bluuebunny/crossref_metadata_2025_split huggingface dataset:
The COVID‐19 Pandemic and the Prevalence of Childhood Obesity in Turkiye
Authors: Salman Hakan , İssi Irlayici Fatma , Akçam Mustafa 
Published: October 2022

Objectives:To examine the prevalence of overweight and obesity in school‐age children in Isparta Province, Turkiye, during the coronavirus disease 2019 (COVID‐19) pandemic, and to compare the results with those of previous studies conducted in Isparta in 2005, 2009, and 2014.Methods:The study was carried out in schools in the city center of Isparta in March 2022, during which the weight and height of students were measured using a scale and stadiometer, and the body mass indices (BMI), BMI percentiles, and z scores were calculated.Results:Of the 8871 students assessed, 4547 (51.3%) were female and the mean age of the sample was 11.92 ± 3.42 (6–18.93) years. The prevalence of overweight was 12%, the prevalence of obesity was 14.5%, and the prevalence of overweight + obesity was 26.5%. A comparison of the figures since 2005 revealed the prevalence of overweight to be stable, while the prevalence of obesity and the prevalence of overweight + obesity were found to have witnessed a increase (χ2: 57.01, P < 0.001). The prevalence of obesity was 13% among girls under 11 years of age and 14.3% among girls over 11 years of age; and 18.2% and 12.8% among boys under and over 11 years of age, respectively (χ2: 23.26, P < 0.001). The prevalence of obesity was significantly higher in boys under 11 years of age.Conclusions:The prevalence of overweight + obesity was nearly stable in the 3 studies conducted over the 17‐year period, but we witnessed an increase in our most recent study conducted during the pandemic. The prevalence of obesity is significantly higher in boys under 11 years of age.
Integration and Implementation of Patient-Reported Outcomes (PRO): A Prospective, Observational Clinical Quality Improvement Study
Authors: Rios-Diaz Arturo J. , Nathan Shelby L. , Cunning Jessica R. , Kozak Geoffrey M. , Messa Charles A. , Whitely Cutler B. , Davis Harrison D. , Thrippleton Sheri , Broach Robyn B. , Fischer John P. 
Published: October 2022

Background:
Implementation of patient-reported outcomes (iPROs) represents a critical barrier to their widespread use and poses challenges to workflow and patient satisfaction. We sought to implement PRO surveys into surgical practice while identifying principles for successful/broader implementation.

Methods:
Outpatient surgical encounters (2016-2019) related to hernia, breast surgery, and post-bariatric body-contouring were assessed for the use of Abdominal-Hernia-Q (AHQ), BREAST-Q™, and BODY-Q™ surveys (implemented in that order). Outcomes were implementation rates/quarter and time to optimal implementation (≥80%). Successful implementation principles were identified during the first implemented PRO instrument and applied to subsequent ones. Logistic regression models were used to estimate increase in rate of implementation/quarter by instrument controlling for clinic volume. Risk-adjusted generalized linear models determined predicted mean differences in total clinic time and patient satisfaction.

Results:
1,206 encounters were identified. Overall survey implementation rate increased from 15% (first-quarter) to 90% (last-quarter; p<0.01). AHQ optimal implementation was reached by 15 months. Principles for successful iPROs were workflow optimization, appropriate patient selection, staff engagement, and electronic survey integration. Consistent application of these principles optimized time to optimal implementation for BREAST-Q™ (9 months; 18.1% increase in implementation/quarter [95% CI 1.5-37.5%]; p<0.01) and BODY-Q™ (3 months; 56.3% increase in implementation/quarter [95% CI 26.8-92.6%]; p=0.03). Neither patient clinic time (p=0.16) nor patient satisfaction differed during the iPRO process (p=0.98).

Conclusions:
Prospective iPROs can be achieved in surgical practice without an adverse effect on patient satisfaction or workflow. The proposed principles of implementation may be used to optimize efficiency for iPROs.
Minimally invasive, nerve and muscle sparing surgical decompression for occipital neuralgia
Authors: Pietramaggiori Giorgio , Scherer Saja 
Published: October 2022

Background:
Occipital Neuralgia (ON) is a well-defined type of headache, whose treatment algorithm is still debated across medical specialties. From the analysis of the literature, it appears that surgical decompression of the occipital nerves is the most effective invasive approach to improve the quality of life of patients suffering from ON refractory to medications. We describe here a minimally invasive nerve and muscle sparing technique to decompress the occipital nerves.

Methods:
The results in terms of reduction of migraine days / month, use of medications, pain evaluation, and decrease in migraine headache index (MHI) were analyzed via a retrospective chart review of 87 patients who underwent nerve and muscle sparing surgical decompression of the greater and lesser occipital nerves mono- or bi-lateral in our institution and were followed up for at least 12 months. The surgical technique is described in detail.

