bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic Value of Chest CT Findings at BOS Diagnosis in Lung Transplant Recipients
Authors: Van Herck Anke , Beeckmans Hanne , Kerckhof Pieterjan , Sacreas Annelore , Bos Saskia , Kaes Janne , Vanstapel Arno , Vanaudenaerde Bart M. , Van Slambrouck Jan , Orlitová Michaela , Jin Xin , Ceulemans Laurens J. , Van Raemdonck Dirk E. , Neyrinck Arne P. , Godinas Laurent , Dupont Lieven J. , Verleden Geert M. , Dubbeldam Adriana , De Wever Walter , Vos Robin 
Published: July 2023

Background.
Bronchiolitis obliterans syndrome (BOS) after lung transplantation is characterized by fibrotic small airway remodeling, recognizable on high-resolution computed tomography (HRCT). We studied the prognostic value of key HRCT features at BOS diagnosis after lung transplantation.

Methods.
The presence and severity of bronchiectasis, mucous plugging, peribronchial thickening, parenchymal anomalies, and air trapping, summarized in a total severity score, were assessed using a simplified Brody II scoring system on HRCT at BOS diagnosis, in a cohort of 106 bilateral lung transplant recipients transplanted between January 2004 and January 2016. Obtained scores were subsequently evaluated regarding post-BOS graft survival, spirometric parameters, and preceding airway infections.

Results.
A high total Brody II severity score at BOS diagnosis (P = 0.046) and high subscores for mucous plugging (P = 0.0018), peribronchial thickening (P = 0.0004), or parenchymal involvement (P = 0.0121) are related to worse graft survival. A high total Brody II score was associated with a shorter time to BOS onset (P = 0.0058), lower forced expiratory volume in 1 s (P = 0.0006) forced vital capacity (0.0418), more preceding airway infections (P = 0.004), specifically with Pseudomonas aeruginosa (P = 0.002), and increased airway inflammation (P = 0.032).

Conclusions.
HRCT findings at BOS diagnosis after lung transplantation provide additional information regarding its underlying pathophysiology and for future prognosis of graft survival.
Loss of Endothelial Glycocalyx During Normothermic Machine Perfusion of Porcine Kidneys Irrespective of Pressure and Hematocrit
Authors: Huijink Tobias M. , van ‘t Hof Cor J. , van Furth L. Annick , de Haan Nora A. , Maassen Hanno , Venema Leonie H. , Lammerts Rosa G.M. , van den Heuvel Marius C. , Hillebrands Jan-Luuk , van den Born Jacob , Berger Stefan P. , Leuvenink Henri G.D. 
Published: July 2023

Background.
Normothermic machine perfusion (NMP) is a promising modality for marginal donor kidneys. However, little is known about the effects of NMP on causing endothelial glycocalyx (eGC) injury. This study aims to evaluate the effects of NMP on eGC injury in marginal donor kidneys and whether this is affected by perfusion pressures and hematocrits.

Methods.
Porcine slaughterhouse kidneys (n = 6/group) underwent 35 min of warm ischemia. Thereafter, the kidneys were preserved with oxygenated hypothermic machine perfusion for 3 h. Subsequently, 4 h of NMP was applied using pressure-controlled perfusion with an autologous blood-based solution containing either 12%, 24%, or 36% hematocrit. Pressures of 55, 75, and 95 mm Hg were applied in the 24% group. Perfusate, urine, and biopsy samples were collected to determine both injury and functional parameters.

Results.
During NMP, hyaluronan levels in the perfusate increased significantly (P < 0.0001). In addition, the positivity of glyco-stained glycocalyx decreased significantly over time, both in the glomeruli (P = 0.024) and peritubular capillaries (P = 0.003). The number of endothelial cells did not change during NMP (P = 0.157), whereas glomerular endothelial expression of vascular endothelial growth factor receptor-2 decreased significantly (P < 0.001). Microthrombi formation was significantly increased after NMP. The use of different pressures and hematocrits did not affect functional parameters during perfusion.

