bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semantic segmentation of plant roots from RGB (mini-) rhizotron images—generalisation potential and false positives of established methods and advanced deep-learning models
Authors: Baykalov Pavel , Bussmann Bart , Nair Richard , Smith Abraham George , Bodner Gernot , Hadar Ofer , Lazarovitch Naftali , Rewald Boris 
Published: November 2023

Abstract
Background
Manual analysis of (mini-)rhizotron (MR) images is tedious. Several methods have been proposed for semantic root segmentation based on homogeneous, single-source MR datasets. Recent advances in deep learning (DL) have enabled automated feature extraction, but comparisons of segmentation accuracy, false positives and transferability are virtually lacking. Here we compare six state-of-the-art methods and propose two improved DL models for semantic root segmentation using a large MR dataset with and without augmented data. We determine the performance of the methods on a homogeneous maize dataset, and a mixed dataset of > 8 species (mixtures), 6 soil types and 4 imaging systems. The generalisation potential of the derived DL models is determined on a distinct, unseen dataset.

Results
The best performance was achieved by the U-Net models; the more complex the encoder the better the accuracy and generalisation of the model. The heterogeneous mixed MR dataset was a particularly challenging for the non-U-Net techniques. Data augmentation enhanced model performance. We demonstrated the improved performance of deep meta-architectures and feature extractors, and a reduction in the number of false positives.

Conclusions
Although correction factors are still required to match human labelled root lengths, neural network architectures greatly reduce the time required to compute the root length. The more complex architectures illustrate how future improvements in root segmentation within MR images can be achieved, particularly reaching higher segmentation accuracies and model generalisation when analysing real-world datasets with artefacts—limiting the need for model retraining.
Incidence and survival of transthyretin amyloid cardiomyopathy from a French nationwide study of in- and out-patient databases
Authors: Damy Thibaud , Bourel Guillaume , Slama Michel , Algalarrondo Vincent , Lairez Olivier , Fournier Pauline , Costa Jérôme , Pelcot Françoise , Farrugia Agnès , Zaleski Isabelle Durand , Lilliu Hervé , Rault Caroline , Bartoli Mathilde , Fievez Stéphane , Granghaud Anna , Rudant Jeremie , Coste Agathe , Cosson Charlotte Noirot , Squara Pierre-Alexandre , Narbeburu Marion , De Neuville Bertrand , Charron Philippe 
Published: November 2023

Abstract
Background
Precise data about ATTR-CM incidence rates at national level are scarce. Consequently, this study aimed to estimate the annual incidence and survival of transthyretin amyloid cardiomyopathy (ATTR-CM) in France between 2011 and 2019 using real world data. We used the French nationwide exhaustive data (SNDS database) gathering in- and out-patient claims. As there is no specific ICD-10 marker code for ATTR-CM, diagnosis required both amyloidosis (identified by E85. ICD-10 code or a tafamidis meglumine delivery) and a cardiovascular condition (identified by ICD-10 or medical procedure codes related to either heart failure, arrhythmias, conduction disorders or cardiomyopathies), not necessarily reported at the same visit. Patients with probable AL-form of amyloidosis or probable AA-form of amyloidosis were excluded.

Results
Between 2011 and 2019, 8,950 patients with incident ATTR-CM were identified. Incidence rates increased from 0.6 / 100,000 person-years in 2011 to 3.6 / 100,000 person-years in 2019 (p < 0.001), reaching 2377 new cases in 2019. Sex ratios (M/F) increased from 1.52 in 2011 to 2.23 in 2019. In 2019, median age at diagnosis was 84.0 years (85.5 for women and 83.5 for men). Median survival after diagnosis was 41.9 months (95% CI [39.6, 44.1]).

