bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Efficacy of Biologics and Small Molecule Therapies in Improving Patient-Reported Outcomes in Ulcerative Colitis: Systematic Review and Network Meta-Analysis
Authors: Shehab Mohammad , Hassan Amro , Alrashed Fatema , Abbas Adnan , Ma Christopher , Narula Neeraj , Jairath Vipul , Singh Siddharth , Bessissow Talat 
Published: August 2024

Abstract

Background
Ulcerative colitis (UC) is a chronic disorder with a considerable negative impact on health-related quality of life (HRQoL), which has been recently recognized as an important treatment target. The purpose of this study is to compare the efficacy of different biologics and small molecule therapies in achieving better patient-reported outcomes and HRQoL in patients with UC.

Methods
We performed a systematic review and network meta-analysis of the EMBASE, MEDLINE, and Cochrane Central databases from inception until February 1, 2024. The primary endpoint was clinical remission in the patient-reported outcome (PRO-2) score in UC patients who were treated with different biologics or small molecules during induction and maintenance phases. PRO-2 score is the sum of both stool frequency and rectal bleeding subscores. The secondary outcome was improvement of HRQoL defined as an increase in Inflammatory Bowel Disease Questionnaire score of ≥16 points from baseline or any change in total score from baseline. A random effects model was used, and outcomes were reported as odds ratio with 95% confidence interval. Interventions were ranked per the SUCRA (surface under the cumulative ranking curve) score.

Results
A total of 54 studies were included in the primary outcome analysis and 15 studies were included in the secondary outcome analysis. The primary analysis showed that during the induction phase all of included drugs were better than placebo in improving the PRO-2 score. Interestingly, upadacitinib was found to be superior to most medications in improving PRO-2 scores. The secondary analysis showed that guselkumab ranked first in the improvement of the Inflammatory Bowel Disease Questionnaire score, followed by upadacitinib during the induction phase.

Conclusion
Upadacitinib ranked first in PRO-2 clinical remission during the induction and maintenance phases. Guselkumab, mirikizumab, tofacitinib, and upadacitinib were the only novel medications that were superior to placebo in improving HRQoL in UC, with guselkumab ranking the highest, followed by tofacitinib and upadacitinib. During maintenance of remission, tofacitinib ranked highest in improving HRQoL.
Reconstitution of Norovirus-Specific T-Cell Responses Following Hematopoietic Stem Cell Transplantation in Patients With Inborn Errors of Immunity and Chronic Norovirus Infection
Authors: Durkee-Shock Jessica , Cohen Ariella , Maghzian Naseem , Pezzella Gloria , Jensen-Wachspress Mariah , Hostal Anna , Barton Karenna , Gangler Krista , Dávila Saldaña Blachy J , Chaimongkol Natthawan , Bollard Catherine M , Sosnovtsev Stanislav V , Cohen Jeffrey , Nagata Bianca M , Alves Derron A , Ghosh Rajarshi , Seifert Bryce A , Freeman Alexandra , Gonzalez Corina , Notarangelo Luigi D , Green Kim Y , Keller Michael D 
Published: August 2024

Abstract

Background
Chronic norovirus infection (CNI) causes significant morbidity in immunocompromised patients. No effective prevention or treatment currently exists.

Methods
Two patients with inborn errors of immunity, X-linked severe combined immunodeficiency (X-SCID) and DOCK8 deficiency, were followed longitudinally for clinical course, immune reconstitution, norovirus-specific T-cell (NST) response, B-cell reconstitution, and norovirus-specific antibody production. Samples were obtained in the peri-hematopoietic stem cell transplant (HSCT) setting before and after CNI clearance. The norovirus strain causing CNI was followed longitudinally for norovirus stool viral loads and sequencing.

Results
The noroviruses were identified as GII.4 Sydney[P4 New Orleans] in 1 patient and GII.17[P17] in the other. An exacerbation of diarrhea post-HSCT in the patient with X-SCID was consistent with norovirus infection but not with graft-versus-host disease on pathologic samples. Both patients recovered polyfunctional NSTs in the CD4 and CD8 T-cell compartments that recognized multiple norovirus structural and nonstructural viral antigens. T-cell responses were minimal during active CNI but detectable after resolution. Mapping of NST responses between the patient with DOCK8 deficiency and his matched sibling donor were nearly identical. B-cell reconstitution or new endogenous antibody production for immunoglobulin A or immunoglobulin G was not observed.

