bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repetitive Transcranial Magnetic Stimulation Promotes Rapid Psychiatric Stabilization in Acutely Suicidal Military Service Members
Authors: Hines Christopher E. , Mooney Scott , Watson Nora L. , Looney Stephen W. , Wilkie David J. 
Published: December 2021

Objective
This study presents data for using accelerated transcranial magnetic stimulation (TMS) as an intervention for suicidal crisis (SC).

Methods
This prospective, single-site, randomized, double-blind trial enrolled active-duty military participants with SC to receive either active TMS (n = 59) or sham TMS (n = 61) 3 times per day for 3 consecutive days. Our primary outcome, the Beck Scale for Suicidal Ideation—current (SSI-C), was measured before each session of TMS. Secondary outcomes measured both the SSI-C and the Beck Scale for Suicidal Ideation—total daily for the 3 intervention days and at 1, 3, and 6 months of follow-up.

Results
In the modified intention to treat (mITT) analysis of SSI-C changes over treatment sessions, the TMS active group had accelerated decline in suicidal ideation as compared with sham: β for interaction was 0.12 points greater SSI-C decline per session (standard error [SE], 0.06) in TMS versus sham (P = 0.04). In both the mITT and per-protocol active TMS groups, the mean final SSI-C scores were below 3. These scores remained below 3 for the entire 6-month follow-up period.

Conclusions
In this military trial of suicidal patients, we found that both active and sham accelerated TMS rapidly reduces SC. Moreover, in the mITT analysis, there was a statistically significant antisuicidal benefit of active TMS versus sham TMS in the primary outcome. Both the mITT and per-protocol groups moved from higher to approximately 7 times lower suicide risk strata and remained there for the duration of the study. Further studies are warranted to understand accelerated TMS' full potential as a treatment for SC.
The role of airborne transmission in a large single source outbreak of SARS-CoV-2 in a Belgian nursing home in 2020
Authors: Vuylsteke Bea , Cuypers Lize , Baele Guy , Stranger Marianne , Paralovo Sarah Lima , André Emmanuel , Dirks Joke , Maes Piet , Laga Marie 
Published: December 2021

AbstractObjectivesTo better understand the conditions which have led to one of the largest COVID-19 outbreaks in Belgian nursing homes in 2020.SettingA nursing home in Flanders, Belgium, which experienced a massive outbreak of COVID-19 after a cultural event. An external volunteer who dressed as a legendary figure visited consecutively the 4 living units and tested positive for SARS-CoV-2 the next day. Within days, residents started to display symptoms and the outbreak spread rapidly within the nursing home.MethodsWe interviewed key informants and collected standardized data from all residents retrospectively. A batch of 115 positive samples with a Ct value of <37 by qRT-PCR were analysed using whole-genome sequencing. Six months after the outbreak, ventilation assessment of gathering rooms in the nursing home was done using a tracer gas test with calibrated CO2sensors.ResultsTimeline of diagnoses and symptom onsets clearly pointed to the cultural event as the start of the outbreak, with the volunteer as index case. The genotyping of positive samples depicted the presence of one large cluster, suggesting a single source outbreak.The global attack rate among residents was 77% with a significant association between infection and presence at the event. Known risk factors such as short distance to or physical contact with the volunteer, and wearing of a mask during the event were not associated with early infection. The ventilation assessment showed a high background average CO2level in four main rooms varying from 657 ppm to 846 ppm.ConclusionsOur investigation shows a rapid and widespread single source outbreak of SARS-CoV-2 in a nursing home, in which airborne transmission was the most plausible explanation for the massive intra-facility spread. Our results underscore the importance of ventilation and air quality for the prevention of future outbreaks in closed facilities.
Toward noninvasive assessment of stroke risk in pediatric cerebrovascular disease
Authors: Horn John D. , Johnson Michael J. , Starosolski Zbigniew , Meoded Avner , Milewicz Dianna M. , Annapragada Ananth , Hossain Shaolie S. 
Published: December 2021