Conclusions
This is the first estimate of nationwide ATTR-CM incidence in France using comprehensive real-world databases. We observed an increased incidence over the study period, consistent with an improvement in ATTR-CM diagnosis in recent years.
Employment, occupation, and income in adults with neurofibromatosis 1 in Denmark: a population- and register-based cohort study
Authors: Kenborg Line , Frederiksen Line E. , Galanakis Michael , Doser Karoline , Nielsen Thomas T. , Doherty Mia Aagaard , Hove Hanne , Østergaard John R. , Handrup Mette M. , Ejerskov Cecilie , Mulvihill John J. , Winther Jeanette F. 
Published: November 2023

Abstract
Background
Little is known about employment status, occupation, and disposable income in adults with NF1.

Methods
From the Danish National Patient Registry and database of two national Centers for Rare Diseases, we identified 1469 adults with NF1, who were matched to 11,991 randomly selected population comparisons on sex and birth year and month. Annual information on employment, occupation and disposable income was ascertained from national registries in 1980–2019.

Results
Adults with NF1 had a lower odds ratio (OR) for employment [OR 0.71, 95% confidence interval (CI) 0.61–0.83] and higher OR for health-related unemployment (OR 2.94, 95% CI 2.16–3.96) at age 30 years than population comparisons, which persisted at age 40 and 50 years. Somatic diagnoses were associated with a higher OR for health-related unemployment in adults with NF1 than in the population comparisons. Adults with NF1 had a slightly lower disposable income, with a 14% (0.82–0.89) reduction observed among the youngest birth cohort. Furthermore, adults with NF1 were less likely to be in a high skilled occupation at ages 30, 40 and 50 years.

Conclusion
Adults with NF1 have a lower employment rate, which was mainly due to health-related reasons and a slightly lower disposable income than adults without NF1. Thus, anticipation guidance for employment should be part of the management of NF1 families.
The political economy of expedience: examining perspectives on military support to Sierra Leone’s Ebola response
Authors: Boland Samuel T. , Balabanova Dina , Mayhew Susannah 
Published: November 2023

AbstractThe 2013–2016 West Africa Ebola Epidemic is the largest outbreak of Ebola in history. By September, 2014 the outbreak was worsening significantly, and the international president of Médecins Sans Frontières called for military assistance. In Sierra Leone, the British and Sierra Leonean militaries intervened. They quickly established a National Ebola Response Centre and a constituent network of District Ebola Response Centres. Thereafter, these inherently militarised centres are where almost all Ebola response activities were coordinated. In order to examine perspectives on the nature of the militaries’ intervention, 110 semi-structured qualitative interviews were conducted and analysed. Military support to Sierra Leone’s Ebola response was felt by most respondents to be a valuable contribution to the overall effort to contain the outbreak, especially in light of the perceived weakness of the Ministry of Health and Sanitation to effectively do so. However, a smaller number of respondents emphasised that the military deployments facilitated various structural harms, including for how the perceived exclusion of public institutions (as above) and other local actors from Ebola response decision making was felt to prevent capacity building, and in turn, to limit resilience to future crises. The concurrent provision of life-saving assistance and rendering of structural harm resulting from the militaries’ intervention is ultimately found to be part of a vicious cycle, which this article conceptualises as the ‘political economy of expedience’, a paradox that should be considered inherent in any militarised intervention during humanitarian and public health crises.
Effect on capillary refill time of volume expansion and increase of the norepinephrine dose in patients with septic shock
Authors: Fage Nicolas , Moretto Francesca , Rosalba Daniela , Shi Rui , Lai Christopher , Teboul Jean-Louis , Monnet Xavier 
Published: November 2023

Abstract
Background
Capillary refill time (CRT) has been suggested as a variable to follow during the course of septic shock. We systematically investigated the effects on CRT of volume expansion and norepinephrine.

Methods
In 69 septic shock patients, we recorded mean arterial pressure (MAP), cardiac index (CI), and 5 consecutive CRT measurements (video method, standardized pressure applied on the fingertip) before and after a 500-mL saline infusion in 33 patients and before and after an increase of the norepinephrine dose in 36 different patients. Fluid responders were defined by an increase in CI ≥ 15%, and norepinephrine responders by an increase in MAP ≥ 15%.

