bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis
Authors: Horstmann Lucas , Lipus Daniel , Bartholomäus Alexander , Arens Felix , Airo Alessandro , Ganzert Lars , Zamorano Pedro , Schulze-Makuch Dirk , Wagner Dirk 
Published: April 2024

AbstractDesert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.
Causal association of genetically determined caffeine intake from tea or coffee with bone health: a two-sample Mendelian randomization study
Authors: Li Gloria Hoi-Yee , Tang Ching-Man , Wu Suet-Man , Cheung Ching-Lung 
Published: April 2024

Abstract

Background
Relationship of caffeine intake and consumption of caffeinated beverages, such as tea and coffee, with bone health remains controversial. This study aimed to evaluate whether genetically determined caffeine intake from tea or coffee has causal effects on overall total body bone mineral density (TB-BMD) and fracture. We also assessed the association with TB-BMD in five age strata.

Methods
Using two-sample Mendelian randomization approach, summary statistics were retrieved from genome-wide association studies (GWAS)/GWAS meta-analyses of caffeine intake from tea (n = 395 866)/coffee (n = 373 522), TB-BMD (n = 66 628), and fracture (n = 426 795). Inverse variance weighted method was adopted as the main univariable analysis. Multivariable analysis was conducted to evaluate whether the causal effect is independent.

Results
In univariable analysis, genetically determined caffeine intake from tea had positive association with overall TB-BMD (per SD increase in genetically determined caffeine intake, beta of TB-BMD [in SD]: 0.166; 95% confidence interval (CI): 0.006–0.326) and inverse association with fracture (OR = 0.79; 95% CI: 0.654–0.954). Genetically determined caffeine intake from coffee was also positively associated with overall TB-BMD (beta = 0.231; 95% CI: 0.093–0.369). The association remained significant after adjustment for smoking in multivariable analysis. Genetically determined caffeine intake from tea or coffee was both positively associated with TB-BMD in the age strata of 45–60 years, but we lacked evidence of association in other strata.

Conclusions
Genetically, caffeine intake from tea or coffee may be beneficial to bone health. Due to the ascertainment method of caffeine intake from tea, our study also implied genetically higher tea consumption may improve TB-BMD and lower fracture risk.
republic: A variability-preserving systematic-correction algorithm for PLATO’s multi-camera light curves
Authors: Barragán Oscar , Aigrain Suzanne , McCormac James 
Published: April 2024

Abstract
Space-based photometry missions produce exquisite light curves that contain a wealth of stellar variability on a wide range of time-scales. Light curves also typically contain significant instrumental systematics – spurious, non-astrophysical trends that are common, in varying degrees, to many light curves. Empirical systematics-correction approaches using the information in the light curves themselves have been very successful, but tend to suppress astrophysical signals, particularly on longer time-scales. Unlike its predecessors, the PLAnetary Transits and Oscillations of stars (PLATO) mission will use multiple cameras to monitor the same stars. We present republic, a novel systematics-correction algorithm which exploits this multi-camera configuration to correct systematics that differ between cameras, while preserving the component of each star’s signal that is common to all cameras, regardless of time-scale. Through simulations with astrophysical signals (star spots and planetary transits), Kepler-like errors, and white noise, we demonstrate republic’s ability to preserve long-term astrophysical signals usually lost in standard correction techniques. We also explore republic’s performance with different number of cameras and systematic properties. We conclude that republic should be considered a potential complement to existing strategies for systematic correction in multi-camera surveys, with its utility contingent upon further validation and adaptation to the specific characteristics of the PLATO mission data.
Major cardiovascular events in patients with cardiovascular monosodium urate deposits in atherosclerotic plaques
Authors: Held Julia , Schwabl Christoph , Haschka David , Maier Sarah , Feuchtner Gudrun , Widmann Gerlig , Duftner Christina , Weiss Günter , Klauser Andrea 
Published: April 2024

Abstract

Objective
To determine the association of cardiovascular atherosclerotic plaque monosodium urate deposits with the occurrence of major cardiovascular events in gout and hyperuricemia patients.

