bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic network of the gut microbiota in inflammatory bowel disease
Authors: Sugihara Kohei , Kamada Nobuhiko 
Published: March 2024

AbstractGut dysbiosis is closely linked to the pathogenesis of inflammatory bowel disease (IBD). Emerging studies highlight the relationship between host metabolism and the modulation of gut microbiota composition through regulating the luminal microenvironment. In IBD, various disease-associated factors contribute to the significant perturbation of host metabolism. Such disturbance catalyzes the selective proliferation of specific microbial populations, particularly pathobionts such as adherent invasive Escherichia coli and oral-derived bacteria. Pathobionts employ various strategies to adapt better to the disease-associated luminal environments. In addition to the host-microbe interaction, recent studies demonstrate that the metabolic network between commensal symbionts and pathobionts facilitates the expansion of pathobionts in the inflamed gut. Understanding the metabolic network among the host, commensal symbionts, and pathobionts provides new insights into the pathogenesis of IBD and novel avenues for treating IBD.
Does preoperative opioid use predict outcomes to 6 months following primary unilateral knee or hip arthroplasty for osteoarthritis? A data-linked retrospective study
Authors: Genel Furkan , Harris Ian A. , Pavlovic Natalie , Lewin Adriane , Mittal Rajat , Huang Andrew Y. , Penm Jonathan , Patanwala Asad E. , Brady Bernadette , Adie Sam , Naylor Justine M. 
Published: March 2024

Abstract
Background
Few Australian studies have examined the incidence of prescribed opioid use prior to primary total knee or total hip arthroplasty (TKA, THA) and whether it predicts post-surgery outcomes. A recent Australian study demonstrated that the prevalence of pre-arthroplasty opioid use was approximately 16%. In the United States, approximately 24% of people undergoing TKA or THA are chronic opioid users preoperatively.

Purpose
This study aimed to determine (i) the proportion of TKA and THA patients who use prescribed opioids regularly (daily) before surgery (i.e., opioid use reported between the time of waitlisting and any time up to 3 months before surgery), (ii) if opioid use before surgery predicts (a) complication/readmission rates to 6-months post-surgery, and (b) patient-reported outcomes to 6-months post-surgery.

Methods
A retrospective cohort study of patients who underwent TKA or THA between January 2013 and June 2018 from two Australian public hospitals was undertaken utilizing linked individual patient-level data from two prospectively collected independent databases comprising approximately 3,500 and 9,500 people (database contained known opioid usage data within the 5-year time frame). Inclusion criteria included (i) primary diagnosis of osteoarthritis of the index joint, (ii) primary elective THA or TKA, and (iii) age ≥ 18 years. Exclusion criteria included (i) revision arthroplasty, (ii) non-elective arthroplasty, (iii) hip hemiarthroplasty, (iv) uni-compartmental knee arthroplasty, and (v) previous unilateral high tibial osteotomy.

Results
Analysis was completed on 1,187 study participants (64% female, 69% TKA, mean (SD) age 67 [9.9]). 30% were using regular opioids preoperatively. Adjusted regression analyses controlling for multiple co-variates indicated no significant association between preoperative opioid use and complications/readmission rates or patient-reported outcomes to 6 months post-surgery. Model diagnostics produced poor discrimination for area under the curves and non-significant goodness of fit tests. Pre-arthroplasty opioid use was associated with lower health-related quality of life (EuroQol-Visual Analogue Scale) compared to non-opioid users undergoing primary THA (mean difference -5.04 [-9.87, -0.22], P = 0.04, Adjusted R2 = 0.06)

Conclusion
In this study, 30% of patients were using prescribed opioids daily prior to primary TKA or THA. Pre-arthroplasty opioid use was not associated with postoperative adverse events or patient-reported pain, function, or global perceived improvement up to six months post-surgery.
An initial typology of approaches used by policy and practice agencies to achieve sustained implementation of interventions to improve health
Authors: Wolfenden Luke , Shoesmith Adam , Hall Alix , Bauman Adrian , Nathan Nicole 
Published: March 2024

Abstract
Background
Scientific investigation of how to sustain the implementation of evidence-based interventions (EBI) is emerging. Sustaining the implementation of EBIs helps ensure their effects on improving health endure. External policy or practice agencies, such as government health departments, are often tasked with supporting individual organisations with sustaining their delivery of EBIs, for example, through financing, training or the provision of other supports. However, to our knowledge, the approaches taken by policy and practice agencies to support the sustainment of EBIs have not been consolidated, categorised and described as a typology.