Results:
Surgical decompression significantly reduced ON burden (at least 50% improvement) in 91% of patients, with 45% reporting a complete remission of occipital pain. Days with pain per month decreased by 80%, chronic background pain intensity decreased by 81% and pain intensity during crisis decreased by 76%. Accordingly, drug usage dropped by about 70%. Only minor complications were reported in 4 patients.

Conclusion:
The described technique could contribute to further attest surgical decompression as the first option among the invasive approaches to treat ON. Results corroborates previous findings adding a less invasive, nerve and muscle sparing approach.
Prevalence and Patterns of Renal Involvement Among Patients With Systemic Lupus Erythematous at a Tertiary Center
Authors: Hasan Manal Ahmed , Alali Lina , Alsadah Fatimah , Alobud Sarah , Alsaif Janat , Alali Zainab 
Published: October 2022

Background
Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder characterized by widespread inflammation and damage to multiple organ systems. One of the most common and severe manifestations of SLE is lupus nephritis (LN).

Objectives
To determine the prevalence of LN among subjects with SLE and to identify the demographic, clinical, and laboratory parameters of SLE in subjects diagnosed with LN.

Methods
This is a descriptive study conducted at a tertiary hospital. Medical records were reviewed from outpatients who visited between January 2015 and October 2019 and who has fulfilled the classification criteria for diagnosis of SLE and had LN.

Results
Among 365 patients with SLE, 36% had LN. The most prevalent World Health Organization class of LN was IV, which significantly correlated with both abnormal creatinine levels and nephrotic range proteinuria. Elevated serum creatinine correlated with the presence of hypertension and thrombocytopenia. Cutaneous manifestations were noted to be present in 100% of LN patients, followed by arthritis and/or arthralgia (82.9%), anemia (94.6%), and lymphopenia (87.6%).

Conclusion
This study aids in the recognition of the demographic, clinical, laboratory features, and the histological patterns of LN patients in Saudi Arabia, that probably has a role in the development and disease progression. A significant correlation was found between abnormal kidney function and hypertension, thrombocytopenia and nephrotic range proteinuria. The presence of World Health Organization class IV LN correlated with both impaired kidney function and nephrotic range proteinuria.
Psychometric Evaluation of the Perceived Research Burden Assessment (PeRBA) in Longitudinal Studies of Alzheimer Disease Using Rasch Analysis
Authors: Keleman Audrey A. , Chang Chih-Hung , Bollinger Rebecca M. , Lingler Jennifer H. , Gabel Matthew , Stark Susan L. 
Published: October 2022

Introduction:
The Perceived Research Burden Assessment (PeRBA) was developed to measure participant perceptions of burden in research studies. This study aimed to examine the psychometric properties of this assessment using Rasch analysis in participants in the longitudinal studies of the Alzheimer disease (AD) and their family members.

Methods:
PeRBA was administered to 443 participants in studies of AD and 212 family members across 4 Alzheimer Disease Research Centers. We used Rasch analysis to examine PeRBA’s psychometric properties, and data-model fit both at item and scale levels.

Results:
PeRBA demonstrated good reliability and item and person fit for participants and family members. A few items did not fit the model for participants or family members. Areas of content redundancy were found in items assessing similar amounts of perceived research burden. Areas of content gaps were also found, with no items assessing certain levels of perceived research burden.

Conclusion:
Analysis results support the good overall psychometric properties of PeRBA among research participants in studies of AD and their family members. Recommendations have been provided to improve the assessment, including rewording items and adding items that could account for a broader range of perceived research burden.
Journey of the mouse primitive endoderm: from specification to maturation
Authors: Chowdhary Sayali , Hadjantonakis Anna-Katerina 
Published: October 2022

The blastocyst is a conserved stage and distinct milestone in the development of the mammalian embryo. Blastocyst stage embryos comprise three cell lineages which arise through two sequential binary cell fate specification steps. In the first, extra-embryonic trophectoderm (TE) cells segregate from inner cell mass (ICM) cells. Subsequently, ICM cells acquire a pluripotent epiblast (Epi) or extra-embryonic primitive endoderm (PrE, also referred to as hypoblast) identity. In the mouse, nascent Epi and PrE cells emerge in a salt-and-pepper distribution in the early blastocyst and are subsequently sorted into adjacent tissue layers by the late blastocyst stage. Epi cells cluster at the interior of the ICM, while PrE cells are positioned on its surface interfacing the blastocyst cavity, where they display apicobasal polarity. As the embryo implants into the maternal uterus, cells at the periphery of the PrE epithelium, at the intersection with the TE, break away and migrate along the TE as they mature into parietal endoderm (ParE). PrE cells remaining in association with the Epi mature into visceral endoderm. In this review, we discuss our current understanding of the PrE from its specification to its maturation.This article is part of the theme issue ‘Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom’.
Embryonic and extraembryonic tissues during mammalian development: shifting boundaries in time and space
Authors: Thowfeequ Shifaan , Srinivas Shankar 
Published: October 2022

