bluuebunny/crossref_metadata_2025_split huggingface dataset:
Memory performance following napping in habitual and non-habitual nappers
Authors: Leong Ruth L F , Yu Nicole , Ong Ju Lynn , Ng Alyssa S C , Jamaluddin S Azrin , Cousins James N , Chee Nicholas I Y N , Chee Michael W L 
Published: December 2020

Abstract

Study Objectives
Afternoon naps benefit memory but this may depend on whether one is a habitual napper (HN; ≥1 nap/week) or non-habitual napper (NN). Here, we investigated whether a nap would benefit HN and NN differently, as well as whether HN would be more adversely affected by nap restriction compared to NN.

Methods
Forty-six participants in the nap condition (HN-nap: n = 25, NN-nap: n = 21) took a 90-min nap (14:00–15:30 pm) on experimental days while 46 participants in the Wake condition (HN-wake: n = 24, NN-wake: n = 22) remained awake in the afternoon. Memory tasks were administered after the nap to assess short-term topographical memory and long-term memory in the form of picture encoding and factual knowledge learning respectively.

Results
An afternoon nap boosted picture encoding and factual knowledge learning irrespective of whether one habitually napped (main effects of condition (nap/wake): ps &lt; 0.037). However, we found a significant interaction for the hippocampal-dependent topographical memory task (p = 0.039) wherein a nap, relative to wake, benefitted habitual nappers (HN-nap vs HN-wake: p = 0.003) compared to non-habitual nappers (NN-nap vs. NN-wake: p = 0.918). Notably for this task, habitual nappers’ performance significantly declined if they were not allowed to nap (HN-wake vs NN-wake: p = 0.037).

Conclusions
Contrary to concerns that napping may be disadvantageous for non-habitual nappers, we found that an afternoon nap was beneficial for long-term memory tasks even if one did not habitually nap. Naps were especially beneficial for habitual nappers performing a short-term topographical memory task, as it restored the decline that would otherwise have been incurred without a nap.

Clinical Trial Information
NCT04044885.
Role of Respiratory Buffering in the Relationship Between Recovery and Performance Fatigability After Aerobic Exercise Training
Authors: Wooten Liana C. , Neville Brian T. , Guccione Andrew A. , Chin Lisa M.K. , Keyser Randall E. 
Published: December 2020

Purpose:
This study characterized the influence of excess expired carbon dioxide (excess V̇co
2) in the relationship between recovery and fatigability.

Methods:
Twenty healthy adults completed peak cardiopulmonary exercise tests (CPXs) and constant work rate tests before and after a vigorous, 4-week aerobic exercise training (AET) regimen. Each test was followed by 10 minutes of recovery and an endurance test at 70% of peak watts attained during CPX. Fatigability was assessed by measures of time to exhaustion and power output. Metabolic and recovery capacity indices were obtained. Data were analyzed using correlations and regressions and compared pre/post AET using paired t tests.

Results:
Significant improvements in recovery and fatigability were observed after AET, along with significant increases in total and excess V̇co
2. Relationships between measures of recovery and fatigability were observed, although strengths of the relationships were diminished after controlling analyses for the effect of excess V̇co
2.

Conclusions:
This study suggests that the ionic buffering capacity may moderate the relationship between recovery and fatigability. These results could have implications regarding AET-induced buffering dynamics, and its role in fatigue resistance when performing activities above moderate intensities. This may be of particular importance in patients with cardiopulmonary complications, unable to improve peak aerobic capacity.
A feature-based network analysis and fMRI meta-analysis reveal three distinct types of prosocial decisions
Authors: Rhoads Shawn A. , Cutler Jo , Marsh Abigail A. 
Published: December 2020

