bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feasibility of reservoir monitoring in the Groningen gas field using ghost reflections from seismic interferometry
Authors: Shirmohammadi Faezeh , Draganov Deyan , Veltmeijer Aukje , Naderloo Milad , Barnhoorn Auke 
Published: March 2024

SUMMARY
Seismic interferometry (SI) retrieves new seismic responses, for example reflections, between either receivers or sources. When SI is applied to a reflection survey with active sources and receivers at the surface, non-physical (ghost) reflections are retrieved as well. Ghost reflections, retrieved from the correlation of two primary reflections or multiples from two different depth levels, are only sensitive to the properties in the layer that cause them to appear in the result of SI, such as velocity, density and thickness. We aim to use these ghost reflections for monitoring subsurface changes, to address challenges associated with detecting and isolating changes within the target layer in monitoring. We focus on the feasibility of monitoring pore-pressure changes in the Groningen gas field in the Netherlands using ghost reflections. To achieve this, we utilize numerical modelling to simulate scalar reflection data, deploying sources and receivers at the surface. To build up subsurface models for monitoring purposes, we perform an ultrasonic transmission laboratory experiment to measure S-wave velocities at different pore pressures. Applying SI by autocorrelation to the modelled data sets, we retrieve zero-offset ghost reflections. Using a correlation operator, we determine time differences between a baseline survey and monitoring surveys. To enhance the ability to detect small changes, we propose subsampling the ghost reflections before the correlation operator and using only virtual sources with a complete illumination of receivers. We demonstrate that the retrieved time differences between the ghost reflections exhibit variations corresponding to velocity changes inside the reservoir. This highlights the potential of ghost reflections as valuable indicators for monitoring even small changes. We also investigate the effect of the sources and receivers’ geometry and spacing and the number of virtual sources and receivers in retrieving ghost reflections with high interpretability resolution.
Antibacterial Agents May Have Shifted Impacts on Inflammatory Bowel Diseases Along with Decrease in Gut Bacteria
Authors: Qin Xiaofa 
Published: March 2024

Lay Summary
This article discussed the likely bell-shaped complicated impacts of antibacterial agents such as food additives like some artificial sweeteners on inflammatory bowel diseases including ulcerative colitis and Crohn’s disease along with decrease in gut bacteria.
Endemic and cryptic: different biogeographic histories of three Italian blister beetles of the genus Meloe (Coleoptera: Meloidae: Meloinae: Meloini)
Authors: Riccieri Alessandra , Spagoni Lucrezia , Bologna Marco A 
Published: March 2024

Abstract
The Italian geographic region is characterized by complex and diversified biogeographic patterns and is represented by a high number of endemic species. Endemic species characterized by a limited distribution range should be a primary concern in conservation. This article aimed to investigate the phylogenetic and biogeographic relationships of 2 Italian endemic species of the wingless blister beetle genus Meloe Linnaeus, 1758: Meloe (Eurymeloe) apenninicus and Meloe (E.) baudii. Our inferences, based on morphological characters, 2 mitochondrial (16S and COI) and 2 nuclear (CAD and 28S) markers and the use of 3 species delimitation analyses approaches, pointed out the presence of a new Italian endemic species (M. (E.) digiuliorumsp. n.), here described, and 3 different patterns of phylogenetic and biogeographic affinities. M. digiuliorum is close to the Spanish endemic M. orobatescomb. n., revealing a possible fragmentation of the ancestor range in the Pleistocene (ca. 0.84 Mya) followed by isolation in Italy and Spain. M. apenninicus is the sister species of the European-Anatolian M. rugous and M. cfr. rugosus, and this pattern originated around the Plio-Pleistocene boundary (ca. 2.83 Mya) likely influenced by the climatic fluctuations and the presence of the Alpine barrier. Finally, 2 subspecies were referred to M. baudii: the nominal one, endemic to Italy, and the Turanian-E European M. b. glazunovistat. n., disclosing a third more recent (ca. 0.64 Mya) pattern of biogeographic disjunction.
Learning competing risks across multiple hospitals: one-shot distributed algorithms
Authors: Zhang Dazheng , Tong Jiayi , Jing Naimin , Yang Yuchen , Luo Chongliang , Lu Yiwen , Christakis Dimitri A , Güthe Diana , Hornig Mady , Kelleher Kelly J , Morse Keith E , Rogerson Colin M , Divers Jasmin , Carroll Raymond J , Forrest Christopher B , Chen Yong 
Published: March 2024

Abstract

Objectives
To characterize the complex interplay between multiple clinical conditions in a time-to-event analysis framework using data from multiple hospitals, we developed two novel one-shot distributed algorithms for competing risk models (ODACoR). By applying our algorithms to the EHR data from eight national children’s hospitals, we quantified the impacts of a wide range of risk factors on the risk of post-acute sequelae of SARS-COV-2 (PASC) among children and adolescents.

