bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterising information gains and losses when collecting multiple epidemic model outputs
Authors: Sherratt Katharine , Srivastava Ajitesh , Ainslie Kylie , Singh David E. , Cublier Aymar , Marinescu Maria Cristina , Carretero Jesus , Cascajo Garcia Alberto , Franco Nicolas , Willem Lander , Abrams Steven , Faes Christel , Beutels Philippe , Hens Niel , Müller Sebastian , Charlton Billy , Ewert Ricardo , Paltra Sydney , Rakow Christian , Rehmann Jakob , Conrad Tim , Schütte Christof , Nagel Kai , Abbott Sam , Grah Rok , Niehus Rene , Prasse Bastian , Sandmann Frank , Funk Sebastian 
Published: July 2023

AbstractBackgroundCollaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during epidemic outbreaks. In the process of collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step. We compared this to directly collecting simulated trajectories. We aimed to explore information on key epidemic quantities; ensemble uncertainty; and performance against data, investigating potential to continuously gain information from a single cross-sectional collection of model results.MethodsWe compared July 2022 projections from the European COVID-19 Scenario Modelling Hub. Five modelling teams projected incidence in Belgium, the Netherlands, and Spain. We compared projections by incidence, peaks, and cumulative totals. We created a probabilistic ensemble drawn from all trajectories, and compared to ensembles from a median across each model’s quantiles, or a linear opinion pool. We measured the predictive accuracy of individual trajectories against observations, using this in a weighted ensemble. We repeated this sequentially against increasing weeks of observed data. We evaluated these ensembles to reflect performance with varying observed data.ResultsBy collecting modelled trajectories, we showed policy-relevant epidemic characteristics. Trajectories contained a right-skewed distribution well represented by an ensemble of trajectories or a linear opinion pool, but not models’ quantile intervals. Ensembles weighted by performance typically retained the range of plausible incidence over time, and in some cases narrowed this by excluding some epidemic shapes.ConclusionsWe observed several information gains from collecting modelled trajectories rather than quantile distributions, including potential for continuously updated information from a single model collection. The value of information gains and losses may vary with each collaborative effort’s aims, depending on the needs of projection users. Understanding the differing information potential of methods to collect model projections can support the accuracy, sustainability, and communication of collaborative infectious disease modelling efforts.Data availabilityAll code and data available on Github:https://github.com/covid19-forecast-hub-europe/aggregation-info-loss
Reliability and validity of physical function tests and ADL survey questions in women living in rural, highland Ethiopia
Authors: Golan Jenna , Thalacker-Mercer Anna , Hoddinott John 
Published: July 2023

AbstractIn rural, highland Ethiopia, physical function, which is the physical ability to fulfill one’s daily roles and responsibilities, may be compromised by a lack of access to nutrition, healthcare, and sanitation. Decreased physical function would be detrimental to health and income-generating activities. Unfortunately, there is a lack of validated methods to measure physical function in adult women in this region. This validity study evaluated the feasibility and reliability of physical tests, including the sit-to-stand (STS) and usual gait speed (UGS). The physical tests were used to assess the validity of context-appropriate activities of daily living (ADL) questions. The results of the STS were used to calculate a power index (Psts) which accounted for body mass and leg length. Feasibility was ascertained qualitatively. Reliability was assessed by comparing the results of the tests and questions between each visit using either Cohen’s κ or Pearson’s ρ. Validity was assessed by regressing the responses to the ADL questions against Psts, controlling for relevant participant characteristics. Study participants consisted of 316 women between the age of 18 and 45 years, living in rural Tigray, Ethiopia, that had previously participated in an impact evaluation of a safety net program. Over a one-week period, participants completed the STS and UGS tests and responded to the ADL questionnaires three times. Pstswas determined to be a feasible, reliable, and valid physical function test for women in rural, highland Ethiopia. UGS lacked feasibility and reliability. The validity of the ADLs was inconclusive. The Pstswill be an essential tool for improving physical function and, subsequently, health and quality of life in rural Ethiopia.
A Randomized Comparison of Radial Artery Intimal Hyperplasia Following Distal vs. Proximal Transradial Access for Coronary Angiography: PRESERVE RADIAL Trial
Authors: Tehrani Behnam N. , Sherwood Matthew W. , Damluji Abdulla A. , Epps Kelly C. , Bakhshi Hooman , Cilia Lindsey , Dassanayake Isuru , Eltebaney Moemen , Gattani Raghav , Howard Edward , Kepplinger David , Ofosu-Somuah Araba , Batchelor Wayne B. 
Published: July 2023