AbstractBackground and PurposeMoyamoya disease (MMD) is a progressive steno-occlusive cerebrovascular disease leading to recurrent stroke. There is a lack of reliable biomarkers to identify unilateral stroke MMD patients who are likely to progress to bilateral disease and experience subsequent contralateral stroke(s). We hypothesized that local hemodynamics are predictive of future stroke and set out to noninvasively assess this stroke risk in pediatric MMD patients.MethodsMR and X-ray angiography imaging were utilized to reconstruct patient-specific models of the circle of Willis of 6 pediatric MMD patients who had previous strokes, along with a control subject. Blood flow simulations were performed by using a Navier-Stokes solver within an isogeometric analysis framework. Vascular regions with a wall shear rate (WSR) above the coagulation limit (> 5000 s−1) were identified to have a higher probability of thrombus formation, potentially leading to ischemic stroke(s). Two metrics, namely, “critical WSR coverage” and “WSR score”, were derived to assess contralateral stroke risk and compared with clinical follow-up data.ResultsIn two patients that suffered a contralateral stroke within two months of the primary stroke, critical WSR coverages exceeding 50% of vessel surface and WSR scores greater than 6x the control were present in multiple contralateral vessels. These metrics were not as conclusive in two additional patients with 3-to-5-year gaps between primary and contralateral strokes. However, a longitudinal study of one of these two cases, where a subsequent timepoint was analyzed, accurately predicted disease stabilization on the primary stroke side and an elevated contralateral stroke risk, thus indicating that post-stroke follow-up at regular intervals might be warranted for secondary stroke prevention.ConclusionsWSR-based metrics could be predictive of future stroke risk after an initial stroke in MMD patients. In addition, more accurate predictions may be possible by performing patient-specific hemodynamic analysis at multiple timepoints during patient follow-up to monitor changes in the WSR-based metrics.
The ground truth of the Data-Iceberg: Correct Meta-data
Authors: Caliskan Aylin , Dangwal Seema , Dandekar Thomas 
Published: December 2021

Short summaryBiological molecular data such as sequence information increase so rapidly that detailed metadata, describing the process and conditions of data collection as well as proper labelling and typing of the data become ever more important to avoid mistakes and erroneous labeling. Starting from a striking example of wrong labelling of patient data recently published in Nature, we advocate measures to improve software metadata and controls in a timely manner to not rapidly loose quality in the ever-growing data flood.
The BioImage Archive - building a home for life-sciences microscopy data
Authors: Hartley Matthew , Kleywegt Gerard J. , Patwardhan Ardan , Sarkans Ugis , Swedlow Jason R. , Brazma Alvis 
Published: December 2021

AbstractDespite the huge impact of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. In its initial development BioImage Archive accepts bioimaging data associated with publications, in any format, from any imaging modality from the molecular to the organism scale, excluding medical imaging. The BioImage Archive will ensure reproducibility of published studies that derive results from image data and reduce duplication of effort. Most importantly, the BioImage Archive will help scientists to generate new insights through reuse of existing data to answer new biological questions, and provision of training, testing and benchmarking data for development of tools for image analysis. The archive is available at https://www.ebi.ac.uk/bioimage-archive/.HighlightsThe BioImage Archive is a new archival data resource at the European Bioinformatics Institute (EMBL-EBI).The BioImage Archive aims to accept all biological imaging data associated with peer-reviewed publications using approaches that probe biological structure, mechanism and dynamics, as well as other important datasets that can serve as reference examples for particular biological or technical domains.The BioImage Archive aims to encourage the use of valuable imaging data, to improve reproducibility of published results that rely on image data, and to facilitate extraction of novel biological insights from existing data and development of new image analysis methods.The BioImage Archive forms the foundation for an ecosystem of related databases, supporting those resources with storage infrastructure and indexing across databases.Across this ecosystem, the BioImage Archive already stores and provides access to over 1.5 petabytes of image data from many different imaging modalities and biological domains.Future development of the BioImage Archive will support the fast-emerging next generation file formats (NGFFs) for bioimaging data, providing access mechanisms tailored toward modern visualisation and data exploration tools, as well as unlocking the power of modern AI-based image-analysis approaches.
Evaluating the Outcomes of Enhanced Adherence Counselling Intervention on Clients with High Viral Loads in Selected Health Facilities in Monze District
Authors: Kaira M. , Sikazwe T. , Simwanza J. , Zambwe M. , Chipimo P. J 
Published: December 2021

