bluuebunny/crossref_metadata_2025_split huggingface dataset:
Somatic mutations in both blood cells and vascular endothelium from patients with severe coronary artery diseases
Authors: Zhang Haotian , Tannous Henry , Mazzeo Christopher , Zheng Haoyi , Zhan Huichun 
Published: January 2022

ABSTRACTIndividuals with clonal hematopoiesis of indeterminate potential (CHIP) is associated with a 2-4 fold increase in cardiovascular diseases (CVDs). While most studies focus on mutant blood cells, we propose that a better insight into the CHIP-CVD connection can be obtained by examining the genetic mutations in both the vascular endothelium and peripheral blood samples from the same patient. In this study, we examined somatic mutations by whole exome sequencing in paired blood and vascular samples from 4 patients with severe coronary artery disease who underwent coronary artery bypass graft surgery. We found that blood and endothelium can acquire the same mutations during aging and CHIP-associated mutations are not uncommon in vascular endothelium in patients with severe CVDs. Since vascular endothelial cells have critical roles in the regulation of cardiovascular function, mutant vascular endothelium offers an opportunity for further investigations to improve our diagnosis and management of individuals with CHIP.
Quantitative proteomics and phosphoproteomics of urinary extracellular vesicles define diagnostic biosignatures for Parkinson’s Disease
Authors: Hadisurya Marco , Li Li , Kuwaranancharoen Kananart , Wu Xiaofeng , Lee Zheng-Chi , Alcalay Roy N. , Padmanabhan Shalini , Tao W. Andy , Iliuk Anton 
Published: January 2022

AbstractMutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been recognized as genetic risk factors for both familial and sporadic forms of Parkinson’s disease (PD). However, compared to cancer, overall lower genetic mutations contribute to the cause of PD, propelling the search for protein biomarkers for early detection of the disease. Utilizing 141 urine samples from four groups, healthy individuals (control), healthy individuals with G2019S mutation in the LRRK2 gene (non-manifesting carrier/NMC), PD individuals without G2019S mutation (idiopathic PD/iPD), and PD individuals with G2019S mutation (LRRK2 PD), we applied a proteomics strategy to determine potential diagnostic biomarkers for PD from urinary extracellular vesicles (EVs). After efficient isolation of urinary EVs through chemical affinity followed by mass spectrometric analyses of EV peptides and enriched phosphopeptides, we identified and quantified 4,480 unique proteins and 2,682 unique phosphoproteins. We detected multiple proteins and phosphoproteins elevated in PD EVs that are known to be involved in important PD pathways, in particular the autophagy pathway, as well as neuronal cell death, neuroinflammation, and formation of amyloid fibrils. Our data revealed that LRRK2 and its Rab substrates are altered but not significant PD biomarkers. We established two panels of proteins and phosphoproteins as novel candidates for disease and risk biomarkers, and substantiated using ROC, machine learning, clinical correlation, and in-depth network analysis. Several disease biomarkers were further validated in patients with PD using parallel reaction monitoring (PRM) and immunoassay for targeted quantitation. These findings demonstrate a general strategy of utilizing biofluid EV proteome/phosphoproteome as an outstanding and non-invasive source for a wide range of disease exploration.
SARS-CoV-2 Omicron variant virus isolates are highly sensitive to interferon treatment
Authors: Bojkova Denisa , Rothenburger Tamara , Ciesek Sandra , Wass Mark N. , Michaelis Martin , Cinatl Jindrich 
Published: January 2022

AbstractRecently, we have shown that SARS-CoV-2 Omicron virus isolates are less effective at inhibiting the host cell interferon response than Delta viruses. Here, we present further evidence that reduced interferon-antagonising activity explains at least in part why Omicron variant infections are inherently less severe than infections with other SARS-CoV-2 variants. Most importantly, we here also show that Omicron variant viruses display enhanced sensitivity to interferon treatment, which makes interferons promising therapy candidates for Omicron patients, in particular in combination with other antiviral agents.
A Machine-Learning Based Objective Measure for ALS Disease Severity
Authors: Vieira Fernando G. , Venugopalan Subhashini , Premasiri Alan S. , McNally Maeve , Jansen Aren , McCloskey Kevin , Brenner Michael P. , Perrin Steven 
Published: January 2022

