bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroconversion following SARS-CoV-2 Infection or Vaccination in Pediatric IBD Patients
Authors: Spencer Elizabeth A. , Klang Eyal , Dolinger Michael , Pittman Nanci , Dubinsky Marla C. 
Published: May 2021

AbstractObjectiveInflammatory bowel disease (IBD) patients are commonly treated with immunomodulatory medications, and the effect of these medications on seroconversion to SARS-CoV-2 infection and vaccination are scant, particularly in pediatrics. We sought to determine serologic responses to SARS-CoV-2 infection and vaccination in pediatric IBD patients.DesignWe conducted a single-center, retrospective study of all pediatric (≤21 years old) IBD patients in whom a SARS-CoV-2 IgG Antibody Assay was performed between April 2020 and May 2021 at our tertiary care center. This assay measures IgG antibody to the full-length SARS-CoV-2 spike protein and was routinely collected at infusion and outpatient clinic visits. The primary outcome was SARS-CoV-2 seroconversion, and the secondary outcome was titer level, with high titer defined as ≥960 titer or >40 AU/mL. Clinical characteristics, including demographics, IBD location, behavior, activity, and therapy, SARS-CoV-2 exposures, COVID-19 testing and symptoms, SARS-CoV-2 infection status (WHO COVID-19: Case Definitions, 2020) and COVID-19 vaccination status and type, were gathered, and univariate analyses examined associations between clinical characteristics and outcome measures.ResultsThere were 340 pediatric patients with SARS-CoV-2 Antibody Testing; 15% for confirmed or probable COVID-19, 2% for suspected COVID-19, 16% for asymptomatic exposure to a close contact with SARS-CoV-2 infection, 61% without any prior symptoms or exposures, and 6% for history of COVID-19 vaccination. Patients with confirmed or probable COVID-19 infection had a 90% rate of seroconversion, with 76% of these patients on biologic therapy. Patients post-infection without seroconversion had a significantly longer interval between infection and antibody assay (P=0.03). Within those with asymptomatic SARS-CoV-2 exposure, 43% had seroconversion, and there were no identified clinical characteristics associated with positive titer.All pediatric patients who received vaccination seroconverted, and all who received mRNA vaccinations, including one after a single dose, achieved high titer levels; 100% of those who received vaccination were on biologic or small molecule therapy, including one on combination therapy with ustekinumab and tofacitinib.ConclusionPediatric IBD patients have strong serologic antibody responses to SARS-CoV-2 infection and COVID-19 vaccination despite high rates of immunomodulatory therapy.
Telecommuting frequency and preference among Japanese workers according to regional cumulative COVID-19 incidence: a cross-sectional study
Authors: Baba Hiroka , Ikegami Kazunori , Ando Hajime , Eguchi Hisashi , Tsuji Mayumi , Tateishi Seiichiro , Nagata Masako , Matsuda Shinya , Fujino Yoshihisa ,   for the CORoNaWork Project
Published: May 2021

AbstractThis study aimed to examine the relationship between telecommuting and the regional cumulative COVID-19 incidence. This was a cross-sectional study analyzing 13,468 office workers. The participant groups, according to the level of cumulative COVID-19 incidence by prefecture, were used as the predictor variable, and telecommuting frequency and preference were used as outcomes. We employed an ordinal logistic regression analysis. In regions with a high cumulative COVID-19 incidence, the proportion of participants who telecommuted more than two days per week was 34.7%, which was approximately 20% higher than in other regions. Telecommuting preference was stronger in areas with higher COVID-19 influence. However, in other regions, the proportion of participants who did not want to telecommute was higher than that of those who wanted to telecommute. We found that telecommuting frequency and preference were higher in regions with high cumulative COVID-19 incidence.
Modeling waning and boosting of COVID-19 in Canada with vaccination
Authors: Childs Lauren , Dick David W , Feng Zhilan , Heffernan Jane M , Li Jing , Röst Gergely 
Published: May 2021

