bluuebunny/crossref_metadata_2025_split huggingface dataset:
SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data
Authors: Liu Yunqing , Li Ningshan , Qi Ji , Xu Gang , Zhao Jiayi , Wang Nating , Huang Xiayuan , Jiang Wenhao , Wei Huanhuan , Justet Aurélien , Adams Taylor S. , Homer Robert , Amei Amei , Rosas Ivan O. , Kaminski Naftali , Wang Zuoheng , Yan Xiting 
Published: October 2024

AbstractSpatial barcoding-based transcriptomic (ST) data require deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method to deconvolve ST data using reference single-cell RNA sequencing (scRNA-seq) data. SDePER tackles platform effects between ST and scRNA-seq data, ensuring a linear relationship between them while addressing sparsity and spatial correlations in cell types across capture spots. SDePER estimates cell-type proportions, enabling enhanced resolution tissue mapping by imputing cell-type compositions and gene expressions at unmeasured locations. Applications to simulated data and four real datasets showed SDePER’s superior accuracy and robustness over existing methods.
Why does malaria transmission continue at high levels despite universal vector control? Quantifying persistent malaria transmission by Anopheles funestus in Western Province, Zambia
Authors: Ashton Ruth A. , Chanda Benjamin , Chishya Chama , Muyabe Rayford , Kaniki Tresford , Mambo Patricia , Mwenya Mwansa , Mwaanga Gift , Arnzen Annie , Orange Erica , Saili Kochelani , Banda Yikona Handrinah , Chulu John , Chitoshi Chanda , Kyomuhangi Irene , Miller John , Silumbe Kafula , Hamainza Busiku , Littrell Megan , Yukich Joshua , Kleinschmidt Immo , Chanda Javan , Wagman Joseph , Eisele Thomas P. 
Published: October 2024

AbstractBackgroundSome settings continue to experience a high malaria burden despite scale-up of malaria vector control to high levels of coverage. Characterisation of persistent malaria transmission in the presence of standard control measures, also termed residual malaria transmission, to understand where and when individuals are exposed to vector biting is critical to inform refinement of prevention and control strategies.MethodsSecondary analysis was performed using data collected during a phase III cluster randomized trial of attractive targeted sugar bait stations in Western Province, Zambia. Two seasonal cohorts of children aged 1–14 years were recruited and monitored monthly during the malaria transmission season, concurrent with entomological surveillance using a combination of human landing catch (HLC) and Centres for Disease Control (CDC) light traps at randomly selected households in study clusters. Behavioural data from cohort participants were combined with measuredAnopheles funestuslanding rates and sporozoite positivity to estimate the human behaviour-adjusted entomological inoculation rate (EIR).ResultsBehavioural data from 1237 children over 5456 child-visits in 20 entomology surveillance clusters were linked with hourly landing rates from 8131 femaleAn.funestustrapped by HLC. Among allAn.funestustested by enzyme-linked immunosorbent assay (ELISA), 3.3% were sporozoite-positive. Mean EIR directly measured from HLC was 0.07 infectious bites per person per night (ib/p/n). When accounting for child locations over the evening and night, the mean behaviour-adjusted EIR was 0.02 ib/p/n. Children not sleeping under insecticide-treated nets (ITNs) experienced 13.6 infectious bites per person per 6 month season, 8% of which occurred outdoors, while ITN users received 1.3 infectious bites per person per 6 month season, 86% of which were received outdoors. Sleeping under an ITN can prevent approximately 90% of potentialAn.funestusbites among children.ConclusionsIn this setting ITNs have a high personal protective efficacy owing to peakAn.funestusbiting occurring indoors while most individuals are asleep. However, despite high household possession of ITNs (>90%) and high individual use (>70%), children in this setting experience more than one infectious bite per person per 6 month transmission season, sufficient to maintain high malaria transmission and burden. New tools and strategies are required to reduce the malaria burden in such settings.Graphical Abstract
Changes in work status after cancer diagnosis and their associations with depressive symptoms among cancer survivors: findings from the Korean longitudinal study of ageing
Authors: Lee Da-eun , Kim Yeonjin , Kim Young-mee , Cho Sung-il 
Published: October 2024

Abstract
Purpose
Cancer survivors encounter significant psychological suffering and are prone to develop depressive symptoms. Work contributes to personal fulfillment and social connections, and by doing so, enhances a cancer survivor’s resilience against adversities. However, maintaining employment can be challenging for some cancer survivors. This research aimed to identify the association between changes in work status and depressive symptoms among cancer survivors in South Korea.

