bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wolverine density distribution reflects past persecution and current management in Scandinavia
Authors: Moqanaki Ehsan , Milleret Cyril , Dupont Pierre , Brøseth Henrik , Bischof Richard 
Published: November 2022

AbstractAfter centuries of intense persecution, several large carnivore species in Europe and North America have experienced a rebound. Today’s spatial configuration of large carnivore populations has likely arisen from the interplay between their ecological traits and current environmental conditions, but also from their history of persecution and protection. Yet, due to the challenge of studying population-level phenomena, we are rarely able to disentangle and quantify the influence of past and present factors driving the spatial distribution and density of these controversial species. Using spatial capture-recapture models and a data set of 742 genetically identified wolverinesGulo gulocollected over ½ million km2across their entire range in Norway and Sweden, we identify landscape-level factors explaining the current population density of wolverines in the Scandinavian Peninsula. Distance from the relic range along the Swedish-Norwegian border, where the wolverine population survived a long history of persecution, remains a key determinant of wolverine density today. However, regional differences in management and environmental conditions also played an important role in shaping spatial patterns in present-day wolverine density. Specifically, we found evidence of slower recolonization in areas that had set lower wolverine population goals in terms of the desired number of annual reproductions. Management of transboundary large carnivore populations at biologically relevant scales may be inhibited by administrative fragmentation. Yet, as our study shows, population-level monitoring is an achievable prerequisite for a comprehensive understanding of the distribution and density of large carnivores across an increasingly anthropogenic landscape.
The repertoire of copy number alteration signatures in human cancer
Authors: Tao Ziyu , Wang Shixiang , Wu Chenxu , Wu Tao , Zhao Xiangyu , Ning Wei , Wang Guangshuai , Wang Jinyu , Chen Jing , Diao Kaixuan , Chen Fuxiang , Liu Xue-Song 
Published: November 2022

AbstractCopy number alterations (CNAs) are a predominant source of genetic alterations in human cancer and play an important role in cancer progression. However comprehensive understanding of the mutational processes and signatures of CNA is still lacking. Here we developed a mechanism-agnostic method to categorize CNA based on various fragment properties, which reflect the consequences of mutagenic processes and can be extracted from different types of data, including whole genome sequencing (WGS) and SNP array. The 14 signatures of CNA have been extracted from 2778 pan-cancer analysis of whole genomes (PCAWG) WGS samples, and further validated with 10851 the cancer genome atlas (TCGA) SNP array dataset. Novel patterns of CNA have been revealed through this study. The activities of some CNA signatures consistently predict cancer patients’ prognosis. This study provides a repertoire for understanding the signatures of CNA in cancer, with potential implications for cancer prognosis, evolution, and etiology.
CRitical Assessment of genomic COntamination detection at several Taxonomic ranks (CRACOT)
Authors: Cornet Luc , Lupo Valérian , Declerck Stéphane , Baurain Denis 
Published: November 2022

AbstractBackgroundGenome contamination is a well-known issue in (meta)genomics. Although it has received a lot of attention, with an increasing number of detection tools made available over the years, no comparison between these tools exists in the literature.ResultsHere, we report the benchmarking of six of the most popular tools using a simulated framework. Our simulations were conducted on six different taxonomic ranks, from phylum to species. The analysis of the estimated contamination levels indicates that the precision of the tools is not good, often due to large overdetection but also underdetection, especially at the genus and species ranks. Furthermore, our results show that only redundant contamination is accurately estimated.ConclusionOur results indicate that using a combination of tools, including Kraken2, is necessary to estimate the contamination level accurately. We also provide a freely available contamination simulation framework, CRACOT, which may be useful for estimating the accuracy of future algorithms.
Taxonomic vs genomic fungi: contrasting evolutionary loss of protistan genomic heritage and emergence of fungal novelties
Authors: Merényi Zsolt , Krizsán Krisztina , Sahu Neha , Liu Xiao-Bin , Bálint Balázs , Stajich Jason , Spatafora Joseph W. , Nagy László G. 
Published: November 2022