AbstractSARS-CoV-2, the causative agent of COVID-19, has caused devastating health and economic impacts around the globe since its appearance in late 2019. The advent of effective vaccines leads to open questions on how best to vaccinate the population. To address such questions, we developed a model of COVID-19 infection by age that includes the waning and boosting of immunity against SARS-CoV-2 in the context of infection and vaccination. The model also accounts for changes to infectivity of the virus, such as public health mitigation protocols over time, increases in the transmissibility of variants of concern, changes in compliance to mask wearing and social distancing, and changes in testing rates. The model is employed to study public health mitigation and vaccination of the COVID-19 epidemic in Canada, including different vaccination programs (rollout by age), and delays between doses in a two-dose vaccine. We find that the decision to delay the second dose of vaccine is appropriate in the Canadian context. We also find that the benefits of a COVID-19 vaccination program in terms of reductions in infections is increased if vaccination of 15-19 year olds are included in the vaccine rollout.
Peripheral Nerve Magnetoneurography with Optically Pumped Magnetometers
Authors: Bu Yifeng , Prince Jacob , Mojtahed Hamed , Kimball Donald , Shah Vishal , Coleman Todd , Sarkar Mahasweta , Rao Ramesh , Huang Mingxiong , Schwindt Peter , Borna Amir , Lerman Imanuel 
Published: May 2021

AbstractElectrodiagnosis is routinely integrated into clinical neurophysiology practice for peripheral nerve disease diagnoses such as neuropathy, demyelinating disorders, nerve entrapment/impingement, plexopathy or radiculopathy. Measured with conventional surface electrodes, the propagation of peripheral nerve action potentials along a nerve is the result of ionic current flow which, according to Ampere’s Law, generates a small magnetic field that is also detected as an “action current” by magnetometers such as superconducting quantum interference device (SQUID) Magnetoencephalography (MEG) systems. Optically pumped magnetometers (OPMs) are an emerging class of quantum magnetic sensors with a demonstrated sensitivity at the 1 fT/√Hz level, capable of cortical action current detection. But OPMs were ostensibly constrained to low bandwidth therefore precluding their use in peripheral nerve electrodiagnosis. With careful OPM bandwidth characterization, we hypothesized OPMs may also detect compound action current signatures consistent with both Sensory Nerve Action Potential (SNAP) and the Hoffmann Reflex (H-Reflex). In as much, our work confirms OPMs enabled with expanded bandwidth can detect the magnetic signature of both the SNAP and H-Reflex. Taken together, OPMs now show potential as an emerging electrodiagnostic tool.
Partial loss of succinate dehydrogenase reduces high red cell distribution width and promotes healthy survival in chronically hypoxic mice
Authors: Baysal Bora E. , Tabaczynski Debra , Curtin Leslie , Seshadri Mukund , Sexton Sandra 
Published: May 2021

AbstractIncreased red cell distribution width (RDW), which measures erythrocyte size variability (anisocytosis), has been linked to early mortality in many diseases and normal aged population through unknown mechanisms. Hypoxia has been proposed to increase both RDW and mortality. However, experimental evidence, especially in animal models, is lacking. Here, we show that chronic hypobaric hypoxia (~10% O2) increases erythrocyte numbers, hemoglobin and RDW, while reducing longevity in male mice. Compound heterozygous knockout (chKO) mutations in succinate dehydrogenase (Sdh; mitochondrial complex II) genes Sdhb, Sdhc and Sdhd reduce high RDW and immature reticulocyte fraction, and increase healthy lifespan in chronic hypoxia. Hemoglobin and erythrocyte numbers in hypoxia do not show statistically significant differences between Sdh chKO and WT mice. These results identify a mitochondrial mechanism regulating both RDW and organismal adaptation to chronic hypoxia, and suggest SDH as a potential therapeutic target to reduce high RDW-associated clinical mortality.
Estimating animal density with camera traps: a practitioner’s guide of the REST model
Authors: Nakashima Yoshihiro , Yajima Gota , Hongo Shun 
Published: May 2021