Main body
To improve conceptual clarity and support both research and practice, we developed an initial working typology of the practical approaches to sustain implementation of EBIs (i.e. sustainment) in order to improve long term health from the perspective of these agencies. The working typology includes three broad approaches. The first, termed ‘Self-Sustainment’, is when implementation of the EBI by an organisation (e.g. hospital, clinic, school) is expected to continue (sustain) in the absence of external (agency) support. The second, termed ‘Static Sustainment Support’, involves the provision of pre-defined external (agency) support to assist organisations to continue implementation of an EBI. The final approach is termed ‘Dynamic Sustainment Support’, whereby support provided by an external agency is dynamic (continues to be adapted) overtime to assist organisations continue implementation of an intervention which may itself also evolve.

Conclusions
We describe the contexts and circumstances where each may be most appropriate in achieving sustained implementation and discuss their research and practice implications.
Evaluating the prediction power and accuracy of two smart response surface experimental designs after revisiting repaglinide floating tablets
Authors: Elsayed Tarek , Hathout Rania M. 
Published: March 2024

Abstract
Background
There is a soar in the figure of companies aiming to achieve efficiency in undergoing experimental processes. Therefore, instead of deploying one-factor-at-a-time, design of experiments is becoming rampantly utilized in order to reduce the resources outflow. There are a copious of different smart designs which could be employed as design of experiments tools. Central composite and d-optimal designs were investigated in this paper. The purpose of this investigation was to compare the two designs and identify the most accurate design at analyzing, interpreting and making predictions with regards to the data offered. The aforementioned purpose was achieved by applying both designs to a preexisting study which sought to prolong the gastrointestinal retention of repaglinide tablets through deploying a full factorial design. Further optimization was performed using Design-Expert software after inducing an outlier point.

Results
R-squared, adjusted R-squared, predicted R-squared and adequate precision were computed in addition to acquiring diagnostics figures such as predicted versus actual, residual versus run, Box–Cox, contour plot and 3D surface plots. Model equations were also produced for each design. Results showed that both designs were successful at modeling the data both scoring r-squared values > 0.7 and adequate precision > 4 implying high fitting, prediction power and ability to navigate the experimental space using a reduced number of experimental runs. The d-optimal design obtained the least relative error of only 3.81%.

Conclusions
In conclusion, the d-optimal design provides a great tool for reduction of experimental testing which in turn diminishes resources consumption. Therefore, this design is favored to be enforced in the pharmaceutical sector.
Unpredicted transformation of acute myeloid leukemia with translocation (16;16) (p13; q22): a case report and review of the literature
Authors: Zaiema Shams ElDoha Galal ElDin , Hafez Heba Mohamed Saber 
Published: March 2024

Abstract
Introduction
The transformation of acute myeloid leukemia with translocation (16;16) (p13; q22) from AML M2 to acute monocytic leukemia (AML M5) during therapy is a rare clinical occurrence, and this is the first time it has been reported.

Clinical complain
A 19-year-old male patient was admitted for severe fatigue with anemic manifestation and weight loss, for more than 1 month, with exacerbation of the condition in the last 2 days.

Diagnosis
A primary diagnosis was made for AML M2 with t (16;16) (p13; q22) established on bone marrow (BM) morphology. A consequential detection of FLT-3 ITD mutation was done. At day 28 follow-up after induction and maintenance therapy, the diagnosis of AML M2 was maintained with a high bone marrow (BM) blast count, prompting the initiation of a more aggressive treatment protocol. After 1 month of implementing the recent protocol, the patient remains morphologically resistant with a notable transformation of bone marrow infiltration by an abnormal monocytic population (monoblasts and promonocytes). The final diagnosis of transforming FLT3-mutated AML with t (16;16) (p13; q22) was established.

Intervention
After the initial diagnosis of AML M2 with t (16;16) (p13; q22), the patient received the 3 + 7 induction protocol. The 2nd induction protocol initiated after the second evaluation and morphological resistance was the FLAG Adrian protocol. The 3rd protocol after transformation to AML M5 was 1 cycle of the MEC protocol. Anti-FLT3 treatment was considered.