Materials and Methods
Our ODACoR algorithms are effectively executed due to their devised simplicity and communication efficiency. We evaluated our algorithms via extensive simulation studies as applications to quantification of the impacts of risk factors for PASC among children and adolescents using data from eight children’s hospitals including the Children’s Hospital of Philadelphia, Cincinnati Children’s Hospital Medical Center, Children’s Hospital of Colorado covering over 6.5 million pediatric patients. The accuracy of the estimation was assessed by comparing the results from our ODACoR algorithms with the estimators derived from the meta-analysis and the pooled data.

Results
The meta-analysis estimator showed a high relative bias (∼40%) when the clinical condition is relatively rare (∼0.5%), whereas ODACoR algorithms exhibited a substantially lower relative bias (∼0.2%). The estimated effects from our ODACoR algorithms were identical on par with the estimates from the pooled data, suggesting the high reliability of our federated learning algorithms. In contrast, the meta-analysis estimate failed to identify risk factors such as age, gender, chronic conditions history, and obesity, compared to the pooled data.

Discussion
Our proposed ODACoR algorithms are communication-efficient, highly accurate, and suitable to characterize the complex interplay between multiple clinical conditions.

Conclusion
Our study demonstrates that our ODACoR algorithms are communication-efficient and can be widely applicable for analyzing multiple clinical conditions in a time-to-event analysis framework.
Race and Antibiotic Use for Children Hospitalized With Acute Respiratory Infections
Authors: Tan Jenna H , McGrath Caitlin L , Brothers Adam W , Fatemi Yasaman , Konold Victoria , Pak Daniel , Weissman Scott J , Zerr Danielle M , Kronman Matthew P 
Published: March 2024

Abstract
We sought to evaluate whether children hospitalized with acute respiratory infections experienced differences in antibiotic use by race and ethnicity. We found that likelihood of broad-spectrum antibiotic receipt differed across racial and ethnic groups. Future work should confirm this finding, evaluate causes, and ensure equitable antibiotic use.
Neuropeptide W protects against ovarian oxidative injury and reinforces ovarian steroidogenic activity via the upregulation of ERα expression
Authors: Arabacı Tamer Sevil , Şen Leyla Semiha , Güneş Kasım , Yüksel Meral , Çetinel Şule , Yeğen Berrak Ç 
Published: March 2024

Abstract

Objectives
The aim of this study was to investigate the protective effect of neuropeptide W (NPW) on ovarian ischemia–reperfusion-induced oxidative injury and ovarian steroid metabolism.

Methods
Rats were randomly divided into control and ischemia groups that received either saline or NPW (0.1 or 5 μg/kg/day). Bilateral ovarian ischemia was performed for 3 h followed by a 72-h reperfusion. Blood, ovary, and uterus samples were collected for biochemical and histological assessments.

Key findings
Treatment with either dose of NPW alleviated oxidative injury of the ovaries with a significant suppression in free radical formation and decreased histopathological injury in both the ovarian and uterine tissues, along with reduced lipid peroxidation and neutrophil accumulation in the uterus. Moreover, NPW treatment reversed the decrease in aromatase expression with a concomitant reduction in the expression of the inactivity enzyme estrogen sulfotransferase. Also, downregulation of estrogen receptor-α (ERα) expression in the injured ovarian tissue was abolished by NPW treatment, which implicates that the protective effect of NPW on the female reproductive system may involve the upregulation of the ERα-mediated signaling pathway.

Conclusions
Our study demonstrated for the first time that NPW protects against ovarian oxidative injury and reinforces ovarian steroidogenic activity, which is accompanied by the upregulation of ERα expression in the ovaries.
Sex differences in cancer outcomes across the range of eGFR
Authors: Shemilt Richard , Sullivan Michael K , Hanlon Peter , Jani Bhautesh D , De La Mata Nicole , Rosales Brenda , Elyan Benjamin M P , Hedley James A , Cutting Rachel B , Wyld Melanie , McAllister David A , Webster Angela C , Mark Patrick B , Lees Jennifer S 
Published: March 2024

ABSTRACT

Background
People with chronic kidney disease (CKD) have increased incidence and mortality of most cancer types. We hypothesized that the odds of presenting with advanced cancer may vary according to differences in estimated glomerular filtration rate (eGFR), that this could contribute to increased all-cause mortality and that sex differences may exist.