AbstractCamera traps are increasingly popular in wildlife research and have the potential to be reliable and cost-effective for estimating animal density. Although density estimation using this automatic technique has long been restricted to species with individually recognizable markings, several analytical approaches have been proposed to target animals lacking such markings (i.e., unmarked populations). Among these approaches, the random encounter and staying time (REST) model may be an efficient and cost-effective approach, even though the procedures for the implementations have not yet been shared with researchers. This paper presents a working protocol for implementing the REST model our research group has been developing. We also present the R code to perform parameter estimation with a maximum likelihood and Bayesian approach. We suggest that this model has potential for further development. We strongly hope that this paper will encourage many researchers to use the REST for density estimation in a wide variety of species in various habitats and make a significant contribution to advancing wildlife conservation and management.
Regions of visual cortex responding to tactile stimulation in an individual with longstanding low vision are not causally involved in tactile processing performance
Authors: Silson Edward H. , Gouws Andre D. , Legge Gordon E. , Morland Antony B. 
Published: May 2021

AbstractBraille reading and other tactile discrimination tasks recruit the visual cortex of both blind and normally sighted individuals undergoing short-term visual deprivation. Prior functional magnetic resonance imaging (fMRI) work in patient ‘S’, a visually impaired adult with the rare ability to read both highly magnified print visually and Braille by touch, found that foveal representations of S’s visual cortex were recruited during tactile perception, whereas peripheral regions were recruited during visual perception. Here, we test the causal nature of tactile responses in the visual cortex of S by combining tactile and visual psychophysics with repetitive transcranial magnetic stimulation (rTMS). First, we replicate this prior fMRI work in S. Second, we demonstrate that transient disruption of S’s foveal visual cortex has no measurable impact on S’s tactile processing performance compared to that of healthy controls – a pattern not predicted by the fMRI results. Third, stimulation of foveal visual cortex maximally disrupted visual processing performance in both S and controls, suggesting the possibility of preserved visual function within S’s foveal cortex. Finally, stimulation of somatosensory cortex induced the expected disruption to tactile processing performance in both S and controls. These data suggest that tactile responses in S’s foveal representation reflect unmasking of latent connections between visual and somatosensory cortices and not behaviourally relevant cross-modal plasticity. Unlike studies in congenitally blind individuals, it is possible that the absence of complete visual loss in S has limited the degree of causally impactful cross-modal reorganisation.Significance statementPrior fMRI work in patient ‘S’ identified that foveal portions of S’s visual cortex respond more to tactile processing, whereas peripheral portions respond more to visual processing. Here, we tested whether this foveal processing was causally related to either tactile or visual processing. First, using fMRI we replicate prior work. Second, we demonstrate that TMS of the foveal representation and of somatosensory cortex interfered with visual and tactile discriminations respectively in controls and crucially also in S. The foveal representation in S, which is responsive to tactile stimulation, does not however play a causal role in mediating S’s ability to discriminate Braille characters and likely reflects the unmasking of latent connections between visual and somatosensory cortices.
Silencing long ascending propriospinal neurons after spinal cord injury improves hindlimb stepping in the adult rat
Authors: Shepard Courtney T. , Pocratsky Amanda M. , Brown Brandon L. , Van Rijswijck Morgan A. , Zalla Rachel M. , Burke Darlene A. , Morehouse Johnny M. , Reigler Amberly S. , Whittemore Scott R. , Magnuson David S.K. 
Published: May 2021

AbstractLong ascending propriospinal neurons (LAPNs) are a subpopulation of spinal cord interneurons that directly connect the lumbar and cervical enlargements. In uninjured animals, conditionally silencing LAPNs resulted in disrupted left-right coordination of the hindlimbs and forelimbs in a context-dependent manner, demonstrating that LAPNs secure alternation of the fore- and hindlimb pairs during overground stepping in the adult rat. Given their ventrolateral location in the spinal cord white matter, many LAPN axons likely remain intact following thoracic spinal cord injury (SCI), suggesting a potential role in the recovery of stepping. Thus, we hypothesized that silencing LAPNs after SCI would result in diminished hindlimb locomotor function. We found instead that silencing of spared LAPNs post-SCI restored the left-right hindlimb coordination associated with alternating gaits that was lost as a result of SCI. Several other fundamental characteristics of hindlimb stepping were also improved and the number of abnormal steps were reduced. However, hindlimb-forelimb coordination was not restored. These data suggest that the temporal information carried between the enlargements by the LAPNs after SCI may be detrimental to hindlimb locomotor function. These observations have implications for our understanding of the relationship between injury severity and functional outcome, for the efforts to develop neuro- and axo-protective therapeutic strategies, and also for the clinical study/implementation of spinal stimulation and neuromodulation.
Cardiovascular Autonomic Neuropathy in Type 1 Diabetes is Associated with Several Metabolic Pathways – New Risk Markers on the Horizon
Authors: Hansen Christian S , Suvitaival Tommi , Theilade Simone , Mattila Ismo , Lajer Maria , Trošt Kajetan , Ahonen Linda , Hansen Tine W , Legido-Quigley Cristina , Rossing Peter , Ahluwalia Tarunveer S 
Published: May 2021

