bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glucosylceramide in cerebrospinal fluid of patients with GBA-associated and idiopathic Parkinson’s disease enrolled in PPMI
Authors: Huh Young Eun , Park Hyejung , Chiang Ming Sum Ruby , Tuncali Idil , Liu Ganqiang , Locascio Joseph J. , Shirvan Julia , Hutten Samantha J. , Rotunno Melissa S. , Viel Catherine , Shihabuddin Lamya S. , Wang Bing , Sardi Sergio Pablo , Scherzer Clemens R. 
Published: November 2021

AbstractProtein-coding variants in the GBA gene modulate susceptibility and progression in ~10% of patients with Parkinson’s disease (PD). GBA encodes the β-glucocerebrosidase enzyme that hydrolyzes glucosylceramide. We hypothesized that GBA mutations will lead to glucosylceramide accumulation in cerebrospinal fluid (CSF). Glucosylceramide, ceramide, sphingomyelin, and lactosylceramide levels were measured by liquid chromatography-tandem mass spectrometry in CSF of 411 participants from the Parkinson’s Progression Markers Initiative (PPMI) cohort, including early stage, de novo PD patients with abnormal dopamine transporter neuroimaging and healthy controls. Forty-four PD patients carried protein-coding GBA variants (GBA-PD) and 227 carried wild-type alleles (idiopathic PD). The glucosylceramide fraction was increased (P = 0.0001), and the sphingomyelin fraction (a downstream metabolite) was reduced (P = 0.0001) in CSF of GBA-PD patients compared to healthy controls. The ceramide fraction was unchanged, and lactosylceramide was below detection limits. We then used the ratio of glucosylceramide to sphingomyelin (the GlcCer/SM ratio) to explore whether these two sphingolipid fractions altered in GBA-PD were useful for stratifying idiopathic PD patients. Idiopathic PD patients in the top quartile of GlcCer/SM ratios at baseline showed a more rapid decline in Montreal Cognitive Assessment scores during longitudinal follow-up compared to those in the lowest quartile with a P-value of 0.036. The GlcCer/SM ratio was negatively associated with α-synuclein levels in CSF of PD patients. This study highlights glucosylceramide as a pathway biomarker for GBA-PD patients and the GlcCer/SM ratio as a potential stratification tool for clinical trials of idiopathic PD patients. Our sphingolipids data together with the clinical, imaging, omics, and genetic characterization of PPMI will contribute a useful resource for multi-modal biomarkers development.
Reduced intrinsic neural timescales in schizophrenia along posterior parietal and occipital areas
Authors: Uscătescu Lavinia Carmen , Said-Yürekli Sarah , Kronbichler Lisa , Stelzig-Schöler Renate , Pearce Brandy-Gale , Reich Luise Antonia , Weber Stefanie , Aichhorn Wolfgang , Kronbichler Martin 
Published: November 2021

AbstractWe computed intrinsic neural timescales (INT) based on resting-state functional magnetic resonance imaging (rsfMRI) data of healthy controls (HC) and patients with schizophrenia spectrum disorder (SZ) from three independently collected samples. Five clusters showed decreased INT in SZ compared to HC in all three samples: right occipital fusiform gyrus (rOFG), left superior occipital gyrus (lSOG), right superior occipital gyrus (rSOG), left lateral occipital cortex (lLOC) and right postcentral gyrus (rPG). In other words, it appears that sensory information in visual and posterior parietal areas is stored for reduced lengths of time in SZ compared to HC. Finally, we found that symptom severity appears to modulate INT of these areas in SZ.
Accessible data curation and analytics for international-scale citizen science datasets
Authors: Murray Benjamin , Kerfoot Eric , Chen Liyuan , Deng Jie , Graham Mark S. , Sudre Carole H. , Molteni Erika , Canas Liane S. , Antonelli Michela , Klaser Kerstin , Visconti Alessia , Hammers Alexander , Chan Andrew T. , Franks Paul W. , Davies Richard , Wolf Jonathan , Spector Tim D. , Steves Claire J. , Modat Marc , Ourselin Sebastien 
Published: November 2021

