bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized multifidelity machine learning for quantum chemistry
Authors: Vinod Vivin , Kleinekathöfer Ulrich , Zaspel Peter 
Published: February 2024

Abstract
Machine learning (ML) provides access to fast and accurate quantum chemistry (QC) calculations for various properties of interest such as excitation energies. It is often the case that high accuracy in prediction using a ML model, demands a large and costly training set. Various solutions and procedures have been presented to reduce this cost. These include methods such as Δ-ML, hierarchical-ML, and multifidelity machine learning (MFML). MFML combines various Δ-ML like sub-models for various fidelities according to a fixed scheme derived from the sparse grid combination technique. In this work we implement an optimization procedure to combine multifidelity models in a flexible scheme resulting in optimized MFML (o-MFML) that provides superior prediction capabilities. This hyperparameter optimization is carried out on a holdout validation set of the property of interest. This work benchmarks the o-MFML method in predicting the atomization energies on the QM7b dataset, and again in the prediction of excitation energies for three molecules of growing size. The results indicate that o-MFML is a strong methodological improvement over MFML and provides lower error of prediction. Even in cases of poor data distributions and lack of clear hierarchies among the fidelities, which were previously identified as issues for multifidelity methods, the o-MFML is advantageous for the prediction of quantum chemical properties.
Anatomical insights into the vascular layout of the barley rachis: implications for transport and spikelet connection
Authors: Rutten Twan , Thirulogachandar Venkatasubbu , Huang Yongyu , Shanmugaraj Nandhakumar , Koppolu Ravi , Ortleb Stefan , Hensel Götz , Kumlehn Jochen , Melzer Michael , Schnurbusch Thorsten 
Published: February 2024

Abstract

Background and Aims
Vascular patterning is intimately related to plant form and function. Here, using barley (Hordeum vulgare) as a model, we studied the vascular anatomy of the spike-type inflorescence. The main aim of the present work was to clarify the relationship between rachis (spike axis) vasculature and spike size, to define vascular dynamics and to discuss the implications for transport capacity and its interaction with the spikelets.

Methods
We used serial transverse internode sections to determine the internode area, vascular area and number of veins along the rachis of several barley lines.

Key Results
Internode area and total vascular area show a clear positive correlation with spike size, whereas the number of veins is only weakly correlated. The lateral periphery of the rachis contains large mature veins of constant size, whereas the central part is occupied by small immature veins. Spikelet-derived veins entering the rachis often merge with the immature rachis veins but never merge with the mature veins. An increase in floret fertility through the conversion of a two-rowed barley into an isogenic six-rowed line, in addition to a decrease in floret fertility owing to enhanced pre-anthesis tip degeneration caused by the mutation tip sterile 2.b (tst2.b), significantly affected vein size but had limited to no effects on the number of veins or internode area.

Conclusions
The rachis vasculature is the result of a two-step process involving an initial layout followed by size adjustment according to floret fertility/spike size. The restriction of large mature vessels to the periphery and that of small immature vessels to the centre of the rachis suggests that long-distance transport and local supply to spikelets are spatially separated processes. The identification of spikelet-derived veins entering the rachis without fusing with its vasculature indicates that a vascular continuity between rachis and spikelets might be non-essential.
Clinical Outcomes at 8-16 Weeks After Upadacitinib Initiation for Acute Severe Ulcerative Colitis: A Case Series in the United States
Authors: Dalal Rahul S , Winter Rachel W , Gupta Sanchit , Sasson Gila F , Hamilton Matthew J , Allegretti Jessica R 
Published: February 2024

Lay Summary
In 9 patients hospitalized for acute severe ulcerative colitis, 8 were successfully discharged without the need for colectomy. Six of 7 patients with sufficient follow-up achieved steroid-free clinical remission at 8 to 16 weeks, and 1 of 2 patients achieved endoscopic response.
Factors influencing the indication of coronary angiography in patients presenting with chest pain unspecified: an analysis of two decades (1994–2014)
Authors: Moreyra Abel E , Mehta Chirag , Cosgrove Nora M , Zinonos Stavros , Sargsyan Davit , Gold Alex , Trivedi Mihir , Kostis John B , Cabrera Javier , Kostis William J 
Published: February 2024