Conclusions.
NMP is accompanied with eGC and vascular endothelial growth factor receptor-2 loss, without significant loss of endothelial cells. eGC loss was not affected by the different pressures and hematocrits used. It remains unclear whether endothelial injury during NMP has harmful consequences for the transplanted kidney.
The Association of Tacrolimus Formulation on Cerebral Blood Flow and Cognitive Function
Authors: Mahaparn Irisa , Lepping Rebecca J. , Montgomery Robert N. , Mukherjee Rishav , Billinger Sandra A. , Brooks William M. , Gupta Aditi 
Published: July 2023

Background.
Calcineurin inhibitors are inherent vasoconstrictors. Cerebral vasoconstriction can reduce cerebral blood flow (CBF), and negatively impact cerebrovascular response (CVR) to exercise, and cognitive function. The once-daily extended-release (LCP) tacrolimus has fewer side effects than the immediate-release (IR) tacrolimus. The role of calcineurin inhibitors on CBF and the impact of specific formulations of tacrolimus on CBF, CVR, and cognitive function are unknown. In this pilot study, we evaluated whether changing from IR tacrolimus to LCP tacrolimus modulates CBF, CVR, or cognitive function in kidney transplant (KT) recipients.

Methods.
We randomized (2:1) 30 stable KT recipients on IR tacrolimus to intervention (switch to LCP tacrolimus) and control (continue IR tacrolimus) arms. We measured CBF, CVR, and cognitive function at baseline and at 12 wk. We used ANCOVA to evaluate changes in outcome variables, with baseline values and study arm as covariates. We used descriptive statistics with mean changes in outcome variables to compare the 2 groups.

Results.
Participants were 51 ± 13 y old. There was no difference in plasma tacrolimus levels at baseline and at 12 wk in the 2 arms. The changes in CBF, resting middle cerebral artery velocity, CVR, and cognitive function were more favorable in the intervention arm than in the control group.

Conclusions.
Changing IR tacrolimus to LCP tacrolimus may improve CBF, cerebrovascular dynamics, and cognitive function in KT recipients. Larger studies are needed to confirm these results.
A Systematic Review and Meta-analysis of Optimized CMV Preemptive Therapy and Antiviral Prophylaxis for CMV Disease Prevention in CMV High-Risk (D+R-) Kidney Transplant Recipients
Authors: Kumar Lakshin , Murray-Krezan Cristina , Singh Nina , Brennan Daniel C. , Rakita Robert M. , Dasgupta Sayan , Fisher Cynthia E. , Limaye Ajit P. 
Published: July 2023

Background.
The optimal strategy for cytomegalovirus (CMV) disease prevention in CMV donor/recipient kidney transplant recipients remains uncertain. Conclusions of prior meta-analyses that CMV disease rates with preemptive therapy (PET) and universal prophylaxis (UP) were comparable may have been affected by inclusion of studies lacking key determinants of efficacy of the respective strategies.

Methods.
We conducted a systematic review and meta-analysis of PET with weekly CMV polymerase chain reaction monitoring for ≥3 mo and UP with 6 mo of valganciclovir. PubMed and Embase databases were reviewed from January 1, 2010, to April 1, 2022. Risk of bias was assessed with 3 instruments (Cochrane RoB, Cochrane RoBINS-I, and an instrument for assessing risk in observational studies). The primary outcome was CMV disease incidence by 1-y posttransplant. Secondary outcomes by 1-y were graft loss, acute allograft rejection, and mortality. Results were synthesized using generalized linear mixed model meta-analysis. PET studies were stratified into low-threshold (LT) and high-threshold (HT) PET based on the viral load threshold for initiation of antiviral therapy.

Results.
Twenty-five studies met inclusion criteria (6 PET, 19 UP). CMV disease incidence was significantly higher in HT (0.30 [95% confidence interval (CI), 0.22-0.39]) versus LT PET (0.06 [95% CI, 0.03-0.12]). LT PET was associated with a significantly lower CMV disease incidence (0.06 [95% CI, 0.03-0.12]) versus UP (0.21 [95% CI, 0.17-0.27]). Incidence of graft loss, acute allograft rejection, or mortality was not significantly different between LT PET and UP (P > 0.05 for all comparisons). Receipt of lymphocyte-depleting antibodies was not associated with a significant difference in CMV disease incidence (odds ratio = 1.34 [95% CI, 0.80-2.25]).

