bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhysioFit: a software to quantify cell growth parameters and extracellular fluxes
Authors: Le Grégam Loïc , Guitton Yann , Bellvert Floriant , Heux Stéphanie , Jourdan Fabien , Portais Jean-Charles , Millard Pierre 
Published: July 2024

Abstract

Summary
Quantification of growth parameters and extracellular uptake and production fluxes is central in systems and synthetic biology. Fluxes can be estimated using various mathematical models by fitting time–course measurements of the concentration of cells and extracellular substrates and products. A single tool is available to non-computational biologists to calculate extracellular fluxes, but it is hardly interoperable and is limited to a single hard-coded growth model. We present our open-source flux calculation software, PhysioFit, which can be used with any growth model and is interoperable by design. PhysioFit includes some of the most common growth models, and advanced users can implement additional models to calculate extracellular fluxes and other growth parameters for metabolic systems or experimental setups that follow alternative kinetics. PhysioFit can be used as a Python library and offers a graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines.

Availability and implementation
PhysioFit v3 is implemented in Python 3 and was tested on Windows, Unix, and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/PhysioFit/ and https://physiofit.readthedocs.io/.
Joint structure learning and causal effect estimation for categorical graphical models
Authors: Castelletti Federico , Consonni Guido , Della Vedova Marco L 
Published: July 2024

ABSTRACT
The scope of this paper is a multivariate setting involving categorical variables. Following an external manipulation of one variable, the goal is to evaluate the causal effect on an outcome of interest. A typical scenario involves a system of variables representing lifestyle, physical and mental features, symptoms, and risk factors, with the outcome being the presence or absence of a disease. These variables are interconnected in complex ways, allowing the effect of an intervention to propagate through multiple paths. A distinctive feature of our approach is the estimation of causal effects while accounting for uncertainty in both the dependence structure, which we represent through a directed acyclic graph (DAG), and the DAG-model parameters. Specifically, we propose a Markov chain Monte Carlo algorithm that targets the joint posterior over DAGs and parameters, based on an efficient reversible-jump proposal scheme. We validate our method through extensive simulation studies and demonstrate that it outperforms current state-of-the-art procedures in terms of estimation accuracy. Finally, we apply our methodology to analyze a dataset on depression and anxiety in undergraduate students.
Longitudinal network-based brain grey matter MRI measures are clinically relevant and sensitive to treatment effects in multiple sclerosis
Authors: Colato Elisa , Stutters Jonathan , Narayanan Sridar , Arnold Douglas L , Chataway Jeremy , Gandini Wheeler-Kingshott Claudia A M , Barkhof Frederik , Ciccarelli Olga , Eshaghi Arman , Chard Declan T 
Published: July 2024

Abstract
In multiple sclerosis clinical trials, MRI outcome measures are typically extracted at a whole-brain level, but pathology is not homogeneous across the brain and so whole-brain measures may overlook regional treatment effects. Data-driven methods, such as independent component analysis, have shown promise in identifying regional disease effects but can only be computed at a group level and cannot be applied prospectively. The aim of this work was to develop a technique to extract longitudinal independent component analysis network-based measures of co-varying grey matter volumes, derived from T1-weighted volumetric MRI, in individual study participants, and assess their association with disability progression and treatment effects in clinical trials. We used longitudinal MRI and clinical data from 5089 participants (22 045 visits) with multiple sclerosis from eight clinical trials. We included people with relapsing–remitting, primary and secondary progressive multiple sclerosis. We used data from five negative clinical trials (2764 participants, 13 222 visits) to extract the independent component analysis-based measures. We then trained and cross-validated a least absolute shrinkage and selection operator regression model (which can be applied prospectively to previously unseen data) to predict the independent component analysis measures from the same regional MRI volume measures and applied it to data from three positive clinical trials (2325 participants, 8823 visits). We used nested mixed-effect models to determine how networks differ across multiple sclerosis phenotypes are associated with disability progression and to test sensitivity to treatment effects. We found 17 consistent patterns of co-varying regional volumes. In the training cohort, volume loss was faster in four networks in people with secondary progressive compared with relapsing–remitting multiple sclerosis and three networks with primary progressive multiple sclerosis. Volume changes were faster in secondary compared with primary progressive multiple sclerosis in four networks. In the combined positive trials cohort, eight independent component analysis networks and whole-brain grey matter volume measures showed treatment effects, and the magnitude of treatment–placebo differences in the network-based measures was consistently greater than with whole-brain grey matter volume measures. Longitudinal network-based analysis of grey matter volume changes is feasible using clinical trial data, showing differences cross-sectionally and longitudinally between multiple sclerosis phenotypes, associated with disability progression, and treatment effects. Future work is required to understand the pathological mechanisms underlying these regional changes.
What makes an event significant: an fMRI study on self-defining memories
Authors: Monsa Rotem , Dafni-Merom Amnon , Arzy Shahar 
Published: July 2024