ABSTRACTTo investigate the changes in Viral Load(VL) during Enhanced Adherence Counselling (EAC) sessions and its determinants among ART clients with unsuppressed VLs in Monze district.MethodA Cross-sectional study involving 616 HVL ART clients from 15 health facilities in Monze district which was conducted between October 1 2019 and March 30 2021.ResultsOut of 616 clients analysed, there was an improvement in viral load suppression following completion of EAC with a final outcome of 61% suppression. 28.7% remained unsuppressed. A total of 9.1% had no final viral load results documented and 0.2 % had been transferred out of their respective facilities and were not included in the study. Collection of repeat Viral loads was done on 84% of the clients with high viral load results while 16% had no record of sample collection. A total of 56 results were not received giving a result return of 89% from repeat samples collected. Females had a 40% likelihood of being unsuppressed at 95% CI (41% to 86%) compared to the males.ConclusionEAC improves the outcomes of HVLs and should be encouraged on all high viral clients. Programs should be developed to improve suppression in females on ART
Mesocorticolimbic system abnormalities in chronic cluster headache patients: a neural signature?
Authors: Ferraro Stefania , Medina Jean Paul , Nigri Anna , Giani Luca , Demichelis Greta , Pinardi Chiara , Bruzzone Maria Grazia , Proietti Alberto , Becker Benjamin , Chiapparini Luisa , Leone Massimo 
Published: December 2021

AbstractBACKGROUNDConverging evidence suggests that anatomical and functional mesocorticolimbic abnormalities support the chronicization of pain disorders.METHODSWe mapped structural and functional alterations of the mesocorticolimbic system in a sample of chronic cluster headache (cCH) patients (n = 28) in comparison to age and sex-matched healthy individuals (n=28) employing structural MRI and resting-state functional MRI (rs-fMRI).RESULTSUnivariate logistic regression models showed that several of the examined structures/areas (i.e., the bilateral nucleus accumbens, ventral diencephalon, hippocampus, and frontal pole, and the right amygdala) differentiated cCH patients from healthy individuals (p<0.05, uncorrected). Specifically, all the significant structures/areas had increased volumes in cCH patients compared to healthy individuals. The examination of the groups suffering from left and right-sided cranial attacks showed a lateralization effect: ipsilateral to the pain ventral diencephalic regions and contralateral to the pain nucleus accumbens discriminated cCH patients from healthy individuals. The rs-fMRI data analyses showed that cCH patients compared to CTRL individuals present robust reduced functional connectivity in the right frontal pole-right amygdala pathway (p<0.05, FDR-corrected).CONCLUSIONOur results showed that cCH patients present anatomical and functional maladaptation of the mesocorticolimbic system, with functional data indicating a possible prefrontal areas’ failure to modulate the mesolimbic structures. These results were opposite to what we hypothesized based on the previous literature on chronic pain conditions. Future studies should assess whether the observed mesocorticolimbic abnormalities are due to the neuroprotective effects of the assumed medications, or to the frequent comorbidity of CH with neuropsychiatric disorders or if they are a genuine neural signature of CH and/or cCH condition.
When self comes to a wandering mind: Brain representations and dynamics of self-generated concepts in spontaneous thought
Authors: Kim Byeol , Andrews-Hanna Jessica R. , Han Jihoon , Lee Eunjin , Woo Choong-Wan 
Published: December 2021