Outcomes
The patient was maintained on the 3rd protocol of chemotherapy. Unfortunately, he was admitted to the ICU unit complaining of neutropenic fever and severe sepsis where he died before final re-evaluation and the anti-FLT3 treatment initiation.

Conclusion
AML with t (16;16) (p13; q22) characterized by favorable outcome. However, identifying additional chromosome abnormality or genetic aberration, especially FLT3 gene mutation, is recognized as an important factor influencing final disease outcome. Therefore, early detection of FLT3 mutations will allow comprehensive disease course prediction and targeted therapy that might achieve longer and more durable remissions.
Predictive accuracy of years score in diagnosis of pulmonary embolism
Authors: Fayiad Hussien , Moussa Heba , Nosair Yara , Mostafa Amira Ismail 
Published: March 2024

Abstract
Background
Pulmonary embolism (PE) is a sudden obstruction of pulmonary arteries usually associated with a high rate of mortality due to acute right ventricular failure. Early diagnosis is of much importance because most patients die within the first hours of presentation. Emergency management is usually highly valuable and right heart failure is potentially reversible. Multidetector computed tomography pulmonary angiography (CTPA) is the best diagnostic imaging modality to document acute pulmonary embolism. Overuse of CTPA increases the unrequired risk of radiation exposure, increasing the risk of malignancy, contrast-related anaphylaxis, and acute kidney injury. To abolish these issues, the simplified score for suspected acute pulmonary embolism using variable D dimer cut-off value in combination with clinical signs can exclude pulmonary embolism safely.

Aim of the study
To evaluate the predictive accuracy of YEARS score in the diagnosis of pulmonary embolism compared to CTPA that might lead to a decrease in the overuse of CTPA.

Methods
The study was held at the chest unit in Kasr ElAini hospitals. It included 50 patients, for which full history, examination, calculation of wells score, D-dimer, YEARS score, and CTPA were done.

Results
The results showed that the YEARS score succeeded in predicting the presence or the absence of PE in 80% of the 50 enrolled patients in our study. YEARS score has a sensitivity of 90% and specificity of 65%.

Conclusion
Patients with zero YEARS score and D-dimer ≥ 1000 ng/ml as well as those with ≥ 1 YEARS score and D-dimer ≥ 500 ng/ml are rendered PE likely by the YEARS algorithm with a sensitivity of 90%. Using years score, we can exclude pulmonary embolism in patients with zero YEARS score and a D-dimer ˂ 1000 ng/ml as well as in patients with ≥ 1 YEARS score and D-dimer ˂ 500 ng/ml with 65% specificity, thus decreasing overuse of CTPA in the diagnosis of PE.
Free-surface multiple attenuation and seismic deghosting for blended data using convolutional neural networks
Authors: Kiraz Mert S. R. , Snieder Roel , Sheiman Jon 
Published: March 2024

Simultaneous source acquisition has become common over the past few decades for marine seismic surveys because of the increased efficiency of seismic acquisition by limiting the time, reducing the cost, and having less environmental impact than conventional single-source (or unblended) acquisition surveys. For simultaneous source acquisition, seismic sources at different locations are fired with time delays, and the recorded data are referred to as the blended data. The air-water interface (or free surface) creates strong multiples and ghost reflections for blended seismic data. The multiples and/or ghost reflections caused by a source in the blended data overlap with the primary reflections of another source, thus creating a strong interference between the primary and multiple events of different sources. We develop a convolutional neural network (CNN) method to attenuate free-surface multiples and remove ghost reflections simultaneously from the blended seismic data. The CNN-based solution that we develop operates on single traces and is not sensitive to the missing near-offset traces, missing traces, and irregular/sparse acquisition parameters (e.g., for ocean-bottom node acquisition and time-lapse monitoring studies). We illustrate the efficacy of our free-surface multiple attenuation and seismic deghosting method by presenting synthetic and field data applications. The numerical experiments demonstrate that our CNN-based approach for simultaneously attenuating free-surface multiples and removing ghost reflections can be applied to the blended data without the deblending step. Although the interference of primaries and multiples from different shots in the blended data makes free-surface multiple attenuation harder than the unblended data, we determine that our CNN-based method effectively attenuates free-surface multiples in the blended synthetic and field data even when the delay time for the blending is different in the training data than in the data to which the CNN is applied.
Characterization of Novel PHEX Variants in X-linked Hypophosphatemic Rickets and Genotype-PHEX Activity Correlation
Authors: Wu Huixiao , Ying Hui , Zhao Wanyi , Sun Yan , Wang Yanzhou , Chen Xinyu , Li Guimei , Yao Yangyang , Xu Shuo , Li Tianyou , Fang Li , Sun Xiaoqing , Wang Ning , Xu Jin , Guan Qingbo , Xia Weibo , Wang Li , Gao Ling , Zhao Jiajun , Xu Chao 
Published: March 2024

