bluuebunny/crossref_metadata_2025_split huggingface dataset:
PoET: automated approach for measuring pore edge tension in giant unilamellar vesicles
Authors: Leomil Fernanda S C , Zoccoler Marcelo , Dimova Rumiana , Riske Karin A 
Published: November 2021

ABSTRACT

Motivation
A reliable characterization of the membrane pore edge tension of single giant unilamellar vesicles (GUVs) requires the measurement of micrometer sized pores in hundreds to thousands of images. When manually performed, this procedure has shown to be extremely time-consuming and to generate inconsistent results among different users and imaging systems. A user-friendly software for such analysis allowing quick processing and generation of reproducible data had not yet been reported.

Results
We have developed a software (PoET) for automatic pore edge tension measurements on GUVs. The required image processing steps and the characterization of the pore dynamics are performed automatically within the software and its use allowed for a 30-fold reduction in the analysis time. We demonstrate the applicability of the software by comparing the pore edge tension of GUVs of different membrane compositions and surface charges. The approach was applied to electroporated GUVs but is applicable to other means of pore formation.

Availability and implementation
The complete software is implemented in Python and available for Windows at https://dx.doi.org/10.17617/3.7h.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Antisense therapies in neurological diseases
Authors: Brunet de Courssou Jean-Baptiste , Durr Alexandra , Adams David , Corvol Jean-Christophe , Mariani Louise-Laure 
Published: November 2021

Abstract
Advances in targeted regulation of gene expression allowed new therapeutic approaches for monogenic neurological diseases. Molecular diagnosis has paved the way to personalized medicine targeting the pathogenic roots: DNA or its RNA transcript. These antisense therapies rely on modified nucleotides sequences (single-strand DNA or RNA, both belonging to the antisense oligonucleotides family, or double-strand interfering RNA) to act specifically on pathogenic target nucleic acids, thanks to complementary base pairing. Depending on the type of molecule, chemical modifications and target, base pairing will lead alternatively to splicing modifications of primary transcript RNA or transient messenger RNA degradation or non-translation. The key to success for neurodegenerative diseases also depends on the ability to reach target cells. The most advanced antisense therapies under development in neurological disorders are presented here, at the clinical stage of development, either at phase 3 or market authorization stage, such as in spinal amyotrophy, Duchenne muscular dystrophy, transthyretin-related hereditary amyloidosis, porphyria and amyotrophic lateral sclerosis; or in earlier clinical phase 1 B, for Huntington's disease, synucleinopathies and tauopathies. We also discuss antisense therapies at the preclinical stage, such as in some tauopathies, spinocerebellar ataxias or other rare neurological disorders. Each subtype of antisense therapy, antisense oligonucleotides or interfering RNA, has proved target engagement or even clinical efficacy in patients; undisputable recent advances for severe and previously untreatable neurological disorders. Antisense therapies show great promise, but many unknowns remain. Expanding the initial successes achieved in orphan or rare diseases to other disorders will be the next challenge, as shown by the recent failure in Huntington disease or due to long-term preclinical toxicity in multiple system atrophy and cystic fibrosis. This will be critical in the perspective of new planned applications to premanifest mutation carriers, or other non-genetic degenerative disorders such as multiple system atrophy or Parkinson disease.
Quantification of visceral perfusion and impact of femoral cannulation: in vitro model of aortic dissection
Authors: Heo Woon , Lee Gyu-Han , Kim Tae-Hoon , Lee Youngjin , Huh Hyungkyu , Ha Hojin , Song Suk-Won , Yoo Kyung-Jong 
Published: November 2021

Abstract

OBJECTIVES
We aimed to simulate blood flow at an aortic dissection in an in vitro vascular model and assess the impact of the cannulation method on visceral perfusion.

METHODS
An aortic-dissection model with an acrylic aortic wall and silicone intimal flap was developed to study visceral perfusion under various cannulation conditions. The primary tear was placed in the proximal descending aorta and the re-entry site in the left common iliac artery. A cardiovascular pump was used to reproduce a normal pulsatile aortic flow and a steady cannulation flow. Axillary and axillary plus femoral cannulation were compared at flow rates of 3–7 l/min. Haemodynamics were analysed by using four-dimensional flow magnetic resonance imaging.