AbstractThe Covid Symptom Study, a smartphone-based surveillance study on COVID-19 symptoms in the population, is an exemplar of big data citizen science. As of May 23rd, 2021, over 5 million participants have collectively logged over 360 million self-assessment reports since its introduction in March 2020. The success of the Covid Symptom Study creates significant technical challenges around effective data curation. The primary issue is scale. The size of the dataset means that it can no longer be readily processed using standard Python-based data analytics software such as Pandas on commodity hardware. Alternative technologies exist but carry a higher technical complexity and are less accessible to many researchers. We present ExeTera, a Python-based open source software package designed to provide Pandas-like data analytics on datasets that approach terabyte scales. We present its design and capabilities, and show how it is a critical component of a data curation pipeline that enables reproducible research across an international research group for the Covid Symptom Study.
Multimodal characterization of Yucatan minipig behavior and physiology through maturation
Authors: Netzley Alesa H. , Hunt Ryan D. , Franco-Arellano Josue , Arnold Nicole , Vazquez Ana I. , Munoz Kirk A. , Colbath Aimee C. , Bush Tamara Reid , Pelled Galit 
Published: November 2021

AbstractBrain injuries induced by external forces are particularly challenging to model experimentally. In recent decades, the domestic pig has been gaining popularity as a highly relevant animal model to address the pathophysiological mechanisms and the biomechanics associated with head injuries. Understanding cognitive, motor, and sensory aspects of pig behavior throughout development is crucial for evaluating cognitive and motor deficits after injury. We have developed a comprehensive battery of tests to characterize the behavior and physiological function of the Yucatan minipig throughout maturation. Behavioral testing included assessments of learning and memory, executive functions, circadian rhythms, gait analysis, and level of motor activity. We applied traditional behavioral apparatus and analysis methods, as well as state-of-the-art sensor technologies to report on motion and activity, and artificial intelligent approaches to analyze behavior. We studied pigs from 16 weeks old through sexual maturity at 35 weeks old. The results show multidimensional characterization of minipig behavior, and how it develops and changes with age. This animal model may capitulate the biomechanical consideration and phenotype of head injuries in the developing brain and can drive forward the field of understanding pathophysiological mechanisms and developing new therapies to accelerate recovery in children who have suffered head trauma.
Quantitative modeling of regular retinal microglia distribution
Authors: Endo Yoshie , Asanuma Daisuke , Namiki Shigeyuki , Sugihara Kei , Hirose Kenzo , Uemura Akiyoshi , Kubota Yoshiaki , Miura Takashi 
Published: November 2021

AbstractMicroglia are resident immune cells in the central nervous system, showing a regular distribution. Advancing microscopy and image processing techniques have contributed to elucidating microglia’s morphology, dynamics, and distribution. However, the mechanism underlying the regular distribution of microglia remains to be elucidated. First, we quantitatively confirmed the regularity of the distribution pattern of microglial soma in the retina. Second, we formulated a mathematical model that includes factors that may influence regular distribution. Next, we experimentally quantified the model parameters (cell movement, process formation, and ATP dynamics). The resulting model simulation from the measured parameters showed that direct cell–cell contact is most important in generating regular cell spacing. Finally, we tried to specify the molecular pathway responsible for the repulsion between neighboring microglia.
Mycoplasma infection and ocular surface diseases: a nationwide cohort study
Authors: Lai Li-Ju , Chen Vincent Chin-Hung , Yang Yao-Hsu , Kao Kai-Liang , Chen Ko-Jung , Wang Ying-Ching , Wu Shu-I 
Published: November 2021

AbstractWhether patients with Mycoplasma infection have an increased risk of ocular surface ulcers. Using a nation-wide database, we identified patients with a new diagnosis of Mycoplasma infection between 1997 and 2013, and compared them with age-, sex-, and index year-matched subjects without the infection. Cox proportional regression was performed to compare the risk of corneal diseases between the two cohorts. The incidence of corneal diseases was significantly higher in the 4223 patients with Mycoplasma infection than in the 16,892 patients without (7.28 vs. 5.94 per 1000 person-years, P < 0.01). The adjusted hazard ratio for the risk of corneal diseases in the study cohort was 1.21 times higher (95% CI 1.02–1.44) than that in the comparison cohort. Mycoplasma infection might be a predisposing factor for patients with keratitis.
Dynamic-boundary-based lateral motion synergistic control of distributed drive autonomous vehicle
Authors: Wang Kai , Ding Weiping , Yang Mingliang , Zhu Qiao 
Published: November 2021