Abstract
Guidelines for cardiac catheterization in patients with non-specific chest pain (NSCP) provide significant room for provider discretion, which has resulted in variability in the utilization of invasive coronary angiograms (CAs) and a high rate of normal angiograms. The overutilization of CAs in patients with NSCP and discharged without a diagnosis of coronary artery disease is an important issue in medical care quality. As a result, we sought to identify patient demographic, socioeconomic, and geographic factors that influenced the performance of a CA in patients with NSCP who were discharged without a diagnosis of coronary artery disease. We intended to establish reference data points for gauging the success of new initiatives for the evaluation of this patient population. In this 20-year retrospective cohort study (1994–2014), we examined 107 796 patients with NSCP from the Myocardial Infarction Data Acquisition System, a large statewide validated database that contains discharge data for all patients with cardiovascular disease admitted to every non-federal hospital in NJ. Patients were partitioned into two groups: those offered a CA (CA group; n = 12 541) and those that were not (No-CA group; n = 95 255). Geographic, demographic, and socioeconomic variables were compared between the two groups using multivariable logistic regression, which determined the predictive value of each categorical variable on the odds of receiving a CA. Whites were more likely than Blacks and other racial counterparts (19.7% vs. 5.6% and 16.5%, respectively; P &lt; .001) to receive a CA. Geographically, patients who received a CA were more likely admitted to a large hospital compared to small- or medium-sized ones (12.5% vs. 8.9% and 9.7%, respectively; P &lt; .05), a primary teaching institution rather than a teaching affiliate or community center (16.1 % vs. 14.3% and 9.1%, respectively; P &lt; .001), and at a non-rural facility compared to a rural one (12.1% vs. 6.5%; P &lt; .001). Lastly from a socioeconomic standpoint, patients with commercial insurance more often received a CA compared to those having Medicare or Medicaid/self-pay (13.7% vs. 9.5% and 6.0%, respectively; P &lt; .001). The utilization of CA in patients with NSCP discharged without a diagnosis of coronary artery disease in NJ during the study period may be explained by differences in geographic, demographic, and socioeconomic factors. Patients with NSCP should be well scrutinized for CA eligibility, and reliable strategies are needed to reduce discretionary medical decisions and improve quality of care.
Intracellular activity and in vivo efficacy in a mouse model of septic arthritis of the novel pseudopeptide Pep16 against Staphylococcus aureus clinical isolates
Authors: Mascary Jean-Baptiste , Bordeau Valérie , Nicolas Irène , Verdier Marie-Clémence , Rocheteau Pierre , Cattoir Vincent 
Published: February 2024

Abstract

Objectives
Assessing the therapeutic potential of a novel antimicrobial pseudopeptide, Pep16, both in vitro and in vivo for the treatment of septic arthritis caused by Staphylococcus aureus.

Methods
Seven clinical isolates of S. aureus (two MRSA and five MSSA) were studied. MICs of Pep16 and comparators (vancomycin, teicoplanin, daptomycin and levofloxacin) were determined through the broth microdilution method. The intracellular activity of Pep16 and levofloxacin was assessed in two models of infection using non-professional (osteoblasts MG-63) or professional (macrophages THP-1) phagocytic cells. A mouse model of septic arthritis was used to evaluate the in vivo efficacy of Pep16 and vancomycin. A preliminary pharmacokinetic (PK) analysis was performed by measuring plasma concentrations using LC-MS/MS following a single subcutaneous injection of Pep16 (10 mg/kg).

Results
MICs of Pep16 were consistently at 8 mg/L for all clinical isolates of S. aureus (2- to 32-fold higher to those of comparators) while MBC/MIC ratios confirmed its bactericidal activity. Both Pep16 and levofloxacin (when used at 2 × MIC) significantly reduced the bacterial load of all tested isolates (two MSSA and two MRSA) within both osteoblasts and macrophages. In MSSA-infected mice, Pep16 demonstrated a significant (∼10-fold) reduction on bacterial loads in knee joints. PK analysis following a single subcutaneous administration of Pep16 revealed a gradual increase in plasma concentrations, reaching a peak of 5.6 mg/L at 12 h.

