bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cerebral Blood Flow in the Salience Network of Individuals with Alcohol Use Disorder
Authors: Butcher Tarah J , Chumin Evgeny J , West John D , Dzemidzic Mario , Yoder Karmen K 
Published: August 2021

AbstractAimsMagnetic resonance imaging (MRI) studies have identified structural and functional differences in salience network nodes of individuals with alcohol use disorders (AUDs) after chronic exposure to alcohol. However, no studies have investigated cerebral blood flow (CBF) in nontreatment-seeking (NTS) individuals with AUD.MethodsIn this work, we sought to quantify putative CBF deficits in NTS individuals relative to social drinking (SD) controls and determine if CBF in the salience network is associated with AUD severity. Fifteen NTS (36.5 ± 11.2 years old, 30.0 ± 22.7 drinks/week) and 22 SD (35.6 ± 11.9 years old, 9.1 ± 5.7 drinks/week) underwent pseudocontinuous arterial spin labeling MRI.ResultsCompared with social drinkers, NTS individuals had significantly lower CBF in the right and left dorsal anterior insula, and the left ventral anterior and posterior insula. The Alcohol Use Disorder Identification Test (AUDIT) score showed a significant negative relationship with CBF in the bilateral caudal anterior cingulate cortex. In addition, a significant negative correlation was present between number of standard drinks consumed per week and the left frontal opercular CBF.ConclusionThese results provide evidence that insular CBF is negatively associated with heavy drinking, and that severity of alcohol use is related to CBF deficits in key nodes of the salience network. Longitudinal data are needed to understand if disruptions of CBF in the insula and the salience network are a predisposition for or a consequence of chronic AUD.
Staging Charisma: Anna Deavere Smith’s Black Feminist Theater of the Multitude
Authors: Winstein-Hibbs Sarah 
Published: August 2021

AbstractRecently, scholars in American studies have begun to trace the literary and cultural history of charisma, an especially slippery term which most often connotes spectacular, individual male leadership. In this article, I suggest that Anna Deavere Smith’s verbatim theatre provides an alternative notion of this term. Specifically, Smith’s plays enact a Black feminist mode of collectivist charisma, one which has been and can be transported from stage to streets and vice versa. I focus here on Smith’s Twilight: Los Angeles, 1992 (1994), a one-woman show that Smith created by interviewing and impersonating dozens of people involved in or affected by the Rodney King “riots.” While the public primarily remembers this moment through King himself, or through spokespeople such as Bill Clinton or George H. W. Bush, Smith refuses either to create protagonists or to channel individualist charisma by staging a multitude. Further, Smith’s decentered theater proffers a collective approach to remembering the broader post-civil rights ethnic and racial tensions that led to the 1992 LA Crisis. Indeed, I suggest that we experience Twilight as part of a performance history of contemporary Left protest by drawing out the similarities between Smith’s multivocal plays and today’s “leaderful,” Black-feminist-led movements for racial justice.
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype
Authors: He Di , Xie Lei 
Published: August 2021

Abstract

Motivation
An unsolved fundamental problem in biology is to predict phenotypes from a new genotype under environmental perturbations. The emergence of multiple omics data provides new opportunities but imposes great challenges in the predictive modeling of genotype-phenotype associations. Firstly, the high-dimensionality of genomics data and the lack of coherent labeled data often make the existing supervised learning techniques less successful. Secondly, it is challenging to integrate heterogeneous omics data from different resources. Finally, few works have explicitly modeled the information transmission from DNA to phenotype, which involves multiple intermediate molecular types. Higher-level features (e.g. gene expression) usually have stronger discriminative and interpretable power than lower-level features (e.g. somatic mutation).

Results
We propose a novel Cross-LEvel Information Transmission (CLEIT) network framework to address the above issues. CLEIT aims to represent the asymmetrical multi-level organization of the biological system by integrating multiple incoherent omics data and to improve the prediction power of low-level features. CLEIT first learns the latent representation of the high-level domain then uses it as ground-truth embedding to improve the representation learning of the low-level domain in the form of contrastive loss. Besides, CLEIT can leverage the unlabeled heterogeneous omics data to improve the generalizability of the predictive model. We demonstrate the effectiveness and significant performance boost of CLEIT in predicting anti-cancer drug sensitivity from somatic mutations via the assistance of gene expressions when compared with state-of-the-art methods. CLEIT provides a general framework to model information transmissions and integrate multi-modal data in a multi-level system.

Availabilityand implementation
The source code is freely available at https://github.com/XieResearchGroup/CLEIT.