Methods
This study used the panel data from the Korean Longitudinal Study of Ageing (KLoSA) and included 199 cancer survivors–799 observations–aged 65 or younger, between 2005 and 2018. Changes in work status consisted of continuous unemployment or employment, quitting a job, and getting a job. We defined depressive symptoms as a CES-D-10 score of 10 or higher and a cut-off of 4 was utilized for sensitivity analysis. Multivariable generalized estimating equation was employed to estimate the odds ratio (OR), adjusting for the number of household members, education level, sex, age, marital status, occupations, cancer treatment, cancer type, catastrophic healthcare expenditure (CHE), and survivorship. Subgroup analysis and interaction between changes in work and cancer types were further explored.

Results
For depressive symptoms, the OR of the continuous unemployment group was 2.27 (95% CI = 1.10–4.69), and the OR of the group that quit a job was 2.20 (95% CI = 1.03–4.72), compared to the continuous employment group. As survivorship increased, the odds of depressive symptoms decreased (OR = 0.94, 95% CI = 0.89–1.00). CHE was associated with depressive symptoms (OR = 2.23, 95% CI = 1.18–4.20). In cancer types with a low tendency to depression, continuous unemployment was associated with depressive symptoms (OR = 3.19, 95% CI = 1.12–9.06). In sensitivity analysis, changes in work, survivorship, and CHE were consistently associated with depressive symptoms.

Conclusions
Cancer survivors who quit a job or continued unemployment were more likely to experience depressive symptoms. The findings of this study imply that assistance for cancer survivors to continue a job or return to employment, including adjustment of workload and hours, may be helpful. Psychological care may be crucial, particularly in the early stage of cancer survivorship. Furthermore, support may be needed to alleviate the burden of healthcare expenditure.
Is informedness the key? An empirical analysis of VET dropouts in Germany
Authors: Herrmann Lisa , Kühn Juliane 
Published: October 2024

AbstractIn 2022, one in four vocational education and training (VET) contracts resulted in premature termination—a potential sign of inefficiency in the training of urgently needed skilled professionals. This study focuses on the level of perceived informedness of trainees and its potential influence on dropout. This includes trainees’ perceived level of information about the characteristics and requirements of an occupation, which may result from various sources of information in the form of social contacts. We draw on theories from the field of career choice and job search to argue that a better level of informedness can reduce uncertainty and enable individuals to make better-informed decisions about their careers. With better informedness, there is a higher probability of finding a suitable match between a trainee and their chosen occupation, ultimately increasing their likelihood of job persistence. This should also lead to a lower probability of dropout among VETs. Using data from the National Educational Panel Study, starting cohort 4, we employed event history analysis. We show that good perceived informedness on the requirements of one’s vocational training and the perception of good school-based vocational preparation reduce the probability of dropping out. In contrast, good informedness about alternative training programs increases dropout risk. We also see that the distinction between closer or more distant groups of people from the social network (strong or weak ties) who provide information about training is not decisive.
Migratory strategies across an ecological barrier: is the answer blowing in the wind?
Authors: Bathrick Rosalyn E. , Johnson James A. , Ruthrauff Daniel R. , Snyder Rebekah , Stager Maria , Senner Nathan R. 
Published: October 2024

Abstract
Background
Ecological barriers can shape the movement strategies of migratory animals that navigate around or across them, creating migratory divides. Wind plays a large role in facilitating aerial migrations and can temporally or spatially change the challenge posed by an ecological barrier, with beneficial winds potentially converting a barrier into a corridor. Here, we explore the role wind plays in shaping initial southbound migration strategy among individuals breeding at two sites along an ecological barrier.