Abstract

Background
X-linked hypophosphatemia (XLHR) is the most common genetic form of hypophosphatemic rickets (HR), which is caused by phosphate regulating endopeptidase homolog X-linked (PHEX) gene mutation. At present, the genotype–phenotype relationship of XLHR and the pathogenic role of PHEX are not fully understood.

Methods
In this study, we summarized clinical features in a new cohort of 49 HR patients and detected 16 novel PHEX and 5 novel non-PHEX variants. Subsequently, we studied the pathogenesis of new variants by protein expression, glycosylation analysis, subcellular localization, and endopeptidase activity.

Results
The results showed that missense variants (Q189H and X750R) slightly reduced protein expression without obviously altering protein length and localization, whereas truncating variants significantly impaired the synthesis of PHEX and produced a shorter immature protein in cells. Interestingly, no evident correlation was observed between mutation types and clinical phenotypes. However, when we analyzed the relationship between PHEX activity and serum phosphorus level, we found that patients with low PHEX activity tended to have severe hypophosphatemia and high rickets severity score. Following this observation, we established 2 new knock-in XLHR mouse models with 2 novel Phex variants (c.T1349C and c.C426G, respectively) using CRISPR/Cas9 technology. Both mouse models demonstrated clinical manifestations of XLHR seen in patients, and PhexC426G mice showed more severe phenotype than PhexT1349C mice, which further confirmed the rationality of genotype–PHEX enzymatic activity correlation analysis.

Conclusion
Therefore, our findings demonstrated that novel PHEX variants could disrupt protein function via affecting protein synthesis, post-translational modification, cellular trafficking, and catalytic activity. Our study facilitates a better understanding of XLHR pathogenic mechanism and PHEX activity-phenotype correlation, which is of crucial importance for future diagnosis and treatment of XLHR.
Pediatric Medullary Thyroid Carcinoma: Clinical Presentations and Long-Term Outcomes in 144 Patients Over 6 Decades
Authors: Hensley Sarah G , Hu Mimi I , Bassett Roland L , Ying Anita K , Zafereo Mark E , Perrier Nancy D , Busaidy Naifa L , Hyde Samuel M , Grubbs Elizabeth G , Waguespack Steven G 
Published: March 2024

Abstract

Context
Sporadic medullary thyroid carcinoma (sMTC) rarely occurs in childhood and no studies have specifically focused on this entity.

Objective
To describe the clinical presentations and long-term outcomes of a large cohort of children and young adults with sMTC compared with hereditary MTC (hMTC).

Methods
Retrospective study of 144 patients diagnosed with MTC between 1961 and 2019 at an age ≤ 21 years and evaluated at a tertiary referral center.

Results
In contrast to hMTC (n = 124/144, 86%), patients with sMTC (n = 20/144, 14%) are older (P &lt; .0001), have larger tumors (P &lt; .0001), a higher initial stage grouping (P = .001) and have more structural disease (P = .0045) and distant metastases (DM) (P = .00084) at last follow-up, but are not more likely to die from MTC (P = .42). Among 77 patients diagnosed clinically, not by family history (20/20 sMTC and 57/124 hMTC), there was no difference in the initial stage (P = .27), presence of DM at diagnosis (P = 1.0), disease status at last follow-up (P = .13), overall survival (P = .57), or disease-specific survival (P = .87). Of the 12 sMTC tumors that underwent somatic testing, 11 (91%) had an identifiable alteration: 10 RET gene alterations and 1 ALK fusion.