Methods
This retrospective cohort study included patients with clinically suspicion of gout, who performed a dual energy computed tomography of the affected limb and thorax between 1 June 2012 and 5 December 2019. Clinical and laboratory parameters were retrieved from patients’ charts. Established cardiovascular risk factors were evaluated. Medical history review identified the presence of major adverse cardiac events with a median follow-up time of 33 months (range 0–108 months) after the performed computed tomography scan.

Results
Full data sets were available for 189 patients: 131 (69.3%) gout patients, 40 (21.2%) hyperuricemia patients and 18 (9.5%) controls. Patients with cardiovascular monosodium urate deposits (n = 85/189, 45%) revealed increased serum acute phase reactants, uric acid levels and calcium scores in computed tomography compared with patients without cardiovascular monosodium urate deposits. Major adverse cardiac events were observed in 35 patients (18.5%) with a higher prevalence in those patients revealing cardiovascular monosodium urate deposits (n = 22/85, 25.9%) compared with those without cardiovascular monosodium urate deposits (n = 13/104, 12.5%, OR 2.4, P = 0.018).

Conclusion
This is the first study demonstrating the higher hazard of major adverse cardiac events in patients with dual energy computed tomography-verified cardiovascular monosodium urate deposits. The higher prevalence of cardiac events in patients with cardiovascular monosodium urate deposits may facilitate risk stratification of gout patients, as classical cardiovascular risk scores or laboratory markers fail in their proper identification.
Exploring the impact of polystyrene microplastics on human health: unravelling the health implications of polystyrene microplastics (PS-MPs): a comprehensive study on cytotoxicity, reproductive health, human exposure, and exposure assessment
Authors: Dilip Bhandare Saurabh 
Published: April 2024

Abstract
This investigation explores the various impacts that polystyrene microplastics (PS-MPs) have on human health. As most of the plastic materials affect human health when they release leachable toxic substances that affect human health, this causes a negative effect that determines poor health conditions and leads to health hazards associated with plastic toxins routed in the human body, such as: Polychlorinated Biphenyls, Polybrominated Biphenyls etc. The study includes micro-plastic exposure assessment on testicular structure analysis, and cytotoxicity evaluations of different human cell types. The findings clarified the possible dangers of PS-MPs exposure from food, medications, and common products, emphasising the necessity of standard specimen handling procedures for precise biomonitoring.
Examining the Association between Immunosuppressants and Wound Healing: A Narrative Review
Authors: Appoo Aria , Christensen Brandon L. , Somayaji Ranjani 
Published: April 2024

ABSTRACT

Objective
To review how different classes of immunosuppressants affect wound healing.

Data Sources
A literature search was conducted in PubMed, Google Scholar, and the University of Calgary Health Sciences Library.

Study Selection
The researchers initially screened article titles using key words such as “immunosuppressive medication,” “wound healing,” and “immunosuppression.” Articles in which the title and/or abstract contained these key words, that addressed wound healing related to immunosuppressant medications, and were published after 2000 were included in the review. When human data were not available for an immunosuppressant (class), animal studies were included.

Data Extraction
The 61 included articles underwent full text review and summarization.

Data Synthesis
All included studies were summarized descriptively including immunosuppressive mechanism of action, study participants or subjects, and evidence of effects on wound healing.

Conclusions
Corticosteroids and mechanistic target of rapamycin inhibitors most consistently demonstrate detrimental effects on wound healing. For other classes of immunosuppressants, evidence is limited with varying effects on wound healing described. Larger, high-quality studies are required to better understand the effects of immunosuppressants, including those with new mechanisms of action, to identify those with the most impact on wound healing.
The Effect of Stoma Site Marking on Stomal Complications: A Long-term Retrospective Study
Authors: Guler Sevil , Eyuboglu Gulcan , Baykara Zehra Gocmen , Hin Aysel Oren , Akdemir Hülya , Akar Emine , Leventoglu Sezai , Yuksel Osman 
Published: April 2024

ABSTRACT

OBJECTIVE
To identify the effect of stoma site marking on stoma-related complications.