AbstractTasks that measure correlates of prosocial decision-making share one common feature: agents can make choices that increase the welfare of a beneficiary. However, prosocial decisions vary widely as a function of other task features. The diverse ways that prosociality is defined and the heterogeneity of prosocial decisions have created challenges for interpreting findings across studies and identifying their neural correlates. To overcome these challenges, we aimed to organize the prosocial decision-making task-space of neuroimaging studies. We conducted a systematic search for studies in which participants made decisions to increase the welfare of others during fMRI. We identified shared and distinct features of these tasks and employed an unsupervised graph-based approach to assess how various forms of prosocial decision-making are related in terms of their low-level components (e.g., task features like potential cost to the agent or potential for reciprocity). Analyses uncovered three clusters of prosocial decisions, which we labeled cooperation, equity, and altruism. This feature-based representation of the task structure was supported by results of a neuroimaging meta-analysis that each type of prosocial decisions recruited diverging neural systems. Results clarify some of the existing heterogeneity in how prosociality is conceptualized and generate insight for future research and task paradigm development.
Regional structural-functional connectome coupling is heritable and associated with age, sex and cognitive scores in adults
Authors: Gu Zijin , Jamison Keith Wakefield , Sabuncu Mert Rory , Kuceyeski Amy 
Published: December 2020

ABSTRACTLarge scale white matter brain connections quantified via the structural connectome (SC) act as the backbone for the flow of functional activation, which can be represented via the functional connectome (FC). Many studies have used statistical analysis or computational modeling techniques to relate SC and FC at a global, whole-brain level. However, relatively few studies have investigated the relationship between individual cortical and subcortical regions’ structural and functional connectivity profiles, here called SC-FC coupling, or how this SC-FC coupling may be heritable or related to age, sex and cognitive abilities. Here, we quantify regional SC-FC coupling in a large group of healthy young adults (22 to 37 years) using diffusion-weighted MRI and resting-state functional MRI data from the Human Connectome Project. We find that while regional SC-FC coupling strengths vary widely across cortical, subcortical and cerebellar regions, they were strongest in highly structurally connected visual and subcortical areas. Additionally, depending on the region, SC-FC coupling varied across sexes and with age and composite cognitive scores. Specifically, SC-FC coupling in the cerebellum tended to decrease with age while coupling in medial fronto-orbital areas tended to increase with age. Males had stronger coupling in many regions, particularly in the right orbito-frontal region and areas in the ventral attention and default mode networks, while females had higher coupling strength in right hippocampus. Furthermore, increased SC-FC coupling in the right insula and decreased coupling in bilateral middle cingulate and supplementary motor areas was associated with higher composite cognitive scores. Finally, we found SC-FC coupling to be highly heritable, particularly in higher order default mode, dorsal/ventral attention and fronto-parietal networks. Taken together, these results suggest regional structure-function coupling in young adults varies with age, is generally stronger in males, is associated with composite cognitive scores and is highly heritable.
Osteoclasts contribute to early development of chronic inflammation by promoting dysregulated hematopoiesis and myeloid skewing
Authors: Madel Maria-Bernadette , Ibáñez Lidia , Ciucci Thomas , Halper Julia , Topi Majlinda , Garchon Henri-Jean , Rouleau Matthieu , Mueller Christopher G , Peyrin-Biroulet Laurent , Moulin David , Blin-Wakkach Claudine , Wakkach Abdelilah 
Published: December 2020

ABSTRACTIncreased myelopoiesis is a hallmark of many chronic inflammatory diseases. However, the mechanisms involved in the myeloid skewing of hematopoiesis upon inflammation are still incompletely understood. Here, we identify an unexpected role of bone-resorbing osteoclasts in promoting hematopoietic stem cell (HSC) proliferation and differentiation towards myeloipoiesis in the early phases of chronic colitis. RNAseq analysis revealed that osteoclasts in colitis differ from control ones and overexpress genes involved in the remodeling of HSC niches. We showed that colitic osteoclasts modulate the interaction of HSCs with their niche and promote myeloid differentiation. Increased osteoclast activity was correlated with an augmentation of myelopoiesis in patients with chronic colitis. Therapeutic blockade of osteoclasts reduced HSC proliferation and myeloid skewing and resulted in a decreased inflammation and severity of colitis. Together, these data identify osteoclasts as potent regulators of HSCs and promising target in chronic colitis.
Extracellular Vesicles Analysis in the COVID-19 Era: Insights on Serum Inactivation Protocols Towards Downstream Isolation and Analysis
Authors: Frigerio Roberto , Musicò Angelo , Brucale Marco , Ridolfi Andrea , Galbiati Silvia , Vago Riccardo , Bergamaschi Greta , Ferretti Anna , Chiari Marcella , Valle Francesco , Gori Alessandro , Cretich Marina 
Published: December 2020