Methods
Using GPS satellite transmitters, we tracked the southbound migrations of Short-billed Dowitchers (Limnodromus griseus caurinus) from two breeding sites in Alaska to nonbreeding sites in coastal Mexico. The breeding sites were positioned in distinct regions along an ecological barrier – the Gulf of Alaska. We investigated potential differences in migratory timing, wind availability, and tailwind support en route across the Gulf of Alaska between individuals breeding at the two sites.

Results
Route choice and arrival timing to wintering sites differed markedly between the two breeding sites: individuals departing from the more westerly site left at the same time as those from further east but crossed the Gulf of Alaska farther west and arrived along the Pacific coast of Mexico an average of 19 days earlier than their counterparts. Dowitchers from both sites departed with slight tailwinds, but once aloft over the Gulf of Alaska, birds from the more westerly site had up to twelve times more tailwind assistance than birds from the more easterly one.

Conclusions
The distinct migration strategies and degree of wind assistance experienced by birds at these two breeding sites demonstrates how differences in wind availability along migratory routes can form the basis for intraspecific variation in migration strategies with potential carryover effects. Future changes in wind regimes may therefore interact with changes in habitat availability to influence migration patterns and migratory bird conservation.
Machine learning based prediction for bulk porosity and static elastic modulus of Yungang Grottoes sandstone
Authors: Zhang Ruoyu , Huang Jizhong , Cheng Yuan , Zhang Yue 
Published: October 2024

Abstract
In this work, four mainstream machine learning (ML) techniques are used to evaluate the bulk porosity and static elastic modulus of weathered Yungang Grottoes sandstone. Datasets are gathered from the experiments, which includes 432 groups effective experimental data including 8 inputs features. bulk porosity and static elastic modulus were considered as outputs to determine the weathering degrees of Yungang Grottoes sandstone. The 4 performance criteria were used to evaluate the ML models. Results demonstrate that the Artificial Neural Network (ANN) is the best-fitted models for estimating the bulk porosity and static elastic modulus compared to Multiple Linear Regression (MLR), Support Vector Regression (SVR), Gaussian Process Regression (GPR). The accuracy of the trained model for static elastic modulus is slightly higher than that of bulk porosity. The GPR and ANN model can accurately predict the bulk porosity and static elastic modulus in training stages. The ANN with multi-hidden layers developed is competent with high degree of precision and generalization ability for bulk porosity and static elastic modulus compared to other selected regression-based ML models (MLR, SVR, and GPR). The coefficient of determinations of ANN in the range of (0.9537–0.9641) during the testing stages is more stable and higher than that of (0.8883–0.9453) other built ML models. The prediction efficiency of pretrained ANN model was well adjusted for the actual and forecast datasets at the training and testing stages, and the error range was no more than 0.7% and 0.15 GPa at both stages of prediction for bulk porosity and static elastic modulus respectively. And the ANN based static elastic modulus prediction model’s error proportions significantly decreased and were confined to a modest range between + 10% and − 10%. The proposed surrogate models are valid for the bulk porosity ranging from 7 to 14% and the static elastic modulus ranging from 0.7 to 1.4 Gpa, which can be utilized for the accurate and fast prediction of the weathering degrees of Yungang Grottoes sandstone.
Impact of environmental change on the indigenous belief system of the Bayso Community of Gidicho Island, Southern Ethiopia
Authors: Fekadu Eshetu , Hebo Mamo , Emirie Gudaye 
Published: October 2024

AbstractThe environment and human existence are inextricably intertwined. Consequently, alterations in the environment’s natural characteristics can lead to severe resource shortages. This affects the institutions that have been crucial in shaping and guiding human lives and preserving the environment’s richness, as well as the endeavours of communities to sustain their livelihoods. This article examines the impact of environmental change on the indigenous belief system of the Bayso community of Gidicho Island, southern Ethiopia. Ethnographic data were collected through interviews, focus group discussions, observation, and photographs. The results showed that environmental change on Gidicho Island and its environs has disrupted the socio-economic and cultural life of the Bayso, essentially their religious rituals. Thus, we advise the federal government to amend the country’s development policies that exacerbate environmental degradation and intervene to reduce the effects of poverty on the resource-use behaviours of its people.
Mechanical thrombectomy for internal carotid artery occlusion beyond a large paraclinoid aneurysm
Authors: Kobayashi Yuya , Kusano Yoshikazu , Watanabe Gen , Yamazaki Ken , Hirayama Shuichi , Kondo Yasufumi , Yamamoto Kanji , Sekijima Yoshiki 
Published: October 2024

Abstract
Background
With the launch of mechanical thrombectomy (MT), the prognosis of patients with cerebral infarction associated with large-vessel occlusion has improved. However, good outcomes are still not achieved in a few patients because of technical difficulties.