ObjectiveCardiovascular autonomic neuropathy (CAN) in diabetes is associated with increased mortality and morbidity and is a non-treatable complication. We investigated associations between circulating metabolites and presence of CAN in persons with type 1 diabetes (T1D).MethodsCAN was assessed by cardiovascular reflex tests (CARTs) in 302 persons with T1D as heart rate response to: deep breathing; lying-to-standing test; and the Valsalva manoeuvre. More than 1 pathological CART defined the CAN diagnosis.Serum metabolomics and lipidomics profiles were analysed with two complementary non-targeted massspectrometry methods. Cross-sectional associations between single metabolites and CAN were assessed by linear regression. Models were fitted with and without adjustments for relevant confounders and multiple testing.ResultsParticipants were mean (IQR) aged 55(49, 63) years, 50% males, with diabetes duration 39(32, 47) years, HbA1c 63(55,69) mmol/mol and 34% had the CAN diagnosis.A total of 75 metabolites and 106 lipids were examined. In crude models, CAN diagnosis was associated with higher levels of hydroxy fatty acids (2,4- and 3,4-dihydroxybutanoic acids, 4–deoxytetronic acid), creatinine, sugar derivates (ribitol, ribonic acid, myo-inositol), citric acid, glycerol, phenols, phosphatidylcholines and lower levels of free fatty acids and amino acid methionine (p<0.05). Upon adjustment, positive associations with CAN were retained with hydroxy fatty acids, tricarboxylic acid (TCA) cycle-based sugar derivates, and citric acid and phenols (Padjusted<0.05).ConclusionsMetabolic pathways, including the TCA cycle, hydroxy fatty acids, phosphatidylcholines and sugar derivatives, were associated with CAN in T1D. These novel metabolic pathways associated with CAN could prove to be future modifiable risk factors.
Continuous Seizure Emergency Evoked in Mice with Pharmacological, Electrographic, and Pathological Features Distinct from Status Epilepticus
Authors: Knox Kevin M. , Zierath Dannielle K. , White H. Steve , Barker-Haliski Melissa 
Published: May 2021

SummaryObjectivesBenzodiazepines are the standard of care for the management of sustained seizure emergencies, including status epilepticus (SE) and seizure clusters. Seizure clusters are a variably defined seizure emergency wherein a patient has multiple seizures above a baseline rate, with intervening periods of recovery, distinguishing clusters from SE. While phenotypically distinct, the precise pathophysiological and mechanistic differences between SE and seizure clusters are under studied. Preclinical interrogation is needed to help uncover the behavioral, physiological, and pathological mechanisms associated with seizure emergencies in order to better manage these events in the susceptible individual.MethodsHerein, we characterize a novel model of sustained seizure emergency induced in CF-1 mice through the combined administration of high-dose phenytoin (PHT; 50 mg/kg, i.p.) and pentylenetetrazol (PTZ; 100 mg/kg, s.c.).ResultsIn the present manuscript we describe a mouse model of sustained seizure emergency that is physiologically, pharmacologically, and histologically distinct from SE. Acute administration of PHT 1 hour prior to s.c.PTZ led to significantly more mice with continuous seizure activity (CSA; 73.4%) versus vehicle-pretreated mice (13.8%; p<0.0001). CSA was sensitive to lorazepam and valproic acid when administered at seizure onset, as well as 30-minutes post-seizure onset. Carbamazepine worsened seizure control and post-CSA survival. Mice in CSA exhibited EEG patterns distinct from kainic acid-induced SE and s.c.PTZ alone, clearly differentiating CSA from SE and s.c.PTZ-induced myoclonic seizures. Neuropathological assessment by FluoroJade-C staining of brains collected 24-hours later revealed no neurodegeneration in any mice with CSA, whereas there was widespread neuronal death in brains from KA-SE mice.SignificanceThis study defines a novel mouse model on which to elucidate the mechanistic differences between sustained seizure emergencies (i.e. SE and seizure clusters) to improve discovery of effective clinical interventions and define mechanisms of seizure termination.Key Points BoxSeizure clusters are a variably defined seizure emergency that is sensitive to benzodiazepines, distinct from status epilepticus.The mechanistic differences between seizure clusters and status epilepticus are not well defined.We report a mouse seizure emergency model that is phenotypically, pathologically, and pharmacologically distinct from status epilepticus.This mouse model provides a novel platform on which to further interrogate the mechanisms underlying seizure emergencies.
Peptimetric: Quantifying and visualizing differences in peptidomic data
Authors: Hartman Erik , Mahdavi Simon , Kjellström Sven , Schmidtchen Artur 
Published: May 2021

