bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis
Authors: Del Chierico Federica , Cardile Sabrina , Baldelli Valerio , Alterio Tommaso , Reddel Sofia , Bramuzzo Matteo , Knafelz Daniela , Lega Sara , Bracci Fiammetta , Torre Giuliano , Maggiore Giuseppe , Putignani Lorenza 
Published: September 2023

Abstract

Background
Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis.

Methods
By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs).

Results
Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients.

Conclusions
We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC.
Co-feeding enhances the yield of methyl ketones
Authors: Ziegler Anita L , Grütering Carolin , Poduschnick Leon , Mitsos Alexander , Blank Lars M 
Published: September 2023

Abstract

The biotechnological production of methyl ketones is a sustainable alternative to fossil-derived chemical production. To date, the best host for microbial production of methyl ketones is a genetically engineered Pseudomonas taiwanensis VLB120 ∆6 pProd strain, achieving yields of 101 mgg−1 on glucose in batch cultivations. For competitiveness with the petrochemical production pathway, however, higher yields are necessary. Co-feeding can improve the yield by fitting the carbon-to-energy ratio to the organism and the target product. In this work, we developed co-feeding strategies for P. taiwanensis VLB120 ∆6 pProd by combined metabolic modeling and experimental work. In a first step, we conducted flux balance analysis with an expanded genome-scale metabolic model of iJN1463 and found ethanol as the most promising among five cosubstrates. Next, we performed cultivations with ethanol and found the highest reported yield in batch production of methyl ketones with P. taiwanensis VLB120 to date, namely, 154 mg g−1 methyl ketones. However, ethanol is toxic to the cell, which reflects in a lower substrate consumption and lower product concentrations when compared to production on glucose. Hence, we propose cofeeding ethanol with glucose and find that, indeed, higher concentrations than in ethanol-fed cultivation (0.84 g Laq−1 with glucose and ethanol as opposed to 0.48 g Laq−1 with only ethanol) were achieved, with a yield of 85 mg g−1. In a last step, comparing experimental with computational results suggested the potential for improving the methyl ketone yield by fed-batch cultivation, in which cell growth and methyl ketone production are separated into two phases employing optimal ethanol to glucose ratios.

One-Sentence Summary
By combining computational and experimental work, we demonstrate that feeding ethanol in addition to glucose improves the yield of biotechnologically produced methyl ketones.
Therapeutic mechanism of Liangxue-Guyuan-Yishen decoction on intestinal stem cells and tight junction proteins in gastrointestinal acute radiation syndrome rats
Authors: Yan Ziqiao , Yin Bofeng , Wang Yuguo , Ni Zhexin , Feng Jian , Yang Qianyu , Li Xiao , Zhu Heng , Dou Yongqi 
Published: September 2023

Abstract
On the basis of the previous research, the Traditional Chinese Medicine theory was used to improve the drug composition for gastrointestinal acute radiation syndrome (GI-ARS). The purpose of this study was to study the therapeutic mechanism of Liangxue-Guyuan-Yishen decoction (LGYD) on GI-ARS and to provide a new scheme for the treatment of radiation injury. Here, we investigated the effects of LGYD on intestinal stem cells (ISCs) in a GI-ARS rat model. Rat health and survival and the protective efficacy of LGYD on the intestines were analyzed. The active principles in LGYD were detected using liquid chromatography-mass spectrometry (LC–MS). ISC proliferation, intestinal epithelial tight junction (TJ) protein expression and regulatory pathways were explored using immunohistochemistry, western blotting (WB) and reverse transcription quantitative polymerase chain reaction (RT-qPCR), respectively. Involvement of the WNT and MEK/ERK pathways in intestinal recovery was screened using network pharmacology analysis and validated by WB and RT-qPCR. LGYD administration significantly improved health and survival in GI-ARS rats. Pathological analysis showed that LGYD ameliorated radiation-induced intestinal injury and significantly promoted LGR5+ stem cell regeneration in the intestinal crypts, upregulated TJ protein, and accelerated crypt reconstruction in the irradiated rats. LC–MS revealed ≥13 constituents that might contribute to LGYD’s protective effects. Collectively, LGYD can promote crypt cell proliferation and ISCs after radiation damage, the above effect may be related to WNT and MEK/ERK pathway.
The Sufi Writing Tradition in Arabic
Authors: Salamah-Qudsi Arin 
Published: September 2023