Case presentation
A 79-year-old Japanese woman was admitted with sudden-onset left hemiplegia. Tissue plasminogen activator was administered and MT was performed for internal carotid artery occlusion distal to a large paraclinoid aneurysm. Some technical difficulties were unique, including contrast agent retention, difficulty in guiding the system, and avoidance of rupture of the aneurysm. Here, we discuss the technical issues and solutions of the MT procedure employed in this case.

Conclusions
The procedure used in flow-diverter devices should be referenced and a stent-retrieving into an aspiration catheter with proximal balloon technique may be the most appropriate method.
Kefir: a fermented plethora of symbiotic microbiome and health
Authors: Tingirikari Jagan Mohan Rao , Sharma Anshul , Lee Hae-Jeung 
Published: October 2024

AbstractIn recent decades, a global shift in lifestyle and the ubiquitous consumption of junk foods have led to dysbiosis and other metabolic disorders significantly impacting human health. Recent studies performed on traditional foods have shown several health benefits and have gained the attention of the scientific community towards ethnic foods. In this regard, the consumption of ethnic foods with symbiotic properties is increasing gradually across the globe. Kefir is one such ethnic food with excellent functional properties. It is a unique traditional fermented drink comprised of kefir grains and probiotic microbes. Kefir grains are a gelatinous consortium of casein, milk solids coupled with yeasts, and lactobacilli-rich microbiota embedded in a poly-saccharide matrix. These components act as starters, initiating fermentation when introduced into fresh milk. This beverage bestows a myriad of symbiotic benefits, encompassing improved gut health and preventing several metabolic and other diseases through various biological mechanisms. Despite its millennia-long history, it has recently gained prominence due to emerging biotechnological and nutraceutical applications and researchers’ burgeoning fascination. In this comprehensive review, we endeavour to provide a meticulous elucidation of the most recent advancements concerning kefir, encompassing its production and processing methodologies for both dairy and water kefir. Furthermore, we delve into the intricate mechanisms underlying its functional properties and the health benefits of kefir as a functional fermented beverage.
The Impact of Minimal Sunlight Exposure on Bone Health: Insights From a Cohort Study in Erythropoietic Protoporphyria
Authors: Kluijver Louisa G , Wagenmakers Margreet A E M , Wilson J H Paul , Langendonk Janneke G 
Published: October 2024

Abstract

Context
Erythropoietic protoporphyria (EPP) is a rare inherited metabolic disease, causing lifelong painful phototoxic reactions, minimal sunlight exposure, and vitamin D deficiency. Previous studies reported a high osteoporosis prevalence in EPP patients.

Objective
To identify those at risk for low bone mineral density (BMD) and assess which factors, including treatment with cholecalciferol and afamelanotide, improve BMD in EPP.

Methods
A longitudinal ambispective single-center cohort study. Data from patient files and two-time questionnaires from adult patients with EPP who underwent at least one dual-energy x-ray absorptiometry (DXA) scan between 2012 and 2023 were used.

Results
BMD is low in EPP patients, with 82.7% of the 139 patients having a Z-score below 0 SD at baseline. Low BMD classified as osteopenia was found in 39.5%, and osteoporosis in 15.3%. There were 50 osteoporosis-related fractures in 34.2% of patients. Aging (odds ratio [OR] 1.08; CI, 1.03-1.12), persistent vitamin D deficiency (OR 1.11; 95% CI, 1.00-1.23) and a low body mass index (OR 0.91; 95% CI, 0.82-0.99) increased the odds of low BMD. Patients with a vitamin D deficiency (OR 5.51; 95% CI, 1.69-17.92) and no cholecalciferol at baseline (OR 0.22; 95% CI, 0.04-1.34) had the highest odds of improving their BMD. Afamelanotide did not improve BMD.