AbstractFungi are among the most ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. However, despite intense interest in their origins, major genomic trends characterising the evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here, we reconstructed gene family evolution across 123 genomes of fungi and relatives and show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and highly episodic innovation via gene duplication. We find that the gene content of early-diverging fungi is protist-like in many respects, owing to the conservation of protist genes in early fungi. While gene loss has been constant and gradual during early fungal evolution, our reconstructions show that gene innovation showed two peaks. Gene groups with the largest contribution to genomic change included extracellular proteins, transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal evolution. Taken together, this work provided a highly resolved genome-wide catalogue of gene family changes across fungal evolution. This suggests that the genome of pre-fungal ancestors may have been transformed into the archetypal fungal genome by a combination of gradual gene loss, turnover and two large duplication events rather than by abrupt changes, and consequently, that the taxonomically defined fungal kingdom does not represent a genomically uniform assemblage of extant species characterized by diagnostic synapomorphies.
An open-access EEG dataset for speech decoding: Exploring the role of articulation and coarticulation
Authors: Moreira João Pedro Carvalho , Carvalho Vinícius Rezende , Mendes Eduardo Mazoni Andrade Marçal , Fallah Ariah , Sejnowski Terrence J. , Lainscsek Claudia , Comstock Lindy 
Published: November 2022

ABSTRACTElectroencephalography (EEG) holds promise for brain-computer interface (BCI) devices as a non-invasive measure of neural activity. With increased attention to EEG-based BCI systems, publicly available datasets that can represent the complex tasks required for naturalistic speech decoding are necessary to establish a common standard of performance within the BCI community. Effective solutions must overcome various kinds of noise in the EEG signal and remain reliable across sessions and subjects without overfitting to a specific dataset or task. We present two validated datasets (N=8 and N=16) for classification at the phoneme and word level and by the articulatory properties of phonemes. EEG signals were recorded from 64 channels while subjects listened to and repeated six consonants and five vowels. Individual phonemes were combined in different phonetic environments to produce coarticulated variation in forty consonant-vowel pairs, twenty real words, and twenty pseudowords. Phoneme pairs and words were presented during a control condition and during transcranial magnetic stimulation targeted to inhibit or augment the EEG signal associated with specific articulatory processes.
Legionella pneumophilamodulates host cytoskeleton by an effector of transglutaminase activity
Authors: Liu Yan , Liu Yao , Luo Zhao-Qing 
Published: November 2022

AbstractThe bacterial pathogenLegionella pneumophiladelivers more than 330 effector proteins into host cells through its Dot/Icm type IV secretion system (T4SS) to facilitate its intracellular replication. A number of these effectors modulate organelle trafficking pathways to create a membrane-bound niche called theLegionellacontaining vacuole (LCV). In this study, we found thatL. pneumophilainduces F-actin accumulation in host cell cortex by its Dot/Icm substrate RavJ (Lpg0944). RavJ harbors an C101H138D170motif associated with human tissue transglutaminases (TGs). We showed that RavJ catalyzes a covalent linkage between actin and the Motin family proteins Angiomotin (AMOT) and Angiomotin-like 1 (AMOTL1), proteins known to regulate tube formation and cell migration. Further study revealed that RavJ-induced crosslink between actin and AMOT occurs on its Gln354residue. Crosslink between actin and AMOT significantly reduces the binding between actin and its binding partner cofilin, suggesting that RavJ inhibits actin depolymerization. We also demonstrated that the metaeffector LegL1 directly interacts with RavJ to antagonize its transglutaminase activity, leading to reduced crosslink between actin and Motin proteins. Our results reveal a novel mechanism of modulating the host actin cytoskeleton byL. pneumophila.
DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43
Authors: Lam Andy Y.W. , Tsuboyama Kotaro , Tadakuma Hisashi , Tomari Yukihide 
Published: November 2022

