bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Genome-Wide Association Study of Respiratory Syncytial Virus Infection Severity in Infants
Authors: Johnson Mari , Chelysheva Irina , Öner Deniz , McGinley Joseph , Lin Gu-Lung , O’Connor Daniel , Robinson Hannah , Drysdale Simon B , Gammin Emma , Vernon Sophie , Muller Jill , Wolfenden Helen , Westcar Sharon , Anguvaa Lazarus , Thwaites Ryan S , Bont Louis , Wildenbeest Joanne , Martinón-Torres Federico , Aerssens Jeroen , Openshaw Peter J M , Pollard Andrew J 
Published: January 2024

Abstract

Background
Respiratory syncytial virus (RSV) is a significant cause of infant morbidity and mortality worldwide. Most children experience at least one 1 RSV infection by the age of two 2 years, but not all develop severe disease. However, the understanding of genetic risk factors for severe RSV is incomplete. Consequently, we conducted a genome-wide association study of RSV severity.

Methods
Disease severity was assessed by the ReSVinet scale, in a cohort of 251 infants aged 1 week to 1 year. Genotyping data were collected from multiple European study sites as part of the RESCEU Consortium. Linear regression models were used to assess the impact of genotype on RSV severity and gene expression as measured by microarray.

Results
While no SNPs reached the genome-wide statistical significance threshold (P &lt; 5 × 10−8), we identified 816 candidate SNPs with a P-value of &lt;1 × 10−4. Functional annotation of candidate SNPs highlighted genes relevant to neutrophil trafficking and cytoskeletal functions, including LSP1 and RAB27A. Moreover, SNPs within the RAB27A locus significantly altered gene expression (false discovery rate, FDR P &lt; .05).

Conclusions
These findings may provide insights into genetic mechanisms driving severe RSV infection, offering biologically relevant information for future investigations.
Identification of CCL20 as a Prognostic Predictor for Severe Fever With Thrombocytopenia Syndrome Based on Plasma Proteomics
Authors: Zhang Yue , Li Lan , Liu Yuanni , Zhang Wei , Peng Wenjuan , Zhang Shuai , Qu Renliang , Ma Yuan , Liu Zishuai , Ge Ziruo , Zhou Yanxi , Tian Wen , Shen Yi , Liu Li , Duan Jianping , Chen Zhihai , Zhu Liuluan 
Published: January 2024

Abstract

Background
Severe fever with thrombocytopenia syndrome (SFTS), a lethal tick-borne hemorrhagic fever, prompted our investigation into prognostic predictors and potential drug targets using plasma Olink Proteomics.

Methods
Employing the Olink assay, we analyzed 184 plasma proteins in 30 survivors and 8 nonsurvivors of SFTS. Validation was performed in a cohort of 154 patients with SFTS via enzyme-linked immunosorbent assay. We utilized the Drug-Gene Interaction Database to identify protein-drug interactions.

Results
Nonsurvivors exhibited 110 differentially expressed proteins as compared with survivors, with functional enrichment in the cell chemotaxis–related pathway. Thirteen differentially expressed proteins—including C-C motif chemokine 20 (CCL20), calcitonin gene–related peptide alpha, and pleiotrophin—were associated with multiple-organ dysfunction syndrome. CCL20 emerged as the top predictor of death, demonstrating an area under the curve of 1 (P = .0004) and 0.9033 (P &lt; .0001) in the discovery and validation cohorts, respectively. Patients with CCL20 levels exceeding 45.74 pg/mL exhibited a fatality rate of 45.65%, while no deaths occurred in those with lower CCL20 levels. Furthermore, we identified 202 Food and Drug Administration–approved drugs targeting 37 death-related plasma proteins.

Conclusions
Distinct plasma proteomic profiles characterize SFTS cases with different outcomes, with CCL20 emerging as a novel, sensitive, accurate, and specific biomarker for predicting SFTS prognosis.
Enrichment Reveals Extensive Integration of Hepatitis B Virus DNA in Hepatitis Delta Virus-Infected Patients
Authors: Ringlander Johan , Strömberg Lucia Gonzales , Stenbäck Joakim B , Andersson Maria E , Abrahamsson Sanna , Skoglund Catarina , Castedal Maria , Larsson Simon B , Rydell Gustaf E , Lindh Magnus 
Published: January 2024

Abstract

Background
Hepatitis B virus (HBV) DNA may become integrated into the human genome of infected human hepatocytes. Expression of integrations can produce the surface antigen (HBsAg) that is required for synthesis of hepatitis D virus (HDV) particles and the abundant subviral particles in the blood of HBV- and HDV-infected subjects. Knowledge about the extent and variation of HBV integrations and impact on chronic HDV is still limited.