Methods
Data were from Secure Anonymised Information Linkage Databank, including people with de novo cancer diagnosis (2011–17) and two kidney function tests within 2 years prior to diagnosis to determine baseline eGFR (mL/min/1.73 m2). Logistic regression models determined the odds of presenting with advanced cancer by baseline eGFR. Cox proportional hazards models tested associations between baseline eGFRCr and all-cause mortality.

Results
eGFR &lt;30 was associated with higher odds of presenting with advanced cancer of prostate, breast and female genital organs, but not other cancer sites. Compared with eGFR &gt;75–90, eGFR &lt;30 was associated with greater hazards of all-cause mortality in both sexes, but the association was stronger in females [female: hazard ratio (HR) 1.71, 95% confidence interval (CI) 1.56–1.88; male versus female comparison: HR 0.88, 95% CI 0.78–0.99].

Conclusions
Lower or higher eGFR was not associated with substantially higher odds of presenting with advanced cancer across most cancer sites, but was associated with reduced survival. A stronger association with all-cause mortality in females compared with males with eGFR &lt;30 is concerning and warrants further scrutiny.
Long non-coding RNA lung cancer-associated transcript-1 promotes glioblastoma progression by enhancing Hypoxia-inducible factor 1 alpha activity
Authors: Huang Haidong , Shah Hariti , Hao Jing , Lin Jianhong , Prayson Richard A , Xie Liangqi , Bao Shideng , Chakraborty Abhishek A , Jankowsky Eckhard , Zhao Jianjun , Yu Jennifer S 
Published: March 2024

Abstract

Background
Hypoxia is associated with poor prognosis in many cancers including glioblastoma (GBM). Glioma stem-like cells (GSCs) often reside in hypoxic regions and serve as reservoirs for disease progression. Long non-coding RNAs (lncRNAs) have been implicated in GBM. However, the lncRNAs that modulate GSC adaptations to hypoxia are poorly understood. Identification of these lncRNAs may provide new therapeutic strategies to target GSCs under hypoxia.

Methods
lncRNAs induced by hypoxia in GSCs were identified by RNA-seq. Lung cancer-associated transcript-1 (LUCAT1) expression was assessed by qPCR, RNA-seq, Northern blot, single molecule FISH in GSCs, and interrogated in IvyGAP, The Cancer Genome Atlas, and CGGA databases. LUCAT1 was depleted by shRNA, CRISPR/Cas9, and CRISPR/Cas13d. RNA-seq, Western blot, immunohistochemistry, co-IP, ChIP, ChIP-seq, RNA immunoprecipitation, and proximity ligation assay were performed to investigate mechanisms of action of LUCAT1. GSC viability, limiting dilution assay, and tumorigenic potential in orthotopic GBM xenograft models were performed to assess the functional consequences of depleting LUCAT1.

Results
A new isoform of Lucat1 is induced by Hypoxia inducible factor 1 alpha (HIF1α) and Nuclear factor erythroid 2-related factor 2 (NRF2) in GSCs under hypoxia. LUCAT1 is highly expressed in hypoxic regions in GBM. Mechanistically, LUCAT1 formed a complex with HIF1α and its co-activator CBP to regulate HIF1α target gene expression and GSC adaptation to hypoxia. Depletion of LUCAT1 impaired GSC self-renewal. Silencing LUCAT1 decreased tumor growth and prolonged mouse survival in GBM xenograft models.

Conclusions
A HIF1α-LUCAT1 axis forms a positive feedback loop to amplify HIF1α signaling in GSCs under hypoxia. LUCAT1 promotes GSC self-renewal and GBM tumor growth. LUCAT1 is a potential therapeutic target in GBM.
Proton versus photon craniospinal irradiation for adult medulloblastoma: A dosimetric, toxicity, and exploratory cost analysis
Authors: Breen William G , Geno Connie S , Waddle Mark R , Qian Jing , Harmsen William S , Burns Terry C , Sener Ugur T , Ruff Michael W , Neth Bryan J , Uhm Joon H , Routman David M , Yan Elizabeth , Kruse Jon J , Laack Nadia N , Brown Paul D , Mahajan Anita 
Published: March 2024

Abstract

Background
This study aimed to determine whether proton craniospinal irradiation (CSI) decreased the dose to normal tissue and resulted in less toxicity than photon CSI for adult patients.