AbstractProtein misfolding and aggregation are characteristic features of neurodegenerative diseases. While molecular chaperones are well-known suppressors of these aberrant events, we recently reported that highly disordered, hydrophilic and charged heat-resistant obscure (Hero) proteins may have similar effects. Specifically, Hero proteins can maintain the activity of other proteins from denaturing conditions in vitro, while their overexpression can suppress cellular aggregation and toxicity associated with aggregation-prone proteins. However, it is unclear how these protective effects are achieved. Here, we utilized single-molecule FRET to monitor the conformations of the aggregation-prone prion-like low complexity domain (LCD) of TAR DNA-binding protein 43 (TDP-43). While we observed high conformational heterogeneity in wild-type LCD, the ALS-associated mutation A315T promoted collapsed conformations. In contrast, an Hsp40 chaperone, DNAJA2, and a Hero protein, Hero11 stabilized extended states of the LCD, consistent with their ability to suppress the aggregation of TDP-43. Our results link single-molecule effects on conformation to macro effects on bulk aggregation, where a Hero protein, like a chaperone, can maintain the conformational integrity of a client protein to prevent its aggregation.
Learning to predict based on self- versus externally induced prediction violations: a direct comparison using a Bayesian inference modelling approach
Authors: Boonstra E.A. , Slagter H.A. 
Published: November 2022

AbstractPredictive processing is quickly gaining ground as a theory of perception and attention. From this perspective the brain is cast as an organism’s predictive model of how its world works and will continue to work in the future. However, research on the brain’s predictive capacities remains beholden to traditional research practices in which participants are passively shown stimuli without their active involvement. The current study is an investigation into ways in which self-generated predictions may differ from externally induced predictions. Participants completed a volatile spatial attention task under both conditions on different days. We used the Hierarchical Gaussian Filter, an approximate Bayesian inference model, to determine subject-specific parameters of belief-updating and inferred volatility. We found preliminary evidence in support of self-generated predictions incurring a larger reaction time cost when violated compared to predictions induced by sensory cue, which translated to participants’ increased sensitivity to changes in environmental volatility. Our results suggest that internally generated predictions may be afforded more weight, but these results are complicated by session order and duration effects, as well as a lack of statistical power. We discuss the limitations of our study preventing us from replicating previous research, and ways to remedy these shortcomings in future studies.
Conscious perception and the role of the basal ganglia: preliminary findings from a deep brain stimulation study
Authors: Boonstra E.A. , Bais M.N. , van Schouwenburg M.R. , van den Munckhof P. , Smit D.J.A. , Denys D. , Slagter H.A. 
Published: November 2022

AbstractConscious perception is thought to depend on global amplification of sensory input. In recent years, the basal ganglia have been implicated in gating conscious access due to their consistent involvement in thalamocortical loops. However, much of the evidence implicating the basal ganglia in these processes in humans is correlational. The current study is a preliminary investigation in four patients to explore whether deep brain stimulation (DBS) in the basal ganglia might improve conscious perception. In our study, treatment-resistant obsessive-compulsive disorder (OCD) patients with a striatal DBS implant completed two canonical conscious perception tasks: emotion-induced blindness and backward masking. We found preliminary evidence in support of a role played by the basal ganglia in conscious perception at the behavioral level: patients performed better when stimulation was active, but we could not establish neural effects corresponding to these behavioral findings, possibly due to our small sample size. We discuss the potential implications and limitations of our study and delineate avenues for future research.
In-depth specificity profiling of Pro-Pro endopeptidases (PPEPs) using combinatorial synthetic peptide libraries
Authors: Claushuis Bart , Cordfunke Robert A. , de Ru Arnoud H. , Otte Annemarie , van Leeuwen Hans C. , Klychnikov Oleg I. , van Veelen Peter A. , Corver Jeroen , Drijfhout Jan W. , Hensbergen Paul J. 
Published: November 2022

