bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative EEG as a Prognostic Tool in Suspected Anti-N-Methyl-d-Aspartate Receptor Antibody Encephalitis
Authors: Blackman Graham , Kumar Kieron , Hanrahan John G. , Dalrymple Anthony , Mullatti Nandini , Moran Nick , Valentin Antonio , Gibson Lucy , Pollak Thomas A. , David Anthony S. 
Published: July 2021

Purpose:
Anti–N-methyl-d-aspartate receptor (anti-NMDAR) encephalitis is a form of autoimmune encephalitis associated with EEG abnormalities. In view of the potentially severe outcomes, there is a need to develop prognostic tools to inform clinical management. The authors explored whether quantitative EEG was able to predict outcomes in patients with suspected anti-NMDAR encephalitis.

Methods:
A retrospective, observational study was conducted of patients admitted to a tertiary clinical neuroscience center with suspected anti-NMDAR encephalitis. Peak power and peak frequency within delta (<4 Hz), theta (4–8 Hz), alpha (8 - 13 Hz), and beta (13–30 Hz) frequency bands were calculated for the first clinical EEG recording. Outcome was based on the modified Rankin Scale (mRS) score at 1 year after hospital discharge. Binomial logistic regression using backward elimination was performed with peak frequency and power, anti-NMDAR Encephalitis One-Year Functional Status score, age, and interval from symptom onset to EEG entered as predictors.

Results:
Twenty patients were included (mean age 48.6 years, 70% female), of which 7 (35%) had a poor clinical outcome (mRS 2–6) at 1 year. There was no association between reported EEG abnormalities and outcome. The final logistic regression model was significant (χ2(1) = 6.35, P < 0.012) with peak frequency in the delta range (<4 Hz) the only retained predictor. The model explained 38% of the variance (Nagelkerke R
2) and correctly classified 85% of cases. Higher peak frequency in the delta range was significantly associated (P = 0.04) with an increased likelihood of poor outcome.

Conclusions:
In this exploratory study, it was found that quantitative EEG on routinely collected EEG recordings in patients with suspected anti-NMDAR encephalitis was feasible. A higher peak frequency within the delta range was associated with poorer clinical outcome and may indicate anti-NMDAR-mediated synaptic dysfunction. Quantitative EEG may have clinical utility in predicting outcomes in patients with suspected NMDAR antibody encephalitis, thereby serving as a useful adjunct to qualitative EEG assessment; however, given the small sample size, replication in a larger scale is indicated.
Scoping review and interpretation of Myofascial Pain/Fibromyalgia syndrome: an attempt to assemble a medical puzzle
Authors: Plaut Shiloh 
Published: July 2021

AbstractBackgroundMyofascial Pain Syndrome (MPS) is a common, overlooked, and underdiagnosed condition and has significant burden. MPS is often dismissed by clinicians while patients remain in pain for years. MPS can evolve into fibromyalgia, however, effective treatments for both are lacking due to absence of a clear mechanism. Many studies focus on central sensitization. Therefore, the purpose of this scoping review is to systematically search cross-disciplinary empirical studies of MPS, focusing on mechanical aspects, and suggest an organic mechanism explaining how it might evolve into fibromyalgia. Hopefully, it will advance our understanding of this disease.MethodsSystematically searched multiple phrases in MEDLINE, EMBASE, COCHRANE, PEDro, and medRxiv, majority with no time limit. Inclusion/exclusion based on title and abstract, then full text inspection. Additional literature added on relevant side topics. Review follows PRISMA-ScR guidelines. PROSPERO yet to adapt registration for scoping reviews.Findings799 records included. Fascia can adapt to various states by reversibly changing biomechanical and physical properties. Trigger points, tension, and pain are a hallmark of MPS. Myofibroblasts play a role in sustained myofascial tension. Tension can propagate in fascia, possibly supporting a tensegrity framework. Movement and mechanical interventions treat and prevent MPS, while living sedentarily predisposes to MPS and recurrence.ConclusionsMPS can be seen as a pathological state of imbalance in a natural process; manifesting from the inherent properties of the fascia, triggered by a disrupted biomechanical interplay. MPS might evolve into fibromyalgia through deranged myofibroblast in connective tissue (“fascial armoring”). Movement is an underemployed requisite in modern lifestyle. Lifestyle is linked to pain and suffering. The mechanism of needling is suggested to be more mechanical than currently thought. A “global percutaneous needle fasciotomy” that respects tensegrity principles may treat MPS/fibromyalgia more effectively. “Functional-somatic syndromes” can be seen as one entity (myofibroblast-generated-tensegrity-tension), sharing a common rheuma-phycho-neurological mechanism.
First detection of SARS-CoV-2 Delta variant (B.1.617.2) in the wastewater of (Ahmedabad), India
Authors: Joshi Madhvi , Kumar Manish , Srivastava Vaibhav , Kumar Dinesh , Rathore Dalipsingh , Pandit Ramesh , Joshi Chaitanya G. 
Published: July 2021