AbstractFinding new sustainable means of diagnosing and treating diseases is one of the most pressing issues of our time. In recent years, several endogenous peptides have been found to be both excellent biomarkers for many diseases and to possess important physiological roles which may be utilized in treatments. The detection of peptides has been facilitated by the rapid development of biological mass spectrometry and now the combination of fast and sensitive high resolution MS instruments and stable nano HP-LC equipment sequences thousands of peptides in one single experiment. In most research conducted with these advanced systems, proteolytically cleaved proteins are analyzed and the specific peptides are identified by software dedicated for protein quantification using different proteomics workflows. Analysis of endogenous peptides with peptidomics workflows also benefit from the novel sensitive and advanced instrumentation, however, the generated peptidomic data is vast and subsequently laborious to visualize and examine, creating a bottleneck in the analysis. Therefore, we have created Peptimetric, an application designed to allow researchers to investigate and discover differences between peptidomic samples. Peptimetric allows the user to dynamically and interactively investigate the proteins, peptides, and some general characteristics of multiple samples, and is available as a web application at https://peptimetric.herokuapp.com. To illustrate the utility of Peptimetric, we’ve applied it to a peptidomic dataset of 15 urine samples from diabetic patients and corresponding data from healthy subjects.
Fork Slowing and Reversal as an Adaptive Response to Chronic ATR Inhibition
Authors: Dibitetto Diego , Sanchi Andrea , Sanford Ethan J. , Lopes Massimo , Smolka Marcus B. 
Published: May 2021

SUMMARYInhibitors of the replication stress response kinase ATR are currently being explored in anti-cancer therapy. Acute ATR inhibition is known to impair the proper control of origin firing, DNA repair, and cell cycle, resulting in DNA breaks and mitotic catastrophe. Less is understood about the effects of clinically relevant regimes of ATR inhibition, which involve chronic and low doses of ATR inhibitors (cATRi) to cells. Here we report unexpected molecular effects ofcATRion replication dynamics.cATRistrongly reduces fork speed but has minimal effects on the accumulation of DNA breaks or cell survival.cATRipromotes extensive fork reversal and RAD51- and PARP-mediated fork slowing that correlate with the accumulation of DNA-RNA hybrids. Our work shows that fork reversal is a critical adaptive response ensuring cell survival duringcATRiand that the manipulation of fork reversal causes hypersensitivity tocATRi, increasing the effectiveness of ATR inhibitors in anti-cancer therapies.
Adapting fundamental concepts from insect societies to the demands of bio-ontologies
Authors: Silva Thiago S.R. 
Published: May 2021

AbstractThe present work provides a logical account for translating fundamental concepts in the study of social insects to bio-ontologies, namely ‘colony’ and ‘caste’, which can be used by researchers for describing and organizing entities belonging to nonhuman societies, as well as for the provision of evidential criteria for evaluating cumulative-constitutive explanations of ‘social’ entities. I explore how different properties can provide connectedness of ‘colonies’ and ‘castes’ and discuss the implications of this approach to biological representation and ontology design. Finally, I briefly discuss some limitations in current approaches to demarcate subcategories of ‘castes’.