AbstractSince the outbreak of COVID-19 crisis, the handling of biological samples from confirmed or suspected SARS-CoV-2 positive individuals demanded the use of inactivation protocols to ensure laboratory operators safety. While not standardized, these practices can be roughly divided in two categories, namely heat inactivation and solvent-detergent treatments. As such, these routine procedures should also apply to samples intended for Extracellular Vesicles (EVs) analysis. Assessing the impact of virus inactivating pre-treatments is therefore of pivotal importance, given the well-known variability introduced by different pre-analytical steps on downstream EVs isolation and analysis. Arguably, shared guidelines on inactivation protocols tailored to best address EVs-specific requirements will be needed among the EVs community, yet deep investigations in this direction haven’t been reported so far.In the attempt of sparking interest on this highly relevant topic, we here provide preliminary insights on SARS-CoV-2 inactivation practices to be adopted prior serum EVs analysis by comparing solvent/detergent treatment vs. heat inactivation. Our analysis entailed the evaluation of EVs recovery and purity along with biochemical, biophysical and biomolecular profiling by means of Nanoparticle Tracking Analysis, Western Blotting, Atomic Force Microscopy, miRNA content (digital droplet PCR) and tetraspanin assessment by microarrays. Our data suggest an increase in ultracentrifugation (UC) recovery following heat-treatment, however accompanied by a marked enrichment in EVs-associated contaminants. On the contrary, solvent/detergent treatment is promising for small EVs (< 150 nm range), yet a depletion of larger vesicular entities was detected. This work represents a first step towards the identification of optimal serum inactivation protocols targeted to EVs analysis.
Effectors with different gears: divergence ofUstilago maydiseffector genes is associated with their temporal expression pattern during plant infection
Authors: Depotter Jasper R.L. , Zuo Weiliang , Hansen Maike , Zhang Boqi , Xu Mingliang , Doehlemann Gunther 
Published: December 2020

AbstractPlant pathogens secrete a variety of effector proteins that enable host colonization but are also typical pathogen detection targets for the host immune system. Consequently, effector genes encounter high selection pressures, which typically makes them fast evolving. The corn smut pathogenUstilago maydishas an effector gene repertoire with a dynamic expression across the different disease stages. We determined the amino acid divergence ofU. maydiseffector candidates withSporisorium reilianumorthologs, a close relative ofU. maydis. Intriguingly, there are two distinct groups of effector candidates, ones with a respective conserved and diverged protein evolution. Conservatively evolving effector genes especially have their peak expression during the (pre-)penetration stages of the disease cycle. In contrast, expression of divergently evolving effector genes generally peaks during fungal proliferation within the host. To test if this interspecific effector diversity corresponds to intraspecific diversity, we sampled and sequenced a diverse collection ofU. maydisstrains from the most important maize breeding and production regions in China. Effector candidates with a diverged interspecific evolution had more intraspecific amino acid variation than candidates with a conserved evolution. In conclusion, we highlight diversity in evolution within theU. maydiseffector repertoire with dynamically and conservatively evolving members.
Efficacy and accuracy responses of DNA mini-barcodes in species identification under a supervised machine learning approach
Authors: Karim Mohimenul , Abid Rashid 
Published: December 2020

AbstractSpecific gene regions in DNA, such as cytochrome c oxidase I (COI) in animals, are defined as DNA barcodes and can be used as identifiers to distinguish species. The standard length of a DNA barcode is approximately 650 base pairs (bp). However, because of the challenges associated with sequencing technologies and the unavailability of high-quality genomic DNA, it is not always possible to obtain the full-length barcode sequence of an organism. Recent studies suggest that mini-barcodes, which are shorter (100-300 bp) barcode sequences, can contribute significantly to species identification. Among various methods proposed for the identification task, supervised machine learning methods are effective. However, any prior work indicating the efficacy of mini-barcodes in species identification under a machine learning approach is elusive to find. In this study, we analyzed the effect of different barcode lengths on species identification using supervised machine learning and proposed a general approximation of the required length of the minibarcode. Since Naïve Bayes is seen to generally outperform other supervised methods in species identification in other studies, we implemented this classifier and showed the effectiveness of the mini-barcode by demonstrating the accuracy responses obtained after varying the length of the DNA barcode sequences.
A pragmatic reevaluation of the efficacy of nonhuman primate optogenetics for psychiatry
Authors: Bliss-Moreau Eliza , Costa Vincent D. , Baxter Mark G. 
Published: December 2020