The first few days of embryonic development in eutherian mammals are dedicated to the specification and elaboration of the extraembryonic tissues. However, where the fetus ends and its adnexa begins is not always as self-evident during the early stages of development, when the definitive body axes are still being laid down, the germ layers being specified and a discrete form or bodyplan is yet to emerge. Function, anatomy, histomorphology and molecular identities have been used through the history of embryology, to make this distinction. In this review, we explore them individually by using specific examples from the early embryo. While highlighting the challenges of drawing discrete boundaries between embryonic and extraembryonic tissues and the limitations of a binary categorization, we discuss how basing such identity on fate is the most universal and conceptually consistent.
This article is part of the theme issue ‘Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom’.
The extended analogy of extraembryonic development in insects and amniotes
Authors: Panfilio Kristen A. , Chuva de Sousa Lopes Susana M. 
Published: October 2022

It is fascinating that the amnion and serosa/chorion, two extraembryonic (EE) tissues that are characteristic of the amniote vertebrates (mammals, birds and reptiles), have also independently evolved in insects. In this review, we offer the first detailed, macroevolutionary comparison of EE development and tissue biology across these animal groups. Some commonalities represent independent solutions to shared challenges for protecting the embryo (environmental assaults, risk of pathogens) and supporting its development, including clear links between cellular properties (e.g. polyploidy) and physiological function. Further parallels encompass developmental features such as the early segregation of the serosa/chorion compared to later, progressive differentiation of the amnion and formation of the amniotic cavity from serosal–amniotic folds as a widespread morphogenetic mode across species. We also discuss common developmental roles for orthologous transcription factors and BMP signalling in EE tissues of amniotes and insects, and between EE and cardiac tissues, supported by our exploration of new resources for global and tissue-specific gene expression. This highlights the degree to which general developmental principles and protective tissue features can be deduced from each of these animal groups, emphasizing the value of broad comparative studies to reveal subtle developmental strategies and answer questions that are common across species.This article is part of the theme issue ‘Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom’.
Extraembryonic tissue in chelicerates: a review and outlook
Authors: Prpic Nikola-Michael , Pechmann Matthias 
Published: October 2022

The formation of extraembryonic membranes (EEMs) contributes to the proper development of many animals. In arthropods, the formation and function of EEMs have been studied best in insects. Regarding the development of extraembryonic tissue in chelicerates (spiders and relatives), most information is available for spiders (Araneae). Especially two populations of cells have been considered to represent EEMs in spiders. The first of these potential EEMs develops shortly after egg deposition, opposite to a radially symmetrical germ disc that forms in one hemisphere of the egg and encloses the yolk. The second tissue, which has been described as being extraembryonic is the so-called dorsal field, which is required to cover the dorsal part of the developing spider germ rudiment before proper dorsal closure. In this review, we summarize the current knowledge regarding the formation of potential extraembryonic structures in the Chelicerata. We describe the early embryogenesis of spiders and other chelicerates, with a special focus on the formation of the potential extraembryonic tissues.This article is part of the theme issue ‘Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom’.
Why are GWASs limp about the X chromosome?
Authors: Amos Christopher I. , Gorlov Ivan P. 
Published: October 2022

AbstractThe X-chromosome is among the largest human chromosomes. It differs from autosomes by a number of important features including hemizygosity in males, an almost complete inactivation of one copy in females, and unique patterns of recombination. We used data from the Catalog of Published Genome Wide Association Studies to compare densities of the GWAS-detected SNPs on the X-chromosome and autosomes. The density of GWAS-detected SNPs on the X-chromosome is 6-fold lower compared to the density of the GWAS-detected SNPs on autosomes. Differences between the X-chromosome and autosomes cannot be explained by differences in the overall SNP density, lower X-chromosome coverage by genotyping platforms or low call rate of X-chromosomal SNPs. Similar differences in the density of GWAS-detected SNPs were found in female-only GWASs (e.g. ovarian cancer GWASs). We hypothesized that the lower density of GWAS-detected SNPs on the X-chromosome compared to autosomes is not a result of a methodological bias, e.g. differences in coverage or call rates, but has a real underlying biological reason – alower density of functional SNPs on the X-chromosome versus autosomes. This hypothesis is supported by the observation that (i) the overall SNP density of X-chromosome is lower compared to the SNP density on autosomes and that (ii) the density of genic SNPs on the X-chromosome is lower compared to autosomes while densities of intergenic SNPs are similar.Author summaryOne of the most striking observations from the Genome Wide Association Studies (GWAS) is that the density of GWAS hits is much lower on X-chromosome compared to autosomes. This was initially explained by technical/analytical reasons such as lower coverage and lack of adequate methods to analyze X-chromosomal SNPs. Since then, a better coverage and better analytical methods to analyze X-chromosomal SNPs were developed. We recently revisited the issue and found that the density of GWAS hits on X-chromosome is at least 5-fold lower compared to autosomes. We demonstrated that the difference cannot be explained by technical or analytical reasons. We proposed a hypothesis of a real biological phenomenon underlying X versus autosomal differences in the density of GWAS-detected SNPs, namely that X-chromosome has a lower density of functional polymorphisms compared to autosomes because of a stronger selection against X-chromosomal mutations since X-chromosomal variants are more exposed to natural selection due to hemizygosity in males and X-chromosome inactivation in females. The hypothesis is supported by the analysis of the densities of intergenic, intronic and exonic SNPs on human chromosomes.
Thymic mesenchymal niche cells drive T cell immune regeneration
Authors: Gustafsson Karin , Isaev Sergey , Kooshesh Kameron A. , Baryawno Ninib , Kokkaliaris Konstantinos D. , Severe Nicolas , Zhao Ting , Scadden Elizabeth W. , Spencer Joel A. , Burns Christian , Akilan Kumaran , Barkas Nikolaos , Gessessew Hayalneh , Lin Charles P. , Kharchenko Peter V. , Scadden David T. 
Published: October 2022