RESULTS
Axillary cannulation (AC) was found to collapse the true lumen at the coeliac and superior mesentery arteries, while combined axillary and femoral cannulation did not change the size of the true lumen. Combined axillary and femoral cannulation resulted in a larger visceral flow than did AC alone. When axillary plus femoral cannulation was used, the visceral flow increased by 125% at 3 l/min, by 89% at 4 l/min, by 67% at 5 L/min, by 98% at 6 l/min and by 101% at 7 l/min, respectively, compared to those with the AC only.

CONCLUSIONS
Our model was useful to understanding the haemodynamics in aortic dissection. In this specific condition, we confirmed that the intimal flap motion can partially block blood flow to the coeliac and superior mesenteric arteries and that additional femoral cannulation can increase visceral perfusion.
Promoting active transport in rural communities through infrastructural modifications: the PABEM needs assessment tool
Authors: Hofer-Fischanger Kathrin , Tuttner Silvia , Amort Frank M , Helms Katja , Unger Julia , Hödl Josef , Strüver Anke , van Poppel Mireille N M 
Published: November 2021

Summary
The design of the built environment in communities influences active transport and physical activity levels of citizens. Existing instruments for quantitatively assessing built environments were developed for use in urban areas and mainly by experts. Participative assessment of built environment modifications (PABEM) is a needs assessment tool that involves citizens and community decision-makers within a structured process for identifying needed changes to promote walking and cycling in rural areas. This article describes the development of the PABEM process and evaluates its initial use in three rural towns in Austria. PABEM consists of the following seven steps: (i) qualitative interviews; (ii) expert assessment of the built environment; (iii) citizen assessment of the built environment; (iv) social media interaction; (v) household questionnaire; (vi) participatory workshop; and (vii) evaluation and scoring workshop. The main modifications identified as necessary in rural towns were the revitalization of existing walking and cycling facilities and the construction of new barrier-free and safe sidewalks. In addition cycling routes to schools, to public transport facilities and to central public places as well as cleaner and inviting seating, a car-free school environment, speed reduction in town centres, more crosswalks and improved cleanliness in public places were also deemed necessary modifications. PABEM’s provisions to ensure collaborative participation of citizens and local decision-makers fostered a continuous dialogue about the requirements of the built environment, user needs and opportunities for realization throughout the whole process.
Health inequity and social determinants of healthcare utilization in the disadvantaged community of Hong Kong
Authors: Tan Joelle Hwee Inn , Goh Amelia Xin Chun , Yi Huso 
Published: November 2021

Summary
Access to appropriate healthcare among disadvantaged populations in countries with universal healthcare requires a critical understanding of the relationships between poverty, social exclusion and health in the local context. The qualitative study explored the experiences of healthcare utilization in an inner-city impoverished community living in slum conditions in Hong Kong. Interviews with 40 slum residents in one of the poorest neighbourhoods in the city explored the following domains: experience and perceptions of the community, housing conditions, informal social capital and support system, interactions with community workers, and experiences in utilizing social and healthcare services. Framework analysis was conducted to identify local themes under the model of healthcare utilization: approachability, acceptability, availability and accommodation, affordability and appropriateness. Despite the subsidized public healthcare system, multiple barriers were identified. Low literacy of healthcare systems was prevalent. Specifically, structural barriers relating mainly to the availability, accommodation and affordability of health services were salient to impede access to healthcare. The barriers related to healthcare providers primarily stemmed from the interactions of healthcare providers, perceived stigma and the lack of patient-centred care. In addition, poverty-related sociocultural norms and personal beliefs of healthcare were found to be significant barriers to healthcare access. Despite the well-established subsidized public healthcare system, healthcare inequity was evident. Lack of quality healthcare access needs to be addressed by providing social and educational resources that facilitate collective efficacy for healthcare, community engagement from public sectors and person-centred care with healthcare providers.
The process of adapting a sexual health intervention for Black early adolescents: a stakeholder engagement approach
Authors: McCabe K , Hotton A , Loyd A B , Floyd B , Donenberg G , Fletcher F E 
Published: November 2021