ABSTRACTBackgroundDistal transradial access (dTRA) is an alternative to conventional forearm transradial access (fTRA) for coronary angiography (CAG). Differences in healing of the radial artery in the forearm (FRA) have not been evaluated between these 2 access strategies. We sought to compare FRA intimal-medial thickening (IMT) in patients randomized to dTRA vs. fTRA for CAG.Methods and ResultsSixty-four consecutive patients undergoing non-emergent CAG were randomized (1:1) to dTRA vs. fTRA. Ultrahigh resolution (55 MHz) vascular ultrasound) of the FRA and distal RA was performed pre-CAG and at 90 days. Primary endpoint was 90-day FRA IMT. Secondary endpoints included procedural characteristics, vascular injury, RA occlusion and ipsilateral hand pain and function. Baseline demographics and clinical characteristics, mean FRA IMT, time to RA access, procedure time, and radiation exposure were similar between the dTRA and fTRA cohorts. There were no between group differences in 90-day FRA IMT (0.37 mm vs 0.38 mm, respectively;p=0.73). No RA occlusions or signs of major vascular injury were observed at 90 days. Ipsilateral hand pain and function (Borg pain scale:12 vs 11,p=0.24; DASH scores: 6 vs 8,p=0.46) were comparable.ConclusionsIn this single center randomized clinical trial, similar patterns of FRA vascular healing at 90 days, procedural results as well as hand pain and function were observed following dTRA vs. fTRA for CAG. Further investigation is warranted to better understand the mechanistics and predictors of RA healing and to identify strategies aimed at preserving RA integrity for future procedures.What is New?DTRA has been proposed as an alternative to traditional fTRA in the wrist for CAG and PCI because of ergonomic and post-procedural recovery benefits to the patient, as well as potential reductions in occlusion of the FRA.There are gaps in knowledge, however, regarding potential differences in remodeling of the FRA in patients undergoing dTRA versus fTRA.In this randomized clinical trial, there were no differences in IMT and patterns of vascular injury and healing, using ultrahigh resolution (55 MHz) ultrasound, at 90 days in patients randomized to dTRA or FTRA for elective and non-emergent CAG and PCI.What Are the Clinical ImplicationsOur findings highlight the need for further inquiry through large multicenter randomized clinical trials to better the understand the mechanistics and predictors of IMT and to identify strategies to mitigate the adverse effects of vessel remodeling in patients undergoing TRA across the entire severity spectrum of cardiovascular disease.
Outbreak risks, cases, and costs of vaccination strategies against wild poliomyelitis in polio-free settings: a modelling study
Authors: Auzenbergs Megan , Abbas Kaja , Voorman Arie , Peak Corey , Jit Mark , O’Reilly Kathleen M 
Published: July 2023