ABSTRACTAmyotrophic Lateral Sclerosis (ALS) disease severity is usually measured using the subjective, questionnaire-based revised ALS Functional Rating Scale (ALSFRS-R). An objective measure for tracking disease severity and progression would be a powerful tool for evaluating real-world drug effectiveness, efficacy in clinical trials, as well as identifying participants for cohort studies. Here we develop a machine learning (ML) based objective measure for ALS disease severity, based on voice samples and accelerometer measurements from a longitudinal dataset collected by the ALS Therapy Development Institute (ALS-TDI) over four years. 584 people living with ALS consented and carried out prescribed speaking and limb-based tasks. 542 participants contributed 5814 voice recordings, and 350 contributed 13009 accelerometer samples, while simultaneously measuring ALSFRS-R scores. Using the data from 475 participants, we trained machine learning (ML) models to predict bulbar-related FRS scores from speech, and limb-related scores from accelerometer samples. On the test set (n=109 participants) the voice models achieved a multiclass AUC of 0.86 (95% CI, 0.85-0.88) on speech FRS prediction, whereas the accelerometer models achieved a median multiclass AUC of 0.73 on 6 limb-related functions. Further, the correlation (and inverse correlations) across different bulbar and limb functions observed in the self-reported ALSFRS-R scores are preserved in the ML-derived scores. Next, we used these models and self-reported ALSFRS-R scores to evaluate the real-world effects of edaravone, a drug recently approved for use in ALS. In the cohort of 54 test participants who received edaravone as part of their usual care, the ML-derived objective scores were consistent with the self-reported ALSFRS-R scores, and both showed highly variable outcomes from edaravone treatment from person to person. At the individual level, the continuous ML-derived score is able to capture a gradual change that is absent in the integer ALSFRS-R scores. This demonstrates the value of these tools for assessing both disease severity and potentially drug effects.
A bite force database of 654 insect species
Authors: Rühr Peter Thomas , Edel Carina , Frenzel Melina , Blanke Alexander 
Published: January 2022

AbstractBite force is a decisive performance trait in animals because it plays a role for numerous life history components such as food consumption, inter- and intraspecific interactions, and reproductive success. Bite force has been studied across a wide range of vertebrate species, but only for 20 species of insects, the most speciose animal lineage. Here we present the insect bite force database with bite force measurements for 654 insect species covering 111 families and 13 orders with body lengths ranging from 4.2 - 180.1 mm. In total we recorded 1906 bite force series from 1290 specimens, and, in addition, present basal head, body, and wing metrics. As such, the database will facilitate a wide range of studies on the characteristics, predictors, and macroevolution of bite force in the largest clade of the animal kingdom and may serve as a basis to further our understanding of macroevolutionary processes in relation to bite force across all biting metazoans.
Host Chitinase 3-like-1 is a Universal Therapeutic Target for SARS-CoV-2 Viral Variants in COVID 19
Authors: Kamle Suchitra , Ma Bing , Lee Chang Min , Schor Gail , Zhou Yang , Lee Chun Geun , Elias Jack A. 
Published: January 2022

