bluuebunny/crossref_metadata_2025_split huggingface dataset:
High risk of lung cancer in surfactant-related gene variant carriers
Authors: Brudon Alexandre , Legendre Marie , Mageau Arthur , Bermudez Julien , Bonniaud Philippe , Bouvry Diane , Cadranel Jacques , Cazes Aurélie , Crestani Bruno , Dégot Tristan , Delestrain Céline , Diesler Rémi , Epaud Ralph , Philippot Quentin , Théou-Anton Nathalie , Kannengiesser Caroline , Ba Ibrahima , Debray Marie-Pierre , Fanen Pascale , Manali Efrosine , Papiris Spyros , Nathan Nadia , Amselem Serge , Gondouin Antoine , Guillaumot Anne , Andréjak Claire , Jouneau Stephane , Beltramo Guillaume , Uzunhan Yurdagul , Galodé François , Westeel Virginie , Mehdaoui Anas , Hirschi Sandrine , Leroy Sylvie , Marchand-Adam Sylvain , Nunes Hilario , Picard Clément , Prévot Grégoire , Reynaud-Gaubert Martine , De Vuyst Paul , Wemeau Lidwine , Defossez Gautier , Zalcman Gérard , Cottin Vincent , Borie Raphael ,   the OrphaLung network
Published: April 2024

BackgroundSeveral rare surfactant-related gene (SRG) variants associated with interstitial lung disease are suspected to be associated with lung cancer, but data are missing. We aimed to study the epidemiology and phenotype of lung cancer in an international cohort of SRG variant carriers.MethodsWe conducted a cross-sectional study of all adults with SRG variants in the OrphaLung network and compared lung cancer risk with telomere-related gene (TRG) variant carriers.ResultsWe identified 99 SRG adult variant carriers (SFTPA1(n=18),SFTPA2(n=31),SFTPC(n=24),ABCA3(n=14) andNKX2-1(n=12)), including 20 (20.2%) with lung cancer (SFTPA1(n=7),SFTPA2(n=8),SFTPC(n=3),NKX2-1(n=2) andABCA3(n=0)). Among SRG variant carriers, the odds of lung cancer was associated with age (OR 1.04, 95% CI 1.01–1.08), smoking (OR 20.7, 95% CI 6.60–76.2) andSFTPA1/SFTPA2variants (OR 3.97, 95% CI 1.39–13.2). Adenocarcinoma was the only histological type reported, with programmed death ligand-1 expression ≥1% in tumour cells in three samples. Cancer staging was localised (I/II) in eight (40%) individuals, locally advanced (III) in two (10%) and metastatic (IV) in 10 (50%). We found no somatic variant eligible for targeted therapy. Seven cancers were surgically removed, 10 received systemic therapy, and three received the best supportive care according to their stage and performance status. The median overall survival was 24 months, with stage I/II cancers showing better survival. We identified 233 TRG variant carriers. The comparative risk (subdistribution hazard ratio) for lung cancer in SRG patientsversusTRG patients was 18.1 (95% CI 7.1–44.7).ConclusionsThe high risk of lung cancer among SRG variant carriers suggests specific screening and diagnostic and therapeutic challenges. The benefit of regular computed tomography scan follow-up should be evaluated.
Multiple phenotype association tests based on sliced inverse regression
Authors: Sun Wenyuan , Jon Kyongson , Zhu Wensheng ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2024

Abstract
Background
Joint analysis of multiple phenotypes in studies of biological systems such as Genome-Wide Association Studies is critical to revealing the functional interactions between various traits and genetic variants, but growth of data in dimensionality has become a very challenging problem in the widespread use of joint analysis. To handle the excessiveness of variables, we consider the sliced inverse regression (SIR) method. Specifically, we propose a novel SIR-based association test that is robust and powerful in testing the association between multiple predictors and multiple outcomes.

Results
We conduct simulation studies in both low- and high-dimensional settings with various numbers of Single-Nucleotide Polymorphisms and consider the correlation structure of traits. Simulation results show that the proposed method outperforms the existing methods. We also successfully apply our method to the genetic association study of ADNI dataset. Both the simulation studies and real data analysis show that the SIR-based association test is valid and achieves a higher efficiency compared with its competitors.

Conclusion
Several scenarios with low- and high-dimensional responses and genotypes are considered in this paper. Our SIR-based method controls the estimated type I error at the pre-specified level $$\alpha $$
α
.
Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice
Authors: Aloryi Kelvin Dodzi , Okpala Nnaemeka Emmanuel , Guo Hong , Karikari Benjamin , Amo Aduragbemi , Bello Semiu Folaniyi , Saini Dinesh Kumar , Akaba Selorm , Tian Xiaohai 
Published: April 2024

Abstract
Background
Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice.

Results
In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation.

