to align root tip growth again along the gravitropic vector. This manuscript shows first insights into cell file movements upon gravitropic stimulus of Arabidopsis thaliana roots that initiate curvature establishment. The roots were grown shaded from light and without exogenous sucrose supplementation, both growth conditions that are known to negatively interfere with directed root growth, which allowed a more uniform tracking of root bending by using a confocal microscope with vertical stage.
CROP: A Retromer-PROPPIN complex mediating membrane fission in the endo-lysosomal system
Authors: Courtellemont Thibault , De Leo Maria Giovanna , Gopaldass Navin , Mayer Andreas 
Published: September 2021

AbstractEndo-lysosomal compartments exchange proteins by fusing, fissioning, and through endosomal transport carriers. Thereby, they sort many plasma membrane receptors and transporters and control cellular signaling and metabolism. How the membrane fission events are catalyzed is poorly understood. Here, we identify the novel CROP complex as a factor acting at this step. CROP joins members of two protein families: the peripheral subunits of retromer, a coat forming endosomal transport carriers, and membrane inserting PROPPINs. Integration into CROP potentiates the membrane fission activity of the PROPPIN Atg18 on synthetic liposomes and confers strong preference for binding PI(3,5)P2, a phosphoinositide required for membrane fission activity. Disrupting CROP blocks fragmentation of lysosome-like yeast vacuoles in vivo. CROP-deficient mammalian endosomes accumulate micrometer-long tubules and fail to export cargo, suggesting that carriers attempt to form but cannot separate from these organelles. PROPPINs compete for retromer binding with the SNX proteins, which recruit retromer to the membrane during the formation of endosomal carriers. Transition from retromer-SNX complexes to retromer-PROPPIN complexes might hence switch retromer activities from cargo capture to membrane fission.
Parallel evolution of phage resistance - virulence trade - offs duringin vitroand nasalPseudomonas aeruginosaphage treatment
Authors: Castledine Meaghan , Padfield Daniel , Sierocinski Pawel , Soria Pascual Jesica , Hughes Adam , Mäkinen Lotta , Friman Ville-Petri , Pirnay Jean-Paul , Merabishvili Maya , De Vos Daniel , Buckling Angus 
Published: September 2021

AbstractWith rising antibiotic resistance, there has been increasing interest in treating pathogenic bacteria with bacteriophages (phage therapy). One limitation of phage therapy is the ease at which bacteria can evolve resistance. Negative effects of resistance may be mitigated when resistance results in reduced bacterial growth and virulence, or when phage coevolve to overcome resistance. Resistance evolution and its consequences are contingent on the bacteria-phage combination and their environmental context, making therapeutic outcomes hard to predict. One solution might be to conduct “in vitroevolutionary simulations” using bacteria-phage combinations from the therapeutic context. Overall, our aim was to investigate parallels betweenin vitroexperiments andin vivodynamics in a human participant. Evolutionary dynamics were similar, with high levels of resistance evolving quickly with limited evidence of phage evolution. Resistant bacteria – evolvedin vitroandin vivo- had lower virulence.In vivo, this was linked to lower growth rates of resistant isolates, whereasin vitrophage resistant isolates evolved greater biofilm production. Population sequencing suggests resistance resulted from selection onde novomutations rather than sorting of existing variants. These results highlight the speed at which phage resistance can evolvein vivo, andin vitroexperiments may give useful insights for clinical evolutionary outcomes.
The transformation of corrosion products on 0Cu2Cr carbon steel in the marine
Authors: Liu Hongyu , Teng Yingxue , Guo Jing , Xiao Qinghe , Wang Miao , Pang QiHang , Li Shengli 
Published: September 2021

Purpose
This paper aims to explore the transformation process and transformation mechanism of carbon steel under the marine environment.

Design/methodology/approach
In this paper, the transformation and rust layers corrosion products on 0Cu2Cr carbon steel with different cycles coupon test was investigated and deeply explored by scanning electron microscope, energy dispersive spectrometer, X-ray diffraction.

Findings
The results showed that the thickness of rust layers grew from 71.83 µm to 533.7 µm with increasing duration of corrosion. The initial corrosion product was γ-FeOOH, then part of the γ-FeOOH continued growing, and under the capillary action, the other part of the γ-FeOOH transformed to α-FeOOH.

Originality/value
To the best of the authors’ knowledge, this paper puts forward for the first time a new viewpoint of the development of corrosion products of low-carbon steel in two ways. This discovery provides a new idea for the future development of steel for marine engineering.
Operational performance improvement through continuous improvement initiatives in micro-enterprises of Turkey
Authors: Inan Guven Gurkan , Gungor Zahit Ergun , Bititci Umit Sezer , Halim-Lim Sarina Abdul 
Published: September 2021

PurposeMicro-enterprises have a vital role in the development of a nation by creating employment, encouraging entrepreneurship, balancing social income and educating the workforce. Yet, micro-enterprises face significant operational challenges such as low productivity, high production costs and long changeover times. These challenges are often overlooked by researchers and practitioners but have a drastic impact on micro-enterprises' operational performance. With over 95% of the economy consisting of micro-enterprises, it is vital to improve operational performance and competitiveness of the micro-enterprises.Design/methodology/approachConsidering the data availability and practical challenges of gathering data from micro-enterprises, an action research methodology was selected as a suitable research method. Following the initial diagnostic visits, planned interventions were prepared and results were observed to gather data and draw conclusions.FindingsFindings suggest that commonly adapted performance improvement initiatives by large enterprises cannot be directly applied in micro-enterprises to enhance operational performance. Micro-enterprises lack the critical resources and company culture to easily adapt these initiatives. On the other hand, when these performance improvement initiatives are filtered according to specific needs of micro-enterprises, continuous improvement initiatives were often found to be effective in improving operational performance. Specifically, 5S, single-minute exchange of dies (SMED), suggestion schemes, layout improvements, management coaching, visual management, empowerment were found to be useful and suitable to address command and control culture, low productivity, unorganised workspace, undelegated authority, low skilled employees and unwillingness to take responsibility problems.Research limitations/implicationsFurther research is required to investigate the specific factors that affect the adaptation of continuous improvement initiatives such as culture and industry type.Originality/valueThis research extends and contributes the current literature on continuous improvement initiatives by revealing how performance improvement initiatives need to be filtered according to the specific needs of micro-enterprises, and how these initiatives can be used to address specific problems to improve operational efficiency. It provides a conceptual framework to guide the decision-making process on operational performance improvement in micro-enterprises.
Toward an understanding of the relationship between LMX and performance over time: the role of trust in leader and appraisal satisfaction
Authors: Gabel-Shemueli Rachel , Riva Zaferson Franco Alberto 
Published: September 2021

PurposeThe purpose of this two-wave longitudinal study was to examine the impact of leader–member exchange (LMX) on employee performance through trust in leader and appraisal satisfaction both cross-sectionally and after one year, and the reciprocal effect of employee performance on LMX one year later.Design/methodology/approachA full panel data design was applied and the sample consisted of 289 employees of a Peruvian insurance organization. Structural equation modeling (SEM) was used to test the research hypotheses.FindingsThe results show the relationship between LMX and performance was sequentially mediated by trust in leader and appraisal satisfaction on both occasions. Additionally, employee performance at Time 1 positively influenced LMX at Time 2.Originality/valueThis study highlights the dynamic and complex relationship between LMX and employee performance over time while identifying relevant variables that influence it.