Conclusion
sMTC is primarily a RET-driven disease that represents 14% of childhood-onset MTC in this cohort. Pediatric sMTC patients are older, present with clinical disease at a more advanced TNM classification, and have more persistent disease at last follow-up compared with hMTC, but these differences disappear when comparing those presenting clinically. Somatic molecular testing should be considered in sMTC patients who would benefit from systemic therapy.
Multicenter Registry of Adenomas of the Pituitary and Related Disorders: Initial Description of Cushing Disease Cohort, Surgical Outcomes, and Surgeon Characteristics
Authors: Little Andrew S. , Karsy Michael , Evans James J. , Kim Won , Pacione Donato R. , Kim Albert H. , Gardner Paul A. , Hendricks Benjamin K. , Sarris Christina E. , Torok Ildiko E. , Low Trevor M. , Crocker Tomiko A. , Valappil Benita , Kanga Mridu , Abdallah Hussein , Collopy Sarah , Fernandez-Miranda Juan C. , Vigo Vera , Ljubimov Vladimir A. , Zada Gabriel , Garrett Norman E. , Delery William , Yuen Kevin C. J. , Rennert Robert C. , Couldwell William T. , Silverstein Julie M. , Kshettry Varun R. , Chicoine Michael R. 
Published: March 2024

BACKGROUND AND OBJECTIVES:
To address the lack of a multicenter pituitary surgery research consortium in the United States, we established the Registry of Adenomas of the Pituitary and Related Disorders (RAPID). The goals of RAPID are to examine surgical outcomes, improve patient care, disseminate best practices, and facilitate multicenter surgery research at scale. Our initial focus is Cushing disease (CD). This study aims to describe the current RAPID patient cohort, explore surgical outcomes, and lay the foundation for future studies addressing the limitations of previous studies.

METHODS:
Prospectively and retrospectively obtained data from participating sites were aggregated using a cloud-based registry and analyzed retrospectively. Standard preoperative variables and outcome measures included length of stay, unplanned readmission, and remission.

RESULTS:
By July 2023, 528 patients with CD had been treated by 26 neurosurgeons with varying levels of experience at 9 academic pituitary centers. No surgeon treated more than 81 of 528 (15.3%) patients. The mean ± SD patient age was 43.8 ± 13.9 years, and most patients were female (82.2%, 433/527). The mean tumor diameter was 0.8 ± 2.7 cm. Most patients (76.6%, 354/462) had no prior treatment. The most common pathology was corticotroph tumor (76.8%, 381/496). The mean length of stay was 3.8 ± 2.5 days. The most common discharge destination was home (97.2%, 513/528). Two patients (0.4%, 2/528) died perioperatively. A total of 57 patients (11.0%, 57/519) required an unplanned hospital readmission within 90 days of surgery. The median actuarial disease-free survival after index surgery was 8.5 years.

CONCLUSION:
This study examined an evolving multicenter collaboration on patient outcomes after surgery for CD. Our results provide novel insights on surgical outcomes not possible in prior single-center studies or with national administrative data sets. This collaboration will power future studies to better advance the standard of care for patients with CD.
Rekonstrukcja zmian paleośrodowiskowych w eemskich zagłębieniach bezodpływowych przedpola lądolodu ostatniego zlodowacenia na przykładzie stanowiska Stara Maryśka II (Północne Mazowsze, Polska Centralna)
Authors: Rychel Joanna , Sieradz Dominika , Massalska Barbara , Standzikowski Karol , Wasiluk Radosław , Woronko Barbara , Nawrocki Jerzy 
Published: March 2024

Odsłonięta w stanowisku Stara Maryśka II sukcesja osadowa obejmuje górną część interglacjału eemskiego po zlodowacenie wisły. Na podstawie ciągłości zapisu palinologicznego w osadach wypełniających zbiornik odtworzony został przebieg zmian klimatu i środowiska w okresie późnego plejstocenu (MIS5e-MIS2). Wyniki datowań metodą OSL pozwoliły wyróżnić okresy funkcjonowania warstwy czynnej wieloletniej zmarzliny podczas zlodowacenia wisły (MIS4-MIS2), która jest wyznacznikiem warunków peryglacjalnych panujących przed czołem lądolodu. Oznaczony został również czas formowania się wydm w rejonie stanowiska.