METHODS
The study sample included 639 individuals with stomas who were followed up in a stomatherapy unit in Turkey between January 1, 2017, and June 20, 2021. Researchers collected patient data from nursing records. Data were evaluated using number, percentage, χ
2, and logistic regression tests.

RESULTS
Of the individuals with stomas, 60.6% (n = 387) were men, and 72.6% (n = 464) had a cancer diagnosis. Their mean age was 60.16 (SD, 14.81) years. The stoma site was marked preoperatively in of 67.1% of patients (n = 429), and 17.1% (n = 109) developed stoma-related complications. The complication rate was higher in individuals with unmarked stoma sites (25.7%; P = .000), emergency surgeries (25.0%; P = .006), colostomies (23.9%; P = .042), and permanent stomas (28.3%; P = .002). The three most common complications were peristomal skin problems (56.9%), mucocutaneous separation (13.8%), and edema (9.2%).

CONCLUSIONS
The incidence of stoma-related complications in the postoperative period was higher in individuals with unmarked stoma sites. The authors recommend that stoma and wound care nurses mark the stoma site in individuals for whom stoma creation is planned.
Multicenter, Prospective, Observational Trial of Nonoperative Versus Operative Treatment for High-Energy Midshaft Clavicle Fractures
Authors: Jeray Kyle J. , Broderick J. Scott , Mullis Brian H. , Everhart Joshua , Tanner Stephanie L. , Snider Becky G. ,   On behalf of Southeastern Fracture Consortium
Published: April 2024

OBJECTIVES:
Evaluate if nonoperative or operative treatment of displaced clavicle fractures delivers reduced rates of nonunion and improved DASH scores

METHODS:

Design: Multicenter, prospective, observational

Setting:
Seven Level 1 Trauma Centers in the United States

Patient Selection Criteria:
Adults with closed, displaced (100% displacement/shortened >1.5cm) midshaft clavicle fractures (OTA 15.2) treated nonoperatively, with plates and screw fixation, or with intramedullary fixation from 2003-2018.

Outcome Measures and Comparisons:
DASH scores (2 weeks, 6 weeks, 3, 6, 12, and 24 months), reoperation, and nonunion were compared between the nonoperative, plate fixation, and intramedullary fixation groups.

RESULTS:
412 patients were enrolled, with 203 undergoing plate fixation, 26 receiving intramedullary fixation, and 183 treated nonoperatively. The average age of the nonoperative group was 40.1 (range 18-79) years versus 35.8 (range 18-74) in the plate group and 39.3 (range 19-56) in the intramedullary fixation group (p=0.06). 140 (76.5%) patients in the nonoperative group were male compared to 154 (75.9%) in the plate group and 18 (69.2%) in the intramedullary fixation group (p=0.69). All groups showed similar DASH scores at 2 weeks, 12 and 24 months (p>0.05). Plate fixation demonstrated better DASH scores (median=20.8) than nonoperative (median=28.3) at 6 weeks (p=0.04). Intramedullary fixation had poorer DASH scores at 6 weeks, 3 and 6 months than plate fixation and worse DASH scores than nonoperative at 6 months (p<0.05). The nonunion rate for nonoperative treatment (14.6%) was significantly higher than the plate group (0%) (p<0.001).

CONCLUSION:
Operative treatment of displaced clavicle fractures provided lower rates of nonunion than nonoperative treatment. Except at 6 weeks, no difference was observed in DASH scores between plate fixation and nonoperative treatment. Intramedullary fixation resulted in worse DASH scores than plate fixation at 6 weeks, 3 and 6 months, and worse DASH scores than nonoperative at 6 months. Implant removal was the leading reason for reoperation in the plate and intramedullary fixation groups, while surgery for nonunion was the primary reason for surgery in the nonoperative group.