Results
The least significant change of CRT was 23%, so that changes in CRT were considered significant if larger than 23%. With volume expansion, CRT remained unchanged on average in patients with baseline CRT < 3 s (n = 7) and in all but one patient with baseline CRT ≥ 3 s in whom fluid increased CI < 15% (n = 13 “fluid non-responders”). In fluid responders with baseline CRT ≥ 3 s (n = 13), CRT decreased in 8 patients and remained unchanged in the others, exhibiting a dissociation between CI and CRT responses. The proportion of patients included > 24 h after starting norepinephrine was higher in patients with such a dissociation than in the other ones (60% vs. 0%, respectively). Norepinephrine did not change CRT significantly (except in one patient) if baseline CRT was ≥ 3 s and the increase in MAP < 15% (n = 6). In norepinephrine responders with prolonged baseline CRT (n = 11), it increased in 4 patients and remained unchanged in the other ones, which exhibited a dissociation between MAP and CRT responses.

Conclusions
In septic shock patients with prolonged CRT, CRT very rarely improves with treatment when volume expansion increases cardiac output < 15% and increasing norepinephrine increases MAP < 15%. When the effects of fluid infusion on cardiac output and of norepinephrine on MAP are significant, the response of CRT is variable, as it decreases in some patients and remains stable in others which exhibit a dissociation between changes in macrohemodynamic variables and in CRT. In this regard, CRT behaves as a marker of microcirculation.
Trial registration: ClinicalTrial.gov (NCT04870892). Registered January15, 2021. Ethics committee approval CE SRLF 21-25.
The ongoing risk of Leishmania donovani transmission in eastern Nepal: an entomological investigation during the elimination era
Authors: Roy Lalita , Cloots Kristien , Uranw Surendra , Rai Keshav , Bhattarai Narayan R. , Smekens Tom , Hendrickx Rik , Caljon Guy , Hasker Epco , Das Murari L. , Van Bortel Wim 
Published: November 2023

Abstract
Background
Visceral leishmaniasis (VL), a life-threatening neglected tropical disease, is targeted for elimination from Nepal by the year 2026. The national VL elimination program is still confronted with many challenges including the increasingly widespread distribution of the disease over the country, local resurgence and the questionable efficacy of the key vector control activities. In this study, we assessed the status and risk of Leishmania donovani transmission based on entomological indicators including seasonality, natural Leishmania infection rate and feeding behavior of vector sand flies, Phlebotomus argentipes, in three districts that had received disease control interventions in the past several years in the context of the disease elimination effort.

Methods
We selected two epidemiologically contrasting settings in each survey district, one village with and one without reported VL cases in recent years. Adult sand flies were collected using CDC light traps and mouth aspirators in each village for 12 consecutive months from July 2017 to June 2018. Leishmania infection was assessed in gravid sand flies targeting the small-subunit ribosomal RNA gene of the parasite (SSU-rRNA) and further sequenced for species identification. A segment (~ 350 bp) of the vertebrate cytochrome b (cytb) gene was amplified from blood-fed P. argentipes from dwellings shared by both humans and cattle and sequenced to identify the preferred host.

Results
Vector abundance varied among districts and village types and peaks were observed in June, July and September to November. The estimated Leishmania infection rate in vector sand flies was 2.2% (1.1%–3.7% at 95% credible interval) and 0.6% (0.2%–1.3% at 95% credible interval) in VL and non-VL villages respectively. The common source of blood meal was humans in both VL (52.7%) and non-VL (74.2%) villages followed by cattle.

Conclusions
Our findings highlight the risk of ongoing L. donovani transmission not only in villages with VL cases but also in villages not reporting the presence of the disease over the past several years within the districts having disease elimination efforts, emphasize the remaining threats of VL re-emergence and inform the national program for critical evaluation of disease elimination strategies in Nepal.