AbstractBackgroundPolio eradication was threatened in 2022 by importation of wild poliovirus serotype 1 into Malawi with subsequent international spread, representing the first wild polio cases in Africa since 2014. Preventing importations and spread of wild poliovirus is critical, and dependent on population immunity provided through routine immunisation and supplementary immunisation activities (SIAs). However, the scale of preventative SIAs has reduced in recent years due to financial constraints.MethodsWe developed a mathematical model of polio transmission dynamics to evaluate the probability of an outbreak, expected number of poliomyelitis cases, and the costs associated with vaccination delivery through routine immunisation (RI), outbreak response SIAs (oSIAs) and preventative SIAs (pSIAs). Across varying levels of routine immunisation coverage, we explore three key strategies: RI+oSIAs, RI+oSIAs+annual pSIAs, and RI+oSIAs+biannual pSIAs.ResultsThe annual pSIA strategy (RI+oSIAs+annual pSIAs) had higher costs but greater probability of no outbreaks: under our model assumptions, annual pSIAs result in 80% probability of no outbreaks when routine immunisation coverage ≥50%. The biannual pSIA strategy (RI+oSIAs+biannual pSIAs) costs less and averts more outbreaks than RI+oSIAs, but RI coverage ≥65% was required to achieve equivalent risk of no outbreaks. The strategy with no pSIAs (RI+oSIAs) had the lowest costs but required ≥75% RI coverage to achieve equivalent risk of no outbreaks.ConclusionPrioritisation of pSIAs must balance outbreak risk against implementation costs, ideally favouring the smallest manageable outbreak risk compatible with elimination. We infer that there are few short-term risks due to population immunity from RI, but without pSIAs, long-term risks accumulate and can result in outbreaks with potential for international spread. We do not consider the costs of further delaying the eradication timeline or societal implications of outbreaks, both of which emphasise the need for pSIAs.
Single-cell transcriptomic analysis of NK cell dynamics in myeloma patients reveal persistent reduction of cytotoxic NK cells from diagnosis to relapse
Authors: Tahri Sabrin , de Jong Madelon M.E. , Fokkema Cathelijne , Papazian Natalie , Kellermayer Zoltán , Vermeulen Michael , van Duin Mark , van Beek Gregory , Hoogenboezem Remco , van de Woestijne Pieter , Nasserinejad Kazem , Saraci Elona , D’Agostino Mattia , Gay Francesca , van der Velden Vincent H.J. , Sanders Mathijs A. , Zweegman Sonja , van de Donk Niels W.J.C. , Broijl Annemiek , Sonneveld Pieter , Cupedo Tom 
Published: July 2023

AbstractNatural killer (NK) cells mediate the cytotoxic immune response against multiple myeloma and are important effector cells in immune therapies through antibody-dependent cellular cytotoxicity. Here, we used single-cell transcriptomics, flow cytometry and functional assays to investigate the bone marrow NK cell compartment of myeloma patients at diagnosis, during treatment and after relapse. The bone marrow of myeloma patients is characterized by a reduction in conventional cytotoxic NK cells that persists throughout treatment. We show in 20% of newly diagnosed myeloma patients that an altered balance between cytotoxic and cytokine-producing NK cells translates into a reduced cytotoxic ability in response to therapeutic antibodies. The relative loss of cytotoxic NK cells persists at relapse and is accompanied by an expansion of IFN-responsive NK cells. These findings reveal previously unappreciated alterations in bone marrow NK cell composition and highlight the importance of understanding the bone marrow immune system in patients receiving immunotherapies.Statement of significanceThe bone marrow of multiple myeloma patients is characterized by a persistent reduction in cytotoxic CD56dimNK cells, accompanied by inferiorin vitroresponses to therapeutic antibodies at diagnosis and an increase in IFN-responsive NK cells at relapse. These findings highlight the importance of understanding the BM microenvironment in multiple myeloma patients receiving immunotherapies.
Leadership and information transfer in groups escaping a (simulated) threat in the wild
Authors: Rathore Akanksha , Vadavalli Bhavya Deepti , Jadhav Vivek , Isvaran Kavita , Guttal Vishwesha 
Published: July 2023