AbstractContrary to the conventional genomic surveillance based on clinical samples (symptomatic patients), the wastewater-based genomic surveillance can identify all the variants shed by the infected individuals in the population, as it does also include RNA fragmented shredded by clinically escaped asymptomatic patients. We analyzed four samples to detect key mutations in the SARS-CoV-2 genome and track circulating variants in Ahmedabad during the first wave (Sep/ Nov 2020) and before the second wave (in Feb 2021) of COVID-19 in India. The analysis showed a total of 35 mutations in the spike protein across four samples categorized into 23 types. We noticed the presence of spike protein mutations linked to the VOC-21APR-02; B.1.617.2 lineage (Delta variant) with 57% frequency in wastewater samples of Feb 2021. The key spike protein mutations were T19R, L452R, T478K, D614G, & P681R and deletions at 22029 (6 bp), 28248 (6 bp), & 28271 (1 bp). Interestingly, these mutations were not observed in the samples of Sep and Nov 2020 but appeared before the devastating second wave of COVID-19, which started in early April 2021 in India, caused rapid transmission and deaths all over India. We found the genetic traces of the B.1.617.2 in samples of early Feb 2021 i.e., more than a month before the first clinically confirmed case of the same variant in March 2021 in Ahmedabad, Gujarat. The present study tells about the circulating variants in Ahmedabad and suggests early prediction VOCs employing the wastewater genomic surveillance approach that must be exploited at a large scale for effective COVID-19 management.HighlightsWhole-genome sequencing of SARS-CoV-2 from the WW samples was carried out.Variant of Concern (VoC: VOC-21APR-02; B.1.617.2) were detected in WW samples.WBE may detect prevalent SARS-CoV-2 variants and monitor their cryptic transmissionWW genomic surveillance can aid the decision-making system for public health policies.
Pre-trial predictors of conflict response efficacy in human dorsolateral prefrontal cortex
Authors: Herman Alexander B. , Smith Elliot H. , Schevon Catherine A. , Yates Mark , McKhann Guy M. , Botvinick Matthew , Hayden Benjamin Y. , Sheth Sameer Anil 
Published: July 2021

ABSTRACTThe ability to perform motor actions depends, in part, on the brain’s initial state, that is, the ensemble firing rate pattern prior to the initiation of action. We hypothesized that the same principle would apply to cognitive functions as well. To test this idea, we examined a unique set of single unit data collected in human dorsolateral prefrontal (dlPFC) cortex. Data were collected in a conflict task that interleaves Simon (motor-type) and Eriksen (flanker-type) conflict trials. In dlPFC, variability in pre-trial firing rate predicted the ability to resolve conflict, as inferred from reaction times. Ensemble patterns that predicted faster Simon reaction times overlapped slightly with those predicting Erikson performance, indicating that the two conflict types are associated with near-orthogonal initial states, and suggesting that there is a weak abstract or amodal conflict preparatory state in this region. These codes became fully orthogonalized in the response state. We interpret these results in light of the initial state hypothesis, arguing that the firing patterns in dlPFC immediately preceding the start of a task predispose it for the efficient implementation of cognitive action.
Nicotine dependence and functional connectivity of insular cortex subregions
Authors: Ghahremani Dara G. , Pochon Jean-Baptiste , Diaz Maylen Perez , Tyndale Rachel F. , Dean Andy C. , London Edythe D. 
Published: July 2021