Abstract
Young Black women are disproportionately affected by sexually transmitted infections (STIs) and HIV. Notably, few sexual health interventions for Black girls have documented the process of utilizing stakeholder input from the Black community to culturally tailor content. We conducted formative work in Chicago to adapt a mother–daughter HIV/STI prevention intervention originally designed for Black adolescent girls aged 14–18 years to meet the needs of early adolescent girls aged 11–13 years. Our iterative process involved three phases: (i) soliciting feedback from an expert panel and community advisory board; (ii) conducting focus groups with experienced research participants; and (iii) theater testing a new curriculum in the target population. Key findings of this process indicate the importance of sophisticated community engagement strategies to shape research design and program implementation. Findings may be used to inform processes for future adaptation work, especially in sexual health programs for young Black girls and their mothers.
In the Shadow of the Gas Chambers: Social Dynamics and Everyday Life around the Killing Center at Bełżec (1941–1944)
Authors: Burzlaff Jan 
Published: November 2021

ABSTRACT
The Nazis’ killing center at Bełżec (1941–1944) poses a fundamental challenge to Holocaust scholars. How can we write the history of a place that has been obliterated and whose records have been destroyed? Twelve untapped non-Jewish video testimonies provide new insights into aspects of daily life around Bełżec. This essay argues that strong social ties dictated who lived and died in the shadow of the gas chambers. The least well-known killing center radicalized social relations in the village, inflected by class, age, and gender. Ultimately, this essay seeks to pave the way for a more systematic approach to the much-debated notion of “social dynamics,” and encourages Holocaust scholars to tackle more directly non-Jewish testimonies.
Parent–child relationship quality and child psychological adjustment in families created using egg donation: children’s perspectives at age 5 years
Authors: Imrie S , Lysons J , Jadva V , Shaw K , Grimmel J , Golombok S 
Published: November 2021

Abstract

STUDY QUESTION
What are children’s perspectives of the quality of their relationships with their parents and their own psychological well-being in families created using egg donation?

SUMMARY ANSWER
Children’s scores indicated good parent–child relationship quality and high levels of psychological well-being, with children in families created using egg donation rating their relationships with their mothers as higher in warmth/enjoyment than children in a comparison group of families created using IVF.

WHAT IS KNOWN ALREADY
Little is known about how children in families created through egg donation view their family relationships and their own psychological well-being. Research with 7-and-10-year-olds in anonymous egg donation families has indicated good parent–child relationship quality from children’s perspectives, but studies have not involved younger children or those conceived following identity-release egg donation.

STUDY DESIGN, SIZE, DURATION
This study included 50 children who had been born through egg donation and a comparison group of 43 children conceived through IVF with the parents’ own gametes. Data were collected between April 2018 and December 2019. The sample forms part of a larger longitudinal study examining family functioning in families created through fertility treatment.

PARTICIPANTS/MATERIALS, SETTING, METHODS
Children were aged 5 years old and had been born into families with different-sex couple parents. All families were visited at home. Children were administered the Berkeley Puppet Interview, a standardized assessment of parent–child relationship quality and psychological well-being.

MAIN RESULTS AND THE ROLE OF CHANCE
Children in egg donation families rated their relationships with their mothers as higher in warmth and enjoyment than did children in IVF families. No differences were found between the two family types in children’s ratings of the father–child relationship, or in children’s ratings of their own psychological well-being.

LIMITATIONS, REASONS FOR CAUTION
It is possible that children who did not consent to take part in the research had less positive perceptions of their family and themselves than children who participated.

WIDER IMPLICATIONS OF THE FINDINGS
The findings are relevant to UK clinics offering identity-release egg donation, to parents who have used egg donation to create their family and to individuals and couples considering their fertility treatment options. That children in egg donation families were more similar than different to children in IVF families in their self-concept and perception of their family relationships should prove reassuring.