Conclusions.
LT PET is associated with a significantly lower incidence of CMV disease compared to UP with similar rates of other clinical outcomes. These findings provide rationale and preliminary data for a randomized superiority trial of optimized LT-PET versus UP in donor seropositive recipient seronegative kidney transplant recipients.
Cross-cultural translation and psychometric validation of the French version of the Fear-Avoidance Components Scale (FACS)
Authors: Duport Arnaud , Bédard Sonia , Raynauld Catherine , Bordeleau Martine , Neblett Randy , Balg Frédéric , Devanne Hervé , Léonard Guillaume 
Published: July 2023

AbstractBackgroundThe Fear-Avoidance Components Scale (FACS) is a reliable and valid instrument widely used to assess fear-avoidance beliefs related to pain and disability. However, there is a scarcity of validated translations of the FACS in different cultural and linguistic contexts, including the French population. This study aimed to translate and validate the French version of the FACS (FACS-Fr/CF), examining its psychometric properties among French-speaking individuals.MethodsA cross-cultural translation process – including forward translation, backward translation, expert committee review, and pre-testing – was conducted to develop the FACS-Fr/CF. The translated version was administered to a sample of French-speaking adults (n=55) with musculoskeletal conditions. Internal consistency (including confirmatory analyses of the 2 factors identified in the Serbian version), test-retest reliability and convergent validity were then assessed.ResultsThe FACS-Fr/CF demonstrated high global internal consistency (α=0.94, 95% CI: 0.91-0.96) as well as high internal consistency of the 2 factors identified in the Serbian version (α=0.90, 95% CI: 0.86-0.94 and α=0.90, 95% CI: 0.85-0.94, respectively). Test-retest analysis revealed a moderate (close to high) reliability (ICC=0.89; 95% CI: 0.82-0.94 and r=0.89;p<0.005). Convergent validity was supported by significant correlations between the FACS-Fr/CF scores and the Tampa Scale for Kinesiophobia (r=0.82;p< 0.005), the Pain Catastrophizing Scale (r=0.72;p< 0.005) and the Hospital Anxiety and Depression Scale (r=0.66;p< 0.005).ConclusionThe present study provides evidence for the cross-cultural translation and psychometric validation of the FACS-Fr/CF. The FACS-Fr/CF exhibits a high internal consistency, a moderate (close to high) test-retest reliability, and good construct validity, suggesting its utility in assessing fear-avoidance beliefs in the French-speaking population. This validated tool can enhance the assessment and understanding of fear-avoidance behaviors and facilitate cross-cultural research in pain-related studies.
Higher ultraviolet light exposure is associated with lower mortality: an analysis of data from the UK Biobank cohort study
Authors: Stevenson Andrew C. , Clemens Tom , Pairo-Castineira Erola , Webb David J. , Weller Richard B. , Dibben Chris 
Published: July 2023

ABSTRACTObjectiveTo examine to what extent UV exposure is associated with all-cause and cause-specific mortality.DesignProspective population-based study.SettingUK Biobank.Participants376,729 participants with white ancestry and no missing data. Two UV exposures were assessed: sun-seeking behaviour (categorised as less active versus more active) and home latitude.Main outcome measuresAll-cause, cardiovascular disease (CVD), cancer and non-CVD/non-cancer mortality. Risk of residual confounding was examined using three negative control outcomes.ResultsThe median follow-up was 12.7 years. Participants with more active sun-seeking behaviour were at a lower risk of all-cause mortality (HR=0.86; 95% confidence interval (CI) 0.80 to 0.93), CVD mortality (HR=0.81; 95% CI 0.68 to 0.95) and cancer mortality (HR=0.86; 95% CI 0.77 to 0.95) compared to participants with less active sun-seeking behaviours, adjusted for demographic, socioeconomic, behavioural and clinical confounders. More active sun seekers had around 50 extra days of survival. Participants whose home latitude was 300km farther south were also at a lower risk of all-cause mortality (HR=0.94; 95% CI 0.92 to 0.96), CVD mortality (HR=0.91; 95% CI 0.86 to 0.95) and cancer mortality (HR=0.93; 95% CI 0.90 to 0.96), adjusted for demographic, socioeconomic, behavioural and clinical confounders. Participants whose home latitude was 300km farther south had around 16 extra days of survival. Sun-seeking behaviour was not associated with two of the three negative controls and home latitude was not associated with any of the negative controls.ConclusionsGreater behavioural and higher geographically related UV exposures were associated with a lower risk of all-cause, CVD and cancer mortality. This study adds to growing evidence that the benefits of UV exposure may outweigh the risks in low sunlight countries. Tailoring public health advice to both the benefits and hazards of UV exposure may reduce the burden of disease and increase life expectancy in low sunlight countries.
Interpretation of wide confidence intervals in meta-analytic estimates: Is the ‘Absence of Evidence’ ‘Evidence of Absence’?
Authors: Miller Sarah L. , Tuia Jordan , Prasad Vinay 
Published: July 2023