Graphical Abstract﻿
Cell fusing agent virus isolated from Aag2 cells does not vertically transmit in Aedes aegypti via artificial infection
Authors: Zhou Ningxin , Huang Enjiong , Guo Xiaoxia , Xiong Yiping , Xie Jingwen , Cai Tong , Du Yutong , Wu Qixing , Guo Sihan , Han Wanrong , Zhang Hengduan , Xing Dan , Zhao Tongyan , Jiang Yuting 
Published: November 2023

Abstract
Background
Cell fusing agent virus (CFAV) was the first insect-specific virus to be characterized, and has been reported to negatively influence the growth of arboviruses such as dengue, Zika, and La Cross, making it a promising biocontrol agent for mosquito-borne disease prevention. Aedes aegypti Aag2 cells were naturally infected with CFAV. However, the ability of this virus to stably colonize an Ae. aegypti population via artificial infection and how it influences the vector competence of this mosquito have yet to be demonstrated.

Methods
CFAV used in this study was harvested from Aag2 cells and its complete genome sequence was obtained by polymerase chain reaction and rapid amplification of complementary DNA ends, followed by Sanger sequencing. Phylogenetic analysis of newly identified CFAV sequences and other sequences retrieved from GenBank was performed. CFAV stock was inoculated into Ae. aegypti by intrathoracic injection, the survival of parental mosquitoes was monitored and CFAV copies in the whole bodies, ovaries, and carcasses of the injected F0 generation and in the whole bodies of the F1 generation on different days were examined by reverse transcription-quantitative polymerase chain reaction.

Results
The virus harvested from Aag2 cells comprised a mixture of three CFAV strains. All genome sequences of CFAV derived from Aag2 cells clustered into one clade but were far from those isolated or identified from Ae. aegypti. Aag2-derived CFAV efficiently replicated in the mosquito body and did not attenuate the survival of Ae. aegypti. However, the viral load in the ovarian tissues was much lower than that in other tissues and the virus could not passage to the offspring by vertical transmission.

Conclusions
The results of this study demonstrate that Aag2-derived CFAV was not vertically transmitted in Ae. aegypti and provide valuable information on the colonization of mosquitoes by this virus.

Graphical abstract
Genetic hypogonadal mouse model reveals niche-specific influence of reproductive axis and sex on intestinal microbial communities
Authors: Sisk-Hackworth Laura , Brown Jada , Sau Lillian , Levine Andrew A. , Tam Lai Ying Ivy , Ramesh Aishwarya , Shah Reeya S. , Kelley-Thackray Evelyn T. , Wang Sophia , Nguyen Anita , Kelley Scott T. , Thackray Varykina G. 
Published: November 2023

AbstractBackgroundThe gut microbiome has been linked to many diseases with sex bias including autoimmune, metabolic, neurological, and reproductive disorders. While numerous studies report sex differences in fecal microbial communities, the role of the reproductive axis in this differentiation is unclear and it is unknown how sex differentiation affects microbial diversity in specific regions of the small and large intestine.MethodsWe used a genetic hypogonadal mouse model that does not produce sex steroids or go through puberty to investigate how sex and the reproductive axis impact bacterial diversity within the intestine. Using 16S rRNA gene sequencing, we analyzed alpha and beta diversity and taxonomic composition of fecal and intestinal communities from the lumen and mucosa of the duodenum, ileum, and cecum from adult female (n = 20) and male (n = 20) wild-type mice and female (n = 17) and male (n = 20) hypogonadal mice.ResultsBoth sex and reproductive axis inactivation altered bacterial composition in an intestinal section and niche-specific manner. Hypogonadism was significantly associated with bacteria from theBacteroidaceae,Eggerthellaceae,Muribaculaceae, andRikenellaceaefamilies,which have genes for bile acid metabolism and mucin degradation. Microbial balances between males and females and between hypogonadal and wild-type mice were also intestinal section-specific. In addition, we identified 3 bacterial genera (EscherichiaShigella,Lachnoclostridium, andEggerthellaceaegenus) with higher abundance in wild-type female mice throughout the intestinal tract compared to both wild-type male and hypogonadal female mice, indicating that activation of the reproductive axis leads to female-specific differentiation of the gut microbiome. Our results also implicated factors independent of the reproductive axis (i.e., sex chromosomes) in shaping sex differences in intestinal communities. Additionally, our detailed profile of intestinal communities showed that fecal samples do not reflect bacterial diversity in the small intestine.ConclusionsOur results indicate that sex differences in the gut microbiome are intestinal niche-specific and that sampling feces or the large intestine may miss significant sex effects in the small intestine. These results strongly support the need to consider both sex and reproductive status when studying the gut microbiome and while developing microbial-based therapies.
Supply-side factors influencing demand for facility-based delivery in Tanzania: a multilevel analysis
Authors: Binyaruka Peter , Foss Anna , Alibrahim Abdullah , Mziray Nicholaus , Cassidy Rachel , Borghi Josephine 
Published: November 2023