Methods
We investigated 50 pieces of liver explant tissue from 5 patients with hepatitis D-induced cirrhosis, using a deep-sequencing strategy targeting HBV RNA.

Results
We found that integrations were abundant and highly expressed, with large variation in the number of integration-derived (HBV/human chimeric) reads, both between and within patients. The median number of unique integrations for each patient correlated with serum levels of HBsAg. However, most of the HBV reads represented a few predominant integrations.

Conclusions
The results suggest that HBV DNA integrates in a large proportion of hepatocytes, and that the HBsAg output from these integrations vary &gt;100-fold depending on clone size and expression rate. A small proportion of the integrations seems to determine the serum levels of HBsAg and HDV RNA in HBV/HDV coinfected patients with liver cirrhosis.
Real-life data of immune recovery using bictegravir/emtricitabine/tenofovir alafenamide in virologically suppressed people living with HIV. Results at 48–96 weeks of RETROBIC Study
Authors: Troya Jesús , Pousada Guillermo , Micán Rafael , Galera Carlos , Sanz José , de los Santos Ignacio , Dueñas Carlos , Cabello Noemí , Martín Cristina , Galindo María Josefa , Garcinuño María Ángeles , Pedrero-Tomé Roberto , Buzón Luis 
Published: January 2024

Abstract

Background
Switching strategy with bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF) has become a gold standard for people living with HIV (PLWH), achieving high efficacy and safety rates. However, data regarding immune status in long-term real-life cohorts of pretreated patients are needed.

Methods
We performed a multicentre, non-controlled, retrospective study in virologically suppressed PLWH switching to B/F/TAF. We evaluated CD4+, CD8+ and CD4+/CD8+ ratio, efficacy and safety at weeks 48 and 96.

Results
The study comprised 1966 PLWH from 12 hospitals in Spain, of whom 80% were men, and the median age was 51.0 [42.0–57.0] years. The median time of HIV infection was 18.0 [10.0–27.0] years. No significant changes in CD4+, CD8+ T cells, or CD4+/CD8+ were observed after 96 weeks. Nevertheless, in women at weeks 48 and 96, we found a significant increase of CD4+ T cells and a significant decrease in CD8+ T cells. In patients ≥60 years at week 96, CD4 T cells significantly increased and CD8+ T cells significantly decreased at week 48. The on-treatment analysis revealed HIV-RNA &lt;50 copies/mL in 95.6% (1700/1779) and 96.7% (1312/1356) of patients at weeks 48 and 96, respectively. The rates increased to 99.2% (1765/1779) and 99.7% (1352/1356) when considering HIV-RNA &lt;200 copies/mL. No resistance mutations were detected in virologic failures. B/F/TAF discontinuations accounted for 10.2% (200). Simplification was the most common reason for discontinuation in 3.8% (74) of patients.

Conclusion
In long-term virologically controlled PLWH, B/F/TAF achieved high efficacy rates and slightly improved immune status in women and individuals aged 60 and over after 48 and 96 of switching.
The combined effect of systemic antibiotics and proton pump inhibitors on Clostridioides difficile infection and recurrence
Authors: Moreels Nele , Boven Annelies , Gressani Oswaldo , Andersson Fredrik L , Vlieghe Erika , Callens Steven , Engstrand Lars , Simin Johanna , Brusselaers Nele 
Published: January 2024

Abstract

Background
Antibiotics and proton pump inhibitors (PPI) are recognized risk factors for acquisition and recurrence of Clostridioides difficile infection (CDI), yet combined effects remain unclear.

Objectives
To assess the short- and long-term effects of antibiotics and PPIs on CDI risk and recurrence.

Methods
Population-based study including all 43 152 patients diagnosed with CDI in Sweden (2006–2019), and 355 172 matched population controls without CDI. The impact of antibiotics and PPIs on CDI risk and recurrence was explored for recent (0–30 days) and preceding (31–180 days) use prior to their first CDI diagnosis, using multivariable conditional logistic regression presented as odds ratios (ORs) and 95% confidence interval, adjusted for demographics, comorbidities and other drugs.