Abstract
This paper addresses Sufi writing in its contemporary third/ninth-fifth/eleventh century CE context, looking at how writing was shaped by other Sufi and non-Sufi forms. Beginning with an overview of the Sufi writing tradition in Arabic during Sufism's formative period, between the early third/ninth and the late sixth/twelfth centuries, the article goes on to discuss early Sufi piety and the ways it challenged common conceptions and epistemological paradigms of early medieval Islamic thought. Looking at the mid fourth/tenth century case of al-Niffarī shows how mystical piety interacterd with a deep-rooted tradition in Arabic literature to forge the unique dynamics of what we know today as Sufi writing.
Using Auxiliary Information in Probability Survey Data to Improve Pseudo-Weighting in Nonprobability Samples: A Copula Model Approach
Authors: Zhu Tingyu , Gamble Laura J , Klapman Matthew , Xue Lan , Lesser Virginia M 
Published: September 2023

Abstract
While probability sampling has been considered the gold standard of survey methods, nonprobability sampling is increasingly popular due to its convenience and low cost. However, nonprobability samples can lead to biased estimates due to the unknown nature of the underlying selection mechanism. In this article, we propose parametric and semiparametric approaches to integrate probability and nonprobability samples using common ancillary variables observed in both samples. In the parametric approach, the joint distribution of ancillary variables is assumed to follow the latent Gaussian copula model, which is flexible to accommodate both categorical and continuous variables. In contrast, the semiparametric approach requires no assumptions about the distribution of ancillary variables. In addition, logistic regression is used to model the mechanism by which population units enter the nonprobability sample. The unknown parameters in the copula model are estimated through the pseudo maximum likelihood approach. The logistic regression model is estimated by maximizing the sample likelihood constructed from the nonprobability sample. The proposed method is evaluated in the context of estimating the population mean. Our simulation results show that the proposed method is able to correct the selection bias in the nonprobability sample by consistently estimating the underlying inclusion mechanism. By incorporating additional information in the nonprobability sample, the combined method can estimate the population mean more efficiently than using the probability sample alone. A real-data application is provided to illustrate the practical use of the proposed method.
Adapting international natural gas and LNG agreements in the light of the energy transition
Authors: Talus Kim 
Published: September 2023

Abstract
This article will examine the bidirectional relationship between private energy contracts and the transition towards a net-zero world. It will focus on long-term take-or-pay natural gas and liquefied natural gas sale and purchase agreements (natural gas and LNG SPAs) that are commonly used in the natural gas sector. These agreements often contain highly restrictive clauses that are designed to ensure stability of supply and demand, which makes them suitable for acquiring the project financing necessary for large capital-intensive energy projects. At the same time, these agreements create an important lock-in effect for the contracting parties. This article will examine the details of gas SPAs from the perspective of this lock-in effect. It will show that current contractual formulations do not provide an adequate solution in the context of the energy transition. Because of this lock-in effect, there is an urgent need to adapt existing contract forms for future use, and to modify the continued application of existing executory contracts to accommodate new realities.
Alone Together: Is Strain Experienced Concurrently by Members of Operating Room Teams?: An Event-based Study
Authors: Keller Sandra , Yule Steven , Smink Douglas S. , Zagarese Vivian , Safford Shawn , Valea Fidel A. , Beldi Guido , Henrickson Parker Sarah 
Published: September 2023

Objective:
To identify which strain episodes are concurrently reported by several team members; to identify triggers of strain experienced by operating room (OR) team members during the intraoperative phase.

Summary:
OR teams are confronted with many sources of strain. However, most studies investigate strain on a general, rather than an event-based level, which does not allow to determine if strain episodes are experienced concurrently by different team members.

Methods:
We conducted an event-based, observational study, at an academic medical center in North America and included 113 operations performed in 5 surgical departments (general, vascular, pediatric, gynecology, and trauma/acute care). Strain episodes were assessed with a guided-recall method. Immediately after operations, participants mentally recalled the operation, described the strain episodes experienced and their content.

Results:
Based on 731 guided recalls, 461 strain episodes were reported; these refer to 312 unique strain episodes. Overall, 75% of strain episodes were experienced by a single team member only. Among different categories of unique strain episodes, those triggered by task complexity, issues with material, or others’ behaviors were typically experienced by 1 team member only. However, acute patient issues (n = 167) and observations of others’ strain (n = 12) (respectively, 58.5%; P < 0.001 and 83.3%; P < 0.001) were often experienced by 2 or more team members.

Conclusions and relevance:
OR team members are likely to experience strain alone, unless patient safety is at stake. This may jeopardize the building of a shared understanding among OR team members.
National ICU Registries as Enablers of Clinical Research and Quality Improvement
Authors: Salluh Jorge I. F. , Quintairos Amanda , Dongelmans Dave A. , Aryal Diptesh , Bagshaw Sean , Beane Abigail , Burghi Gaston , López Maria del Pilar Arias , Finazzi Stefano , Guidet Bertrand , Hashimoto Satoru , Ichihara Nao , Litton Edward , Lone Nazir I. , Pari Vrindha , Sendagire Cornelius , Vijayaraghavan Bharath Kumar Tirupakuzhi , Haniffa Rashan , Pisani Luigi , Pilcher David ,   on behalf of Linking of Global Intensive Care (LOGIC) and Japanese Intensive care PAtient Database (JIPAD) Working Group
Published: September 2023

OBJECTIVES:
Clinical quality registries (CQRs) have been implemented worldwide by several medical specialties aiming to generate a better characterization of epidemiology, treatments, and outcomes of patients. National ICU registries were created almost 3 decades ago to improve the understanding of case-mix, resource use, and outcomes of critically ill patients. This narrative review describes the challenges, proposed solutions, and evidence generated by National ICU registries as facilitators for research and quality improvement.