Conclusions
Pep16 is a promising option for the treatment of septic arthritis due to S. aureus, particularly owing to its robust intracellular activity.
Effect of Selective Enrichment Storage Temperature and Duration Time on the Detection of Salmonella in Food
Authors: Hu Lijun , Zhang Guodong 
Published: February 2024

Abstract

Background
For pathogen detection in food, there are occasions where samples cannot be processed immediately after selective enrichment or need to be reexamined days or weeks later for confirmation or retest.

Objective
This study aimed to investigate the effect of different prolonged period of storage of selective enrichments of food at 4 ± 2°C and room temperature (20–22°C) on the detection and isolation of Salmonella.

Method
This study included two experiments involving 34 types of foods to compare the effect of 4 ± 2°C and room temperature storage on the detection of Salmonella in 204 selective enrichments (Rappaport-Vassiliadis [RV] and Tetrathionate [TT] broths) during a 42-day storage (Experiment I); and to monitor the survival of Salmonella in 300 selective enrichments (RV and TT) with different pre-enrichment broths (Lactose broth [LB] or Buffered peptone water broth [BPW]), stored at 4°C for 60 days (Experiment II). All the samples were subjected to Salmonella analysis following the FDA BAM method.

Results
During multiple samplings, the positive detection rate for Salmonella remained consistent through Day 42 after selective enrichment, irrespective of Salmonella serotype, storage temperature, pre-enrichment broth, or selective enrichment broth in both Experiment I and II. However, on Day 60 sampling in Experiment II, seven previously positive results turned to negatives. These data indicated that storage of RV and TT enrichments at 4 ± 2°C or room temperature for up to 42 days after selective enrichment did not compromise the detection of Salmonella in the tested food categories, regardless of Salmonella serotypes and the broths used for pre-enrichment and selective enrichment.

Conclusions
At least for the food types studied in this experiment, the recovery of Salmonella from selective enrichments could be postponed for a limited period of time (e.g., &lt;42 days) if needed without adversely affecting the test results. However, the delayed analysis of TT and RV enrichments does pose a risk of reduced detection sensitivity, as evidenced by the seven negative results on Day 60 compared to previous positives. We do not recommend or endorse delaying the analysis of TT and RV enrichments.

Highlights
In the food matrixes investigated in this experiment, the plating and isolation of Salmonella from selective TT and RV enrichments stored at 4 ± 2°C or room temperature could be deferred for a period (up to 42 days) without any negative effect on the test results, if necessary.
Contested Legitimating Agents: The Regional “Battle” for Legitimacy in Venezuela
Authors: Wajner Daniel F 
Published: February 2024

Abstract
Practitioners, pundits, and scholars increasingly recognize the role that international organizations play in conflicts. Regional organizations (ROs), as brokers of collective security, welfare, and identity, have become particularly active agents during violent crises by granting legitimacy to certain protagonists and discrediting the legitimacy of others, thus affecting international policymaking. However, existing research generally assesses the legitimizing effects of ROs in either a static way, in which the stances of their member states do not change over time, or in an institutional vacuum, where ROs are not challenged by other ROs. This study aims to shed light on the impact of multiple ROs dynamically and simultaneously intervening in legitimation struggles. It focuses on the 2014–2020 regional “battle” over the legitimate authority of the Chavista–Madurista regime in Venezuela, examining how multiple Latin American ROs articulated their discourse seeking to influence the crisis’ outcomes. To this end, a multi-step process tracing based on four phases (opening, deliberation, judgment, and denouement) is applied. The findings reveal the lively competition between involved actors for the recognition of ROs as the relevant legitimating agents, and the limits faced in achieving collective action when polarization over such a regional legitimating role prevails. The study has novel implications for scholarly understanding of the role of legitimation dynamics in promoting international cooperation during periods of disruption.
An adult right inguinal hernia and cryptorchidism treated simultaneously with laparoscopic transabdominal preperitoneal repair and laparoscopic orchiectomy: a case report
Authors: Kimura Dai , Miyagawa Yusuke , Miyao Masafumi , Matumura Hideyasu , Koike Shoichiro 
Published: February 2024