AbstractTranslational neuroscience is committed to generating discoveries in the laboratory that ultimately can improve human lives. Optogenetics has received considerable attention because of its demonstrated promise in rodent brains to manipulate cells and circuits. In a recent report, Tremblay and colleagues (2020) introduce an open resource detailing optogenetic studies of the nonhuman primate (NHP) brain and make robust claims about the translatability of the technology. We propose that their quantitative (e.g., a 91% success rate) and theoretical claims are questionable because the data were analyzed at a level relevant to the rodent but not NHP brain, injections were clustered within a few monkeys in a few studies in a few brain regions, and their definitions of success was not clearly relevant to human neuropsychiatric disease. A reanalysis of the data with a modified definition of success that included a behavioralandbiological effect revealed an 62.5% success rate that was lower when considering only strong outcomes (53.1%). This calls into question the current efficacy of optogenetic techniques in the NHP brain and suggests that we are a long way from being able to leverage them in “the service of patients with neurological or psychiatric conditions” as the Tremblay report claims.
A traditional medicine, Respiratory Detox Shot (RDS), inhibits the infection of SARS-CoV, SARS-CoV-2, and the Influenza A virusin vitro
Authors: Hetrick Brian , Yu Dongyang , Olanrewaju Adeyemi A. , Chilin Linda D. , He Sijia , Debbagh Deemah , Ma Yuan-Chun , Hofmann Lewis A. , Hakami Ramin M. , Wu Yuntao 
Published: December 2020

ABSTRACTThe ongoing global pandemic of coronavirus disease 2019 (COVID-19) has resulted in the infection of over 60 million people and has caused over 1.4 million deaths as of December 2020 in more than 220 countries and territories. Currently, there is no effective treatment for COVID-19 to reduce mortality. We investigated the potential anti-coronavirus activities from an oral liquid of traditional medicine, Respiratory Detox Shot (RDS), which contains mostly herbal ingredients traditionally used to manage lung diseases. Here we report that RDS inhibited the infection of target cells by SARS-CoV and SARS-CoV-2 pseudoviruses, and by infectious wild-type SARS-CoV-2. We further demonstrated that RDS inhibits viral early infection steps. In addition, we found that RDS can also block the infection of target cells by Influenza A virus. These results suggest that RDS may broadly inhibit the infection of respiratory viruses.
Identification of a family of Vibrio type III secretion system effectors that contain a conserved serine/threonine kinase domain
Authors: Plaza N , Urrutia IM , Garcia K , Waldor MK , Blondel CJ 
Published: December 2020

ABSTRACTVibrio parahaemolyticus is a marine Gram-negative bacterium that is a leading cause of seafood-borne gastroenteritis. Pandemic strains of V. parahaemolyticus rely on a specialized protein secretion machinery known as the type III secretion system 2 (T3SS2) to cause disease. The T3SS2 mediates the delivery of effector proteins into the cytosol of infected cells, where they subvert multiple cellular pathways. Here, we identify a new T3SS2 effector protein encoded by VPA1328 (VP_RS21530) in V. parahaemolyticus RIMD2210633. Bioinformatic analysis revealed that VPA1328 is part of a larger family of uncharacterized T3SS effector proteins with homology to the VopG effector protein in V. cholerae AM-19226. These VopG-like proteins are found in many but not all T3SS2 gene clusters and are distributed among diverse Vibrio species including V. parahaemolyticus, V. cholerae, V. mimicus, and V. diabolicus and also in Shewanella baltica. Structure-based prediction analyses uncovered the presence of a conserved C-terminal kinase domain in VopG orthologs, similar to the serine/threonine kinase domain found in the NleH family of T3SS effector proteins. However, in contrast to NleH effector proteins, in tissue culture-based infections, VopG did not impede host cell death or suppress IL-8 secretion, suggesting a yet undefined role for VopG during V. parahaemolyticus infection. Collectively, our work reveals that VopG effector proteins, a new family of likely serine/threonine kinases, is widely distributed in the T3SS2 effector armamentarium among marine bacteria.IMPORTANCEVibrio parahaemolyticus is the leading bacterial cause of seafood-borne gastroenteritis worldwide. The pathogen relies on a type III secretion system to deliver a variety of effector proteins into the cytosol of infected cells to subvert cellular function. In this study, we identified a novel Vibrio parahaemolyticus effector protein that is similar to the VopG effector of Vibrio cholerae. VopG-like effectors were found in diverse Vibrio species and contain a conserved serine/threonine kinase domain that bears similarity to the kinase domain in the EHEC and Shigella NleH effectors that manipulate host cell survival pathways and host immune responses. Together our findings identify a new family of Vibrio effector proteins and highlight the role of horizontal gene transfer events among marine bacteria in shaping T3SS gene clusters.
Multidisciplinary Interrogation of a Crucial Protein Interface in the Type II Secretion System
Authors: Escobar Cristian A. , Douzi Badreddine , Ball Geneviève , Barbat Brice , Alphonse Sebastien , Quinton Loïc , Voulhoux Romé , Forest Katrina T. 
Published: December 2020