Results
Compared to controls, the combined effect of recent PPIs and antibiotics [ORAB+PPI = 17.51 (17.48–17.53)] on CDI risk was stronger than the individual effects [ORAB = 15.37 (14.83–15.93); ORPPI = 2.65 (2.54–2.76)]. Results were less pronounced for exposure during the preceding months. Dose–response analyses showed increasing exposure correlated with CDI risk [recent use: ORAB = 6.32 (6.15–6.49); ORPPI = 1.65 (1.62–1.68) per prescription increase].
Compared to individuals without recurrence (rCDI), recent [ORAB = 1.30 (1.23–1.38)] and preceding [ORAB = 1.23 (1.16–1.31); ORPPI = 1.12 (1.03–1.21)] use also affected the risk of recurrence yet without significant interaction between both. Recent macrolides/lincosamides/streptogramins; other antibacterials including nitroimidazole derivates; non-penicillin beta lactams and quinolones showed the strongest association with CDI risk and recurrence, particularly for recent use. PPI use, both recent and preceding, further increased the CDI risk associated with almost all antibiotic classes.

Conclusion
Recent and less recent use of PPIs and systemic antibiotics was associated with an increased risk of CDI, particularly in combination.
Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals
Authors: Aoki Yu-ichi , Taguchi Keiko , Anzawa Hayato , Kawashima Junko , Ishida Noriko , Otsuki Akihito , Hasegawa Atsushi , Baird Liam , Suzuki Takafumi , Motoike Ikuko N , Ohneda Kinuko , Kumada Kazuki , Katsuoka Fumiki , Kinoshita Kengo , Yamamoto Masayuki 
Published: January 2024

Abstract
Whole blood transcriptome analysis is a valuable approachin medical research, primarily due to the ease of sample collection and the richness of the information obtained. Since the expression profile of individual genes in the analysis is influenced by medical traits and demographic attributes such as age and gender, there has been a growing demand for a comprehensive database for blood transcriptome analysis. Here, we performed whole blood RNA sequencing (RNA-seq) analysis on 576 participants stratified by age (20–30s and 60–70s) and gender from cohorts of the Tohoku Medical Megabank (TMM). A part of female segment included pregnant women. We did not exclude the globin gene family in our RNA-seq study, which enabled us to identify instances of hereditary persistence of fetal hemoglobin based on the HBG1 and HBG2 expression information. Comparing stratified populations allowed us to identify groups of genes associated with age-related changes and gender differences. We also found that the immune response status, particularly measured by neutrophil-to-lymphocyte ratio (NLR), strongly influences the diversity of individual gene expression profiles in whole blood transcriptome analysis. This stratification has resulted in a data set that will be highly beneficial for future whole blood transcriptome analysis in the Japanese population.
Sphingosine-1-phosphate promotes osteogenesis by stimulating osteoblast growth and neovascularization in a vascular endothelial growth factor–dependent manner
Authors: Wille Annalena , Weske Sarah , von Wnuck Lipinski Karin , Wollnitzke Philipp , Schröder Nathalie H , Thomas Nadine , Nowak Melissa K , Deister-Jonas Jennifer , Behr Björn , Keul Petra , Levkau Bodo 
Published: January 2024

Abstract
Sphingosine-1-phosphate (S1P) plays multiple roles in bone metabolism and regeneration. Here, we have identified a novel S1P-regulated osteoanabolic mechanism functionally connecting osteoblasts (OBs) to the highly specialized bone vasculature. We demonstrate that S1P/S1PR3 signaling in OBs stimulates vascular endothelial growth factor a (VEGFa) expression and secretion to promote bone growth in an autocrine and boost osteogenic H-type differentiation of bone marrow endothelial cells in a paracrine manner. VEGFa-neutralizing antibodies and VEGF receptor inhibition by axitinib abrogated OB growth in vitro and bone formation in male C57BL/6J in vivo following S1P stimulation and S1P lyase inhibition, respectively. Pharmacological S1PR3 inhibition and genetic S1PR3 deficiency suppressed VEGFa production, OB growth in vitro, and inhibited H-type angiogenesis and bone growth in male mice in vivo. Together with previous work on the osteoanabolic functions of S1PR2 and S1PR3, our data suggest that S1P-dependent bone regeneration employs several nonredundant positive feedback loops between OBs and the bone vasculature. The identification of this yet unappreciated aspect of osteoanabolic S1P signaling may have implications for regular bone homeostasis as well as diseases where the bone microvasculature is affected such as age-related osteopenia and posttraumatic bone regeneration.
A novel fluid identification method based on a high-precision spectral decomposition method
Authors: Miao Fawei , He Yanxiao , Wang Shangxu , Huang Handong 
Published: January 2024

