bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomic analysis reveals gene regulation mediated by caspase activity in a chordate organism
Authors: Krasovec Gabriel , Karaiskou Anthi , Quéinnec Éric , Chambon Jean-Philippe 
Published: October 2021

Abstract
Background
Apoptosis is a caspase regulated cell death present in all metazoans defined by a conserved set of morphological features. A well-described function of apoptosis is the removal of excessive cells during development and homeostasis. Recent studies have shown an unexpected signalling property of apoptotic cells, affecting cell fate and/or behaviour of neighbouring cells. In contrast to the apoptotic function of cell elimination, this new role of apoptosis is not well understood but seems caspase-dependent. To deepen our understanding of apoptotic functions, it is necessary to work on a biological model with a predictable apoptosis pattern affecting cell fate and/or behaviour. The tunicate Ciona intestinalis has a bi-phasic life cycle with swimming larvae which undergo metamorphosis after settlement. Previously, we have shown that the tail regression step during metamorphosis, characterized by a predictable polarized apoptotic wave, ensures elimination of most tail cells and controls primordial germ cells survival and migration.

Results
We performed differential transcriptomic analysis between control metamorphosing larvae and larvae treated with the pan-caspase inhibitor Z-VAD-fmk in order to explore the transcriptional control of apoptotic cells on neighbouring cells that survive and migrate. When caspase activity was impaired, genes known to be involved in metamorphosis were downregulated along with other implicated in cell migration and survival molecular pathways.

Conclusion
We propose these results as a confirmation that apoptotic cells can control surrounding cells fate and as a reference database to explore novel apoptotic functions in animals, including those related to migration and differentiation.
Repertoire analysis of γδ T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires
Authors: Dixon Robert , Preston Stephen G. , Dascalu Stefan , Flammer Patrik G. , Fiddaman Steven R. , McLoughlin Kirstie , Boyd Amy , Volf Jiri , Rychlik Ivan , Bonsall Michael B. , Kaspers Bernd , Smith Adrian L. 
Published: October 2021

AbstractBackgroundDespite increasing interest in γδ T cells and their non-classical behaviour, most studies focus on animals with low numbers of circulating γδ T cells, such as mice and humans. Arguably, γδ T cell functions might be more prominent in chickens where these cells form a higher proportion of the circulatory T cell compartment. The TCR repertoire defines different subsets of γδ T cells, and such analysis is facilitated by well-annotated TCR loci. γδ T cells are considered at the cusp of innate and adaptive immunity but most functions have been identified in γδ low species. A deeper understanding of TCR repertoire biology in γδ high and γδ low animals is critical for defining the evolution of the function of γδ T cells. Repertoire dynamics will reveal populations that can be classified as innate-like or adaptive-like as well as those that straddle this definition.ResultsHere, a recent discrepancy in the structure of the chicken TCR gamma locus is resolved, demonstrating that tandem duplication events have shaped the evolution of this locus. Importantly, repertoire sequencing revealed large differences in the usage of individual TRGV genes, a pattern conserved across multiple tissues, including thymus, spleen and the gut. A single TRGV gene, TRGV3.3, with a highly diverse private CDR3 repertoire dominated every tissue in all birds. TRGV usage patterns were partly explained by the TRGV-associated recombination signal sequences. Public CDR3 clonotypes represented varying proportions of the repertoire of TCRs utilising different TRGVs, with one TRGV dominated by super-public clones present in all birds.ConclusionsThe application of repertoire analysis enabled functional annotation of the TCRG locus in a species with a high circulating γδ phenotype. This revealed variable usage of TCRGV genes across multiple tissues, a pattern quite different to that found in γδ low species (human and mouse). Defining the repertoire biology of avian γδ T cells will be key to understanding the evolution and functional diversity of these enigmatic lymphocytes in an animal that is numerically more reliant on them. Practically, this will reveal novel ways in which these cells can be exploited to improve health in medical and veterinary contexts.
Prevalence and factors associated with severe anaemia post-caesarean section at a tertiary Hospital in Southwestern Uganda
Authors: Sivahikyako Sylvie Atosa , Owaraganise Asiphas , Tibaijuka Leevan , Agaba David Collins , Kayondo Musa , Ngonzi Joseph , Mugisha Julius , Kanyesigye Hamson 
Published: October 2021

Abstract
Background
Severe anaemia after caesarean section adversely affects the woman and the new-born. While prenatal anaemia is extensively studied, the literature on post-caesarean section anaemia is limited and characteristics of women at the highest risk of developing severe anaemia after caesarean section are unknown. This study aimed to determine the prevalence and factors associated with severe anaemia on day three post caesarean section.