AbstractCollective motion in many species is believed to be driven by predation, which is considered a crucial evolutionary force. However, there are limited studies on how information about predators spreads through a group, particularly in natural settings. Here, using high-resolution drone-based recordings, we analyze the collective escape dynamics of a group living species – blackbuck (Antilope cervicara), an Indian antelope – under the conditions of a simulated threat in their natural grassland habitat. Our analysis reveals that, in response to the simulated threat, group cohesion first increases, followed by a simultaneous increase in median speed and polarization. We also observe the emergence of a temporary leader-follower relationship during the collective escape. Interestingly, we found that the distance of individuals from the “predator” affected only their response time, not their influence on the group movement. The individuals furthest from the threat were the least likely to initiate movement and were uncoordinated with the group’s speed. Additionally, we discovered that the most influential individuals during the collective escape were the least likely to occupy front positions during group movement. Instead, our results indicate that individuals at the rear “push” individuals at the front during collective escape events. This contrasts with the typical notion of individuals at the front determining group movement and those at the back trying to catch up.
Mental fatigue has only marginal effects on static balance control in healthy young adults
Authors: Weissinger Kerstin , Bach Margit Midtgaard , Brachmann Anna , Stins John F. , Beek Peter Jan 
Published: July 2023

AbstractWe examined the influence of mental fatigue on static balance control in healthy young adults to gain greater clarity about this issue than provided in previous research. Based on the prevailing assumption in pertinent literature, we hypothesized that mental fatigue leads to a reduced cognitive regulation of quiet upright standing, as reflected in center of pressure (COP) excursions. More specifically, we hypothesized that the influence of mental fatigue on balance control depends on the attentional effort required by the balance tasks being performed. To test these hypotheses, 44 young adults (24 women and 20 men) were quasi-randomly assigned to either an experimental group that was mentally fatigued (using the TloadDback-task with individualized settings) or a control group (who watched a documentary). Before and after the intervention the participants performed six balance tasks that differed in (attentional) control requirements, while their COP was being recorded. From these time-series sway variability, mean speed, and sample entropy were calculated and analyzed statistically. Additionally, mental fatigue was assessed using VAS scales. Statistical analyses confirmed that the balance tasks differed in control characteristics and that mental fatigue was elevated in the experimental group, but not in the control group. Nevertheless, no significant main effects of mental fatigue were found on any of the COP measures of interest, except for some non-robust and difficult to interpret interaction effects involving the factor group. These results suggest that, in young adults, postural control in static balance tasks is largely automatic and unaffected by mental fatigue.
Lasting dynamic effects of the psychedelic 2,5-dimethoxy-4-iodoamphetamine ((±)-DOI) on cognitive flexibility
Authors: Šabanović Merima , Lazari Alberto , Blanco-Pozo Marta , Lerch Jason P. , Walton Mark E. , Bannerman David M. 
Published: July 2023

AbstractPsychedelic drugs can aid fast and lasting remission from various neuropsychiatric disorders, though the underlying mechanisms remain unclear. Preclinical studies suggest serotonergic psychedelics enhance neuronal plasticity, but whether neuroplastic changes can also be seen at cognitive and behavioural levels is unexplored. Here we show that a single dose of the psychedelic 2,5-dimethoxy-4-iodoamphetamine ((±)-DOI) affects structural brain plasticity and cognitive flexibility in young adult mice beyond the acute drug experience. Usingex vivomagnetic resonance imaging, we show increased volumes of several sensory and association areas one day after systemic administration of 2mgkg−1(±)-DOI. We then demonstrate lasting effects of (±)-DOI on cognitive flexibility in a two-step probabilistic reversal learning task where 2mgkg−1(±)-DOI improved the rate of adaptation to a novel reversal in task structure occurring one-week post-treatment. Strikingly, (±)-DOI-treated mice started learning from reward omissions, a unique strategy not typically seen in mice in this task, suggesting heightened sensitivity to previously overlooked cues. Crucially, further experiments revealed that (±)-DOI’s effects on cognitive flexibility were contingent on the timing between drug treatment and the novel reversal, as well as on the nature of the intervening experience. (±)-DOI’s facilitation of both cognitive adaptation and novel thinking strategies may contribute to the clinical benefits of psychedelic-assisted therapy, particularly in cases of perseverative behaviours and a resistance to change seen in depression, anxiety, or addiction. Furthermore, our findings highlight the crucial role of time-dependent neuroplasticity and the influence of experiential factors in shaping the therapeutic potential of psychedelic interventions for impaired cognitive flexibility.
Revealing abrupt transitions from goal-directed to habitual behavior
Authors: Moore Sharlen , Wang Zyan , Zhu Ziyi , Sun Ruolan , Lee Angel , Charles Adam , Kuchibhotla Kishore V. 
Published: July 2023