LEVEL OF EVIDENCE:
Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.
Characteristics and Outcomes of Occult Infections in Presumed Aseptic Nonunions: A Retrospective Cohort Study
Authors: Wagner Robert Kaspar , Emmelot Mees P. , van Trikt Clinton , Visser Caroline E. , Peters Edgar J.G. , Janssen Stein J. , Kloen Peter 
Published: April 2024

OBJECTIVES:
To determine (1) the rate of positive cultures in presumed aseptic nonunions, (2) the rate and microbial spectrum of positive cultures that represented occult infection, and (3) rates of nonunion healing.

METHODS:

Design:
Retrospective cohort study.

Setting:
Tertiary referral center.

Patients Selection Criteria:
Adult patients with a presumed aseptic nonunion treated with single-stage revision between 2002 and 2022.

Outcome Measures and Comparisons:
The rate of positive cultures compared for 2 protocols: old: 1–2 samples cultured 7 days versus new: 5 samples cultured 14 days. The rate of positive cultures meeting occult infection criteria with the new protocol (≥2 samples with phenotypically indistinguishable microorganisms, or ≥1 sample with a high virulent microorganism). Nonunion healing rates between protocols and between groups based on culture results with the new protocol.

RESULTS:
One hundred seventy-nine patients were included. The rate of positive cultures was 14% (n = 15/105) with the old protocol and 51% (n = 38/74) with the new protocol (P < 0.001). With the new protocol, the rate of positive cultures meeting occult infection criteria was 19% (n = 14/74), and coagulase-negative staphylococci (48%) and Cutibacterium acnes (38%) were the most common microorganisms. Nonunion healing rates after the primary revision did not differ between protocols (old: 82% vs. new: 86%, P = 0.41) and groups based on culture result (sterile: 86% vs. occultly infected: 93%, P = 0.66). The final overall nonunion healing rate was 97%.

CONCLUSIONS:
Occult infections were identified in 1 in 5 presumed aseptic nonunions using a standardized protocol with 5 intraoperative samples cultured 14 days and were predominantly caused by slow growing, gram-positive microorganisms. The local spectrum and antimicrobial sensitivity of occult infections should be considered when developing empiric antimicrobial protocols. Patients with presumed aseptic nonunions can expect high healing rates, regardless of the culture result.

LEVEL OF EVIDENCE:
Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
JFH1-based Core-NS2 genotype variants of HCV with genetic stability in vivo and in vitro: Important tools in the evaluation of virus neutralization
Authors: Collignon Laura , Holmbeck Kenn , Just Ashley , Verhoye Lieven , Velázquez-Moctezuma Rodrigo , Fahnøe Ulrik , Carlsen Thomas H. R. , Law Mansun , Prentoe Jannick , Scheel Troels K. H. , Gottwein Judith M. , Meuleman Philip , Bukh Jens 
Published: April 2024

Background and Aims:
HCV infection continues to be a major global health burden despite effective antiviral treatments. The urgent need for a protective vaccine is hindered by the scarcity of suitable HCV-permissive animal models tractable in vaccination and challenge studies. Currently, only antibody neutralization studies in infectious cell culture systems or studies of protection by passive immunization of human liver chimeric mice offer the possibility to evaluate the effect of vaccine-induced antibodies. However, differences between culture-permissive and in vivo–permissive viruses make it a challenge to compare analyses between platforms. To address this problem, we aimed at developing genotype-specific virus variants with genetic stability both in vitro and in vivo.

Approach and Results:
We demonstrated infection of human liver chimeric mice with cell culture–adapted HCV JFH1-based Core-NS2 recombinants of genotype 1–6, with a panel of 10 virus strains used extensively in neutralization and receptor studies. Clonal re-engineering of mouse-selected mutations resulted in virus variants with robust replication both in Huh7.5 cells and human liver chimeric mice, with genetic stability. Furthermore, we showed that, overall, these virus variants have similar in vitro neutralization profiles as their parent strains and demonstrated their use for in vivo neutralization studies.