AbstractProteases comprise the class of enzymes that catalyze the hydrolysis of peptide bonds, thereby playing a pivotal role in many aspects of life. The amino acids surrounding the scissile bond determine the susceptibility towards protease-mediated hydrolysis. A detailed understanding of the cleavage specificity of a protease can lead to the identification of its endogenous substrates, while it is also essential for the design of inhibitors. We developed a new method which combines the high diversity of a combinatorial synthetic peptide library with the sensitivity and detection power of mass spectrometry to determine protease cleavage specificity. We applied this method to study a group of bacterial metalloproteases that have the unique specificity to cleave between two prolines, i.e. Pro-Pro endopeptidases (PPEPs). We not only confirmed the prime-side specificity of PPEP-1 and PPEP-2, but also revealed some new unexpected peptide substrates. Moreover, we have characterized a new PPEP (PPEP-3) which has a prime-side specificity that is very different from that of the other two PPEPs. Importantly, the approach that we present in this study is generic and can be extended to investigate the specificity of other proteases.
Elevated α-synuclein attenuates phagocytosis inSNCAtriplication human iPSC-derived neuron:microglia co-cultures
Authors: Lieberman Richard , Elnaggar Khaled , Jesseman Kimberly , DeFrancisco Sarah , Degouveia Kelsey , Suneby Emma , Wu Hao , Rojas L. Alejandro , Graef John D. 
Published: November 2022

AbstractSynucleinopathies such as Parkinson’s disease (PD) are characterized by pathologic production, aggregation, and cell-to-cell transmission of α-synuclein (α-syn) protein that results in impaired cellular function. While neurons of the substantia nigra pars compacta express high levels of α-synuclein and are highly vulnerable to its aberrant expression or conformation, brain-resident macrophages (microglia) are also sensitive to abnormal α-synuclein, with recent reports indicating that elevated levels impair phagocytic abilityin vivoandin vitro. To explore the impact of elevated α-syn on microglial function we employed a co-culture model containing iPSC-derived neurons and microglia-like cells. iPSCs from healthy control donors and a Parkinson’s donor with an allelic triplication of theSNCAgene locus were differentiated into neurons and microglia-like cells. In monoculture, neurons and microglia generated from theSNCAtriplication donor expressed higher levels ofSNCAtranscript and protein. Neurons were found to have significantly greater expression ofSNCAcompared to microglia, regardless of donor genotype. Co-cultures of neurons and microglia revealed that microglia cultured withSNCAtriplication neurons displayed reduction in phagocytosis of fluorescentE. coli, irrespective of microglia donor genotype.SNCAmRNA and protein expression could be reduced with treatment with an antisense oligonucleotide (ASO) targetingSNCA. ASO treatment partially rescued microglia phagocytosis inSNCAtriplication co-cultures and in co-cultures containingSNCAtriplication neurons and healthy control microglia. Our results complement and extend previous findings of impaired microglial function in the presence of elevated α-synuclein in a novel patient-derived co-culture model that utilizes more disease-relevant conditions rather than the relaying on the addition of exogenous α-synuclein.
Extracting electromyographic signals from multi-channel local-field-potentials using independent component analysis without direct muscular recording
Authors: Osanai Hisayuki , Yamamoto Jun , Kitamura Takashi 
Published: November 2022