ABSTRACTThe type IV filament superfamily comprises widespread membrane-associated polymers in prokaryotes. The Type II secretion system (T2SS), a significant virulence pathway in many pathogens, belongs to this superfamily. A knowledge gap in the understanding of the T2SS is the molecular role of a small ‘pseudopilin’ protein. Using multiple biophysical techniques, we have deciphered how this missing component of the Xcp T2SS architecture is structurally integrated, and thereby also unlocked its function. We demonstrate that the low abundance XcpH is the adapter that bridges a trimeric initiating tip complex XcpIJK with a periplasmic filament of XcpG subunits. Our model reveals that each pseudopilin protein caps an XcpG protofilament in an overall pseudopilus compatible with the dimensions of the periplasm and the outer membrane-spanning secretin through which substrates of the T2SS pass. Unexpectedly, to fulfill its adapter function, the XcpH N-terminal helix must be unwound, a property shared with the XcpG subunits. We provide the first complete structural model of a type IV filament, a result immediately transferable to understanding of other T2SS and the type IV pili.
Kaposi’s Sarcoma Herpesvirus Is Associated with Osteosarcoma in Xinjiang Uyghur Population
Authors: Chen Qian , Chen Jiangtao , Li Yuqing , Liu Dawei , Zeng Yan , Tian Zheng , Yunus Akbar , Yang Yong , Lu Jie , Song Xinghua , Yuan Yan 
Published: December 2020

AbstractOsteosarcoma is the most common malignant tumor of bone predominately affecting adolescents and young adults. Viral etiology of osteosarcoma has been proposed more than a half-century ago but never been proven by identifying any virus authentically associated with human osteosarcoma. The Uyghur ethnic population in Xinjiang China has an unusually high prevalence of Kaposi’s sarcoma-associated herpesvirus (KSHV) infection and elevated incidence of osteosarcoma. In the current study, we explored the possible association of KSHV infection and osteosarcoma occurrence. Our seroepidemiological study revealed that KSHV prevalence was significantly elevated in osteosarcoma patients versus the general population in the Xinjiang Uyghur population (OR, 10.23; 95%CI, 4.25, 18.89). The KSHV DNA genome and viral latent nuclear antigen LANA were detected in most osteosarcoma tumor cells. Gene expression profiling analysis showed that KSHV positive osteosarcoma represents a distinct subtype of osteosarcomas with viral gene-driven signaling pathways that are important for osteosarcoma development. We conclude that KSHV infection is a risk factor for osteosarcoma and KSHV is associated with some osteosarcomas, representing a newly identified viral-associated endemic cancer.SignificanceViral etiology of osteosarcoma was proposed previously but has never been proven by identifying any virus that is authentically associated with human osteosarcoma. The current study revealed an association of human osteosarcoma with KSHV infection in Uyghur osteosarcoma patients. First, this study provides the first evidence that supports the possible viral etiology of human osteosarcoma. The gene expression profiling study showed that KSHV-positive osteosarcoma represents a distinct subtype of osteosarcomas, which is of diagnostic, prognostic and therapeutic significance. Second, KSHV-associated osteosarcomas preferentially occur in children and young adults, predicting that KSHV-positive children in KSHV endemic region may be at great risk for osteosarcoma. Third, the finding extended the range of human cancers associated with viruses.