Supplementary information
Supplementary data are available at Bioinformatics online.
PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images
Authors: Fernandez-Gonzalez Rodrigo , Balaghi Negar , Wang Kelly , Hawkins Ray , Rothenberg Katheryn , McFaul Christopher , Schimmer Clara , Ly Michelle , do Carmo Ana Maria , Scepanovic Gordana , Erdemci-Tandogan Gonca , Castle Veronica 
Published: August 2021

AbstractSummaryOur increasing ability to resolve fine details using light microscopy is matched by an increasing need to quantify images in order to detect and measure phenotypes. Despite their central role in cell biology, many image analysis tools require a financial investment, are released as proprietary software, or are implemented in languages not friendly for beginners, and thus are used as black boxes. To overcome these limitations, we have developed PyJAMAS, an open-source tool for image processing and analysis written in Python. PyJAMAS provides a variety of segmentation tools, including watershed and machine learning-based methods; takes advantage of Jupyter notebooks for the display and reproducibility of data analyses; and can be used through a cross-platform graphical user interface or as part of Python scripts via a comprehensive application programming interface.Availability and implementationPyJAMAS is open-source and available at https://bitbucket.org/rfg_lab/pyjamas.Supplementary informationSupplementary data are available at Bioinformatics online.
CLPP deficiency ameliorates neurodegeneration caused by impaired mitochondrial protein synthesis
Authors: Rumyantseva Anastasia , Popovic Milica , Trifunovic Aleksandra 
Published: August 2021

Abstract
Mitochondria are essential organelles found in every eukaryotic cell, required to convert food into usable energy. Therefore, it is not surprising that mutations in either mtDNA or nuclear DNA-encoded genes of mitochondrial proteins cause diseases affecting the oxidative phosphorylation system, which are heterogeneous from a clinical, genetic, biochemical and molecular perspective and can affect patients at any age. Despite all this, it is surprising that our understanding of the mechanisms governing mitochondrial gene expression and its associated pathologies remain superficial and therapeutic interventions largely unexplored.
We recently showed that loss of the mitochondrial matrix protease caseinolytic protease proteolytic subunit (CLPP) ameliorates phenotypes in cells characterized by defects in oxidative phosphorylation maintenance. Here, we build upon this finding by showing that CLPP depletion is indeed beneficial in vivo for various types of neuronal populations, including Purkinje cells in the cerebellum and cortical and hippocampal neurons in the forebrain, as it strongly improves distinct phenotypes of mitochondria encephalopathy, driven by the deficiency of the mitochondrial aspartyl tRNA synthase DARS2. In the absence of CLPP, neurodegeneration of DARS2-deficient neurons is delayed as they present milder oxidative phosphorylation dysfunction. This in turn leads to a decreased neuroinflammatory response and significantly improved motor functions in both double-deficient models (Purkinje cell-specific or forebrain neuron-specific Dars2/Clpp double knockout mice). We propose that diminished turnover of respiratory complex I caused by the loss of CLPP is behind the improved phenotype in Dars2/Clpp double knockout animals, even though this intervention might not restore respiratory complex I activity but rather improve mitochondrial cristae morphology or help maintain the NAD+/NADH ratio inside mitochondria.
These results also open the possibility of targeting CLPP activity in many other mitochondrial encephalopathies characterized by respiratory complex I instability.
Neurofilament light chain and glial fibrillary acidic protein levels in metachromatic leukodystrophy
Authors: Beerepoot Shanice , Heijst Hans , Roos Birthe , Wamelink Mirjam M C , Boelens Jaap Jan , Lindemans Caroline A , van Hasselt Peter M , Jacobs Edwin H , van der Knaap Marjo S , Teunissen Charlotte E , Wolf Nicole I 
Published: August 2021