Methods
This single-institution retrospective analyzed differences in radiation doses, acute toxicity, and cost between proton and CSI for adult medulloblastoma patients.

Results
Of 39 total patients, 20 were treated with photon CSI prior to 2015, and 19 were treated with proton CSI thereafter. Median age was 28 years (range 18–66). The molecular subtype was most commonly sonic hedgehog (68%). Patients most commonly received 36 Gy CSI in 20 fractions with a boost to 54–55.8 Gy (92%). Proton CSI delivered significantly lower mean doses to cochleae, lacrimal glands, lens, parotid glands, pharyngeal constrictors, esophagus, lungs, liver, and skin (all P &lt; .001). Patients receiving proton CSI had significantly lower rates of acute dysphagia of any grade (5% versus 35%, P = .044) and decreased median weight loss during radiation (+1.0 versus –2.8 kg, P = .011). Weight loss was associated with acute hospitalization (P = .009). Median follow-up was 2.9 and 12.9 years for proton and photon patients, respectively, limiting late toxicity and outcome comparisons. At the last follow-up, 5 photon patients had died (2 of progressive disease, 3 without recurrence ages 41–63) and 21% had experienced major cardiovascular events. At 10 years, 89% were alive and 82% were recurrence free.

Conclusions
This study demonstrates dosimetric improvements with proton CSI, potentially leading to decreased acute toxicity including dysphagia and weight loss during treatment.
Basis risk and the demand for catastrophic rainfall insurance
Authors: Negi Digvijay S , Ramaswami Bharat 
Published: March 2024

Abstract
Rainfall is an important source of covariate shock in developing countries. Insurance against a rainfall index has, therefore, held much promise as a formal insurance product to protect the livelihoods of poor farmers. But how good is rainfall as a measure of covariate shocks? The imperfect association between them has been flagged as a reason for low demand for index insurance. Using district crop yields and rainfall data for India, we find that tail dependence characterizes the association between aggregate crop yields and rainfall. Could this property be exploited to design catastrophic loss insurance programs that have low basis risk? Using simulations of the estimated copulas, we show that the value of index-based insurance relative to actuarial cost is higher for insurance against extreme losses (of the index) than for insurance against all losses. We conclude that index insurance could find greater acceptability if it only insured extreme losses.
Identification of early risk factors for anti-citrullinated-protein-antibody positive rheumatoid arthritis—a prospective cohort study
Authors: Cîrciumaru Alexandra , Kisten Yogan , Hansson Monika , Mathsson-Alm Linda , Joshua Vijay , Wähämaa Heidi , Loberg Haarhaus Malena , Lindqvist Joakim , Padyukov Leonid , Catrina Sergiu-Bogdan , Fei Guozhong , Vivar Nancy , Rezaei Hamed , af Klint Erik , Antovic Aleksandra , Réthi Bence , Catrina Anca I , Hensvold Aase 
Published: March 2024

Abstract

Objective
Individuals positive for anti-cyclic-peptide-antibodies (anti-CCP) and musculoskeletal complaints (MSK-C) are at risk for developing rheumatoid arthritis (RA). In this study we aimed to investigate factors involved in arthritis progression.

Methods
Anti-CCP2-positive individuals with MSK-C referred to a rheumatologist were recruited. Individuals lacked arthritis at clinical and ultrasound examination and were followed for ≥3 years or until clinical arthritis diagnosis. Blood samples from inclusion were analysed for nine ACPA reactivities (citrullinated α-1-enolase, fibrinogen, filaggrin, histone, vimentin and tenascin peptides); 92 inflammation-associated proteins; and HLA-shared epitope alleles. Cox regression was applied to the data to identify independent predictors in a model.

Results
Two hundred and sixty-seven individuals were included with median follow-up of 49 months (interquartile range [IQR]: 22–60); 101 (38%) developed arthritis after a median of 14 months (IQR: 6–27). The analysis identified that presence of at least one ACPA reactivity (hazard ratio [HR] 8.0; 95% CI: 2.9, 22), ultrasound-detected tenosynovitis (HR 3.4; 95% CI: 2.0, 6.0), IL-6 levels (HR 1.5; 95% CI: 1.2, 1.8) and IL-15 receptor α (IL-15Rα) levels (HR 0.6; 95% CI: 0.4, 0.9) are significant independent predictors for arthritis progression in a prediction model (Harrell’s C 0.76 [s.e. 0.02], AUC 0.82 [95% CI: 0.76, 0.89], cross-validated AUC 0.70 [95% CI: 0.56, 0.85]).