Conclusion
This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.
Genetic characterizations of Cryptosporidium spp. from children with or without diarrhea in Wenzhou, China: high probability of zoonotic transmission
Authors: Zhao Wei , Ren Guangxu , Jiang Weiyan , Wang Long , Wang Jiayang , Yuan Zhongying , Yan Lanzhu , Li Yongtai , Sun Yanbin , Xue Xinjie , Jiang Yanyan , Lu Gang , Huang Huicong 
Published: April 2024

AbstractBackgroundCryptosporidiumis a highly pathogenic parasite responsible for diarrhea in children worldwide. Here, the epidemiological status and genetic characteristics ofCryptosporidiumin children with or without diarrhea were investigated with tracking of potential sources in Wenzhou City, China.MethodsA total of 1032 children were recruited, 684 of whom had diarrhea and 348 without, from Yuying Children’s Hospital in Wenzhou, China. Samples of stool were collected from each participant, followed by extraction of DNA, genotyping, and molecular identification ofCryptosporidiumspecies and subtypes.ResultsTwenty-two of the 1032 (2.1%) children were infected withCryptosporidium spp. with 2.5% (17/684) and 1.4% (5/348) in diarrhoeic and asymptomatic children, respectively. FourCryptosporidiumspecies were identified, includingC. parvum(68.2%; 15/22),C. felis(13.6%; 3/22),C. viatorum(9.1%; 2/22), andC. baileyi(9.1%; 2/22). TwoC. parvumsubtypes named IIdA19G1 (n = 14) and IInA10 (n = 1), and one each ofC. felis(XIXa) andC. viatorum(XVaA3g) subtype was found as well.ConclusionsThis is the first research that identifiedCryptosporidiumin children of Wenzhou, China, using PCR. Identification of zoonoticC. parvum, C. felis,C. viatorum, and their subtypes indicate potential cross-species transmission ofCryptosporidiumbetween children and animals. Additionally, the presence ofC. baileyiin children suggests that this species has a wider host range than previously believed and that it possesses the capacity to infect humans.
Exploring how people achieve recommended levels of physical activity, despite self-reported economic difficulties: a sense of coherence perspective
Authors: Johansson Lisbeth M. , Fransson Eleonor I. , Lingfors Hans , Golsäter Marie 
Published: April 2024

Abstract
Background
The salutogenic theory forms the basis for health promotion and describes health as a continuum from a dis-ease pole of health to an ease pole. The core concept for the salutogenic theory is sense of coherence (SOC). For a strong SOC, general resistance resources, such as solid economic situation, are essential. The aim was to explore how people – despite self-reported economic difficulties – comprehend, manage and find it meaningful to achieve the level of physical activity recommended by World Health Organisation (WHO).

Method
The study is based on interviews with people achieving the recommended physical activity (PA) level despite economic difficulties. The interviews were conducted at primary health care centres and family centres after a targeted health dialogue. We used a qualitative deductive content analysis based on sense of coherence as the main category, with the three generic categories of comprehensibility, manageability and meaningfulness.

Result
The findings elucidate a pattern of a process. In this process, the participants comprehend their knowledge of the health benefits of PA and have a plan for performing their PA. They utilise their resources in order to manage to apply their knowledge and plan for PA in their lives despite their challenges. When PA becomes meaningful to them, they have an intrinsic motivation to perform it and experience its benefits.

Conclusion
This study suggests a possible process that might help in achieving the recommended PA level among people with economic difficulties and other challenges. The findings might be used in health promotion work, such as targeted health dialogues in primary health care, to reduce health inequalities when supporting people who are not achieving the recommended levels of PA.

Trial registration
Not applicable.
Relapsing bronchopneumonia due to community-associated methicillin-resistant Staphylococcus aureus: a case report
Authors: Shimada Sho , Yamaguchi Tetsuo , Mikoshiba Satsuki , Sato Kazuaki , Mitsumura Takahiro , Komori Kohji , Yamana Takashi , Iijima Yuki , Sakakibara Rie , Shibata Sho , Honda Takayuki , Shirai Tsuyoshi , Okamoto Tsukasa , Furusawa Haruhiko , Tateishi Tomoya , Miyazaki Yasunari 
Published: April 2024

Abstract
Background
The emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has increased the incidence of community-onset MRSA infection. Respiratory tract infections caused by MRSA has been noted for their severity; however, repeated relapses that require extended antibiotic therapy are rare.

Case presentation
We report a case of relapsing bronchopneumonia caused by CA-MRSA in a 56-year-old man. The patient responded to antibiotics, but repeatedly relapsed after stopping treatment. MRSA was consistently isolated from airway specimens during each relapse. Extended oral antibiotic treatment with trimethoprim/sulfamethoxazole (TMP/SMX) for 6 months achieved infection control. Whole-genome sequencing of the isolated strain revealed that the causative agent was sequence type (ST)1/staphylococcal cassette chromosome mec (SCCmec) type IVa, a clone that is rapidly increasing in Japan.