Abstract
Self-defining memories are highly significant personal memories that contribute to an individual’s life story and identity. Previous research has identified 4 key subcomponents of self-defining memories: content, affect, specificity, and self-reflection. However, these components were not tested under functional neuroimaging. In this study, we first explored how self-defining memories distinguish themselves from everyday memories (non-self-defining) through their associated brain activity. Next, we evaluated the different self-defining memory subcomponents through their activity in the underlying brain system. Participants recalled both self-defining and non-self-defining memories under functional MRI and evaluated the 4 subcomponents for each memory. Multivoxel pattern analysis uncovered a brain system closely related to the default mode network to discriminate between self-defining and non-self-defining memories. Representational similarity analysis revealed the neural coding of each subcomponent. Self-reflection was coded mainly in the precuneus, middle and inferior frontal gyri, and cingulate, lateral occipital, and insular cortices. To a much lesser extent, content coding was primarily in the left angular gyrus and fusiform gyrus. No region was found to represent information on affect and specificity. Our findings highlight the marked difference in brain processing between significant and non-significant memories, and underscore self-reflection as a predominant factor in the formation and maintenance of self-defining memories, inviting a reassessment of what constitutes significant memories.
It is time to address the contribution of cholesterol in all apoB-containing lipoproteins to atherosclerotic cardiovascular disease
Authors: Toth Peter P , Banach Maciej 
Published: July 2024

Abstract
On average, LDL particles are the most populous lipoprotein in serum under fasting conditions. For many reasons, it has been the primary target of lipid-lowering guidelines around the world. In the past 30 years, we have witnessed remarkable changes in each iteration of dyslipidaemia guidelines, with LDL-cholesterol (LDL-C) targets becoming lower and lower among patients at high and very high risk for atherosclerotic cardiovascular disease (ASCVD). The world over, goal attainment rates are low, and hence, ASCVD prevalence remains unacceptably high. Inadequate LDL-C lowering is a major issue in contemporary cardiovascular (CV) medicine. Another issue that vexes even the most astute clinician is that of ‘residual risk’, meaning the excess risk that remains even after LDL-C is appropriately reduced. In recent years, an important new component of residual risk has emerged: triglyceride-enriched lipoproteins or remnant lipoproteins. These precursors to LDL particles can assume outsized importance among patients with derangements in triglyceride metabolism (e.g. genetic variants, insulin resistance, and diabetes mellitus) and may be more atherogenic than LDL species. Consequently, to reduce total risk for acute CV events, the time has come to include the entire spectrum of apoB-containing lipoproteins in approaches to both risk evaluation and treatment.
Candida albicans PPR proteins are required for the expression of respiratory Complex I subunits
Authors: Wenda Joanna Maria , Drzewicka Katarzyna , Mulica Patrycja , Tetaud Emmanuel , di Rago Jean Paul , Golik Paweł , Łabędzka-Dmoch Karolina 
Published: July 2024

Abstract
Pentatricopeptide repeat (PPR) proteins bind RNA and are present in mitochondria and chloroplasts of Eukaryota. In fungi, they are responsible for controlling mitochondrial genome expression, mainly on the posttranscriptional level. Candida albicans is a human opportunistic pathogen with a facultative anaerobic metabolism which, unlike the model yeast Saccharomyces cerevisiae, possesses mitochondrially encoded respiratory Complex I (CI) subunits and does not tolerate loss of mtDNA. We characterized the function of 4 PPR proteins of C. albicans that lack orthologs in S. cerevisiae and found that they are required for the expression of mitochondrially encoded CI subunits. We demonstrated that these proteins localize to mitochondria and are essential to maintain the respiratory capacity of cells. Deletion of genes encoding these PPR proteins results in changes in steady-state levels of mitochondrial RNAs and proteins. We demonstrated that C. albicans cells lacking CaPpr4, CaPpr11, and CaPpr13 proteins show no CI assembly, whereas the lack of CaPpr7p results in a decreased CI activity. CaPpr13p is required to maintain the bicistronic NAD4L–NAD5 mRNA, whereas the other 3 PPR proteins are likely involved in translation-related assembly of mitochondrially encoded CI subunits. In addition, we show that CaAep3p, which is an ortholog of ScAep3p, performs the evolutionary conserved function of controlling expression of the ATP8–ATP6 mRNA. We also show that C. albicans cells lacking PPR proteins express a higher level of the inducible alternative oxidase (AOX2) which likely rescues respiratory defects and compensates for oxidative stress.
Sociodemographic Determinants of Extreme Heat and Ozone Risk Among Older Adults in 3 Sun Belt Cities
Authors: Crank Peter J , O’Lenick Cassandra R , Baniassadi Amir , Sailor David J , Wilhelmi Olga , Hayden Mary 
Published: July 2024

Abstract

Background
Vulnerable populations across the United States are frequently exposed to extreme heat, which is becoming more intense due to a combination of climate change and urban-induced warming. Extreme heat can be particularly detrimental to the health and well-being of older citizens when it is combined with ozone. Although population-based studies have demonstrated associations between ozone, extreme heat, and human health, few studies focused on the role of social and behavioral factors that increase indoor risk and exposure among older adults.