AbstractIntroductionRecently, a Cochrane review by Jefferson et al. on physical interventions to slow the spread of respiratory viruses concluded that, “Wearing masks in the community probably makes little or no difference to the outcome of laboratory-confirmed influenza/SARS-CoV-2 compared to not wearing masks”, though this finding had a wide confidence interval. Cochrane issued a rare clarifying statement, fueling controversy. We sought to contextualize the findings of the review by Jefferson et al.MethodsWe searched for consecutive reviews by Cochrane published on or before March 9th, 2023. We included studies where a central finding showed an intervention offered no statistically significant benefit, and ascertained the language used by reviewers to describe that result. We compare this to the report by Jefferson et al., and deemed it consistent or inconsistent with the language of their report.ResultsWe found between November 21st, 2022, and March 9th, 2023, there were 20 Cochrane reviews that met the inclusion criteria. We found that 95% (n = 19) of the reviews used language that was consistent with Jefferson’s findings, while 5% (n = 1) used language inconsistent with Jefferson’s conclusion, describing the effect of the intervention on the outcome as “unclear”.DiscussionMost reviews performed by Cochrane conclude that interventions which fail to show statistically significant benefits make “no difference” have “no effect” or do not “increase or decrease” the outcome, and this occurs despite wide confidence intervals. The conclusions by Jefferson et al. are consistent with Cochrane reporting guidelines and clarification from the organization was unjustified.
ReDirection: a numerically robust R-package to characterize every reaction of a user-defined biochemical network with the probable dissociation constant
Authors: Kundu Siddhartha 
Published: July 2023

AbstractBiochemical networks integrate enzyme-mediated substrate conversions with non-enzymatic complex formation and disassembly to accomplish complex biochemical and physiological function. The multitude of theoretical studies utilizing empirical/clinical data notwithstanding, the parameters used in these analyses whilst being theoretically sound are likely to be of limited biomedical relevance. There is need for a computational tool which can ascribe functionality to and generate potentially testable hypotheses for a biochemical network. “ReDirection” characterizes every reaction of a user-defined biochemical network with the probable dissociation constant and does so by combinatorially summing all non-redundant and non-trivial vectors of a null space generated subspace from the stoichiometry number matrix of the modelled biochemical network. This is followed by defining and populating a reaction-specific sequence vector with numerical values drawn from each row of this subspace, computing several descriptors and partitioning selected terms into distinct subsets in accordance with the expected outcomes (forward, reverse, equivalent) for a reaction. “ReDirection” computes the sums of all the terms that comprise each outcome-specific subset, maps these to strictly positive real numbers and bins the same to a reaction-specific outcome vector. The p1-norm of this vector is the probable dissociation constant for a reaction and is used to assign and annotate the reaction. “ReDirection” iterates these steps recursively until every reaction of the modelled biochemical network has been assigned an unambiguous outcome. “ReDirection” works on first principles, does not discriminate between enzymatic and non-enzymatic reactions, offers a mathematically rigorous and biochemically relevant environment to explore user-defined biochemical networks under naive and perturbed conditions and can be used to address empirically intractable biochemical problems. The utility and relevance of “ReDirection” is highlighted with an investigation of a constrained biochemical network of human Galactose metabolism. “ReDirection” is freely available and accessible from the comprehensive R archive network (CRAN) with the URL (https://cran.r-project.org/package=ReDirection).
Reconfiguration of Behavioral Signals in the Anterior Cingulate Cortex based on Emotional State
Authors: Lindsay Adrian J , Gallello Isabella , Caracheo Barak F , Seamans Jeremy K 
Published: July 2023

AbstractBehaviours and their execution depend on the context and emotional state in which they are performed. The contextual modulation of behavior likely relies on regions such as the anterior cingulate cortex (ACC) that multiplex information about emotional/autonomic states and behaviours. The objective of the present study was to understand how the representations of behaviors by ACC neurons become modified when performed in different emotional states. A pipeline of machine learning techniques was developed to categorize and classify complex, spontaneous behaviors from video. This pipeline, termed HUB-DT, discovered a range of statistically separable behaviors during a task in which motivationally significant outcomes were delivered in blocks of trials that created 3 unique ‘emotional contexts’. HUB-DT was capable of detecting behaviors specific to each emotional context and was able to identify and segregate the portions of a neural signal related to a behaviour and to emotional context. Overall, ∼10x as many neurons responded to behaviors in a contextually dependent versus a fixed manner, highlighting the extreme impact of emotional state on representations of behaviors that were precisely defined based on detailed analyses of limb kinematics. This type of modulation may be a key mechanism that allows the ACC to modify behavioral output based on emotional states and contextual demands.
DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning
Authors: Liu Guole , Niu Tongxin , Qiu Mengxuan , Zhu Yun , Sun Fei , Yang Ge 
Published: July 2023