Discussion and conclusions
This patient had an unusual course of MRSA bronchopneumonia with repeated relapses. Although the choice of antibiotics for long-term use in MRSA respiratory tract infections has not been well established, TMP/SMX was effective and well tolerated for long-term therapy in this case. The clinical course of infections related to the rapid emerging clone, ST1/SCCmec type IVa warrants further attention.
Smoking during pregnancy and its effect on placental weight: a Mendelian randomization study
Authors: Jaitner Annika , Vaudel Marc , Tsaneva-Atanasova Krasimira , Njølstad Pål R. , Jacobsson Bo , Bowden Jack , Johansson Stefan , Freathy Rachel M. 
Published: April 2024

Abstract
Background
The causal relationship between maternal smoking in pregnancy and reduced offspring birth weight is well established and is likely due to impaired placental function. However, observational studies have given conflicting results on the association between smoking and placental weight. We aimed to estimate the causal effect of newly pregnant mothers quitting smoking on their placental weight at the time of delivery.

Methods
We used one-sample Mendelian randomization, drawing data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (N = 690 to 804) and the Norwegian Mother, Father and Child Cohort Study (MoBa) (N = 4267 to 4606). The sample size depends on the smoking definition used for different analyses. The analysis was performed in pre-pregnancy smokers only, due to the specific role of the single-nucleotide polymorphism (SNP) rs1051730 (CHRNA5 – CHRNA3 – CHRNB4) in affecting smoking cessation but not initiation.

Results
Fixed effect meta-analysis showed a 182 g [95%CI: 29,335] higher placental weight for pre-pregnancy smoking mothers who continued smoking at the beginning of pregnancy, compared with those who stopped smoking. Using the number of cigarettes smoked per day in the first trimester as the exposure, the causal effect on placental weight was 11 g [95%CI: 1,21] per cigarette per day. Similarly, smoking at the end of pregnancy was causally associated with higher placental weight. Using the residuals of birth weight regressed on placental weight as the outcome, we showed evidence of lower offspring birth weight relative to the placental weight, both for continuing smoking at the start of pregnancy as well as continuing smoking throughout pregnancy (change in z-score birth weight adjusted for z-score placental weight: -0.8 [95%CI: -1.6,-0.1]).

Conclusion
Our results suggest that continued smoking during pregnancy causes higher placental weights.
Sertaconazole 300 mg versus clotrimazole 500 mg vaginal suppository for treating pregnant women with acute vaginal candidiasis: a double-blinded, randomized trial
Authors: Chayachinda Chenchit , Thamkhantho Manopchai , Rekhawasin Thanapa , Klerdklinhom Chanakarn 
Published: April 2024

Abstract
Background
Vaginal candidiasis (VC) commonly affects pregnant women. Traditionally, clotrimazole vaginal tablets (CLO) have been the cornerstone of management. However, sertaconazole ovules (SER) offer a novel topical antimycotic option. This double-blinded, randomized trial evaluated the efficacy of single-dose SER and CLO in treating acute VC during pregnancy.

Methods
From June 2020 to May 2021, this trial recruited pregnant women aged ≥ 18 years with VC symptoms (abnormal vaginal discharge and/or vulvar/vaginal itching) confirmed by microscopy. Participants with ≥ 4 VC episodes in the prior year, immunocompromised status, or imidazole contraindications and those who were absent at the 2-week follow-up were excluded. Participants were randomized to receive either 300 mg SER or 500 mg CLO. Evaluations 2 weeks after the initial medication administration included clinical cure (self-reported resolution of all symptoms), microscopic cure (pseudohyphal absence), patient satisfaction, side effects, and time to clinical cure. Participants with persistent VC received weekly SER doses until delivery. Assessments of recurrence and pregnancy outcomes were done.

Results
The analysis included 96 participants (48 per group, mean age 27.4 ± 7.4 years, gestational age at diagnosis 22.9 ± 6.4 weeks). Without statistical significance, SER achieved a higher clinical cure rate (62.5% vs 50%, p = 0.217; a mean difference of 12.5%, 95%CI: -17.5% to 42.5%; and a rate ratio of 1.25, 95%CI: 0.71 to 2.23) and a lower microscopic cure (47.9% vs. 62.5%, p = 0.151; a mean difference of -14.6%, 95%CI: -44.3% to 15.1%; and a rate ratio of 0.77, 95%CI: 0.43 to 1.37). The two groups had comparable times to clinical cure (SER: 3.1 ± 1.8 days, CLO: 3.4 ± 2.7 days; p = 0.848) and substantial satisfaction rates (SER: 66.7%, CLO: 60.4%; p = 0.753). No side effects were reported. Of 60 participants who gave birth at Siriraj Hospital, there were no significant differences in pregnancy outcomes. Repeated SER dosing eradicated symptoms and enhanced the microscopic cure rate. Recurrence was observed in four SER and two CLO participants within 1–2 months.