Abstract
Pediatric health checkups have been mandatory for all citizens since 1966 based on the Maternal and Child Health Law in Japan, and cryptorchidism or undescended testis in adult males are rare. We report a case of an adult right inguinal hernia and cryptorchidism treated simultaneously with laparoscopic transabdominal preperitoneal repair and laparoscopic orchiectomy. A 35-year-old man came to our department with a chief complaint of bulging in the right inguinal region for several months. He was diagnosed with a right inguinal hernia and was scheduled for transabdominal preperitoneal repair. During intraoperative intraperitoneal observation, a white 30-mm mass was found in the hernia orifice. A diagnosis of right cryptorchidism was made, and transabdominal preperitoneal repair and laparoscopic orchiectomy were performed. Laparoscopic simultaneous surgery could be safely performed in an adult patient with a hernia complicated by a cryptorchidism. It can be recommended as a surgical option in such cases.
A rare manifestation of IgG4-related disease and secondary hypereosinophilic syndrome: A case report
Authors: Takeuchi Miyoshi , Shojima Masumi , Matsueda Shumei , Nagae Hiroshi , Kuroiwa Mika , Fujita Aya , Kawano Mitsuhiro , Inoue Dai , Komori Takahiro , Takeuchi Mai , Ooshima Koichi , Kuroki Yusuke , Katafuchi Ritsuko 
Published: February 2024

ABSTRACT
We report a case of IgG4-related disease (IgG4-RD) with marked eosinophilia. A 79-year-old woman was admitted due to diarrhoea and weight loss. Cervical lymphadenopathy, bilateral submandibular glands swelling, anaemia (Hb8.5 g/dl), hypereosinophilia (9750/μl), elevated serum creatinine (1.57 mg/dl), pancreatic amylase (191 IU/l), and IgG4 (3380 mg/dl) were found. Diffusion-weighted image on magnetic resonance imaging showed high-intensity signals inside both the pancreas and the kidneys. The echogram of submandibular glands revealed cobblestone pattern. Kidney biopsy revealed acute tubulointerstitial nephritis. Biopsies of lip, gastrointestinal tract, and bone marrow showed infiltration of lymphoplasmacytic cells and IgG4-positive plasma cells (30–67/HPF). Gastrointestinal and bone marrow biopsies also showed eosinophilic infiltration. Adrenal insufficiency, rheumatic disease, tuberculosis, parasite infection, drug-induced eosinophilia, and eosinophilic leukaemia were all ruled out. We started treatment with 40 mg of prednisolone (PSL) and her general condition rapidly improved. The eosinophil count, serum IgG4, and serum creatinine decreased. We gradually tapered PSL and maintained 5 mg/day. During the 5 years of treatment, she had no recurrence of the symptom. According to the 2019 American College of Rheumatology/European League Against Rheumatism classification criteria for IgG4-RD, eosinophils &gt;3000/μl is one of the exclusion criteria. If we comply with this criterion, the diagnosis of IgG4-RD should be avoided. However, our case fit the diagnostic criteria of type I autoimmune pancreatitis, IgG4-related sialadenitis, and global diagnosis of IgG4-RD. We finally diagnosed our case as IgG4-RD with secondary hypereosinophilic syndrome. This case suggests that IgG4-RD with eosinophils &gt;3000/μl does exist in the real world.
Changes in muscle strength and risk of cardiovascular disease among middle-aged and older adults in China: Evidence from a prospective cohort study
Authors: Yang Ze , Wei Jiemin , Liu Hongbo , Zhang Honglu , Liu Ruifang , Tang Naijun , Yang Xueli 
Published: February 2024

Abstract

Background:
Evidence indicates that low muscle strength is associated with an increased cardiovascular diseases (CVDs) risk. However, the association between muscle strength changes based on repeated measurements and CVD incidence remains unclear.

Methods:
The study used data from the China Health and Retirement Longitudinal Study in 2011 (Wave 1), 2013 (Wave 2), 2015 (Wave 3), and 2018 (Wave 4). Low muscle strength was defined as handgrip strength <28 kg for men or <18 kg for women, or chair-rising time ≥12 s. Based on changes in muscle strength from Waves 1 to 2, participants were categorized into four groups of Normal–Normal, Low–Normal, Normal–Low, and Low–Low. CVD events, including heart disease and stroke, were recorded using a self-reported questionnaire during Waves 3 and 4 visits. Cox proportional hazards models were used to investigate the association between muscle strength changes and CVD incidence after multivariable adjustments. Hazard ratios (HRs) and 95% confidence intervals (95% CIs) were estimated with the Normal–Normal group as the reference.