Abstract
Metachromatic leukodystrophy is a lethal metabolic leukodystrophy, with emerging treatments for early disease stages. Biomarkers to measure disease activity are required for clinical assessment and treatment follow-up.
This retrospective study compared neurofilament light chain and glial fibrillary acidic protein (GFAP) levels in CSF (n = 11) and blood (n = 92) samples of 40 patients with metachromatic leukodystrophy (aged 0–42 years) with 38 neurologically healthy children (aged 0–17 years) and 38 healthy adults (aged 18–45 years), and analysed the associations between these levels with clinical phenotype and disease evolution in untreated and transplanted patients. Metachromatic leukodystrophy subtype was determined based on the (expected) age of symptom onset. Disease activity was assessed by measuring gross motor function deterioration and brain MRI. Longitudinal analyses with measurements up to 23 years after diagnosis were performed using linear mixed models.
CSF and blood neurofilament light chain and GFAP levels in paediatric controls were negatively associated with age (all P &lt; 0.001). Blood neurofilament light chain level at diagnosis (median, interquartile range; picograms per millilitre) was significantly increased in both presymptomatic (14.7, 10.6–56.7) and symptomatic patients (136, 40.8–445) compared to controls (5.6, 4.5–7.1), and highest among patients with late-infantile (456, 201–854) or early-juvenile metachromatic leukodystrophy (291.0, 104–445) and those ineligible for treatment based on best practice (291, 57.4–472). GFAP level (median, interquartile range; picogram per millilitre) was only increased in symptomatic patients (591, 224–1150) compared to controls (119, 78.2–338) and not significantly associated with treatment eligibility (P = 0.093). Higher blood neurofilament light chain and GFAP levels at diagnosis were associated with rapid disease progression in late-infantile (P = 0.006 and P = 0.051, respectively) and early-juvenile patients (P = 0.048 and P = 0.039, respectively). Finally, blood neurofilament light chain and GFAP levels decreased during follow-up in untreated and transplanted patients but remained elevated compared with controls. Only neurofilament light chain levels were associated with MRI deterioration (P &lt; 0.001).
This study indicates that both proteins may be considered as non-invasive biomarkers for clinical phenotype and disease stage at clinical assessment, and that neurofilament light chain might enable neurologists to make better informed treatment decisions. In addition, neurofilament light chain holds promise assessing treatment response. Importantly, both biomarkers require paediatric reference values, given that their levels first decrease before increasing with advancing age.
Golfing with Trump. Social capital, decline, inequality, and the rise of populism in the US
Authors: Rodríguez-Pose Andrés , Lee Neil , Lipp Cornelius 
Published: August 2021

AbstractIn 2000, Robert Putnam forecast that United States (US) democracy was at risk from the twin challenges of declining civic engagement and rising interpersonal inequality. Sixteen years later, his predictions were vindicated by the election of Donald Trump as president of the US. This paper analyses the extent to which the 2016 election of Donald Trump—and his failed re-election bid in 2020—have been related to levels of social capital and interpersonal inequalities. We posit an alternative: that the rise in votes for Trump has been the result of long-term economic and population decline in areas with strong social capital. This hypothesis is confirmed by the econometric analysis conducted for US counties. Long-term declines in employment and population—rather than in earnings, salaries, or wages—in places with relatively strong social capital propelled Donald Trump to the presidency and almost secured his re-election. By contrast, low social capital and high interpersonal inequality were not connected to a surge in support for Trump. These results are robust to the introduction of control variables and different inequality measures. The analysis also shows that the discontent at the base of the Trump margin is not just a consequence of the 2008 crisis but had been brewing for a long time. Places in the US that remained cohesive but witnessed an enduring decline are no longer bowling alone, they have golfed with Trump and will, in all likelihood, continue to golf with Trumpism or other forms of populism.
Specifying and Model Checking Distributed Control Algorithms at Meta-level
Authors: Doan Ha Thi Thu , Ogata Kazuhiro 
Published: August 2021

Abstract
This paper proposes an approach to the specification and model checking of a large, important class of distributed algorithms called control algorithms (CAs), which are superimposed on underlying distributed systems (UDSs). The approach is based on rewriting logic by moving from its object level to the meta-level. We introduce the idea of specifying CAs as meta-programs that take the specifications of UDSs and automatically generate the specifications of the UDSs on which the CAs are superimposed (UDS-CAs). Due to many options, such as network topologies, even fixing the number of each kind of entities, such as mobile support stations (MSSs) and mobile hosts (MHs) in a mobile checkpointing algorithm, there are many instances of a UDS. To address the problem, we generate all possible initial states of a UDS for a fixed number of each kind of entities such that some constraints, such as MSSs strongly connected with a wired network, are fulfilled and conduct model checking for each of the initial states. We demonstrate the usefulness by reporting on a case study where a counterexample is found for some specific initial states but not for the other initial states, detecting a subtle flaw lurking in a mobile checkpointing algorithm.
Cluster Randomized Trials: Lessons for Inflammatory Bowel Disease Trials
Authors: Caron Bénédicte , D’Amico Ferdinando , Danese Silvio , Peyrin-Biroulet Laurent 
Published: August 2021

AbstractRandomized clinical trials are the gold standard for the development of new drugs. Clinical trials have become increasingly complex, in particular in the field of inflammatory bowel diseases. For this reason, a new study design called ‘cluster randomized trial’ has been introduced. Cluster randomized trials randomly assign groups of individuals within a population of interest, such as people in a particular research site, clinic or hospital, and measure the effects of an intervention at the individual level. In contrast to individual randomization, cluster randomization permits the evaluation of a cluster-level intervention, may be logistically simpler and less expensive than a conventional randomized trial, and can help reduce the effect of treatment contamination. An important aspect requiring particular attention in cluster randomized trials is the risk for imbalance of covariates at baseline which decreases the statistical power and precision of the results, and reduces face validity and credibility of the trial results. A variety of restricted randomization methods have been proposed to minimize risk of imbalance. Our aim here is to clarify the advantages and drawbacks of cluster randomized trials in order to properly interpret study results and to identify their role in upcoming inflammatory bowel disease trials.
Outcomes in patients with acute myocardial infarction and history of illicit drug use: a French nationwide analysis
Authors: Ma Iris , Genet Thibaud , Clementy Nicolas , Bisson Arnaud , Herbert Julien , Semaan Carl , Bouteau Jérémie , Angoulvant Denis , Ivanes Fabrice , Fauchier Laurent 
Published: August 2021