AbstractSelf-relevant concepts are major building blocks of spontaneous thought, and their dynamics in a natural stream of thought are likely to reveal one’s internal states important for mental health. Here we conducted an fMRI experiment (n= 62) to examine brain representations and dynamics of self-generated concepts in the context of spontaneous thought using a newly developed free association-based thought sampling task. The dynamics of conceptual associations were predictive of individual differences in general negative affectivity, replicating across multiple datasets (n= 196). Reflecting on self-generated concepts strongly engaged brain regions linked to autobiographical memory, conceptual processes, emotion, and autonomic regulation, including the medial prefrontal and medial temporal subcortical structures. Multivariate pattern-based predictive modeling revealed that the neural representations of valence became more person-specific as the level of perceived self-relevance increased. Overall, this study provides a hint of how self-generated concepts in spontaneous thought construct inner affective states and idiosyncrasies.
A mechanistically interpretable model of the retinal neural code for natural scenes with multiscale adaptive dynamics
Authors: Ding Xuehao , Lee Dongsoo , Grant Satchel , Stein Heike , McIntosh Lane , Maheswaranathan Niru , Baccus Stephen 
Published: December 2021

AbstractThe visual system processes stimuli over a wide range of spatiotemporal scales, with individual neurons receiving input from tens of thousands of neurons whose dynamics range from milliseconds to tens of seconds. This poses a challenge to create models that both accurately capture visual computations and are mechanistically interpretable. Here we present a model of salamander retinal ganglion cell spiking responses recorded with a multielectrode array that captures natural scene responses and slow adaptive dynamics. The model consists of a three-layer convolutional neural network (CNN) modified to include local recurrent synaptic dynamics taken from a linear-nonlinear-kinetic (LNK) model [1]. We presented alternating natural scenes and uniform field white noise stimuli designed to engage slow contrast adaptation. To overcome difficulties fitting slow and fast dynamics together, we first optimized all fast spatiotemporal parameters, then separately optimized recurrent slow synaptic parameters. The resulting full model reproduces a wide range of retinal computations and is mechanistically interpretable, having internal units that correspond to retinal interneurons with biophysically modeled synapses. This model allows us to study the contribution of model units to any retinal computation, and examine how long-term adaptation changes the retinal neural code for natural scenes through selective adaptation of retinal pathways.
Time Between Viral Loads for People with HIV during the COVID-19 Pandemic
Authors: El-Nahal Walid G. , Shen Nicola M. , Keruly Jeanne C. , Jones Joyce L. , Fojo Anthony T. , Manabe Yukari C. , Moore Richard D. , Gebo Kelly A. , Chander Geetanjali , Lesko Catherine R. 
Published: December 2021

AbstractBackgroundDuring the COVID-19 pandemic, patients experienced significant care disruptions, including lab monitoring. We investigated changes in the time between viral load (VL) checks for people with HIV associated with the pandemic.MethodsThis was an observational analysis of VLs of people with HIV in routine care at a large subspecialty clinic. At pandemic onset, the clinic temporarily closed its onsite laboratory. The exposure was time period (time-varying): pre-pandemic (January 1st 2019-March 15th, 2020); pandemic lab-closed (March 16th-July 12th, 2020); and pandemic lab-open (July 13th-December 31st, 2020). We estimated time from an index VL to a subsequent VL, stratified by whether the index VL was suppressed (≤200 copies/mL). We also calculated cumulative incidence of a non-suppressed VL following a suppressed index VL, and of re-suppression following a loss of viral suppression.ResultsCompared to pre-pandemic, hazard ratios for next VL check were: 0.34 (95% CI: 0.30, 0.37, lab-closed) and 0.73 (CI: 0.68, 0.78, lab-open) for suppressed patients; 0.56 (CI: 0.42, 0.79, lab-closed) and 0.92 (95% CI: 0.76, 1.10, lab-open) for non-suppressed patients. The 12-month cumulative incidence of loss of suppression was the same in the pandemic lab-open (4%) and pre-pandemic period (4%). The hazard of re-suppression following loss of suppression was lower during the pandemic lab-open versus the pre-pandemic period (hazard ratio: 0.68, 95% CI: 0.50, 0.92).ConclusionsEarly pandemic restrictions and lab closure significantly delayed VL monitoring. Once the lab re-opened, non-suppressed patients resumed normal monitoring. Suppressed patients still had a delay, but no significant loss of suppression.SummaryDuring the early COVID-19 pandemic, people with HIV experienced disruptions in viral load monitoring due to lab closure and pandemic restrictions. Loosening restrictions resolved delays for non-suppressed, but not suppressed patients. Delays did not significantly increase proportion of non-suppressed patients.
Effectiveness of different booster regimens for preventing infection and adverse outcomes in Puerto Rico
Authors: Robles-Fontán M.M. , Irizarry R.A. 
Published: December 2021