STUDY FUNDING/COMPETING INTEREST(S)
This research was supported by a Wellcome Trust Collaborative Award [208013/Z/17]. The authors have no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER
N/A.
Assay for the peptide:N-glycanase/NGLY1 and disease-specific biomarkers for diagnosing NGLY1 deficiency
Authors: Hirayama Hiroto , Suzuki Tadashi 
Published: November 2021

Abstract
Cytosolic peptide:N-glycanase (NGLY1 in mammals), a highly conserved enzyme in eukaryotes, catalyses the deglycosylation of N-glycans that are attached to glycopeptide/glycoproteins. In 2012, an autosomal recessive disorder related to the NGLY1 gene, which was referred to as NGLY1 deficiency, was reported. Since then, more than 100 patients have been identified. Patients with this disease exhibit various symptoms, including various motor deficits and other neurological problems. Effective therapeutic treatments for this disease, however, have not been established. Most recently, it was demonstrated that the intracerebroventricular administration of an adeno-associated virus 9 vector expressing human NGLY1 during the weaning period allowed some motor functions to be recovered in Ngly1−/− rats. This observation led us to hypothesize that a therapeutic intervention for improving these motor deficits or other neurological symptoms found in the patients might be possible. To achieve this, it is critical to establish robust and facile methods for assaying NGLY1 activity in biological samples, for the early diagnosis and evaluation of the therapeutic efficacy for the treatment of NGLY1 deficiency. In this mini review, we summarize progress made in the development of various assay methods for NGLY1 activity, as well as a recent progress in the identification of NGLY1 deficiency-specific biomarkers.
Length of Stay per Total Body Surface Area Burn Relative to Mechanism: A Pediatric Injury Quality Improvement Collaborative Study
Authors: Patterson Kelli N , Onwuka Amanda , Horvath Kyle Z , Fabia Renata , Giles Sheila , Marx Daniel , Aguayo Pablo , Ziegfeld Susan , Garcia Alejandro , Stewart F Dylan , Fritzeen Jennifer , Burd Randall S , Vitale Lisa , Klein Justin , Thakkar Rajan K 
Published: November 2021

Abstract
Studies on length of stay (LOS) per total body surface area (TBSA) burn in pediatric patients are often limited to single institutions and are grouped in ranges of TBSA burn which lacks specific detail to counsel patients and families. A LOS to TBSA burn ratio of 1 has been widely accepted but not validated with multi-institution data. The objective of this study is to describe the current relationship of LOS per TBSA burn and LOS per TBSA burn relative to burn mechanism with the use of multi-institutional data. Data from the Pediatric Injury Quality Improvement Collaborative (PIQIC) were obtained for patients across five pediatric burn centers from July 2018 to September 2020. LOS per TBSA burn ratios were calculated. Descriptive statistics and generalized linear regression which modeled characteristics associated with LOS per TBSA ratio are described. Among the 1267 pediatric burn patients, the most common mechanism was scald (64%), followed by contact (17%) and flame (13%). The average LOS/TBSA burn ratio across all cases was 1.2 (SD = 2.1). In adjusted models, scald burns and chemical burns had similar LOS/TBSA burn ratios of 0.8 and 0.9, respectively, whereas all other burns had a significantly higher LOS/TBSA burn ratio (p&lt;0.0001). LOS/TBSA burn ratios were similar across races, although Hispanics had a slightly higher ratio at 1.4 days. These data establish a multi-institution LOS per TBSA ratio across PIQIC centers and demonstrate a significant variation in the LOS per TBSA burn relative to the burn mechanism sustained.
Suppression of uterine and placental ferroptosis by N-acetylcysteine in a rat model of polycystic ovary syndrome
Authors: Hu Min , Zhang Yuehui , Ma Shuting , Li Juanli , Wang Xu , Liang Mengmeng , Sferruzzi-Perri Amanda Nancy , Wu Xiaoke , Ma Hongxia , Brännström Mats , Shao Linus R , Billig Håkan 
Published: November 2021