Methods
On the third day after caesarean section, women were consecutively enrolled in a cross-sectional study at Mbarara Regional Referral Hospital (MRRH). Women who got transfused peripartum were excluded. For every woman, we measured haemoglobin (Hb) concentration and collected data on sociodemographic, obstetric, and medical characteristics. The primary outcome was severe anaemia after caesarean section, defined as Hb < 7 g/dl. We used logistic regression analysis to determine factors associated with severe anaemia after caesarean section. P-value < 0.05 was considered statistically significant.

Results
From December 2019 to March 2020, 427 of 431 screened women were enrolled in the study. Their mean age was 26.05 (SD ± 5.84) years. Three hundred thirteen (73.3%) had attended at least four antenatal care visits. The prevalence of severe anaemia post-caesarean section was 6.79%. Foetus with macrosomia (aOR 7.9 95%CI: 2.18–28.85, p <  0.01) and having mild or moderate anaemia pre-caesarean section (aOR:9.6, 95%CI: 3.91–23.77, p <  0.01) were the factors associated with severe anaemia after caesarean section.

Conclusion
Severe anaemia in women post-caesarean section is relatively uncommon at our institution. It is associated with preoperative anaemia and macrosomic birth. Women with a low preoperative Hb concentration and those whose foetus have macrosomia could be targeted for haemoglobin optimisation before and during caesarean section.
Family support on intensive care units during the COVID-19 pandemic: a qualitative evaluation study into experiences of relatives
Authors: Klop Hanna T. , Nasori Mana , Klinge Tjitske W. , Hoopman Rianne , de Vos Mirjam A. , du Perron Chantal , van Zuylen Lia , Steegers Monique , ten Tusscher Birkitt L. , Abbink Floor C. H. , Onwuteaka-Philipsen Bregje D. , Pasman H. Roeline W. 
Published: October 2021

Abstract
Background
During the first peak of the COVID-19 pandemic in the Netherlands, relatives of patients with COVID-19 admitted to Intensive Care Units (ICUs) were severely restricted in visiting their relatives and in communicating with treating physicians. Family communication is a core element of critical care, however, this pandemic forced medical ICU staff to arrange alternative family support for instance by Family Support Teams (FSTs), consisting of non-ICU affiliated staff who telephonically contacted relatives. This study aims to examine relatives’ experiences with FSTs on two ICUs of a Dutch university medical centre, and to evaluate its working strategies. .

Methods
In a semi-structured interview study, relatives of patients with COVID-19 admitted to ICU’s, who had been supported by the FSTs, were sampled purposively. Twenty-one interviews were conducted telephonically by three researchers. All interviews were topic list guided and audio-recorded. Data was analysed thematically.

Results
All participants indicated they went through a rough time. Almost all evaluated the FSTs positively. Four major themes were identified. First, three important pillars of the FSTs were providing relatives with transparency about the patients’ situation, providing attention to relatives’ well-being, and providing predictability and certainty by calling on a daily basis in a period characterised by insecurity. Second, relatives appeared to fulfil their information needs by calls of the FSTs, but also by calling the attending ICU nurse. Information provided by the FSTs was associated with details and reliability, information provided by nurses was associated with the patient’s daily care. Third, being a primary family contact was generally experienced as both valuable and as an emotional burden. Last, participants missed proper aftercare. Family support often stopped directly after the patient died or had left the ICU. Relatives expressed a need for extended support after that moment since they had strong emotions after discharge or death of the patient.