AbstractRecent laboratory and observational studies have demonstrated that the COVID-19 vaccine effectiveness wanes over time. In response, several jurisdictions have authorized the administration of booster doses. Since August 13, 2021, Puerto Rico has administered 540,140 booster shots. We used data collected and made public by the Puerto Rico Department of Health (PRDH) to evaluate the effectiveness of four different booster regimens at preventing SARS-CoV-2 laboratory confirmed infections and adverse COVID-19 outcomes. Specifically, we analyzed data from all 115,995 SARS-CoV-2 infections occurring since the vaccination process commenced on December 15, 2020. We combined vaccination status, SARS-CoV-2 test results, and COVID-19 hospitalizations and deaths data, and fit a statistical model that adjusted for time-varying incidence rates and age group, to estimate time-varying vaccine effectiveness against infection and adverse outcomes. We find that, after 6 months, the mRNA-1273 and BNT162b2 effectiveness against infection wanes substantially to 61% (58%-63%) and 36% (34%-39%), respectively, while the Ad26.COV2.S wanes to 35% (31%-39%) after two months. However, after a booster shot of the corresponding initial vaccine manufacturer, effectiveness increased to 87% (83%-91%) and 82% (79%-85%) for mRNA-1273 and BNT162b2, respectively. The effectiveness for Ad26.COV2.S followed by either a mRNA-1273 or BNT162b2 booster increased to 88% (71%-100%), substantially higher than 65% (59%-70%), the peak effectiveness reached with just one shot. We also found that heterologous booster regimens restored effectiveness. Furthermore, we did not observe waning after two months of the booster shot. Finally, we found that all booster regimens provided increased protection against COVID-19 hospitalizations and deaths. Code and data to reproduce the analyses are provided here: https://github.com/rafalab/booster-eff-pr.
Parental provisioning drives brain size in birds
Authors: Griesser Michael , Drobniak Szymon M. , Graber Sereina M. , van Schaik Carel P. 
Published: December 2021

AbstractLarge brains support numerous cognitive adaptations and therefore may appear to be highly beneficial. Nonetheless, the high energetic costs of brain tissue may have prevented the evolution of large brains in many species. This problem may also have a developmental dimension: juveniles, with their immature and therefore poorly performing brains, would face a major energetic hurdle if they were to pay for the construction of their own brain, especially in larger-brained species. Here we explore the possible role of parental provisioning for the development and evolution of adult brain size in birds. A comparative analysis of 1,176 bird species shows that various measures of parental provisioning (precocial vs altricial state at hatching, relative egg mass, time spent provisioning the young) strongly predict relative brain size across species. The parental provisioning hypothesis also provides an explanation for the well-documented but so far unexplained pattern that altricial birds have larger brains than precocial ones. We therefore conclude that the evolution of parental provisioning allowed species to overcome the seemingly insurmountable energetic constraint on growing large brains, which in turn enabled bird species to increase survival and population stability. Because including adult eco-and socio-cognitive predictors only marginally improved the explanatory value of our models, these findings also suggest that the traditionally assessed cognitive abilities largely support successful parental provisioning. Our results therefore indicate that the cognitive adaptations underlying successful parental provisioning also provide the behavioral flexibility facilitating reproductive success and survival.Significance StatementThe young of large brained species, if left to grow their own brain, would face a seemingly insurmountable energetic constraint, because brain tissue is energetically costly but adequate cognitive benefits arise only after a delay. We therefore hypothesize that protracted parental provisioning was a precondition for the evolution of large brains. Comparative analyses of 1,176 bird species confirmed that parental provisioning strongly predicts variation in relative brain size, suggesting that these two traits coevolved. These results provide the first explanation for the well-known difference in relative brain size between altricial and precocial birds. They also cast doubt on the explanatory value of previously considered social or technological cognitive abilities, suggesting we rethink our approach to cognitive evolution.