Results:
A total of 1164 CVD cases were identified among 6608 participants. Compared to participants with sustained normal muscle strength, the CVD risks increased progressively across groups of the Low–Normal (HR = 1.20, 95% CI: 1.01–1.43), the Normal–Low (HR = 1.35, 95% CI: 1.14–1.60), and the Low–Low (HR = 1.76, 95% CI: 1.49–2.07). Similar patterns were observed for the significant associations between muscle strength status and the incidence risks of heart disease and stroke. Subgroup analyses showed that the significant associations between CVD and muscle strength changes were consistent across age, sex, and body mass index (BMI) categories.

Conclusions:
The study found that muscle strength changes were associated with CVD risk. This suggests that continuous tracking of muscle status may be helpful in screening cardiovascular risk.
Validation of a screening panel for pediatric metabolic dysfunction–associated steatotic liver disease using metabolomics
Authors: Huneault Helaina E. , Gent Alasdair E. , Cohen Catherine C. , He Zhulin , Jarrell Zachery R. , Kamaleswaran Rishikesan , Vos Miriam B. 
Published: February 2024

Background:
Metabolic dysfunction–associated steatotic liver disease (MASLD), formerly known as NAFLD, is the most common liver disease in children. Liver biopsy remains the gold standard for diagnosis, although more efficient screening methods are needed. We previously developed a novel NAFLD screening panel in youth using machine learning applied to high-resolution metabolomics and clinical phenotype data. Our objective was to validate this panel in a separate cohort, which consisted of a combined cross-sectional sample of 161 children with stored frozen samples (75% male, 12.8±2.6 years of age, body mass index 31.0±7.0 kg/m2, 81% with MASLD, 58% Hispanic race/ethnicity).

Methods:
Clinical data were collected from all children, and high-resolution metabolomics was performed using their fasting serum samples. MASLD was assessed by MRI-proton density fat fraction or liver biopsy and cardiometabolic factors. Our previously developed panel included waist circumference, triglycerides, whole-body insulin sensitivity index, 3 amino acids, 2 phospholipids, dihydrothymine, and 2 unknowns. To improve feasibility, a simplified version without the unknowns was utilized in the present study. Since the panel was modified, the data were split into training (67%) and test (33%) sets to assess the validity of the panel.

Results:
Our present highest-performing modified model, with 4 clinical variables and 8 metabolomics features, achieved an AUROC of 0.92, 95% sensitivity, and 80% specificity for detecting MASLD in the test set.

Conclusions:
Therefore, this panel has promising potential for use as a screening tool for MASLD in youth.
Applying human-centered design to the construction of a cirrhosis management clinical decision support system
Authors: Ge Jin , Buenaventura Ana , Berrean Beth , Purvis Jory , Fontil Valy , Lai Jennifer C. , Pletcher Mark J. 
Published: February 2024

Background:
Electronic health record (EHR)-based clinical decision support is a scalable way to help standardize clinical care. Clinical decision support systems have not been extensively investigated in cirrhosis management. Human-centered design (HCD) is an approach that engages with potential users in intervention development. In this study, we applied HCD to design the features and interface for a clinical decision support system for cirrhosis management, called CirrhosisRx.

Methods:
We conducted technical feasibility assessments to construct a visual blueprint that outlines the basic features of the interface. We then convened collaborative-design workshops with generalist and specialist clinicians. We elicited current workflows for cirrhosis management, assessed gaps in existing EHR systems, evaluated potential features, and refined the design prototype for CirrhosisRx. At the conclusion of each workshop, we analyzed recordings and transcripts.

Results:
Workshop feedback showed that the aggregation of relevant clinical data into 6 cirrhosis decompensation domains (defined as common inpatient clinical scenarios) was the most important feature. Automatic inference of clinical events from EHR data, such as gastrointestinal bleeding from hemoglobin changes, was not accepted due to accuracy concerns. Visualizations for risk stratification scores were deemed not necessary. Lastly, the HCD co-design workshops allowed us to identify the target user population (generalists).

Conclusions:
This is one of the first applications of HCD to design the features and interface for an electronic intervention for cirrhosis management. The HCD process altered features, modified the design interface, and likely improved CirrhosisRx’s overall usability. The finalized design for CirrhosisRx proceeded to development and production and will be tested for effectiveness in a pragmatic randomized controlled trial. This work provides a model for the creation of other EHR-based interventions in hepatology care.