Conclusions
Family support in times of the extreme COVID-19 situation is important, as relatives are restricted in communication and have a strong need for information and support. Relatives feel encouraged by structure, frequency, support and understanding by FSTs. However, remote family support should be tailored to the needs of relatives. A fixed contact person on de ICU and video calling might be good extra options for family support, also in future post COVID-19 care, but cannot replace physical visits.
Activated gut-homing CD8+ T cells for coeliac disease diagnosis on a gluten-free diet
Authors: Fernández-Bañares Fernando , López-Palacios Natalia , Corzo María , Arau Beatriz , Rubio Mercedes , Fernández-Prieto Marta , Tristán Eva , Pujals Mar , Farrais Sergio , Horta Saúl , Hernández Juana María , Gomez-Perosanz Marta , Reche Pedro A. , Esteve María , Núñez Concepción 
Published: October 2021

Abstract
Background
The diagnosis of coeliac disease (CD) in individuals that have started a gluten-free diet (GFD) without an adequate previous diagnostic work-out is a challenge. Several immunological assays such as IFN-γ ELISPOT have been developed to avoid the need of prolonged gluten challenge to induce the intestinal damage. We aimed to evaluate the diagnostic accuracy of activated gut-homing CD8+ and TCRγδ+ T cells in blood after a 3-day gluten challenge and to compare it with the performance of IFN-γ ELISPOT in a HLA-DQ2.5 subsample.

Methods
A total of 22 CD patients and 48 non-CD subjects, all of them following a GFD, underwent a 3-day 10-g gluten challenge. The percentage of two T cell subsets (CD8+ CD103+ β7hi CD38+/total CD8+ and TCRγδ+ CD103+ β7hi CD38+/total TCRγδ+) in fresh peripheral blood drawn baseline and 6 days after the challenge was determined by flow cytometry. IFN-γ ELISPOT assays were also performed in HLA-DQ2.5 participants. ROC curve analysis was used to assess the diagnostic performance of the CD8+ T cell response and IFN-γ ELISPOT.

Results
Significant differences between the percentage of the two studied subsets of CD8+ and TCRγδ+ cells at days 0 and 6 were found only when considering CD patients (p < 10−3 vs. non-CD subjects). Measuring activated CD8+ T cells provided accurate CD diagnosis with 95% specificity and 97% sensitivity, offering similar results than IFN-γ ELISPOT.

Conclusions
The results provide a highly accurate blood test for CD diagnosis in patients on a GFD of easy implementation in daily clinical practice.
The downgrading of pain sufferers’ credibility
Authors: Tosas Mar Rosàs 
Published: October 2021

AbstractBackgroundThe evaluation of pain remains one of the most difficult challenges that healthcare practitioners face. Chronic pain appears to affect more than 35% of the population in the West, and indeed, pain is the most common reason patients seek medical care. Despite its ubiquity, studies in the last decades reveal that many patients feel their pain is dismissed by healthcare practitioners and that, as a result, they are denied proper medical care. Buchman, Ho, and Goldberg (J Bioethic Inq 14:31-42, 2017) point to this phenomenon as a form of “epistemic injustice”: an unfair and harmful downgrading of credibility affecting some individuals and groups, which prevents them from receiving appropriate and beneficial medical care.MethodsBy exploring the existing literature on this downgrading of patients’ credibility written by healthcare professionals and scholars in medical humanities, I identify and examine the reasons patients are often not believed about their pain and why healthcare is too-often unhelpful or hurtful to people presenting with chronic pain. I also explore to what extent it is possible to forge an alternative epistemological model.ResultsI suggest that most of the causes of this downgrading of patient’s credibility result from either thedifficulty in communicating painor the widespread belief that pathology is always the result ofobjective tissue damage. I examine whether pain has to be effectively communicated and have an objective cause in order for it to be deemed credible. In the end, I argue that in the case of pain, both communication and objectivity are highly problematic.ConclusionsI conclude by suggesting that, although alternative epistemological models might be impossible to build, believing patients has both moral and clinical benefits, and this warrants further research.
Spontaneous recovery from sunitinib-induced disruption of sarcomere in human iPSC-cardiomyocytes and possible involvement of the Hippo pathway
Authors: Matsui Toshikatsu , Shinozawa Tadahiro 
Published: October 2021

Abstract
Background
Sunitinib is known to cause cardiotoxicity in clinical settings. However, among sunitinib-treated patients experiencing adverse cardiac events, decreased cardiac function was reportedly reversible in > 50% of the patients. We previously showed that anti-cancer drugs such as sunitinib cause marked sarcomere disruption in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), and the extent of sarcomere disruption can be used to predict drug-induced cardiotoxicity in humans. The aim of this study is to investigate whether the reversibility of sunitinib-induced cardiac events in clinical settings can be mimicked in vitro, and to examine the molecular mechanism responsible for sunitinib-induced cardiotoxicity focusing on the Hippo pathway.