AbstractThe insular cortex has been identified as a promising target in brain-based therapies for Tobacco Use Disorder, and has three major sub-regions (ventral anterior, dorsal anterior, and posterior) that serve distinct functional networks. How these subregions and associated networks contribute to nicotine dependence has not been well understood, and therefore was the subject of this study. Forty-seven individuals (24 women; 18-45 years old) who smoked cigarettes daily rated their dependence using the Fagerström Test for Nicotine Dependence (FTND), abstained from smoking overnight (~12 h), and underwent resting-state functional MRI. Correlations between dependence and resting-state functional connectivity (RSFC) of the major insular sub-regions were evaluated using whole-brain-corrected voxel-wise analyses and post-hoc region-of-interest (ROI) analyses. Dependence was analyzed both as a unitary (FTND total score) and bivariate construct – two FTND factors (“morning smoking” and “daytime smoking”). Dependence was negatively correlated with connectivity of both the right dorsal and left ventral anterior insula with the left precuneus, and with connectivity of the left posterior insula to the left putamen. In post-hoc analyses, dependence correlated negatively with connectivity between all anterior insula subregions and the left precuneus, and with bilateral posterior insula connectivity with the left posterior putamen. The latter finding was driven by “daytime smoking”. These results suggest an anterior-posterior distinction in functional insular networks associated with different dimensions of nicotine dependence, with greater dependence linked to weaker connectivity. They may inform therapeutic approaches involving brain stimulation that may elicit differential clinical outcomes depending on the insular subnetwork targeted.
A natural marmoset model of genetic generalized epilepsy
Authors: Yang Xiangyu , Chen Zhitang , Wang Ziying , He Guang , Li Zhiqiang , Shi Yongyong , Gong Neng , Zhao Binglei , Takahashi Eiki , Li Weidong 
Published: July 2021

SummaryAs a common neurological disease, epilepsy has been extensively studied. Efforts have been made on rodent and other animal models to reveal the pathogenic mechanisms of epilepsy and develop new drugs as treatment. However, the features of current epilepsy models cannot fully mimic different kinds of epilepsy in human, asking for non-human primates models of epilepsy. The common marmoset (Callithrix jacchus) is a New World monkey that is widely used to study brain function. Here, we show a natural marmoset model of generalized epilepsy. In this unique marmoset family, generalized epilepsy was successfully induced by handling operation in some individuals. We mapped the marmoset family with handling-sensitive epilepsy and found that epileptic marmoset had an autosomal dominant genetic predisposition. Those marmosets were more sensitive to epilepsy inducers pentylenetetrazol (PTZ). By electrocorticogram (ECoG) recording, we detected epileptic discharge in marmoset with history of seizures. However, there was no significant change in the overall structure of epileptic marmoset brain. In summary, we report a family of marmosets with generalized seizures induced by handling operation. This epileptic marmoset family provides insights to better understand the mechanism of generalized epilepsy and helps to develop new therapeutic methods.Short summaryDespite the rodent and other animal models on epilepsy, a common neurological disease, the understanding of the pathogenic mechanisms of epilepsy and treatment are yet to be advanced., Non-human primates are good experimental animals for modelling neurological disease. Here we report a common marmoset family with generalized epilepsy induced by handling stimulation. We mapped the epileptic marmoset family and found that epilepsy had a genetic predisposition. The present report deals in detail with the phenotypes and characteristics of epileptic marmosets. This natural marmoset reflect epilepsy model will help to better understand the mechanism of epilepsy and develop new therapeutic methods.
Dissociable Multi-scale Patterns of Development in Personalized Brain Networks
Authors: Pines Adam R. , Larsen Bart , Cui Zaixu , Sydnor Valerie J. , Bertolero Maxwell A. , Adebimpe Azeez , Alexander-Bloch Aaron F. , Davatzikos Christos , Fair Damien A. , Gur Ruben C. , Gur Raquel E. , Li Hongming , Milham Michael P. , Moore Tyler M. , Murtha Kristin , Parkes Linden , Thompson-Schill Sharon L. , Shanmugan Sheila , Shinohara Russell T. , Weinstein Sarah M. , Bassett Danielle S. , Fan Yong , Satterthwaite Theodore D. 
Published: July 2021