Conclusion
In the treatment of acute VC during pregnancy, 300 mg SER and 500 mg CLO exhibited comparable efficacy in terms of clinical and microscopic cure rates, satisfaction, side effects, time to clinical cure, recurrence rates, and pregnancy outcomes.

Trial registration
TCTR20190308004 (registration date March 8, 2019).
Is a tiered restrictions system an effective intervention for COVID-19 control? Results from Portugal, November-December 2020
Authors: Moniz Marta , Soares Patrícia , Nunes Baltazar , Leite Andreia 
Published: April 2024

Abstract
Background
In November 2020, similar to other European countries, Portugal implemented a tiered restrictions system to control the COVID-19 pandemic. We aimed to compare the COVID-19 growth rate across tiers to assess the effect of a tiered restrictions system in Portugal, using models with different times between tiers assessment. Our hypothesis was that being in a higher tier brings a faster deceleration in the growth rate than being in a lower tier.

Methods
The national database of notified COVID-19 cases and publicly available data were used to analyse the effect of the tiered restrictions system on the COVID-19 incidence growth rate. The tiers were based on the European Centre for Disease Control risk classification: moderate, high, very and extremely high. We used a generalised mixed-effects regression model to estimate the growth rate ratio (GRR) for each tier, comparing the growth rates of higher tiers using moderate tier as reference. Three models were fitted using different times between tiers assessment, separated by 14 days.

Results
We included 156 034 cases. Very high tier was the most frequent combination in all the three moments assessed (21.2%), and almost 50% of the municipalities never changed tier during the study period. Immediately after the tiers implementation, a reduction was identified in the municipalities in high tier (GRR high tier: 0.90 [95%CI: 0.79; 1.02]) and very high tier (GRR very high tier: 0.68 [95%CI: 0.61; 0.77]), however with some imprecision in the 95% confidence interval for the high tier. A reduction in very high tier growth rate was identified two weeks (GRR: 0.79 [95%CI: 0.71; 0.88]) and four weeks (GRR: 0.77 [95%CI: 0.74; 0.82]) after the implementation, compared to moderate tier. In high tier, a reduction was also identified in both times, although smaller.

Conclusions
We observed a reduction in the growth rate in very high tier after the tiered restriction system was implemented, but we also observed a lag between tiered restriction system implementation and the onset of consequent effects. This could suggest the importance of early implementation of stricter measures for pandemic control. Thus, studies analysing a broader period of time are needed.
Characterization of adults concerning the use of a hypothetical mHealth application addressing stress-overeating: an online survey
Authors: Lurz Martin , Gemesi Kathrin , Holzmann Sophie Laura , Kretzschmar Birgit , Wintergerst Monika , Groh Georg , Böhm Markus , Gedrich Kurt , Hauner Hans , Krcmar Helmut , Holzapfel Christina 
Published: April 2024

Abstract
Background
About 40% of people respond to stress by consuming more unhealthy foods. This behavior is associated with increased energy intake and the risk of obesity. As mobile health (mHealth) applications (apps) have been shown to be an easy-to-use intervention tool, the characterization of potential app users is necessary to develop target group-specific apps and to increase adherence rates.

Methods
This cross-sectional online survey was conducted in the spring of 2021 in Germany. Sociodemographic data and data on personality (Big Five Inventory, BFI-10), stress-eating (Salzburg Stress Eating Scale, SSES), and technology behavior (Personal Innovativeness in the Domain of Information Technology, PIIT; Technology Acceptance Model 3, TAM 3) were collected.

Results
The analysis included 1228 participants (80.6% female, mean age: 31.4 ± 12.8 years, mean body mass index (BMI): 23.4 ± 4.3 kg/m2). Based on the TAM score, 33.3% (409/1228) of the participants had a high intention to use a hypothetical mHealth app to avoid stress-overeating. These persons are characterized by a higher BMI (24.02 ± 4.47 kg/m2, p < 0.001), by being stress-overeaters (217/409, 53.1%), by the personality trait “neuroticism” (p < 0.001), by having specific eating reasons (all p < 0.01), and by showing a higher willingness to adopt new technologies (p < 0.001).

Conclusion
This study suggests that individuals who are prone to stress-overeating are highly interested in adopting an mHealth app as support. Participants with a high intention to use an mHealth app seem to have a general affinity towards new technology (PIIT) and appear to be more insecure with conflicting motives regarding their diet.

Trial registration
This survey was registered in the German Clinical Trials Register (Registration number: DRKS00023984).