Methods
iPSC-CMs were stimulated with sunitinib for 72 h and the morphology of sarcomere structures were analyzed by high-content analysis before and after sunitinib washout. To examine the involvement of the Hippo pathway in the sunitinib-induced sarcomere disruption, the extent of nuclear localization of YAP1 (yes-associated protein 1, a Hippo signaling target) was determined. iPSC-CMs were also stimulated with sunitinib and a small molecule inhibitor of the Hippo pathway, XMU-MP-1 and sarcomere structures were analyzed.

Results
We observed a spontaneous recovery in cardiac sarcomeres in iPSC-CMs that were significantly disrupted by sunitinib treatment after a 72 h or 144 h washout of sunitinib. The extent of nuclear localization of YAP1 was significantly reduced after sunitinib stimulation and tended to return to normal levels after drug washout. Simultaneous stimulation of iPSC-CM with sunitinib and XMU-MP-1 suppressed the sunitinib-induced disruption of sarcomeres.

Conclusions
These results indicate that iPSC-CMs have the ability to recover from sunitinib-induced sarcomere disruption, and the Hippo pathway plays a role in the process of sunitinib-induced disruption of sarcomere and its recovery. Inhibition of the Hippo pathway may help to develop a co-medication strategy for mitigating the risk of sunitinib-induced adverse cardiac events.
Left atrial wall thickness and its relationship with reconnection after pulmonary vein isolation in patients with atrial fibrillation evaluated using a three-dimensional wall thickness map
Authors: Oh Seil , Joo Yoon Ha , Lee Euijae , Lee So-Ryoung , Cha Myung-Jin , Choi Eue-Keun , Lee Jung Chan , Lee Whal 
Published: October 2021

Abstract
Background
The major cause of recurrence after pulmonary vein (PV) isolation for atrial fibrillation (AF) is PV reconnection, and thicker wall could be associated with reconnection.

Objectives
This study aimed to evaluate the wall thickness of the PV antrum in reconnection sites using a three-dimensional (3D) wall thickness map.

Methods
A total of 91 patients who underwent a second ablation procedure due to AF recurrence were evaluated. The locations of the PV reconnection sites were confirmed in electroanatomical maps. A 3D atrial wall thickness (AWT) map was created using computed tomography scan data. The AWT values of the ablation lines of the index procedure were graded in each segment of the PV antrum: grade 1, 0.5 < AWT ≤ 1.0 mm; grade 2, 1.0 < AWT ≤ 1.5 mm; grade 3, 1.5 < AWT ≤ 2.0 mm; grade 4, 2.0 < AWT ≤ 2.5 mm; grade 5, AWT > 2.5 mm.

Results
A total of 281 PV reconnection sites among 1256 segments of the PV antrum in 79 patients were detected. The average AWT grades were 2.7 ± 1.0 and 2.2 ± 1.0 in the reconnected and non-reconnected segments, respectively (P < 0.01). Higher AWT grades were observed in the reconnected superior segments of the left superior PV, carina and inferior segments of the left inferior PV, superior and posterior segments of the right superior PV, and posterior and inferior segments of the right inferior PV.