Abstract
The mechanisms that link hyperandrogenism and insulin (INS) resistance (HAIR) to the increased miscarriage rate in women with polycystic ovary syndrome (PCOS) remain elusive. Previous studies demonstrate that increased uterine and placental ferroptosis is associated with oxidative stress-induced fetal loss in a pre-clinical PCOS-like rat model. Here, we investigated the efficacy and molecular mechanism of action of the antioxidant N-acetylcysteine (NAC) in reversing gravid uterine and placental ferroptosis in pregnant rats exposed to 5α-dihydrotestosterone (DHT) and INS. Molecular and histological analyses showed that NAC attenuated DHT and INS-induced uterine ferroptosis, including dose-dependent increases in anti-ferroptosis gene content. Changes in other molecular factors after NAC treatment were also observed in the placenta exposed to DHT and INS, such as increased glutathione peroxidase 4 protein level. Furthermore, increased apoptosis-inducing factor mitochondria-associated 2 mRNA expression was seen in the placenta but not in the uterus. Additionally, NAC was not sufficient to rescue DHT + INS-induced mitochondria-morphological abnormalities in the uterus, whereas the same treatment partially reversed such abnormalities in the placenta. Finally, we demonstrated that NAC selectively normalized uterine leukemia inhibitory factor, osteopontin/secreted phosphoprotein 1, progesterone receptor, homeobox A11 mRNA expression and placental estrogen-related receptor beta and trophoblast-specific protein alpha mRNA expression. Collectively, our data provide insight into how NAC exerts beneficial effects on differentially attenuating gravid uterine and placental ferroptosis in a PCOS-like rat model with fetal loss. These results indicate that exogenous administration of NAC represents a potential therapeutic strategy in the treatment of HAIR-induced uterine and placental dysfunction.
Inflammation and physical dysfunction: responses to moderate intensity exercise in chronic kidney disease
Authors: Watson Emma L , Baker Luke A , Wilkinson Tom J , Gould Doug W , Xenophontos Soteris , Graham-Brown Matthew , Major Rupert W , Ashford Robert U , Viana Joao L , Smith Alice C 
Published: November 2021

ABSTRACT

Background
People with chronic kidney disease (CKD) experience skeletal muscle wasting, reduced levels of physical function and performance, and chronic systemic inflammation. While it is known that a relationship exists between inflammation and muscle wasting, the association between inflammation and physical function or performance in CKD has not been well studied. Exercise has anti-inflammatory effects, but little is known regarding the effect of moderate intensity exercise. This study aimed to (i) compare systemic and intramuscular inflammation between CKD stage G3b–5 and non-CKD controls; (ii) establish whether a relationship exists between physical performance, exercise capacity and inflammation in CKD; (iii) determine changes in systemic and intramuscular inflammation following 12 weeks of exercise; and (iv) investigate whether improving inflammatory status via training contributes to improvements in physical performance and muscle mass.

Methods
This is a secondary analysis of previously collected data. CKD patients stages G3b–5 (n = 84, n = 43 males) and non-CKD controls (n = 26, n = 17 males) underwent tests of physical performance, exercise capacity, muscle strength and muscle size. In addition, a subgroup of CKD participants underwent 12 weeks of exercise training, randomized to aerobic (AE, n = 21) or combined (CE, n = 20) training. Plasma and intramuscular inflammation and myostatin were measured at rest and following exercise.

Results
Tumour necrosis factor-α was negatively associated with lower $^{^{^{.}}}{\rm V}$O2Peak (P = 0.01), Rectus femoris-cross sectional area (P = 0.002) and incremental shuttle walk test performance (P &lt; 0.001). Interleukin-6 was negatively associated with sit-to-stand 60 performances (P = 0.006) and hand grip strength (P = 0.001). Unaccustomed exercise created an intramuscular inflammatory response that was attenuated following 12 weeks of training. Exercise training did not reduce systemic inflammation, but AE training did significantly reduce mature myostatin levels (P = 0.02). Changes in inflammation were not associated with changes in physical performance.

Conclusions
Systemic inflammation may contribute to reduced physical function in CKD. Twelve weeks of exercise training was unable to reduce the level of chronic systemic inflammation in these patients, but did reduce plasma myostatin concentrations. Further research is required to further investigate this.