AbstractTo improve the path tracking accuracy and yaw stability of distributed drive autonomous vehicles (DDAVs) under extreme working conditions, a cooperative lateral motion control method based on the dynamic boundary is proposed to prevent different road adhesion conditions from affecting the motion stability of DDAVs. Based on the analysis of the DDAV lateral dynamics system coordination mechanism, a dynamic boundary considering the pavement adhesion coefficient is proposed, and the Lateral Motion Synergistic Control System (LMSCS) is designed. The LMSCS is divided into the coordination, control, and executive layers. The coordination layer divides the control domain into the stable, quasi-stable, and unstable domains by the dynamic boundary, and coordinates the control strength of the path following control and yaw stability control. In the control layer, the path following control and yaw stability control laws are designed based on the global fast terminal sliding mode. The executive layer estimates the expected steering wheel angle and expected additional wheel torque. Joint simulations under double line shifting conditions confirmed that LMSCS reflects the impact of the road attachment conditions and improves the path tracking accuracy and vehicle yaw stability. The LMSCS has better overall performance than existing lateral motion control methods.
Clinicopathological characteristics and outcomes of 23 patients with secretory carcinoma of major salivary glands
Authors: Sun Jingjing , Liu Sirui , Fu Kun , Gao Ning , Li Rui , He Wei , Gao Zhenjie 
Published: November 2021

AbstractThis retrospective study investigated the clinicopathological characteristics of secretory carcinoma of salivary glands (SCSG) in 23 patients with histopathologically confirmed SCSG between January 2010 and December 2020. In total, 13 males and 10 females (ratio, 1.3:1) aged 10 − 69 years (median, 45 years) were enrolled in this study; the average disease duration was 2.44 years (0.25–20 years). Twenty-one patients (91.3%) had SCSG in the parotid gland, and two (8.7%) in the submandibular gland. All patients had single nodules of diameters 0.8–4.8 cm (average 2.6 cm); five with lymph node metastases, and two with distant metastases. Immunohistochemically, tumors stained positive for S-100, mammaglobin, CK7, GATA3 and pan-Trk, and negative for DOG1, P63, and calponin, with Ki-67 positivity from 1 to 50%. ETV6 gene rearrangement was confirmed in 15 patients. All patients underwent oncological resection, four had radioactive particles implanted postoperatively, one received chemotherapy, and seven underwent chemoradiotherapy. Six patients had regional recurrences, two distant metastases, and one died before the last follow-up. SCSGs are typically indolent, with a low locoregional recurrence rate and excellent survival. Prognosis is correlated to clinical stage, pathological grade, and surgical procedures.
Closed-loop wearable naloxone injector system
Authors: Chan Justin , Iyer Vikram , Wang Anran , Lyness Alexander , Kooner Preetma , Sunshine Jacob , Gollakota Shyamnath 
Published: November 2021

AbstractOverdoses from non-medical use of opioids can lead to hypoxemic/hypercarbic respiratory failure, cardiac arrest, and death when left untreated. Opioid toxicity is readily reversed with naloxone, a competitive antagonist that can restore respiration. However, there remains a critical need for technologies to administer naloxone in the event of unwitnessed overdose events. We report a closed-loop wearable injector system that measures respiration and apneic motion associated with an opioid overdose event using a pair of on-body accelerometers, and administers naloxone subcutaneously upon detection of an apnea. Our proof-of-concept system has been evaluated in two environments: (i) an approved supervised injection facility (SIF) where people self-inject opioids under medical supervision and (ii) a hospital environment where we simulate opioid-induced apneas in healthy participants. In the SIF (n = 25), our system identified breathing rate and post-injection respiratory depression accurately when compared to a respiratory belt. In the hospital, our algorithm identified simulated apneic events and successfully injected participants with 1.2 mg of naloxone. Naloxone delivery was verified by intravenous blood draw post-injection for all participants. A closed-loop naloxone injector system has the potential to complement existing evidence-based harm reduction strategies and, in the absence of bystanders, help make opioid toxicity events functionally witnessed and in turn more likely to be successfully resuscitated.
Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis
Authors: Alberdi Antton , Martin Bideguren Garazi , Aizpurua Ostaizka 
Published: November 2021

AbstractThe gut microbiota is recognised as an essential asset for the normal functioning of animal biology. When wild animals are moved into captivity, the modified environmental pressures are expected to rewire the gut microbiota, yet whether this transition follows similar patterns across vertebrates is still unresolved due to the absence of systematic multi-species analyses. We performed a meta-analysis of gut microbiota profiles of 322 captive and 322 wild specimens from 24 vertebrate species. Our analyses yielded no overall pattern of diversity and compositional variation between wild and captive vertebrates, but a heterogeneous landscape of responses, which differed depending on the components of diversity considered. Captive populations showed enrichment patterns of human-associated microorganisms, and the minimal host phylogenetic signal suggests that changes between wild and captive populations are mainly driven by case-specific captivity conditions. Finally, we show that microbiota differences between wild and captive populations can impact evolutionary and ecological inferences that rely on hierarchical clustering-based comparative analyses of gut microbial communities across species.
Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics
Authors: López-Pérez Ana R. , Balwierz Piotr J. , Lenhard Boris , Muller Ferenc , Wardle Fiona C. , Manfroid Isabelle , Voz Marianne L. , Peers Bernard 
Published: November 2021

AbstractRetinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) inverse-agonist BMS493 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. RAR ChIP-seq further defined the direct RAR target genes in zebrafish, includinghoxgenes as well as several pancreatic regulators likemnx1,insm1b,hnf1baandgata6. Comparison of zebrafish and murine RAR ChIP-seq data highlighted the conserved direct target genes and revealed that some RAR sites are under strong evolutionary constraints. Among them, a novel highly conserved RAR-induced enhancer was identified downstream of theHoxBlocus and driving expression in the nervous system and in the gut in a RA-dependent manner. Finally, ATAC-seq data unveiled the role of the RAR-direct targets Hnf1ba and Gata6 in opening chromatin at many regulatory loci upon RA treatment.
Effect of dual-rotation on MHD natural convection of NEPCM in a hexagonal-shaped cavity based on time-fractional ISPH method
Authors: Raizah Zehba , Aly Abdelraheem M. 
Published: November 2021

AbstractThe time-fractional derivative based on the Grunwald–Letnikove derivative of the 2D-ISPH method is applying to emulate the dual rotation on MHD natural convection in a hexagonal-shaped cavity suspended by nano-encapsulated phase change material (NEPCM). The dual rotation is performed between the inner fin and outer hexagonal-shaped cavity. The impacts of a fractional time derivative$$\alpha$$α$$\left( {0.92 \le \alpha \le 1} \right)$$0.92≤α≤1, Hartmann number Ha$$\left( {0 \le Ha \le 80} \right)$$0≤Ha≤80, fin length$$\left( {0.2 \le L_{Fin} \le 1} \right)$$0.2≤LFin≤1, Darcy parameter Da$$\left( {10^{ - 2} \le Da \le 10^{ - 4} } \right)$$10-2≤Da≤10-4, Rayleigh number Ra$$\left( {10^{3} \le Ra \le 10^{6} } \right)$$103≤Ra≤106, fusion temperature$$\theta_{f}$$θf$$\left( {0.05 \le \theta_{f} \le 0.8} \right)$$0.05≤θf≤0.8, and solid volume fraction$$\varphi$$φ$$\left( {0 \le \varphi \le 0.06} \right)$$0≤φ≤0.06on the velocity field, isotherms, and mean Nusselt number$$\overline{Nu}$$Nu¯are discussed. The outcomes signaled that a dual rotation of the inner fin and outer domain is affected by a time-fractional derivative. The inserted cool fin is functioning efficiently in the cooling process and adjusting the phase change zone within a hexagonal-shaped cavity. An increment in fin length augments the cooling process and changes the location of a phase change zone. A fusion temperature$$\theta_{f}$$θfadjusts the strength and position of a phase change zone. The highest values of$$\overline{Nu}$$Nu¯are obtained when$$\alpha = 1$$α=1. An expansion in Hartmann number$$Ha $$Hareduces the values of$$\overline{Nu}$$Nu¯. Adding more concentration of nanoparticles is improving the values of$$\overline{Nu}$$Nu¯.
Possible impacts of the predominant Bacillus bacteria on the Ophiocordyceps unilateralis s. l. in its infected ant cadavers
Authors: Tu Kai-Wen , Chiu Ming-Chung , Lin Wei-Jiun , Hsueh Yen-Ping , Lin Chung-Chi , Chou Jui-Yu 
Published: November 2021