Methods
We conducted a household survey that aimed to understand how older adults are affected by extreme heat and ozone pollution inside and outside of their homes across Houston, Phoenix, and Los Angeles. We examine contributing factors to the risk of self-reported health effects using a generalized linear mixed-effects regression model of telephone survey data of 909 older adults in 2017.

Results
We found an increased occurrence of self-reported symptoms for extreme heat with preexisting respiratory health conditions and a lack of air conditioning access; self-reported ozone symptoms were more likely with preexisting respiratory health conditions. The risk of heat-related symptoms was slightly higher in Los Angeles than Houston and Phoenix. We found several demographic, housing, and behavioral characteristics that influenced the risk of heat- and ozone-related symptoms.

Conclusions
The increased risk among older adults based on specific social and behavioral factors identified in this study can inform public health policy and help cities tailor their heat and ozone response plans to the specific needs of this vulnerable population.
Site-specific N-glycoproteomic analysis reveals up-regulated fucosylation in seminal plasma of asthenozoospermia
Authors: Xin Miaomiao , Li Cheng , You Shanshan , Zhu Bojing , Shen Jiechen , Dong Wenbo , Xue Xia , Shi Wenhao , Xiong Yao , Shi Juanzi , Sun Shisheng 
Published: July 2024

Abstract
N-linked glycoproteins are rich in seminal plasma, playing essential roles in supporting sperm function and fertilization process. The alteration of seminal plasma glycans and its correspond glycoproteins may lead to sperm dysfunction and even infertility. In present study, an integrative analysis of glycoproteomic and proteomic was performed to investigate the changes of site-specific glycans and glycoptoteins in seminal plasma of asthenozoospermia. By large scale profiling and quantifying 5,018 intact N-glycopeptides in seminal plasma, we identified 92 intact N-glycopeptides from 34 glycoproteins changed in asthenozoospermia. Especially, fucosylated glycans containing lewis x, lewis y and core fucosylation were significantly up-regulated in asthenozoospermia compared to healthy donors. The up-regulation of fucosylated glycans in seminal plasma may interfere sperm surface compositions and regulation of immune response, which subsequently disrupts sperm function. Three differentiated expression of seminal vesicle-specific glycoproteins (fibronectin, seminogelin-2, and glycodelin) were also detected with fucosylation alteration in seminal plasma of asthenozoospermia. The interpretation of the altered site-specific glycan structures provides data for the diagnosis and etiology analysis of male infertility, as well as providing new insights into the potential therapeutic targets for male infertility.
Surgical timing for asphyxiating thoracic dystrophy
Authors: Chen Xingfei , Ye Huilan , Dang Run , Yang Yiyu 
Published: July 2024

Abstract
This report describes a 4-year-old girl diagnosed with asphyxiating thoracic dystrophy who experienced severe respiratory distress and multiple complications after undergoing a corrective operation for a thoracic deformity. The optimal age for children with asphyxiating thoracic dystrophy to receive a corrective operation is between 6 and 12 years old. For children under 6 years old, the decision to undergo an operation should be carefully evaluated.
Iraq's Authoritarian Democracies: A Conceptual Framework through Tawfiq al-Suwaydi's Political Memoirs
Authors: Al-Kalisy Abdulla 
Published: July 2024

Abstract
Political memoirs have been typically utilized for their historical reference, neglecting the wide array of conceptualizations of the political sphere and the state that politicians' narratives represent. Critical discourse analysis methodologies, by focusing on perceptions and interpretations of discourse, provide the tools to uncover these conceptualizations of elites and those that represent the state. This is particularly important in states like Iraq, which struggle against hybridity, where the democratic system is actioned through authoritarianist tendencies that define the political sphere. This manipulation of an otherwise democratic structure requires an analysis of the conceptual framework that informs the manipulation. The political memoirs of Tawfiq al-Suwaydi, an Iraqi PM on multiple occasions throughout the Monarchy Era, cover significantly more than identity construction, confirmation of historical narratives, and his defenses. The discursive foundation of the state and the way it is actioned against a democratic system is qualified throughout his writing. In his narration, we will see a significant outpour of fundamentally authoritarian views of rule rooted in efficiency through domination and absolute control. Meanwhile, the democratic system was conceptualized as serving the purpose of appeasing an otherwise inconsolable people. This article highlights the way memoirs of political elites, through the justificatory and analytical language, are gateways to understanding the perceptions of rule upon which their mode of operation, and so the foundation of hybridity, is based. This aims to further illuminate oppressive continuities within the Iraqi political sphere as we have seen a return to a similar form of hybridity post-2003.
Examining the long-term impacts of ergot alkaloids on fetal heifer development and subsequent growth and reproductive performance
Authors: Haimon McKenzie L J , Poole Rebecca K , Newsome McKayla A , Brown Alecia R , Dudley Harrison , Poole Daniel H 
Published: July 2024