ABSTRACTCOVID 19 is the disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2; SC2) which has caused a world-wide pandemic with striking morbidity and mortality. Evaluation of SC2 strains demonstrated impressive genetic variability and many of these viral variants are now defined as variants of concern (VOC) that cause enhanced transmissibility, decreased susceptibility to antibody neutralization or therapeutics and or the ability to induce severe disease. Currently, the delta (δ) and omicron (o) variants are particularly problematic based on their impressive and unprecedented transmissibility and ability to cause break through infections. The delta variant also accumulates at high concentrations in host tissues and has caused waves of lethal disease. Because studies from our laboratory have demonstrated that chitinase 3-like-1 (CHI3L1) stimulates ACE2 and Spike (S) priming proteases that mediate SC2 infection, studies were undertaken to determine if interventions that target CHI3L1 are effective inhibitors of SC2 viral variant infection. Here we demonstrate that CHI3L1 augments epithelial cell infection by pseudoviruses that express the alpha, beta, gamma, delta or omicron S proteins and that the CHI3L1 inhibitors anti-CHI3L1 and kasugamycin inhibit epithelial cell infection by these VOC pseudovirus moieties. Thus, CHI3L1 is a universal, VOC-independent therapeutic target in COVID 19.
‘Holey’ niche! Finding holes in niche hypervolumes using persistence homology
Authors: Conceição Pedro , Morimoto Juliano 
Published: January 2022

AbstractHutchinson’s niche hypervolume concept has enabled significant progress in our understanding of species’ ecological needs and distributions across environmental gradients. Nevertheless, the properties of Hutchinson’s n-dimensional hypervolumes can be challenging to calculate and several methods have been proposed to extract meaningful measurements of hypervolumes’ properties (e.g., volume).One key property of hypervolumes are holes, which provide important information about the ecological occupancy of species. However, to date, current methods rely on volume estimates and set operations to identify holes in hypervolumes. Yet, this approach can be problematic because in high-dimensions, the volume of region enclosing a hole tends to zero.Here, we propose the use of the topological concept of persistence homology (PH) to identify holes in hypervolumes and in ecological datasets more generally. PH allows for the estimates of topological properties in n-dimensional niche hyper-volumes and is independent of the volume estimates of the hypervolume. We demonstrate the application of PH to canonical datasets and to the identification of holes in the hypervolumes of five vertebrate species with diverse niches, highlighting the potential benefits of this approach to gain further insights into animal ecology.Overall, our approach enables the study of an yet unexplored property of Hutchinson’s hypervolumes (i.e., holes), and thus, have important implications to our understanding of animal ecology.
Border closure and travel restrictions to control the spread of COVID-19: an update to a Cochrane review
Authors: Abou-Setta Ahmed M. , Lam Otto LT , Kasireddy Viraj , Askin Nicole , Tricco Andrea C. 
Published: January 2022

AbstractBackgroundCOVID-19 has proven to be more difficult to manage for many reasons including its high infectivity rate. One of the potential ways to limit its spread is by limiting free travel across borders, including via air travel. The objective of this systematic review is to identify, critically-appraise and summarize evidence on border closures and travel restrictions.MethodsThis review is based on the Cochrane review: “International travel-related control measures to contain the COVID-19 pandemic” and followed the same methodology. In brief, we searched for clinical and modelling studies in general health and COVID-19-specific bibliographic databases. The primary outcome categories were (i) cases avoided, (ii) cases detected, and (iii) a shift in epidemic development. Secondary outcomes were other infectious disease transmission outcomes, healthcare utilisation, resource requirements and adverse effects if identified in studies assessing at least one primary outcome.ResultsWe included 43, mostly modelling, studies that met our inclusion criteria. Fourteen new studies were identified in the updated search, as well as updated companions (e.g., peer-reviewed publications that were previously only available as pre-prints). Most studies were of moderate to high quality. The added studies did not change the main conclusions of the Cochrane review nor the quality of the evidence (very low to low certainty). However, it did add to the evidence base for most outcomes.ConclusionsWeak evidence supports the use of border closures to limit the spread of COVID-19 via air travel. Real-world studies are required to support these conclusions.
Segmentation stability of human head and neck cancer medical images for radiotherapy applications under de-identification conditions: benchmarking data sharing and artificial intelligence use-cases
Authors: Sahlsten Jaakko , Wahid Kareem A. , Glerean Enrico , Jaskari Joel , Naser Mohamed A. , He Renjie , Kann Benjamin H. , Mäkitie Antti , Fuller Clifton D. , Kaski Kimmo 
Published: January 2022