Abstract
Background
Improving access to facility-based delivery care has the potential to reduce maternal and newborn deaths across settings. Yet, the access to a health facility for childbirth remains low especially in low-income settings. To inform evidence-based interventions, more evidence is needed especially accounting for demand- and supply-side factors influencing access to facility-based delivery care. We aimed to fill this knowledge gap using data from Tanzania.

Methods
We used data from a cross-sectional survey (conducted in January 2012) of 150 health facilities, 1494 patients and 2846 households with women who had given births in the last 12 months before the survey across 11 districts in three regions in Tanzania. The main outcome was the place of delivery (giving birth in a health facility or otherwise), while explanatory variables were measured at the individual woman and facility level. Given the hierarchical structure of the data and variance in demand across facilities, we used a multilevel mixed-effect logistic regression to explore the determinants of facility-based delivery care.

Results
Eighty-six percent of 2846 women gave birth in a health facility. Demand for facility-based delivery care was influenced more by demand-side factors (76%) than supply-side factors (24%). On demand-side factors, facility births were more common among women who were educated, Muslim, wealthier, with their first childbirth, and those who had at least four antenatal care visits. On supply-side factors, facility births were more common in facilities offering outreach services, longer consultation times and higher interpersonal quality. In contrast, facilities with longer average waiting times, longer travel times and higher chances of charging delivery fees had few facility births.

Conclusions
Policy responses should aim for strategies to improve demand like health education to raise awareness towards care seeking among less educated groups and those with higher parity, reduce financial barriers to access (including time costs to reach and access care), and policy interventions to enhance interpersonal quality in service provision.
Safety and efficacy of human ESC-derived corneal endothelial cells for corneal endothelial dysfunction
Authors: Yu Juan , Yu Nianye , Tian Yao , Fang Yifan , An Bin , Feng Guihai , Wu Jun , Wang Liu , Hao Jie , Wang Liqiang , Zhou Qi , Li Wei , Wang Yukai , Hu Baoyang 
Published: November 2023

Abstract
Background
Research on human pluripotent stem cells (hPSCs) has shown tremendous progress in cell-based regenerative medicine. Corneal endothelial dysfunction is associated with the loss and degeneration of corneal endothelial cells (CECs), rendering cell replacement a promising therapeutic strategy. However, comprehensive preclinical assessments of hPSC-derived CECs for this cell therapy remain a challenge.

Results
Here we defined an adapted differentiation protocol to generate induced corneal endothelial cells (iCECs) consistently and efficiently from clinical-grade human embryonic stem cells (hESCs) with xeno-free medium and manufactured cryopreserved iCECs. Cells express high levels of typical CECs markers and exhibit transendothelial potential properties in vitro typical of iCECs. After rigorous quality control measures, cells meeting all release criteria were available for in vivo studies. We found that there was no overgrowth or tumorigenicity of grafts in immunodeficient mice. After grafting into rabbit models, the surviving iCECs ameliorated edema and recovered corneal opacity.

Conclusions
Our work provides an efficient approach for generating iCECs and demonstrates the safety and efficacy of iCECs in disease modeling. Therefore, clinical-grade iCECs are a reliable source for future clinical treatment of corneal endothelial dysfunction.