Abstract
Time-frequency decomposition technology is an effective tool for analyzing non-stationary signals. Improving resolution of spectral decomposition techniques is important to extract more useful information from the received signal. The Wigner-Ville distribution (WVD) has been widely applied in seismic signal analysis, it can better analyze seismic signals due to many excellent mathematical properties, but this method has a drawback that cross terms interference exists in the analyzing of multicomponent signals, which severely limits its application. The combination of the complex-domain matching pursuit (CDMP) with this approach effectively solves this problem. However, the conventional CDMP-WVD does not take the influence of the scale parameter on the Morlet wavelet waveform into account, which reduces the time-frequency resolution of CDMP-WVD. Therefore, to correct the defect that the atomic waveforms change only with the frequency parameter, we propose an improved spectral decomposition method ICDMP-WVD that considers the scale parameter. In this study, we first analyze influences of the scale parameter on Morlet wavelet waveform and make the scale parameter a search parameter that improves the computational efficiency and time-frequency resolution of the traditional CDMP-WVD method. Accordingly, the seismic dispersion-dependent attributes are calculated via combing the improved CDMP-WVD algorithm and the frequency-dependent AVO inversion. We adopt a two-step frequency-dependent AVO inversion method to improve the stability of the conventional frequency-dependent AVO inversion. Theoretical data and real data application show that the approach in this study can identify gas reservoirs efficiently and accurately.
Fine characterization of interbedding sand-mudstone based on waveform indication inversion
Authors: Shi Suzhen , Gao Weixu , Long Teng , Xie Dongshan , Li Li , Pei Jinbo , Cai Jianchao 
Published: January 2024

Abstract
Owing to the increasing challenges associated with coal mine exploration and development, extremely precise surveys with high-resolution images are required to support production. Conventional inversion methods cannot provide sufficiently precise images of the complex lithologies in coal measure strata. Accordingly, this study performed research in Qiyuan mining area, Shanxi Province, China, and predicted the complex lithology on the basis of facies control using waveform indication inversion and waveform indication simulation. Horizontal changes in seismic waveforms were used to reflect lithologic assemblage characteristics for facies-controlled constraints, and the vertical mapping the connection between seismic waveform and logging curves was shown. Moreover, high-resolution inversions of wave impedance and natural gamma parameters were conducted. Combined with lithologic shielding and accurate time–depth conversion, the inversions enabled the precise characterization of the lithological assemblage distribution in the study area. Our results showed that waveform indication inversion could distinguish between coal seams and limestone, whereas waveform indication simulation based on natural gamma could effectively distinguish between sandstone and mudstone. Furthermore, the horizontal resolution was improved and the vertical resolution extended to a thickness of 2–3 m. In addition, the inversion results were highly consistent with drilling results, with an error &lt;0.1 m. Therefore, waveform indication inversion and simulation could be applied to coal mines for safe and efficient production.
Noninvasive EEG measurement of sleep in the family cat and comparison with the dog
Authors: Bálint Anna , Reicher Vivien , Csibra Barbara , Gácsi Márta 
Published: January 2024

Abstract
We have successfully measured the sleep electroencephalogram (EEG) of 12 family cats during an afternoon nap using a completely noninvasive methodology originally developed and validated for family dogs. Extracting both macrostructural and spectral sleep variables from the acquired data, we: (1) provided a descriptive analysis of sleep structure in cats and the power spectral density (PSD) distribution considering 3 sleep stages—drowsiness, non-rapid eye movement (NREM), and rapid eye movement (REM) sleep; and (2) compared the results to those obtained in family dogs measured under the same conditions and using the same methodology. Importantly, our description of sleep structure and PSD distribution in cats proved to be comparable to those of earlier invasive studies, highlighting that appropriate noninvasive methodologies may provide a viable alternative to those that are invasive in some cases. While no macrostructural differences were found between the sleep of cats and dogs, and the characteristic PSDs were mostly similar across sleep stages within the 2 species, the high-frequency resolution comparison of PSD distributions revealed differences between the 2 species in all sleep stages (concerning the delta, theta, alpha, sigma, and beta bands in drowsiness and NREM sleep; and the delta, alpha, and sigma bands in REM sleep). Potential factors underlying these differences are discussed, including differences in circadian rhythms, sleep homeostatic regulation, experienced stress, or even differential attitudes toward owners—highlighting important links between sleep characteristics and often more complex neural and behavioral features.
Three new shrews (Soricidae: Crocidura) from West Sumatra, Indonesia: elevational and morphological divergence in syntopic sister taxa
Authors: Nations Jonathan A , Handika Heru , Mursyid Ahmad , Darma Busta Ryski , Apandi  , Achmadi Anang S , Esselstyn Jacob A 
Published: January 2024