AbstractBackgroundDemand for head and neck cancer (HNC) radiotherapy data in algorithmic development has prompted increased image dataset sharing. Medical images must comply with data protection requirements so that re-use is enabled without disclosing patient identifiers. Defacing, i.e., the removal of facial features from images, is often considered a reasonable compromise between data protection and re-usability for neuroimaging data. While defacing tools have been developed by the neuroimaging community, their acceptability for radiotherapy applications have not been explored. Therefore, this study systematically investigated the impact of available defacing algorithms on HNC organs at risk (OARs).MethodsA publicly available dataset of magnetic resonance imaging scans for 55 HNC patients with eight segmented OARs (bilateral submandibular glands, parotid glands, level II neck lymph nodes, level III neck lymph nodes) was utilized. Eight publicly available defacing algorithms were investigated: afni_refacer, DeepDefacer, defacer, fsl_deface, mask_face, mri_deface, pydeface, and quickshear. Using a subset of scans where defacing succeeded (N=29), a 5-fold cross-validation 3D U-net based OAR auto-segmentation model was utilized to perform two main experiments: 1.) comparing original and defaced data for training when evaluated on original data; 2.) using original data for training and comparing the model evaluation on original and defaced data. Models were primarily assessed using the Dice similarity coefficient (DSC).ResultsMost defacing methods were unable to produce any usable images for evaluation, while mask_face, fsl_deface, and pydeface were unable to remove the face for 29%, 18%, and 24% of subjects, respectively. When using the original data for evaluation, the composite OAR DSC was statistically higher (p ≤ 0.05) for the model trained with the original data with a DSC of 0.760 compared to the mask_face, fsl_deface, and pydeface models with DSCs of 0.742, 0.736, and 0.449, respectively. Moreover, the model trained with original data had decreased performance (p ≤ 0.05) when evaluated on the defaced data with DSCs of 0.673, 0.693, and 0.406 for mask_face, fsl_deface, and pydeface, respectively.ConclusionDefacing algorithms may have a significant impact on HNC OAR auto-segmentation model training and testing. This work highlights the need for further development of HNC-specific image anonymization methods.
Hepatitis B virus infection in the Lao PDR: A systematic review
Authors: Hefele Lisa , Nouanthong Phonethipsavanh , Hübschen Judith M. , Muller Claude P , Black Antony P 
Published: January 2022

AbstractIntroductionEven though hepatitis B is endemic in the Lao PDR, the understanding of the epidemiology of hepatitis B infection is incomplete. This article reviews the available literature about hepatitis B seroprevalence, risk factors and genotypes in the Lao population in order to provide an up- to date summary of the HBV epidemiology in the Lao PDR, identify knowledge gaps and provide public health recommendations.MethodsUsing PubMed/Medline and ScienceDirect, all studies reporting the prevalence of hepatitis B markers or genotype distribution in the Lao PDR published were systematically reviewed.ResultsThe 21 studies included focused on the general population, blood donors, women, children, health care workers and garment factory workers. The studies varied extensively in sample size, target population, methods, study location and time periods. The prevalence of the hepatitis B surface antigen (HBsAg) in blood donors was reported to be 8.7%-9.6% in 2003-2006. In the years 2011-2012, the reported HBsAg prevalence among women (including pregnant women) ranged from 0%-9.5% and among children aged 5-9 years from 1.7%-8.7%, depending on study location and age. The majority of strains characterized in Lao PDR belonged to genotypes B and C.ConclusionStudies displayed considerable heterogeneity in populations, design and laboratory methods. A high HBsAg prevalence was reported in adults including pregnant women. Low infant vaccination coverage and compromised vaccine immunogenicity were found. Only two studies focused on HBV in risk populations, emphasizing the need for further studies to characterize hepatitis B epidemiology in potentially vulnerable groups. Hepatitis B infection continues to represent a substantial public health threat in the Lao PDR and needs to be monitored to inform health authorities and to counteract over-burdening of the health care system. In order to end mother to child transmission, vaccination coverage with the hepatitis B birth dose should be increased.
Are allergic diseases a risk factor for systemic side effects after COVID-19 vaccines?
Authors: Atayik Emel , Aytekіn Gökhan 
Published: January 2022