Conclusions:
These mouse-selected HCV recombinants enable the triage of new vaccine-relevant antibodies in vitro and further allow characterization of protection from infection in vivo using identical viruses in human liver chimeric mice. As such, these viruses will serve as important resources in testing novel antibodies and can thus guide strategies to develop an efficient protective vaccine against HCV infection.
Prevalence and Predictors of Follow-up Endoscopic Biopsy in Patients With Celiac Disease in the United States
Authors: Venkat Manu V. , Chen Ling , Wright Jason D. , Lebwohl Benjamin 
Published: April 2024

Objective:
To characterize the frequency and predictors of follow-up endoscopic biopsy in patients with celiac disease.

Background:
The utility of routine follow-up biopsy in patients after a diagnosis of celiac disease is uncertain, especially in patients whose symptoms resolve on the gluten-free diet.

Patients and Methods:
Using the Merative MarketScan U.S. commercial insurance and Medicare databases, we identified 30,737 patients with biopsy-diagnosed celiac disease. We followed them until they had a second duodenal biopsy (our primary outcome) or insurance coverage ended.

Results:
Among the patients with celiac disease we identified, 5976 (19.4%) underwent a follow-up biopsy. The median time between initial and follow-up biopsies was 16.8 months. Compared with younger patients, those aged 20 years or older had an increased likelihood of undergoing a follow-up biopsy (cumulative incidence rate at 5 y for patients age ≥20 y was 36.0%, 95% CI: 35.0%-37.1% vs 21.9%, 95% CI: 20.5%-23.4% in patients age ≤19 y). Follow-up biopsies occurred less frequently in more recent calendar years. Follow-up biopsy was more common among patients with an Elixhauser Comorbidity Index of 1 (hazard ratio: 1.09; 95% CI: 1.01-1.17) or ≥2 (hazard ratio: 1.28; 95% CI: 1.20-1.37) compared with patients with an index of zero. Among patients who had a follow-up biopsy, 57% had a celiac disease-related symptom recorded in the 30 days before the procedure.

Conclusions:
Follow-up duodenal biopsy is performed in a substantial minority of U.S. patients with celiac disease. Adult age and increased comorbidity burden were associated with a greater likelihood of follow-up biopsy. Just under half of follow-up biopsies are performed for routine surveillance, in the absence of persistent symptoms.
Nomogram predicting survival in patients with lymph node-negative hepatocellular carcinoma based on the SEER database and external validation
Authors: Li Ziqiang , Hong Qingyong , Li Kun 
Published: April 2024

Background
The relationship between lymph node (LN) status and survival outcome in hepatocellular carcinoma (HCC) is a highly controversial topic. The aim of this study was to investigate the prognostic factors in patients without LN metastasis (LNM) and to construct a nomogram to predict cancer-specific survival (CSS) in this group of patients.

Methods
We screened 6840 eligible HCC patients in the Surveillance, Epidemiology and End Results（SEER）database between 2010 and 2019 and randomized them into a training cohort and an internal validation cohort, and recruited 160 patients from Zhongnan Hospital of Wuhan University as an external validation cohort. Independent prognostic factors obtained from univariate and multivariate analysis were used to construct a nomogram prediction model. The concordance index (C-index), area under curve (AUC), calibration plots and decision curve analysis (DCA) were used to assess the predictive power and clinical application of the model.

Results
Univariate and multivariate analysis revealed age, gender, bone metastasis, lung metastasis, AFP, T stage, surgery and chemotherapy as independent prognostic factors. The C-index of the constructed nomogram for the training cohort, internal validation cohort and external validation cohort are 0.746, 0.740, and 0.777, respectively. In the training cohort, the AUC at 1-, 3-, and 5-year were 0.81, 0.800, and 0.800, respectively. Calibration curves showed great agreement between the actual observations and predictions for the three cohorts. The DCA results suggest that the nomogram model has more clinical application potential.

Conclusion
We constructed a nomogram to predict CSS in HCC patients without LNM. The model has been internally and externally validated to have excellent predictive performance and can help clinicians determine prognosis and make treatment decisions.