SUMMARYThe brain is organized into networks at multiple resolutions, or scales, yet studies of functional network development typically focus on a single scale. Here, we derived personalized functional networks across 29 scales in a large sample of youths (n=693, ages 8-23 years) to identify multi-scale patterns of network re-organization related to neurocognitive development. We found that developmental shifts in inter-network coupling systematically adhered to and strengthened a functional hierarchy of cortical organization. Furthermore, we observed that scale-dependent effects were present in lower-order, unimodal networks, but not higher-order, transmodal networks. Finally, we found that network maturation had clear behavioral relevance: the development of coupling in unimodal and transmodal networks dissociably mediated the emergence of executive function. These results delineate maturation of multi-scale brain networks, which varies according to a functional hierarchy and impacts cognitive development.
Dug: A Semantic Search Engine Leveraging Peer-Reviewed Knowledge to Span Biomedical Data Repositories
Authors: Waldrop Alexander M. , Cheadle John B. , Bradford Kira , Preiss Alexander , Chew Robert , Holt Jonathan R. , Braswell Nathan , Watson Matt , Crerar Andrew , Ball Chris M. , Kebede Yaphet , Schreep Carl , Linebaugh PJ , Hiles Hannah , Boyles Rebecca , Bizon Chris , Krishnamurthy Ashok , Cox Steve 
Published: July 2021

AbstractMotivationAs the number of public data resources continues to proliferate, identifying relevant datasets across heterogenous repositories is becoming critical to answering scientific questions. To help researchers navigate this data landscape, we developed Dug: a semantic search tool for biomedical datasets utilizing evidence-based relationships from curated knowledge graphs to find relevant datasets and explain why those results are returned.ResultsDeveloped through the National Heart, Lung, and Blood Institute’s (NHLBI) BioData Catalyst ecosystem, Dug has indexed more than 15,911 study variables from public datasets. On a manually curated search dataset, Dug’s total recall (total relevant results/total results) of 0.79 outperformed default Elasticsearch’s total recall of 0.76. When using synonyms or related concepts as search queries, Dug (0.36) far outperformed Elasticsearch (0.14) in terms of total recall with no significant loss in the precision of its top results.Availability and ImplementationDug is freely available at https://github.com/helxplatform/dug. An example Dug deployment is also available for use at https://search.biodatacatalyst.renci.org/.Contactawaldrop@rti.org or scox@renci.org
Ecological inference using data from accelerometers needs careful protocols
Authors: Garde Baptiste , Wilson Rory P. , Fell Adam , Cole Nik , Tatayah Vikash , Holton Mark D. , Rose Kayleigh A. R. , Metcalfe Richard S. , Robotka Hermina , Wikelski Martin , Tremblay Fred , Whelan Shannon , Elliott Kyle H. , Shepard Emily L. C. 
Published: July 2021

AbstractAccelerometers in animal-attached tags have proven to be powerful tools in behavioural ecology, being used to determine behaviour and provide proxies for movement-based energy expenditure. Researchers are collecting and archiving data across systems, seasons and device types. However, in order to use data repositories to draw ecological inference, we need to establish the error introduced according to sensor type and position on the study animal and establish protocols for error assessment and minimization.Using laboratory trials, we examine the absolute accuracy of tri-axial accelerometers and determine how inaccuracies impact measurements of dynamic body acceleration (DBA), as the main acceleration-based proxy for energy expenditure. We then examine how tag type and placement affect the acceleration signal in birds using (i) pigeons Columba livia flying in a wind tunnel, with tags mounted simultaneously in two positions, (ii) back- and tail-mounted tags deployed on wild kittiwakes Rissa tridactyla. Finally, we (iii) present a case study where two generations of tag were deployed using different attachment procedures on red-tailed tropicbirds Phaethon rubricauda foraging in different seasons.Bench tests showed that individual acceleration axes required a two-level correction (representing up to 4.3% of the total value) to eliminate measurement error. This resulted in DBA differences of up to 5% between calibrated and uncalibrated tags for humans walking at different speeds. Device position was associated with greater variation in DBA, with upper- and lower back-mounted tags in pigeons varying by 9%, and tail- and back-mounted tags varying by 13% in kittiwakes. Finally, DBA varied by 25% in tropicbirds between seasons, which may be attributable to tag attachment procedures.Accelerometer accuracy, tag placement, and attachment details critically affect the signal amplitude and thereby the ability of the system to detect biologically meaningful phenomena. We propose a simple method to calibrate accelerometers that should be used prior to deployments and archived with resulting data, suggest a way that researchers can assess accuracy in previously collected data, and caution that variable tag placement and attachment can increase sensor noise and even generate trends that have no biological meaning.
The multilayered organization of water-soluble proteins
Authors: Wang Lincong 
Published: July 2021