Conclusions
This report is the first to demonstrate reconstitution of NST immunity after HSCT closely temporally aligned with clearance of CNI, suggesting that cellular immunity is sufficient for norovirus clearance.
Potentially avoidable hospitalizations and associated factors among older people in French Guiana using the French National Health Data System
Authors: Clarke Loreinzia , Castor-Newton Marie Josiane , Jalles Constanca , Lapeyre-Mestre Maryse , Gardette Virginie 
Published: August 2024

Abstract
Knowing the prevalence of potentially avoidable hospitalizations (PAHs) and the factors associated with them is essential if preventive action is to be taken. Studies on PAHs mainly concern adults, and very few have been carried out in South America. To the best of our knowledge, there has been no study on PAHs in French Guiana, particularly among older adults. This case–control study aimed to estimate the prevalence of PAHs in the Guianese population aged over 65 and to analyze their associated factors. We used the 2017–2019 data from the French National Health Service database (Système National des Données de Santé). The patients were age- and sex-matched 1 : 3 with controls without any PAH in 2019. Factors associated with PAHs were investigated through two conditional logistic regression models [one including the Charlson comorbidity index (CCI) and one including each comorbidity of the CCI], with calculation of the adjusted odds ratio (aOR) and 95% confidence interval (CI). The PAH incidence was 17.4 per 1000 inhabitants. PAHs represented 6.6% of all hospitalizations (45.6% related to congestive heart failure or hypertension). A higher CCI was associated with PAHs [aOR 2.2 (95% CI: 1.6, 3.0) and aOR 4.8 (95% CI: 2.4, 9.9) for 1–2 and ≥3 comorbidities, respectively, versus 0], as was immigrant health insurance status [aOR 2.3 (95% CI: 1.3, 4.2)]. Connective tissue disease, chronic pulmonary disease, congestive heart failure, diabetes, and peripheral vascular disease were comorbidities associated with an increased risk of PAHs. While the prevention of PAHs among immigrants is probably beyond the reach of the Guianese authorities, primary care and a public health policy geared toward prevention should be put in place for the French Guianese population suffering from cardiovascular disease in order to reduce PAHs.
Redefining the History and Historiography on American Evangelicalism in the Era of the Religious Right
Authors: Sutton Matthew Avery 
Published: August 2024

Abstract
Writing in the shadow of the religious right, a group of historians beginning in the 1980s crafted a new history of American evangelicalism to counter the politicized, right-wing faith of their era. Rather than focus on the movement as a product of specific historical, cultural, and political contexts, they defined it by a set of abstract theological principles. Then they identified those people from the colonial period to the present who fit their definition and who made positive contributions to North American history. The result was a new, singular, multi-century, “evangelical consensus” in the literature that decoupled the movement from politics, race, class, gender, and sexuality. I assess the historiography they created and then argue that we should drop the use of the term evangelical from our eighteenth- and nineteenth-century histories, and I offer a new definition of postwar evangelicalism that embeds it in its cultural context.
Simultaneous Extraction of Bone Marrow RNA and DNA from Patients with Hematologic Diseases Using a Combined Magnetic Bead Method within 1 Hour
Authors: Mu Huijun , Zou Jian , Zhang Haiping 
Published: August 2024

Abstract

Background
TRIzolTM is widely used for RNA and DNA extraction. However, this method is laborious and time-consuming. The objective of this study was to validate a time-effective and labor-saving protocol.

Methods
The TRIzol method was used to separate the aqueous phase, protein, and phenol layer of bone marrow samples from 12 patients with hematological diseases. Subsequently, RNA and DNA were extracted from the aqueous layer containing RNA and phenol layer containing DNA, respectively, using magnetic bead extraction kits. The quantity and purity of extracted RNA and DNA were examined using a NanoDrop spectrophotometer. Quantitative fluorescence PCR amplification of the ABL1 gene was performed to verify the effectiveness of the extracted RNA and DNA for downstream experiments. RNA and DNA from another 16 bone marrow samples were extracted to compare the performance of the two methods.

Results
Co-extraction of RNA and DNA was completed within 1 h. The data showed that RNA and DNA yield ranged from 13.1 to 204.5 ng/µL and 33.1 to 228.8 ng/µL, respectively. The A260/A280 ratios of RNA and DNA samples ranged from 1.82 to 2.01 and 1.73 to 1.91, respectively. RNA and DNA extracted using this scheme exhibited ideal performance in quantitative fluorescence PCR. The present protocol showed better quality and effectiveness in extracting RNA and DNA compared to the TRIzol method.