Abstract

Aims
Several reports suggest that illicit drug use may be a major cause of acute myocardial infarction (AMI) independently of smoking habits and associated with a poorer prognosis. The aim of our study was to evaluate the impact of illicit drug use on (i) the risk of AMI and (ii) its prognosis.

Methods and results
This French longitudinal cohort study was based on the administrative hospital-discharge database from the entire population. First, we collected data for all patients admitted in hospital in 2013 with at least 5 years of follow-up to identify potential predictors of AMI. In a second phase, we collected data for all patients admitted with AMI from January 2010 to December 2018. We identified patients with a history of illicit drug use (cannabis, cocaine, or opioid). These patients were matched with patients without illicit drug use to assess their prognosis. In 2013, 3 381 472 patients were hospitalized with a mean follow-up of 4.7 ± 1.8 years. In multivariable analysis, among all drugs under evaluation, only cannabis use was significantly associated with a higher risk of AMI [HR 1.32 (95% CI 1.09–1.59), P = 0.004]. Between January 2010 and December 2018, we then identified 738 899 AMI patients. Among these patients, 3827 (0.5%) had a known history of illicit drug use. These patients were younger, most often male and had less comorbidities. After 1:1 propensity score matching, during a mean follow-up of 1.9 ± 2.3 years, there was no significant difference between patients without illicit drug use and patients with illicit drug use regarding all-cause death, cardiovascular death, stroke, or heart failure.

Conclusion
In a large and systematic nationwide analysis, cannabis use was an independent risk factor for the incidence of AMI. However, the prognosis of illicit drug users presenting with AMI was similar to patients without illicit drug use.
Aortic coarctation with cardiac fibroma in a young patient: a case report
Authors: Shen Linghong , Xu Ke , Kong Ye , He Ben 
Published: August 2021

Abstract

Background
Cardiac fibroma and aortic coarctation are rarely observed concomitantly in the same patient. We report a case of cardiac fibroma with aortic coarctation treated with a hybrid surgical procedure. To the best of our knowledge, this is the first case of these two abnormalities existing in one patient.

Case summary
A 22-year-old female patient visited the clinic with a 10-year history of hypertension. Physical examination revealed blood pressure of the upper extremities 50 mmHg higher than that of the lower extremities. Computed tomography angiography revealed a post-ductal-type aortic coarctation at the beginning segment of the descending aorta along with a 7.7 cm × 5.1 cm left ventricular mass. Transthoracic echocardiogram showed a mass at the middle segments of the lateral wall and apex and posterior wall of the left ventricle. Cardiac magnetic resonance imaging also showed the mass with hypointense signal on T1, hyperintense signal on T2, and intense signal on late gadolinium enhancement. No evidences of metastatic lesions were observed on 18F-fluorodeoxyglucose positron emission tomography. The patient underwent a hybrid surgery involving aortic stent implantation and complete left ventricular mass removal. The gradient between stenosis returned to &lt;10 mmHg after the procedure. Pathologic findings revealed cardiac fibroma.

Discussion
It is rare to encounter a patient suffering from both cardiac fibroma and aortic coarctation. No evidences indicated a single cause or syndrome resulting in the coexistence of these two abnormalities. A hybrid surgery involving aortic stent implantation and complete cardiac mass resection could optimize the treatment in such cases.
Employment protection and fertility decisions: the unintended consequences of the Italian Jobs Act
Authors: De Paola Maria , Nisticò Roberto , Scoppa Vincenzo 
Published: August 2021

SUMMARY
We study the effect of a reduction in employment protection on workers’ fertility decisions. Using data from the Italian Labor Force Survey for 2013–18, we analyse how the propensity to have a child has been affected by the 2015 labour market reform dubbed the ‘Jobs Act’, which reduced employment protection for employees of larger firms while leaving small firms essentially untouched. We take a Difference-in-Differences identification approach and compare the change in fertility decisions of women employed in large firms with that of women in small firms. We find that the former’s probability of having a child is 1.4 percentage points lower. A battery of robustness checks confirms this finding. The effect also holds when possible sorting issues are accounted for by an instrumental variable approach. We document substantial heterogeneous effects by age, marital status, parity and geographical area as well as by education and earnings. Our findings suggest the potential unintended consequences on fertility that labour market reforms introducing greater flexibility may have by heightening career insecurity.