Abstract
Consumption of toxic endophyte-infected tall fescue (EI) results in poor reproductive performance in domestic livestock. In this study, the objective was to evaluate the effects of ergovaline exposure during mid-gestation (days 93 through 188 of gestation) on dam performance, the growing female fetus, and the subsequent growth and reproductive performance of the gestationally exposed heifer calves. Pregnant Angus and Simmental-Angus cows were blocked by age (2 to 3, to 7, and &gt;7 y), body weight (BW), and breed; and then randomly assigned to graze either novel endophyte-infected tall fescue (EN; &lt;5% infection rate; n = 27 year 1, n = 16 year 2) or toxic EI (99% infection rate; n = 27 year 1, n = 17 year 2). Weekly BW, body condition scores (BCS), hair coat scores, hair shedding scores (HSS), and blood samples for progesterone (P4) analysis were collected from mid-April through July of 2017 (year 1) and 2018 (year 2). Gestation length, birth weight, placental characteristics, heifer calf growth, onset of puberty, ovarian characteristics, and artificial insemination pregnancy rates were measured. Data were analyzed using the MIXED procedure of SAS. Cows grazing EI pastures had reduced average daily gain, reduced BCS, greater HSS, and decreased P4 concentrations compared to cows on EN pasture (P &lt; 0.01). Birth weights were decreased for heifers whose dams were exposed to EI pastures during their second trimester (P &lt; 0.01). Heifer pregnancy rates were not impacted by EI pasture exposure during gestation for either year of the study. However, a treatment-by-year effect was seen for the pregnancy rate for EI-exposed heifers in year 2; EI-exposed heifers in year 2 had increased pregnancy rates at two of the inseminations. Combined, these data reinforce that consumption of toxic EI during gestation can negatively impact both dam and offspring performance. More studies are needed to evaluate more parameters in an effort to elucidate the possible life-long impacts of ergovaline exposure during gestation.
Perforated neonatal appendicitis mimicking necrotizing enterocolitis in a premature neonate: a case report and literature review
Authors: Manasra Mahmoud R , Alhroob Thaer , Marrawani Mohammad , Batanje Dalia , Imran Yahya , Harahsha Moatz , Amleh Abdul-Karim , Zugayar Diaa 
Published: July 2024

Abstract
Necrotizing enterocolitis (NEC) predominantly affects preterm infants and can mimic other conditions like acute appendicitis. Neonatal appendicitis (NA) is extremely rare, with an incidence of 0.04–0.2% and high fatality rates. Due to its rarity and resemblance to other neonatal conditions, NA diagnosis is often delayed. We report a case of a 2220-g male preterm neonate delivered at 31 + 5 weeks via urgent cesarean section due to chorioamnionitis, initially misdiagnosed with NEC but later found to have a perforated appendix. The neonate recovered well post-surgery, with the ileostomy reversed 10 weeks later. Prompt surgical intervention is crucial for NA, as it requires different management than NEC. This case underscores the importance of considering NA in preterm infants with severe abdominal symptoms and emphasizes timely surgical intervention to improve outcomes. Additionally, it supports the hypothesis that localized NEC involving the appendix may have a better prognosis than generalized NEC.
Sudden onset presentation of giant primary thyroid hemangioma: a rare case report
Authors: Al-Maghrabi Haneen , Alardati Hosam , Waggass Ghouth , Aref Mohammed , Heaphy John 
Published: July 2024

Abstract
Hemangiomas are considered slow growing benign neoplasms. Primary thyroid hemangiomas are uncommon and may pose difficulty in diagnosis due to absence of distinctive imaging characteristics and related clinical symptoms. It is crucial to precisely identify these lesions to aid in implementing nonsurgical treatment plans rather than resorting to surgical procedures in certain cases. In this report we present a case of a 76-year-old female who presented with painless, rapid, and sudden notice of right-side neck swelling over a 1-day duration. Her radiological examinations raised the concern of a vascular lesion that was emoblized endovascularly. Then, it was surgically removed, which was eventually determined to be primary thyroid hemangioma. In addition, we present a literature review of previously published cases and discuss tumor pathophysiology, clinical presentations, radiology features, and differential diagnosis.