Conclusions
This protocol for RNA and DNA co-extraction is fast, labor-saving, and high throughput. It can be adopted for routine molecular biology analyses, particularly for non-reproducible specimens.
Enhancing Repo Market Transparency: The EU Securities Financing Transactions Regulation
Authors: Bassi Claudio , Grill Michael , Hermes Felix , Mirza Harun , O’Donnell Charles , Wedow Michael 
Published: August 2024

Abstract
The introduction of the Securities Financing Transactions Regulation into EU law provides a unique opportunity to obtain an in-depth understanding of repo markets. Based on the transaction-level data reported under the regulation, this article contributes to the literature with key facts about the euro area repo market. We start by providing the regulatory background, as well as highlighting some of its advantages for financial stability analysis. We then go on to present three sets of findings that are highly relevant to financial stability and focus on the dimensions of the different market segments, counterparties, and collateral, including haircut practices. Finally, we outline how the data reported under the regulation can support the policy work of central banks and supervisory authorities and contribute to the existing literature on repo markets. We demonstrate that these data can be used to make several important contributions to enhancing our understanding of the repo market from a financial stability perspective, ultimately assisting international efforts to increase repo market resilience.
X-ray afterglow limits on the viewing angles of short gamma-ray bursts
Authors: O’Connor Brendan , Beniamini Paz , Gill Ramandeep 
Published: August 2024

ABSTRACT
The behaviour of a short gamma-ray burst (sGRB) afterglow light curve can reveal the angular structure of the relativistic jet and constrain the observer’s viewing angle $\theta _\textrm {obs}$. The observed deceleration time of the jet, and, therefore, the time of the afterglow peak, depends on the observer’s viewing angle. A larger viewing angle leads to a later peak of the afterglow and a lower flux at peak. We utilize the earliest afterglow detections of 58 sGRBs detected with the Neil Gehrels Swift Observatory X-ray Telescope to constrain the ratio of the viewing angle $\theta _\textrm {obs}$ to the jet’s core $\theta _\textrm {c}$. We adopt a power-law angular jet structure in both energy $E(\theta)\propto \theta ^{-a}$ and Lorentz factor $\Gamma (\theta)\propto \theta ^{-b}$ beyond the core. We find that either sGRBs are viewed within $\theta _\textrm {obs}/\theta _\textrm {c}\lt 1$ or the initial Lorentz factor of material in their jet’s core is extremely high ($\Gamma _0\gt 500$). If we consider tophat jets, we constrain 90 per cent of our sample to be viewed within $\theta _\textrm {obs}/\theta _\textrm {c}\lt 1.06$ and 1.15 for our canonical and conservative afterglow scenarios. For a subset of events with measurements of the jet break, we can constrain $\Gamma _0\theta _\textrm {c}\gtrsim 30$. This confirmation that cosmological sGRBs are viewed either on-axis or very close to their jet’s core has significant implications for the nature of the prompt gamma-ray production mechanism and for the rate of future sGRB detections coincident with gravitational waves, implying that they are extremely rare.
Formation of the AlCl molecule through radiative association of Al with Cl
Authors: Jones (nee Burdakova) Daria , Nyman Gunnar 
Published: August 2024

ABSTRACT
Detection of the AlCl molecule in IRC+10216 has been reported in the literature. We here report calculations of reaction rate constants for formation of AlCl through radiative association of Al and Cl for a temperature interval of 1000 to 14000 K. Potential energy and permanent/transition dipole moment curves were taken from the literature. Quantum mechanical and semiclassical/classical methods were used to obtain the reaction cross-sections and thermal rate constants, accounting for shape resonances with Breit–Wigner theory. Both the A$^1 \Pi \rightarrow$ X$^1 \Sigma ^+$ transition and the X$^1 \Sigma ^+\rightarrow$ X$^1 \Sigma ^+$ transition have been treated, with results showing that the former dominates for the temperatures considered in this study. Our rate constants are a factor of two to three larger than previously calculated values, where the latter were obtained without considering resonances or the X$^1 \Sigma ^+\rightarrow$ X$^1 \Sigma ^+$ transition. Our new values do however not change the previous conclusion that radiative association can only contribute modestly to the formation of AlCl under the given conditions.
Association of human papillomavirus genotype and phylogenic clade with oropharyngeal cancer outcomes
Authors: Wotman Michael T , Ivic-Pavlicic Tara , Westra William H , Gold Brandon , D’Andrea Megan , Genden Eric M , Misiukiewicz Krzysztof , Roof Scott A , Taioli Emanuela , Posner Marshall 
Published: August 2024

Abstract

Background
Human papillomavirus (HPV)+ oropharynx cancer (OPC) has a more favorable prognosis than HPV-negative disease, but the impact of specific HPV genotype and phylogenic clade on patient outcomes is not well understood and has profound implications for treatment de-intensification.