Abstract
We describe 3 new species of shrews (Eulipotyphla, Soricidae, Crocidura) from West Sumatra, Indonesia. Two of these taxa were found above 1,800 m on Mt. Singgalang. The third taxon was found above 1,660 m on Mt. Talamau, 65 km northwest of Mt. Singgalang. We also resurrect Crocidura aequicauda based on 2 specimens from Mts. Tujuh and Kerinci, which lie near the border between West Sumatra and Jambi provinces. Several methodological approaches support our findings: linear cranial morphometrics, landmark-based 2D geometric morphometrics, and molecular phylogenetics using both mtDNA and 6 nuclear exons. A multilocus species-tree analysis places the 3 new species and C. aequicauda in a clade with the Javan endemics C. monticola and C. umbra. Although the 2 taxa from Mt. Singgalang are recovered as sister species, 1 is nearly twice the size of the other, and they are divergent in several other morphological characters, such as tail length, cranium size, and pelage color and texture. Recently diverged yet morphologically disparate sister taxa living syntopically in an isolated habitat “island,” like the montane forests of Mt. Singgalang, is unusual in mammals but documented in other Crocidura on neighboring Java and Borneo; these 2 new taxa represent the first known case of this phenomenon on Sumatra. Our results bring the number of Sumatran Crocidura to 10, 9 of which are endemic to the island. All 3 of the new species appear to be endemic to a single mountain and were not detected in similar surveys of nearby mountains. If this local endemism pattern is common, it would indicate that Sumatra’s mammal diversity may be severely underestimated, largely due to the paucity of small-mammal surveys and museum specimens.
Changes in smoking use and subsequent lung cancer risk in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study
Authors: Gutiérrez-Torres Daniela S , Kim Sungduk , Albanes Demetrius , Weinstein Stephanie J , Inoue-Choi Maki , Albert Paul S , Freedman Neal D 
Published: January 2024

Abstract

Background
Reducing cigarettes per day may lower the risk of lung cancer compared with continuing to smoke at the same intensity. Other changes in smoking behaviors, such as increasing cigarette consumption or quitting for a period and relapsing, may also affect lung cancer risk.

Methods
We examined changes in smoking status and cigarettes per day among 24 613 Finnish male smokers aged 50-69 years who participated in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study. Longitudinal data on smoking were collected during study follow-up visits 3 times a year (approximately every 4 months) between 1985 and 1993. Incident lung cancer patients through 2012 were identified by the Finnish Cancer Registry. Risk ratios (RRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards regression.

Results
Compared with smoking 20 cigarettes per day continuously across the intervention period, reducing an average of 5 cigarettes per day per year while smoking was associated with a 20% lower risk of lung cancer (95% CI = 0.71 to 0.90). A substantially lower risk of lung cancer was also observed when participants smoked at 50% (RR = 0.72, 95% CI = 0.57 to 0.90) and 10% (RR = 0.55, 95% CI = 0.36 to 0.83) of study visits, relative to smoked at 100% of study visits.

Conclusions
Smokers may lower their risk of lung cancer by reducing smoking intensity (cigarettes per day while smoking) and the time they smoke. However, quitting smoking completely is the most effective way for smokers to reduce their risk of lung cancer.
Shifts in local governments’ corporatization intensity: evidence from German cities
Authors: Rackwitz Maike , Raffer Christian 
Published: January 2024

Abstract
Why do local governments create and reform public service companies, given their uncertain economic benefits and potential damage to accountability and service transparency? Taking an extended transaction cost perspective, we argue that corporatization—the provision of public services by publicly owned companies—is a function of fiscal hardship, the decision maker’s economic orientation and the level of operator transparency. Using a two-way fixed effects regression, we test this expectation on 680 investment reports of 34 German cities from 1998 to 2017, representing 11,062 year-corporatized entity combinations. We show that the drivers of corporatization are sensitive to the depth of local ownership analyzed. In doing so, we highlight the theoretical need and potential for conceptual differentiation between ownership levels along a corporation’s lineage. Exploiting the data’s panel structure, we also find that the intensity of corporatization has heightened since the late 1990s, largely due to increasingly complex corporate structures of indirect ownership.