Conclusion
We propose a high RA risk phase characterized by presence of ACPA reactivity, tenosynovitis, IL-6 and IL-15Rα and suggest that these factors need to be further investigated for their biological effects and clinical values, to identify individuals at particular low risk and high risk for arthritis progression.
Biomarker analysis from the phase 2b randomized placebo-controlled trial of riociguat in early diffuse cutaneous systemic sclerosis
Authors: Khanna Dinesh , Kramer Frank , Höfler Josef , Ghadessi Mercedeh , Sandner Peter , Allanore Yannick , Denton Christopher P , Kuwana Masataka , Matucci-Cerinic Marco , Pope Janet E , Atsumi Tatsuya , Bečvář Radim , Czirják László , De Langhe Ellen , Hachulla Eric , Ishii Tomonori , Ishikawa Osamu , Johnson Sindhu R , Riccieri Valeria , Schiopu Elena , Silver Richard M , Smith Vanessa , Stagnaro Chiara , Steen Virginia , Stevens Wendy , Szücs Gabriella , Truchetet Marie-Elise , Wosnitza Melanie , Distler Oliver 
Published: March 2024

Abstract

Objective
To examine disease and target engagement biomarkers in the RISE-SSc trial of riociguat in early diffuse cutaneous systemic sclerosis and their potential to predict the response to treatment.

Methods
Patients were randomized to riociguat (n = 60) or placebo (n = 61) for 52 weeks. Skin biopsies and plasma/serum samples were obtained at baseline and week 14. Plasma cyclic guanosine monophosphate (cGMP) was assessed using radio-immunoassay. α-Smooth muscle actin (αSMA) and skin thickness were determined by immunohistochemistry, mRNA markers of fibrosis by qRT-PCR in skin biopsies, and serum CXC motif chemokine ligand 4 (CXCL-4) and soluble platelet endothelial cell adhesion molecule-1 (sPECAM-1) by enzyme-linked immunosorbent assay.

Results
By week 14, cGMP increased by 94 (78)% with riociguat and 10 (39)% with placebo (P &lt; 0.001, riociguat vs placebo). Serum sPECAM-1 and CXCL-4 decreased with riociguat vs placebo (P = 0.004 and P = 0.008, respectively). There were no differences in skin collagen markers between the two groups. Higher baseline serum sPECAM-1 or the detection of αSMA-positive cells in baseline skin biopsies was associated with a larger reduction of modified Rodnan skin score from baseline at week 52 with riociguat vs placebo (interaction P-values 0.004 and 0.02, respectively).

Conclusion
Plasma cGMP increased with riociguat, suggesting engagement with the nitric oxide–soluble guanylate cyclase–cGMP pathway. Riociguat was associated with a significant reduction in sPECAM-1 (an angiogenic biomarker) vs placebo. Elevated sPECAM-1 and the presence of αSMA-positive skin cells may help to identify patients who could benefit from riociguat in terms of skin fibrosis.

Trial registration
Clinicaltrials.gov, NCT02283762.
Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush
Authors: Fedosov Alexander E , Zaharias Paul , Lemarcis Thomas , Modica Maria Vittoria , Holford Mandë , Oliverio Marco , Kantor Yuri I , Puillandre Nicolas 
Published: March 2024

Abstract
The molluskan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in the early stages of diversification, generating a “bush” at the base of their evolutionary tree, which has been hard to resolve even with high throughput molecular data. In the present study to resolve the bush, we use a variety of phylogenetic inference methods and a comprehensive exon capture dataset of 1817 loci (79.6% data occupancy) comprising 112 taxa of 48 out of 60 Neogastropoda families. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolving most backbone nodes, 3 prove problematic: First, the uncertain placement of Cancellariidae, as the sister group to either a Ficoidea-Tonnoidea clade or to the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major “core Neogastropoda” grouping. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analyzed phylogenetic signal of targeted loci in relation to potential biases, and we propose the most probable resolutions in the latter 2 recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to differential paralog loss shortly after the whole genome duplication, which should be resolved with a curated set of longer loci.