AbstractThe structural analysis of proteins has focused primarily on secondary structure, three-dimensional fold and active site while whole surface has been analyzed to a lesser extent and interior has not received much attention. Here we present an analysis of both the surfaces and the interiors of a set of water-soluble monomeric proteins in terms of solvent-excluded surface (SES) and atomic partial charge. The analysis shows that the surface of a soluble monomer has a net negative charge and is much smoother than the interior. Most interestingly with regard to both atomic partial charge and SES-defined geometric property there exists a multilayered organization from the exterior to the interior of a soluble monomer. The multilayered organization is closely related to protein-solvent interaction and should be a general feature of a water-soluble protein. Particularly the multilayered organization may set an upper limit for the size of a water-soluble monomer and plays an important role in the determination of its overall shape in solution.Significance statementThe analysis of the solvent-excluded surfaces (SESs) of a large set of water-soluble monomers with crystal structures shows that in any soluble monomer there exists a multilayered organization in terms of SES-defined electric and geometric properties. It means that the atoms in a soluble monomer are not randomly distributed but organized into successive layers to optimize its interaction with solvent molecules. The SES-derived multi-layered organization should be a general feature of a water-soluble protein and likely plays a vital role in its solvation, folding and structure.
Differential effects of high versus low linear energy transfer (LET) radiation on type-I interferon (IFNβ) and TREX1 responses
Authors: Miles Devin , Cao Ning , Sandison George , Stewart Robert D. , Moffitt Greg , Pulliam Thomas , Parvathaneni Upendra , Goff Peter , Nghiem Paul , Stantz Keith 
Published: July 2021

PurposeCancer cells produce innate immune signals following radiation damage, with STING pathway signaling as a critical mediator. High linear energy transfer (LET) radiations create larger numbers of DNA double-strand breaks (DSBs) per unit dose than low-LET radiations and may therefore be more immunogenic. We studied the dose response characteristics of pro-immunogenic type-I interferon, interferon-beta (IFNβ), and its reported suppressor signal, three-prime repair exonuclease 1 (TREX1), in vitro with low-LET x-rays and high-LET fast neutrons.MethodsMerkel cell carcinoma cells (MCC) were irradiated by graded doses of x-rays (1-24 Gy) or fast neutrons (1-8 Gy). IFNβ was measured as a function of dose via ELISA assay, and exonuclease TREX1 expression via immunofluorescence microscopy. The Monte Carlo damage simulation (MCDS) was used to model fast neutron relative biological effectiveness for DSB induction (RBEDSB) and compared to laboratory measurements of the RBE for IFNβ production (RBEIFNβ) and TREX1 upregulation (RBETREX1). RBEIFNβ models were also applied to radiation transport simulations to quantify the potential secretion of IFNβ in representative clinical beams.ResultsPeak IFNβ secretion occurred at 5.7 Gy for fast neutrons and at 14.0 Gy for x-rays, i.e., an effective RBEIFNβ of 2.5 ± 0.2. The amplitude (peak value) of secreted IFNβ signal did not significantly differ between x-rays and fast neutrons (P > 0.05). TREX1 signal increased linearly with absorbed dose, with a four-fold higher upregulation per unit dose for fast neutrons relative to x-rays (RBETREX1 of 4.0 ± 0.1). Monte Carlo modeling of IFNβ suggests Bragg peak-to-entrance ratios of IFNβ production of 40, 100, and 120 for proton, alpha, and carbon ion beams, respectively, a factor of 10-20-fold higher compared to their corresponding physical dose peak-to-entrance ratios. The spatial width of the Bragg peak for IFNβ production is also a factor of two smaller.ConclusionHigh-LET fast neutrons initiate a larger IFNβ response per unit absorbed dose than low-LET x-rays (i.e., RBEIFNβ value of 2.5). The RBE value for IFNβ is quite similar to data reported in the literature for DSB induction and cellular, post-irradiation micronucleation formation for neutrons and x-rays. The increased IFNβ release after high-LET radiation may be a contributing factor in stimulating a systemic anti-tumor, adaptive immune response (abscopal effect). However, our results indicate that TREX1 anti-inflammatory signaling in vitro for MCC cells is larger per unit dose for fast neutrons than for x-rays (RBETREX1 of 4.0). Given these competing effects, additional studies are needed to clarify whether or not high-LET radiations are therapeutically advantageous over low-LET radiation for pro-inflammatory immune signaling in other cell lines in vitro and for in vivo cancer models.