AbstractThymic atrophy and the progressive immune decline that accompanies it is a major health problem, chronically with age and acutely with immune injury. No solution has been defined. Here we demonstrate that one of the three mesenchymal cell subsets identified by single-cell analysis of human and mouse thymic stroma is a critical niche component for T lymphopoiesis. The Postn+ subset is located perivascularly in the cortical-medullary junction, medulla and subcapsular regions. Cell depletion demonstrated that it recruits T competent cells to the thymus and initiates T lymphopoiesisin vivo. This subset distinctively expresses the chemokineCcl19necessary for niche functions. It markedly declines with age and in the acute setting of hematopoietic stem cell transplant conditioning. When isolated and adoptively transferred, these cells durably engrafted the atrophic thymus, recruited early T progenitors, increased T cell neogenesis, expanded TCR complexity and enhanced T cell response to vaccination. These data define a thymus lymphopoietic niche cell type that may be manipulated therapeutically to regenerate T lymphopoiesis.
Rapid and Efficient Ambient Temperature X-ray Crystal Structure Determination at Turkish Light Source
Authors: Gul Mehmet , Ayan Esra , Destan Ebru , Johnson J Austin , Shafiei Alaleh , Kepceoğlu Abdullah , Yilmaz Merve , Ertem Fatma Betül , Yapici İlkin , Tosun Bilge , Baldir Nilüfer , Tokay Nurettin , Nergiz Zeliş , Karakadioğlu Gözde , Paydos Seyide Seda , Kulakman Cahine , Ferah Cengiz Kaan , Güven Ömür , Atalay Necati , Akcan Enver Kamil , Cetinok Haluk , Arslan Nazlı Eylül , Şabanoğlu Kardelen , Aşci Bengisu , Tavli Serra , Gümüsboğa Helin , Altuntaş Sevde , Otsuka Masami , Fujita Mikako , Tekin Şaban , Çiftçi Halilibrahim , Durdaği Serdar , Karaca Ezgi , Kaplan Türköz Burcu , Kabasakal Burak Veli , Kati Ahmet , DeMirci Hasan 
Published: October 2022

ABSTRACTHigh-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish Light Source (Turkish DeLight). The complete dataset was collected in 18.5 mins with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme.Turkish DeLightprovides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.
Cross-sex cecal microbiota transfer alters depressive-like behaviours in mice
Authors: Hinks Meagan , Martin Yellow , Burke Francine , Bambico Francis R. , Swift-Gallant Ashlyn 
Published: October 2022

AbstractMajor depressive disorder (MDD) is a leading cause of non-fatal global disease burden, with females being two-fold more likely than males to be diagnosed with the disorder. Despite this distinct sex-linked disparity of diagnosis, it is unclear what underlies the sex bias of MDD prevalence. Recent findings suggest a role for the gut in mediating affective disorders through the gut-brain-axis (GBA). However, few studies have included sex as a biological variable. For this study, cross-sex transfer of cecal microbiota was performed between male and female C57Bl/6 mice to elucidate the effects of sex and the gut microbiome on a standard battery of tests measuring depressive-like behaviours. Specifically, regardless of sex, recipients of male cecal content had a greater sucrose preference than controls and recipients of female cecum. Conversely, in the splash test, recipients of female cecum displayed a decrease in grooming behaviour compared to both controls and recipients of male cecum, suggestive of an increase in depressive-like behaviour. These results support a role for female-specific gut microbes in contributing to female vulnerability to depression, while male-specific gut microbes may protect in part against an anhedonia-like phenotype