DATA SOURCES:
English language articles were identified in PubMed using phrases related to ICU registries, CQRs, outcomes, and case-mix.

STUDY SELECTION:
Original research, review articles, letters, and commentaries, were considered.

DATA EXTRACTION:
Data from relevant literature were identified, reviewed, and integrated into a concise narrative review.

DATA SYNTHESIS:
CQRs have been implemented worldwide by several medical specialties aiming to generate a better characterization of epidemiology, treatments, and outcomes of patients. National ICU registries were created almost 3 decades ago to improve the understanding of case-mix, resource use, and outcomes of critically ill patients. The initial experience in European countries and in Oceania ensured that through locally generated data, ICUs could assess their performances by using risk-adjusted measures and compare their results through fair and validated benchmarking metrics with other ICUs contributing to the CQR. The accomplishment of these initiatives, coupled with the increasing adoption of information technology, resulted in a broad geographic expansion of CQRs as well as their use in quality improvement studies, clinical trials as well as international comparisons, and benchmarking for ICUs.

CONCLUSIONS:
ICU registries have provided increased knowledge of case-mix and outcomes of ICU patients based on real-world data and contributed to improve care delivery through quality improvement initiatives and trials. Recent increases in adoption of new technologies (i.e., cloud-based structures, artificial intelligence, machine learning) will ensure a broader and better use of data for epidemiology, healthcare policies, quality improvement, and clinical trials.
Ray-Tracing Transepithelial Excimer Laser Central Corneal Remodeling Plus Pachymetry-Guided Accelerated Corneal Crosslinking for Keratoconus
Authors: Mazzotta Cosimo , Stojanovic Aleksandar , Romano Vito , Addabbo Giuseppe , Borroni Davide , Balamoun Ashraf Armia , Ferrise Marco 
Published: September 2023

Purpose:
The aim of this study was to report the 12 to 96 months results of a tissue-preservation algorithm based on ray-tracing-guided transepithelial excimer laser central corneal ablation (RT t-PRK) combined with individualized pachymetry-guided accelerated crosslinking (M nomogram ACXL) in young adult patients with stable keratoconus (KC).

Methods:
This was a prospective interventional study including 38 eyes of 38 young adult patients (stage II KC) with a mean age of 35 years (range 26–46 years) who underwent simultaneous RT with t-PRK plus pachymetry-based ACXL in the worst eye. The treatments were performed using the iViS Suite iRES Excimer Laser (Ligi, Taranto, Italy). Ray-tracing–guided treatments were planned using the customized interactive programmed transepithelial ablation (CIPTA) 2 web software and diagnostic data were assessed by the Precisio 2 tomographer (Ligi, Taranto, Italy) and Sirius tomographer (C.S.O., Florence, Italy). The main outcome measures included uncorrected distance visual acuity, best spectacle–corrected visual acuity, Kmax, high-order aberrations, minimum corneal thickness, and posterior elevation, with a mean follow-up of 52 months (range 12–96 m).

Results:
The mean UDVA improved + 3.5 ±1.28 Snellen lines (SL); 38% gained ≥ 4 ±1.34 SLs, 35% ≥ 3 ±1.21 SLs, 22% ≥ 2 ±1.12 SLs, and 5% ≥ 1 ±0.75 SLs. The mean best spectacle–corrected visual acuity increased by + 4.3 ±1.3 SL. Sixty-eight percent gained ≥ 4 ±0.88 SLs and 30% ≥ 3 ±0.78 SL. No SLs were lost.

Conclusions:
RT t-PRK plus ACXL significantly improved the quality of vision in patients with KC, preventing overcorrection and minimizing tissue consumption.
Residual Dialkyl Phosphate Metabolite Concentrations of Organophosphate Pesticides Among Indian Farmworkers
Authors: Lari Summaiya , Pandiyan Arun , Vanka Janardhan , Jee Babban , Yamagani Praveen , Kumar Senthil Balakrishnan , Naidu Mohan , Jonnalagadda Padmaja 
Published: September 2023

Objective
Biomonitoring of urinary dialkyl phosphate (DAP) metabolites, a sensitive biomarker to assess pesticides exposure and also to study the impact of the use of personal protective equipment (PPE).