Methods
The objective of this single-institution cohort study was to investigate the association of HPV genotype (16 vs high-risk non-16) and clade (A9 vs A7) with OPC outcomes. The primary endpoints were overall survival (OS) and event-free survival (EFS) in patients with M0 disease treated with curative intent.

Results
The cohort included 598 patients (87% HPV16, 98% A9). Compared to those with HPV16 OPC, individuals with non-HPV16 OPC had a higher age, comorbidity index, and proportion of non-whites, HIV+ patients, T4 tumors, and stage IV disease (AJCC 7th edition). Non-HPV16 genotype was associated with worse OS in univariate (HR = 2.17, 95% CI, 1.24-3.80, P = .0066), but not in multivariate analysis (HRadj = 0.84, 95% CI, 0.43-1.62, P = .5921). A7 clade was associated with worse OS in univariate (HR = 4.42, 95% CI, 1.60-12.30, P = .0041), but not in multivariate analysis (HRadj = 2.39, 95% CI, 0.57-9.99, P = .2325). Neither HPV genotype (HR = 1.60, 95% CI, 0.99-2.60, P = .0566) nor phylogenic clade (HR = 2.47, 95% CI, 0.91-6.72, P = .0761) was associated with EFS.

Conclusion
Non-HPV16 genotype and A7 clade were associated with worse OS and trended toward worse EFS in univariate analyses. The survival differences were more pronounced by phylogenic clade than by HPV16 status, suggesting that the former may be a more useful classification for future studies. However, neither HPV16 status nor phylogenic clade was prognostic when adjusting for patient and tumor covariates, raising the question as to whether possible differences in outcomes are related to distinct clinical profiles rather than inherent viral properties.
An intuitionistic interpretation of Bishop’s philosophy
Authors: Bentzen Bruno 
Published: August 2024

Abstract
The constructive mathematics developed by Bishop in Foundations of Constructive Analysis succeeded in gaining the attention of mathematicians, but discussions of its underlying philosophy are still rare in the literature. Commentators seem to conclude, from Bishop’s rejection of choice sequences and his severe criticism of Brouwerian intuitionism, that he is not an intuitionist–broadly understood as someone who maintains that mathematics is a mental creation, mathematics is meaningful and eludes formalization, mathematical objects are mind-dependent constructions given in intuition, and mathematical truths are experienceable. This paper develops and defends an intuitionistic interpretation of Bishop’s philosophical views.
Conserved cis-elements enable NODULES WITH ACTIVATED DEFENSE1 regulation by NODULE INCEPTION during nodulation
Authors: Yu Haixiang , Xiao Aifang , Zou Zhongmin , Wu Qiujin , Chen Lin , Zhang Dandan , Sun Yuzhang , Wang Chao , Cao Jianbo , Zhu Hui , Zhang Zhongming , Cao Yangrong 
Published: August 2024

Abstract
Symbiotic nitrogen fixation within nitrogen-fixing clade (NFC) plants is thought to have arisen from a single gain followed by massive losses in the genomes of ancestral non-nodulating plants. However, molecular evidence supporting this model is limited. Here, we confirm through bioinformatic analysis that NODULES WITH ACTIVATED DEFENSE1 (NAD1) is present only in NFC plants and is thus an NFC-specific gene. Moreover, NAD1 was specifically expressed in nodules. We identified three conserved nodulation-associated cis-regulatory elements (NACE1–3) in the promoter of LjNAD1 from Lotus japonicus that are required for its nodule specific expression. A survey of NFC plants revealed that NACE1 and NACE2 are specific to the Fabales and Papilionoideae, respectively, while NACE3 is present in all NFC plants. Moreover, we found that nodule inception (NIN) directly binds to all three NACEs to activate NAD1 expression. Mutation of L. japonicus LjNAD1 resulted in the formation of abnormal symbiosomes with enlarged symbiosome space and frequent breakdown of bacteroids in nodules, resembling phenotypes reported for Medicago truncatula Mtnad1 and Mtnin mutants. These data point to NIN–NAD1 as an important module regulating rhizobial accommodation in nodules. The regulation of NAD1 by NIN in the NFC ancestor represent an important evolutionary adaptation for nodulation.
Systemic sclerosis and cancer in the UK: an epidemiological analysis using the clinical practice research datalink
Authors: Pauling John D , McHugh Neil J , McGrogan Anita 
Published: August 2024

Abstract

Background
Cancer can cause mortality in systemic sclerosis (SSc). We investigated the association between cancer and SSc using the Clinical Practice Research Datalink (CPRD).