AbstractAnimal hosts infected and killed by parasitoid fungi become nutrient-rich cadavers for saprophytes. Bacteria adapted to colonization of parasitoid fungi can be selected and can predominate in the cadavers, actions that consequently impact the fitness of the parasitoid fungi. In Taiwan, the zombie fungus, Ophiocordyceps unilateralis sensu lato (Clavicipitaceae: Hypocreales), was found to parasitize eight ant species, with preference for a principal host, Polyrhachis moesta. In this study, ant cadavers grew a fungal stroma that was predominated by Bacillus cereus/thuringiensis. The bacterial diversity in the principal ant host was found to be lower than the bacterial diversity in alternative hosts, a situation that might enhance the impact of B. cereus/thuringiensis on the sympatric fungus. The B. cereus/thuringiensis isolates from fungal stroma displayed higher resistance to a specific naphthoquinone (plumbagin) than sympatric bacteria from the environment. Naphthoquinones are known to be produced by O. unilateralis s. l., and hence the resistance displayed by B. cereus/thuringiensis isolates to these compounds suggests an advantage to B. cereus/thuringiensis to grow in the ant cadaver. Bacteria proliferating in the ant cadaver inevitably compete for resources with the fungus. However, the B. cereus/thuringiensis isolates displayed in vitro capabilities of hemolysis, production of hydrolytic enzymes, and antagonistic effects to co-cultured nematodes and entomopathogenic fungi. Thus, co-infection with B. cereus/thuringiensis offers potential benefits to the zombie fungus in killing the host under favorable conditions for reproduction, digesting the host tissue, and protecting the cadaver from being taken over by other consumers. With these potential benefits, the synergistic effect of B. cereus/thuringiensis on O. unilateralis infection is noteworthy given the competitive relationship of these two organisms sharing the same resource.
Saliva is superior over nasopharyngeal swab for detecting SARS-CoV2 in COVID-19 patients
Authors: Beyene Getachew Tesfaye , Alemu Fekadu , Kebede Eyerusalem Solomon , Alemayehu Dawit Hailu , Seyoum Tamirayehu , Tefera Dessalegn Abeje , Assefa Gebeyehu , Tesfaye Abebech , Habte Anteneh , Bedada Gadissa , Tegene Birhanemeskel , Yeshambaw Melese , Wassie Liya , Mihret Adane , Abdissa Alemseged , Mulu Andargachew 
Published: November 2021

AbstractScaling up of diagnostic capacity is needed to mitigate the global pandemic of SARS-CoV2. However, there are challenges including shortage of sample collection swabs and transport medium. Saliva has been recommended as a simple, low-cost, non-invasive option. However, data from different populations and settings are limited. Here, we showed that saliva could be a good alternative sample to diagnose COVID-19 patients. Pair of NPS-saliva samples was collected from 152 symptomatic; confirmed COVID-19 patients, and compared their positivity rate, viral load, and duration of viral shedding. From 152 patients, 80 (52.63%) tested positive and 72 (47.37%) were negative for SARSA-CoV2 in NPS sample. In saliva, 129 (92.14%) were tested positive and 11 (7.86%) were negative on the day of admission to hospital. The overall percent agreement of RT-PCR result of Saliva to NPS was 70% (196/280). A comparison of viral load from 72 NPS-saliva pair samples on day of admission shows saliva contains significantly higher viral load (P < 0.001). In conclusion, saliva has higher yield in detecting SARS-CoV2, and COVID-19 patients show higher viral load and prolonged period of viral shedding in saliva. Therefore, we recommend saliva as a better alternative sample to NPS to diagnose COVID-19 patients.
Lockdowns lose one third of their impact on mobility in a month
Authors: Joshi Yogesh V. , Musalem Andres 
Published: November 2021

AbstractAs the novel coronavirus (COVID‐19) pandemic spread across the world over the past year, many countries imposed lockdowns in the form of stay at home requirements on their citizens to mitigate its spread. We analyze mobility data from 93 countries implementing lockdowns to investigate their immediate impact on mobility and the subsequent evolution of mobility. We find that at the start of a lockdown, median mobility is reduced to 36% below the baseline, and by another 18% in the subsequent 2 weeks. 70 countries had lockdowns lasting beyond 4 weeks and showed a significant reduction in mobility compared to that prior to the lockdown. Mobility was at its minimum 18 days into the lockdown for the median country. Comparing this minimum mobility to the average mobility 2 weeks before the lockdown, we observe a median reduction of 50 percentage points, evidencing that lockdowns reduce mobility. For 59 of these 70 countries, lockdowns lasted at least 4 weeks after reaching minimum mobility and most observed a significant rebound in mobility during the lockdown period. For the median country, 30.1% of the mobility reduction achieved is lost within 4 weeks, and lockdowns lose all their impact on mobility in 112.1 days. Overall, our findings show that while lockdowns significantly reduce mobility, this impact is also subject to fatigue as the lockdown period extends longer. The magnitude of mobility reductions achieved and fatigues reported in this research can help policy makers anticipate the likely impact of their lockdown policies.