AbstractA fundamental tenet of animal behavior is that decision-making involves multiple ‘controllers.’ Initially, behavior is goal-directed, driven by desired outcomes, shifting later to habitual control, where cues trigger actions independent of motivational state. Clark Hull’s question from 1943 still resonates today: “Is this transition abrupt, or is it gradual and progressive?”1Despite a century-long belief in gradual transitions, this question remains unanswered2,3as current methods cannot disambiguate goal-directed versus habitual control in real-time. Here, we introduce a novel ‘volitional engagement’ approach, motivating animals by palatability rather than biological need. Offering less palatable water in the home cage4,5reduced motivation to ‘work’ for plain water in an auditory discrimination task when compared to water-restricted animals. Using quantitative behavior and computational modeling6, we found that palatability-driven animals learned to discriminate as quickly as water-restricted animals but exhibited state-like fluctuations when responding to the reward-predicting cue—reflecting goal-directed behavior. These fluctuations spontaneously and abruptly ceased after thousands of trials, with animals now always responding to the reward-predicting cue. In line with habitual control, post-transition behavior displayed motor automaticity, decreased error sensitivity (assessed via pupillary responses), and insensitivity to outcome devaluation. Bilateral lesions of the habit-related dorsolateral striatum7blocked transitions to habitual behavior. Thus, ‘volitional engagement’ reveals spontaneous and abrupt transitions from goal-directed to habitual behavior, suggesting the involvement of a higher-level process that arbitrates between the two.
scARE: Attribution Regularization for Single Cell Representation Learning
Authors: Inecik Kemal , Theis Fabian 
Published: July 2023

AbstractSingle-cell data generation techniques have provided valuable insights into the intricate nature of cellular heterogeneity. However, effectively unraveling subtle variations within a specific gene set of interest, while mitigating the confounding presence of higher-order variability, remains challenging. To address this, we propose scARE, a novel end-to-end generative deep learning model, amplifies model sensitivity to a preselected subset of features while minimizing others. scARE incorporates an auxiliary attribution loss term during model training, which empowers researchers to manipulate the model’s behavior robustly and flexibly. In this study, we showcased scARE’s applicability in two concrete scenarios: uncovering subclusters associated with the expression patterns of two cellular pathway genes, and its ability to optimize the model training procedure by leveraging time-points metadata, resulting in improved downstream performance.
Multivariate and Regional Age-Related Change in Basal Ganglia Iron in Neonates
Authors: Cabral L. , Calabro F.J. , Foran W. , Parr A.C. , Ojha A. , Rasmussen J. , Ceschin R. , Panigrahy A. , Luna B. 
Published: July 2023

AbstractIn the perinatal period, reward and cognitive systems begin trajectories, influencing later psychiatric risk. The basal ganglia is important for reward and cognitive processing but early development has not been fully characterized. To assess age-related development, we used a measure of basal ganglia physiology, specifically brain tissue iron, obtained from nT2* signal in rsfMRI, associated with dopaminergic processing. We used data from the Developing Human Connectome Project (N=464) to assess how moving from the prenatal to the postnatal environment affects rsfMRI nT2*, modeling gestational and postnatal age separately for basal ganglia subregions in linear models. We did not find associations with tissue iron and gestational age [Range: 24.29-42.29] but found positive associations with postnatal age [Range:0-17.14] in the pallidum and putamen, but not the caudate. We tested if there was an interaction between preterm birth and postnatal age, finding early preterm infants (GA<35 weeks) had higher iron levels and changed less over time. To assess multivariate change, we used support vector regression to predict age from voxel-wise-nT2* maps. We could predict postnatal but not gestational age when maps were residualized for the other age term. This provides evidence subregions differentially change with postnatal experience and preterm birth may disrupt trajectories.