SummaryElectromyography (EMG) has been commonly used for precise identification of animal behavior. However, they are often not recorded together with in vivo electrophysiology due to the need for additional surgeries and setups and the high risk of mechanical wire disconnection. While independent component analysis (ICA) has been used to reduce noise from field potential data, there has been no attempt to proactively use the removed “noise”, of which EMG signals are thought to be one of the major sources. Here, we demonstrate that EMG signals can be reconstructed without direct EMG recording, using the “noise” ICA component from local field potentials. The extracted component is highly correlated with directly measured EMG, termed as IC-EMG. IC-EMG is useful for measuring an animal’s sleep/wake, freezing response and NREM/REM sleep states consistently with actual EMG. Our method has advantages in precise and long-term behavioral measurement in wide-ranged in vivo electrophysiology experiments.Highlights-EMG signals can be extracted from LFP signals without direct muscular recording-The extracted signal is highly correlated with direct EMG recording signals-The extracted signal is useful in measuring animal behaviors as well as actual EMG-This method contributes to precise and stable long-term behavior measurementIn briefOsanai et al. demonstrate electromyography (EMG) signals can be extracted from multi-channel local field potential (LFP) recordings using blind-source-separation technique without direct measurement of muscle activity. The proposed method adds precise and long-term behavioral measurements with EMG information in wide-ranged in vivo electrophysiology experiments.
The relationship between electronic human resource management and employee job satisfaction in organizational value-creation in Africa: the case of Zimbabwe
Authors: Nyathi Musa , Kekwaletswe Ray 
Published: November 2022

PurposeThe purpose of this paper is to examine the mediating effect of employee job satisfaction on the relationship between electronic human resource management (e-HRM) use and e-HRM macro-level consequences.Design/methodology/approachData were collected through a survey involving 32 organizations, using e-HRM applications. A purposive sampling technique was employed. A structural equation modeling technique with the use of the process macro approach was used to analyze collected data.FindingsE-HRM use has a positive and significant effect on e-HRM macro-level consequences and constituent elements of e-HRM operational, relational and transactional consequences. Employee job satisfaction partially mediates the relationship between e-HRM use and e-HRM macro-level consequences.Practical implicationsThe use of e-HRM, complemented by human resource best practices, enhances employee job satisfaction. At an indirect level, job satisfaction partially mediates the effect of e-HRM use on e-HRM macro-level consequences. Organizations should invest in job satisfaction-enhancing practices to ensure attainment of intended organization-wide consequences on a more consistent basis.Originality/valueThe study broadens the scope through which the association between e-HRM use, e-HRM macro-level consequences and employee job satisfaction are viewed. The study illustrates the limitations of the deterministic view of e-HRM use, while supporting the assumptions of the moderate determinism approach, which pin the success of e-HRM systems on the performance and satisfaction of e-HRM actors. The level of employee job satisfaction mediates the relationship between e-HRM use and e-HRM macro-level consequences. The study, to the authors' knowledge, is the first in establishing such an effect.
Copyright implications for the aggregation of audiovisual content in Greece
Authors: Malliari Afrodite , Nitsos Ilias , Zapounidou Sofia , Doropoulos Stavros 
Published: November 2022

Purpose
This paper aims to attempt to provide an overview of the copyright legal framework for audiovisual resources in Europe and Greece, how Audiovisual (AV) content is currently licensed by Greek providers and how licenses or copyright exceptions enable its reuse. The motivation for this work was the development of an aggregation service for audiovisual resources in Greece, the Open AudioVisual Archives (OAVA) platform.

Design/methodology/approach
Copyright licenses and exceptions in the European Union and in Greek Legislation have been thoroughly reviewed along with the reuse of content, based on the terms of Fair Use, Rights Statements and Creative Commons. Licensing issues for the most well-known aggregation services, such as Europeana, Digital Public Library of America, Trove, Digital New Zealand and the National Digital Library of India, have also been studied and considered. Audiovisual content providers in Greece have been recorded, and their licensing preferences have been analyzed. Pearson’s chi-square test was applied to test the relationship between the provider’s type, resources’ genre and licenses used.

Findings
Despite the abundance of copyright legislation in the European Union and in Greece, audiovisual content providers in Greece seem to ignore it or find it difficult to choose the right license. More than half of them choose to publish their resources on popular audiovisual platforms using the default licensing option provided. Creative Commons licenses are preferred for audiovisual content that falls into the following categories: open courses (almost exclusively) and interviews and digital collection/research projects (about half of the content).

Originality/value
This paper examines audiovisual content aggregation, in the EU and Greece, from a legal point of view. To the best of the authors’ knowledge, it is the first attempt to record and analyze the licensing preferences of Greek AV content providers.