Conclusion
The reconnected segments of the PV antrum showed thicker myocardium than the non-reconnected ones in patients with recurrent AF after catheter ablation. A wall thickness map for PV isolation could be considered for customized ablation in order to reduce PV reconnection.
A clade of telosma mosaic virus from Thailand is undergoing geographical expansion and genetic differentiation in passionfruit of Vietnam and China
Authors: Yu Chaowei , Lian Qin , Lin Huihuang , Chen Lei , Lu Yizhong , Zhai Yingying , Han Xing , Du Zhenguo , Gao Fangluan , Wu Zujian 
Published: October 2021

AbstractPassionfruit (Passiflora edulis) is widely cultivated in tropical and subtropical regions around the world. Several viruses of the genus Potyvirus pose serious threat to passion fruit production. The origin, dispersal and evolution of these potyviruses, however, are poorly understood. Here, we investigated the genetic structure of telosma mosaic virus (TelMV), a potyvirus that infects passionfruit in East and Southeast Asia, after a survey of its incidence in passionfruit plants of China. The phylogeny inferred from 140 nucleotide sequences of the coat protein (CP) gene of TelMV, including 96 determined in this study, separated this virus into 4 clades. TelMV isolates from passionfruit were placed into Clade 1–3, while those from other plant species into Clade 4. Interestingly, TelMV isolates of passionfruit from Thailand were found in all the three clades of Clade 1–3, but those from China and Vietnam were found exclusively in Clade 1. Nevertheless, TelMV isolates within Clade 1 tended to cluster according to their geographical origin. Geographical populations from Thailand, Taiwan and Hainan islands of China showed significant genetic differences with one another and with those from Guangxi, Fujian, Guangdong, Yunnan and Jiangsu provinces of China. Altogether, these data suggest that several distinct TelMV clades had arisen from the passionfruit of Thailand, but only one of which was dispersed. In expanding its distribution, this clade of TelMV has undergone geography-associated evolution. Further studies on this hypothesis may shed new insights into mechanisms underlying the emergence of potyviral diseases in passionfruit plants.
Anxiety and depression in the elderly due to COVID-19 pandemic: a pilot study
Authors: Das Subhash , Arun Priti , Rohilla Ravi , Parashar Kantadorshi , Roy Aratrika 
Published: October 2021

Abstract
Background
The elderly are a vulnerable section of the population who are prone to physical, mental, social, and economic deprivation. The effect of COVID-19 had a worldwide impact on all age groups, with a particularly higher mortality and morbidity rate among the elderly population. The present study was undertaken to know about the psychological morbidity in the geriatric population during the period of the COVID-19 pandemic. The study was cross-sectional and was done through a telephonic survey. Eligible elderly subjects were contacted telephonically, and the Geriatric Anxiety Scale and the Geriatric Depression Scale were administered. To evaluate the functional ability of elderly subjects, the Everyday Abilities Scale for India (EASI) scale was administered. For the telephonic survey, verbal consent was sought.

Results
A total of 92 elderly subjects were included. Male outnumbered the females with a ratio of 1.8:1. Spouse and children were primary caregivers in 83.7% of the subjects. 90.2% were married, and 66.3% had earned a graduate/professional level of education. Chronic illness was present in 50% of subjects. The most common co-morbidities were hypertension (27.2%) and diabetes (21.7%). The proportion of elderly with anxiety and depression was 8.7% and 15.2% respectively.

Conclusion
The elderly showed lower levels of anxiety and depression. Higher resilience among the elderly and good family support may be the reasons for such an unexpected finding. However, more studies are required to validate the findings of the current study.
Participatory eco-landscape design: the case of NRIAG eco-park in Helwan, Egypt
Authors: Okasha Alia Sameh , Mekkawy Asmaa Aly El 
Published: October 2021

AbstractAs cities get more crowded and polluted, eco-landscape design gains increasing attention. Open spaces play a vital role in healing the natural environment as well as the physical and mental health of the citizens. This paper presents an exploratory eco-park design project in Helwan, Egypt. The project focuses on the opportunity of integrating marginalised natural environments, such as Wadis (dry streams), with the urban fabric through Eco-landscape design. The current work explores the complex environment, characterised by detailed multidisciplinary data, which requires multi-layer analysis. The discussion evaluates the tremendous effect of integrating the participatory qualitative method with other analytical and digital tools, such as modelling and Geographic Information Systems (GIS), to deduce scientific details and activities in the preliminary phases of zoning plans. This results in a constructive framework for merging these multi-methods and tools within the participatory eco-landscape design process. In addition, the conclusion highlights the peculiarity of the eco-landscape design and practice in the current Egyptian situation in a broad sense.