Methods
A validated case-ascertainment strategy identified SSc patients in the CPRD. A cohort study design examined cancer occurrence following SSc, with SSc patients matched to six non-SSc comparators by age, sex and GP practice. Prevalent and incident cases of SSc were analysed separately. Descriptive statistics and Cox analyses determined hazard ratios for cancer occurrence. A case-control study (matched 1:6) examined cancer occurrence prior to SSc.

Results
From 10.1 million individuals in CPRD, 1588 of cases of SSc were identified. Two hundred and six cancers followed SSc diagnosis (116 in prevalent and 90 in incident cohort). Commonest cancers were mucocutaneous (4.5%), lung (2.1%) and breast (1.9%). The proportion of SSc patients developing cancer was significantly higher than non-SSc in both incident (11.2% vs 9.7%, P = 0.02) and prevalent cohorts (14.8% vs 12.1%, P = 0.03); particularly for lung cancer (2.6% vs 0.9% in prevalent cohort, P &lt; 0.001). Overall incidence of cancer in the SSc groups was 17.6/1000 person years, compared with 13.9/1000 person years in the non-SSc group. The adjusted hazard ratios for cancer were 1.41 (95% CI 1.14–1.75) and 1.32 (95% CI 1.04–1.67) for prevalent and incident SSc, respectively. No increased risk of cancer prior to SSc diagnosis was identified in the case-control study.

Conclusion
We have identified an increased risk of cancer diagnosis following, but not before, SSc diagnosis. Our findings could support screening recommendations for cancer in SSc.
Amphetamine-Induced Dopamine Release Predicts 1-Year Outcome in First-Episode Psychosis: A Naturalistic Observation
Authors: Weidenauer Ana , Sauerzopf Ulrich , Bauer Martin , Bum Carina , Diendorfer Cornelia , Dajic Irena , Bartova Lucie , Kastner Alina , Bamminger Karsten , Nics Lukas , Philippe Cecile , Hacker Marcus , Rujescu Dan , Wadsak Wolfgang , Praschak-Rieder Nicole , Willeit Matthäus 
Published: August 2024

Abstract

Background and Hypothesis
The dopamine theory of schizophrenia suggests that antipsychotics alleviate symptoms by blocking dopamine D2/3 receptors, yet a significant subset of patients does not respond adequately to treatment. To investigate potential predictors, we evaluated d-amphetamine-induced dopamine release and 1-year clinical outcomes in 21 antipsychotic-naive patients with first-episode schizophrenia.

Study Design
Twenty-one antipsychotic-naive patients (6 female) underwent dopamine D2/3 receptor radioligand [11C]-(+)-PHNO positron emission tomography. For estimating dopamine release, scans were performed with and without d-amphetamine pretreatment. The Positive and Negative Syndrome Scale was performed at regular intervals over 1 year while receiving treatment in a naturalistic setting (Clinical Trial Registry: EUDRACT 2010-019586-29).

Study Results
A group analysis revealed no significant differences in d-amphetamine-induced dopamine release between patients with or without clinically significant improvement. However, d-amphetamine-induced dopamine release in ventral striatum was significantly associated with reductions in positive symptoms (r = 0.54, P = .04; uncorrected P-values); release in globus pallidus correlated with a decrease in PANSS negative (r = 0.58, P = .02), general (r = 0.53, P = .04), and total symptom scores (r = 0.063, P = .01). Higher dopamine release in substantia nigra/ventral tegmental area predicted larger reductions in general symptoms (r = 0.51, P = .05). Post-amphetamine binding in putamen correlated positively with negative symptom scores at baseline (r = 0.66, P = .005) and throughout all follow-up visits.

Conclusions
These exploratory results support a relationship between d-amphetamine-induced dopamine release and the severity and persistence of symptoms during the first year of psychosis.
Regulatory agencies as innovation enablers: a conceptualization
Authors: Bonnin Roca Jaime 
Published: August 2024

Abstract
Regulatory agencies are usually tasked with a dual mission of assessing the benefits and risks posed by products reaching the market, and ensuring the competitiveness of the industries they oversee. Although literature usually presents regulators as agents hampering innovation, that is not always the case. The purpose of this paper is to discuss, under which conditions, and why, regulatory agencies may enable innovation. I propose a conceptual framework to connect the literatures on regulatory processes and innovation processes. Based on this framework, I analyse three connections between the innovation and regulatory processes, which create opportunities for agencies’ innovation intermediation. I provide real-life examples of three different mechanisms through which such intermediation may take place, and propose four modes of intermediation which are characteristic of regulatory agencies.