AbstractBackground/ aimMass vaccination seems to be the most effective way to turn back to the pre-pandemic period and end the pandemic. Unfortunately, COVID-19 vaccines have some side effects. In phase studies of currently-approved COVID-19 vaccines, patients with a known allergy or a history of anaphylaxis were excluded from the studies. This situation creates doubts about the course of atopy and the presence of allergic disease related to the side effects of COVID-19 vaccines in patients with allergic diseases. Therefore, our aim with this study was to evaluate local side effects (LSE) and systemic side effects (SSE) after COVID-19 vaccines in patients with allergic diseases and to determine possible risk factors.Materials and MethodsSix hundred forty-eight adult patients who received any COVID-19 vaccine between April 1, 2021 and September 30, 2021 and agreed to participate in the study were included in this case-control retrospective study.ResultsSix hundred forty-eight adult patients [Female: 446 (68.8%), Male: 202 (32.2%)] participated in the study. After the 1st dose of COVID-19 vaccine, 24.1% of patients reported SSE. After the 2nd dose of COVID-19 vaccine, 67 patients (12.3%) developed SSE. Female gender (OR: 1.757, 95%Cl: 1.143-2.702, p: 0.010), history of previous COVID-19 infection (OR: 1.762, 95%Cl: 1.068-2.906, p: 0.026), and COVID-19 vaccine type administered (OR: 4.443, 95% CI: 2.640-7.476, p<0.001) were found to be independent risk factors for SSE after COVID-19 vaccines. Premedication (OR: 0.454, 95% Cl: 0.281-0.733, p<0.001), was found to be a protective factor for SSE developing after COVID-19 vaccines.ConclusionCoronoVac and Pfizer-BioNTech COVID-19 vaccines are shown to be well tolerated. Patients with allergic disease do not have an increased risk for SSE that may develop after COVID-19 vaccines. Moreover, doubts or fears about possible side effects in the allergic patient group should not be an obstacle to COVID-19 vaccination.
A brain atlas of the camouflaging dwarf cuttlefish,Sepia bandensis
Authors: Montague Tessa G. , Rieth Isabelle J. , Gjerswold-Selleck Sabrina , Garcia-Rosales Daniella , Aneja Sukanya , Elkis Dana , Zhu Nanyan , Kentis Sabrina , Rubino Frederick A. , Nemes Adriana , Wang Katherine , Hammond Luke A. , Emiliano Roselis , Ober Rebecca A. , Guo Jia , Axel Richard 
Published: January 2022

SummaryThe coleoid cephalopods (cuttlefish, octopus, and squid) are a group of soft-bodied marine mollusks that exhibit an array of interesting biological phenomena, including dynamic camouflage, complex social behaviors, prehensile regenerating arms, and large brains capable of learning, memory, and problem-solving [1–10]. The dwarf cuttlefish,Sepia bandensis, is a promising model cephalopod species due to its small size, substantial egg production, short generation time, and dynamic social and camouflage behaviors [11]. Cuttlefish dynamically camouflage to their surroundings by changing the color, pattern and texture of their skin. Camouflage is optically-driven, and is achieved by expanding and contracting hundreds of thousands of pigment-filled saccules (chromatophores) in the skin, which are controlled by motor neurons emanating from the brain. We generated a dwarf cuttlefish brain atlas using magnetic resonance imaging (MRI), deep learning, and histology, and we built an interactive web tool (cuttlebase.org) to host the data. Guided by observations in other cephalopods [12–20], we identified 32 brain lobes, including two large optic lobes (75% the total volume of the brain), chromatophore lobes whose motor neurons directly innervate the chromatophores of the color-changing skin, and a vertical lobe that has been implicated in learning and memory. This brain atlas provides a valuable tool for exploring the neural basis of cuttlefish behavior.