Conclusion
25-hydroxyvitamin D (25(OH)D) status plays a crucial role in both preventing low BMD and improving BMD. EPP is a natural model for lack of sunlight exposure and vitamin D deficiency, underlining the importance of lifelong adequate vitamin D status for bone health in the general population.
Functions and Mechanism of Thyroid Hormone Receptor Action During Amphibian Development
Authors: Louis Emeric , Fu Liezhen , Shi Yun-Bo , Sachs Laurent M 
Published: October 2024

Abstract
Thyroid hormones and their receptors (TRs) play critical roles during vertebrate development. One of the most dramatic developmental processes regulated by thyroid hormones is frog metamorphosis, which mimics the postembryonic (perinatal) period in mammals. Here, we review some of the findings on the developmental functions of thyroid hormones and TRs as well as their associated mechanisms of action obtained from this model system. More than 2 decades ago, a dual function model was proposed for TR in anuran development. During larval development, unliganded receptors recruit corepressors to repress thyroid hormone response genes to prevent premature metamorphic changes. Subsequently, when thyroid hormone levels rise, liganded receptors recruit coactivators to activate thyroid hormone response genes, leading to metamorphic changes. Over the years, molecular and genetic approaches have provided strong support for this model and have shown that it is applicable to mammalian development as well as to understanding the diverse effects of thyroid hormones in normal physiology and diseases caused by thyroid hormone signaling dysfunction.
Target gene responses differ when transcription factor levels are acutely decreased by nuclear export versus degradation
Authors: McGehee James , Stathopoulos Angelike 
Published: October 2024

ABSTRACT
Defining the time of action for morphogens requires tools capable of temporally controlled perturbations. To study how the transcription factor Dorsal affects patterning of the Drosophila embryonic dorsal-ventral axis, we used two light-inducible tags that trigger either nuclear export or degradation of Dorsal under blue light. Nuclear export of Dorsal leads to loss of the high-threshold, ventrally expressed target gene snail (sna), while the low-threshold, laterally expressed target gene short-gastrulation (sog) is retained. In contrast, degradation of Dorsal results in retention of sna, loss of sog, and lower nuclear levels compared to when Dorsal is exported from the nucleus. To understand why nuclear export causes loss of sna but degradation does not, we investigated Dorsal kinetics using photobleaching and found that it rapidly re-enters the nucleus even under blue-light conditions favoring export. The associated kinetics of Dorsal being rapidly imported and exported continuously are likely responsible for loss of sna but, alternatively, can support sog. Collectively, our results indicate that this dynamic patterning process is influenced by both Dorsal concentration and nuclear retention.
Loss of STING impairs lactogenic differentiation
Authors: Vickers Ramiah R. , Wyatt Garhett L. , Sanchez Lilia , VanPortfliet Jordyn J. , West A. Phillip , Porter Weston W. 
Published: October 2024

ABSTRACT
Heightened energetic and nutrient demand during lactogenic differentiation of the mammary gland elicits upregulation of various stress responses to support cellular homeostasis. Here, we identify the stimulator of interferon genes (STING) as an immune supporter of the functional development of mouse mammary epithelial cells (MECs). An in vitro model of MEC differentiation revealed that STING is activated in a cGAS-independent manner to produce both type I interferons and proinflammatory cytokines in response to the accumulation of mitochondrial reactive oxygen species. Induction of STING activity was found to be dependent on the breast tumor suppressor gene single-minded 2 (SIM2). Using mouse models of lactation, we discovered that loss of STING activity results in early involution of #3 mammary glands, severely impairing lactational performance. Our data suggest that STING is required for successful functional differentiation of the mammary gland and bestows a differential lactogenic phenotype between #3 mammary glands and the traditionally explored inguinal 4|9 pair. These findings affirm unique development of mammary gland pairs that is essential to consider in future investigations into normal development and breast cancer initiation.