Methods
A preintervention-postintervention study to biomonitor dimethylphosphate, diethylphosphate, diethylthiophosphate, and diethyl-dithiophosphate using liquid chromatography with tandem mass spectrometry among Indian farmworkers (n = 120).

Results
Dimethylphosphate was detected in all samples at a mean concentration of 74.91 μg · L−1 (17.616 μg · g−1 creatinine), whereas diethylthiophosphate and diethyl-dithiophosphate were detected in 88% and 82% of samples, respectively, among farmworkers who adopted unsafe pesticide-handling practices. Intervention studies showed a significant reduction in the urinary DAP metabolites detected among the farmworkers using PPE provided to them (P < 0.01).

Conclusions
Study confirms the exposure to pesticides among farmworkers and highlights the importance of the use of PPE to minimize exposure.
Correlation between the preoperative maximum soleal vein diameter and the postoperative bilateral deep venous thrombosis in THA: a case–control study
Authors: Kimura Fumihiko , Watarai Keisuke , Okada Nobuhiko , Moronuki Takahisa , Kamatsuda Yoko , Nomura Kazuhiro , Kim Yoon Taek , Oda Hiromi , Kadono Yuho 
Published: September 2023

Background:
Patients with bilateral lower limb deep venous thrombosis (DVT) have a higher risk of pulmonary thromboembolism (PTE) and mortality than patients with unilateral lower limb DVT. Preoperative dilatation of the soleal vein (SV) diameter is a predictor of postoperative DVT. The purpose of this study is to investigate the cutoff value for SV diameter as a risk factor for VTE development.

Materials and methods:
The authors examined 274 patients with unilateral THA who met the inclusion criteria in a retrospective study. The mean age of the patients was 65.7±11.2 years, with 70 males and 204 females. Bilateral lower limb vein ultrasonography was performed preoperatively and ~1 week after THA. The frequency and localization of DVT were investigated in postoperative ultrasonography. The patients were divided into three groups: no DVT (non-DVT), unilateral lower limb DVT (Uni-DVT), and bilateral lower limb DVT (Bi-DVT). The three groups were compared in terms of preoperative venous vessel maximum diameter.

Results:
There were 62 patients (22.6%) who had postoperative DVT. There are no symptomatic PTE patients. DVT was found in 44 patients (16.0%) of the Uni-DVT group and 18 patients (6.6%) of the Bi-DVT group. The SV maximum diameter was 6.41±1.79 mm in the non-DVT group, 7.06±2.13 mm in the Uni-DVT group, and 8.06±2.26 mm in the Bi-DVT group, with a significant difference (P=0.001) between the non-DVT and Bi-DVT groups. In the Bi-DVT group, the cutoff value for preoperative SV maximum diameter was 6.75 mm (95% CI: 0.625–0.831; P=0.001; sensitivity, 77.8%; specificity, 60.4%; area under the curve, 0.728).

Conclusions:
In THA, preoperative ultrasonography with a maximum SV diameter of 6.75 mm or greater was the risk of bilateral DVT leading to fatal PTE is increased.
Prospective quantitative study: Doppler ultrasound in the evaluation of chronic renal allograft disease and correlation with histopathological finding
Authors: Katwal Shailendra , Suwal Sundar , Bhandari Rajan M. , Chataut Dinesh , Ansari Mukhtar Alam , Lamichhane Suman 
Published: September 2023

Background and Objectives:
Renal allograft biopsy is the gold standard for diagnosing chronic allograft nephropathy, but noninvasive methods are needed to avoid unnecessary biopsies. Doppler ultrasonography, particularly the resistive index (RI), correlates with renal allograft dysfunction. This study aims to assess the relationship between renal sonographic parameters and biochemical parameters in diagnosing graft interstitial fibrosis.

Methods:
The study evaluated 60 renal allograft recipients for sonographic renal morphological features and Doppler indices. The estimated glomerular filtration rate (eGFR) was calculated, and cortical fibrosis after the biopsy was determined using the Banff score. Continuous variables like mean and SD were calculated, and categorical variables were reported using frequencies and proportions. Associations were examined using independent sample t-tests, χ
2tests, and multivariate regression analysis.

Results:
The mean eGFR was 75.23±25.45 ml/min/1.73 m2. A significant correlation of eGFR with RI (r=0.341, P=0.008) was seen. A significant difference in mean RI (F=10.167; df=2,57; P<0.001) was seen among the histological grades of fibrosis. Among the histological grades of fibrosis, significant differences in RI among mild and moderate (S.E. 0.033, P=0.043), mild and severe (S.E. 0.026, P=0.001) as well as moderate and severe (S.E. 0.036, P=0.029) was seen.

Conclusion:
Doppler was able to noninvasively predict allograft fibrosis and could be used as a complementary imaging tool during the follow-up of renal allograft patients. Future research is needed to improve evidence, diagnostic criteria, guidelines, and long-term impact.