ABSTRACTPicking particles of biological macromolecules from their cryo-electron tomograms is critical to solving their 3D structuresin situ. To reach sub-nanometre resolution, large numbers of particles often need to be picked, a laborious and time-consuming task if performed manually. To date, however, the adoption of automated particle-picking methods remains limited because of the limitations in their accuracy, processing speed and, for those based on learning models, manual annotation cost. To overcome the limitations, we develop DeepETPicker, a deep learning model for fast and accurate picking of 3D particles from cryo-electron tomograms. The training of DeepETPicker requires only weak supervision with low numbers of simplified Gaussian-type labels, reducing the burden of manual annotation of tomograms under very low signal-to-noise ratios. The simplified labels combined with the customized and lightweight model architecture of DeepETPicker as well as GPU-accelerated pooling enable substantially improved accuracy and accelerated processing speed. When tested on simulated as well as real tomograms, DeepETPicker outperforms the competing state-of-the-art methods by achieving the highest overall accuracy and speed, which translate into better quality of picked particles and higher resolutions of final reconstruction maps. DeepETPicker is provided in open source with a user-friendly interface to support automated particle picking for high-resolution cryo-electron tomographyin situ.
EnrichMiner: a biologist-oriented web server for mining biological insights from functional enrichment analysis results
Authors: Liu Xian , Xu Kaikun , Tao Xin , Bo Xiaochen , Chang Cheng 
Published: July 2023

AbstractFunctional enrichment analysis has been widely used to help researchers obtain biological insights from -omics data. However, the results are often redundant and difficult to digest. The key is developing tools to help users explore the relationships between the enriched terms, remove the redundant terms, and finally select representative terms. However, existing tools hardly make a good integration between enrichment analysis and representative terms selection in a biological-friendly manner. Here, we developed a biologist-oriented web server named EnrichMiner to provide a one-stop solution. It is a complete analysis pipeline from a gene list or a ranked gene table to published-style figures. More importantly, it provides user-friendly interfaces and rich interactive operations to help users explore the term relationships and remove redundancy. EnrichMiner has been integrated into the ExpressVis platform, and is freely accessible athttps://omicsmining.ncpsb.org.cn/ExpressVis/EnrichMinerand does not require login.
Radial glia promote microglial development through integrin αVβ8-TGFβ1 signaling
Authors: McKinsey Gabriel L. , Santander Nicolas , Zhang Xiaoming , Kleemann Kilian , Tran Lauren , Katewa Aditya , Conant Kaylynn , Barraza Matthew , Waddell Kian , Lizama Carlos , La Russa Marie , Koo Hyun Ji , Lee Hyunji , Mukherjee Dibyanti , Paidassi Helena , Anton E. S. , Atabai Kamran , Sheppard Dean , Butovsky Oleg , Arnold Thomas D. 
Published: July 2023

SummaryMicroglia diversity emerges from interactions between intrinsic genetic programs and environment-derived signals, but how these processes unfold and interact in the developing brain remains unclear. Here, we show that radial glia-expressed integrin beta 8 (ITGB8) expressed in radial glia progenitors activates microglia-expressed TGFβ1, permitting microglial development. Domain-restricted deletion ofItgb8in these progenitors establishes complementary regions with developmentally arrested “dysmature” microglia that persist into adulthood. In the absence of autocrine TGFβ1 signaling, we find that microglia adopt a similar dysmature phenotype, leading to neuromotor symptoms almost identical toItgb8mutant mice. In contrast, microglia lacking the TGFβ signal transducersSmad2andSmad3have a less polarized dysmature phenotype and correspondingly less severe neuromotor dysfunction. Finally, we show that non-canonical (Smad-independent) signaling partially suppresses disease and development associated gene expression, providing compelling evidence for the adoption of microglial developmental signaling pathways in the context of injury or disease.