bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibration Control Solutions for Microscopy
Authors: Morgan John , Wigglesworth Wes 
Published: July 2024

Abstract
Vibration is always present in our environment at some level. It can have a deleterious effect on all types of microscopes and should always be considered when installing a microscope in a facility. Some microscope manufacturers, particularly those who make charged electron or particle beam microscopes, have detailed vibration specifications; others do not. In this article we discuss sources of vibration, techniques for mitigating vibration, and some general rules about which types of vibration control to use based on the type of microscope being used.
Tests of subgrid models for star formation using simulations of isolated disc galaxies
Authors: Nobels Folkert S J , Schaye Joop , Schaller Matthieu , Ploeckinger Sylvia , Chaikin Evgenii , Richings Alexander J 
Published: July 2024

ABSTRACT
We use smoothed particle hydrodynamics simulations of isolated Milky Way-mass disc galaxies that include cold, interstellar gas to test subgrid prescriptions for star formation (SF). Our fiducial model combines a Schmidt law with a gravitational instability criterion, but we also test density thresholds and temperature ceilings. While SF histories are insensitive to the prescription for SF, the Kennicutt–Schmidt (KS) relations between SF rate and gas surface density can discriminate between models. We show that our fiducial model, with an SF efficiency per free-fall time of 1 per cent, agrees with spatially resolved and azimuthally averaged observed KS relations for neutral, atomic, and molecular gas. Density thresholds do not perform as well. While temperature ceilings selecting cold, molecular gas can match the data for galaxies with solar metallicity, they are unsuitable for very low-metallicity gas and hence for cosmological simulations. We argue that SF criteria should be applied at the resolution limit rather than at a fixed physical scale, which means that we should aim for numerical convergence of observables rather than of the properties of gas labelled as star-forming. Our fiducial model yields good convergence when the mass resolution is varied by nearly 4 orders of magnitude, with the exception of the spatially resolved molecular KS relation at low surface densities. For the gravitational instability criterion, we quantify the impact on the KS relations of gravitational softening, the SF efficiency, and the strength of supernova feedback, as well as of observable parameters such as the inclusion of ionized gas, the averaging scale, and the metallicity.
Sulphur storage in cold molecular clouds: the case of the NH4+SH- salt on interstellar dust grains
Authors: Vitorino J , Loison J -C , Wakelam V , Congiu E , Dulieu F 
Published: July 2024

ABSTRACT
In comets and in the cold phase of the interstellar medium (ISM), ammonium salts are key molecular species due to their role in the retention of volatile compounds on cold surfaces. In the case of sulphur, the H$_2$S/OCS ratio observed in protostars could be explained by the presence of ammonium hydrosulphide (NH$_4$SH) salts. However, laboratory data on the properties of NH4SH in ISM cold relevant conditions are rather scarce, as they usually focus on the atmosphere of Jupiter. We propose to consolidate the laboratory data regarding NH$_4$SH on grains, by performing temperature programmed desorption experiments and Fourier transform infrared reflection spectroscopy. The salt was also exposed to H atoms to mimic the ISM conditions. NH$_4$SH was found to form in situ at 10 K, from a mixture of ammonia (NH$_3$) and hydrogen sulphide (H$_2$S). The NH$_4^+$ infrared feature (1485 cm$^{-1}$) is the most prominent one at 80 K. As pure species, H$_2$S and NH$_3$ desorb at 76 and 90 K, respectively, whereas they are released into the gas phase at 153 K when adsorbed in the form of salt. The presence of water delays the desorption of the salt until the very end of the water desorption, but does not affect the desorption kinetics. During H-exposure, the salt is dissociated and no new product was detected. As a comparative study, salts have been included in the Nautilus gas–grain model. The results show a good correlation with the observations of IRAS 16293−2422B, as opposed to when NH$_4$SH is not included in the model.
PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era
Authors: Huang Yu-Hao , Sun Yi-Fei , Li Hao , Li Hao-Sen , Pang Hong 
Published: July 2024

Abstract
The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, prior to core analyses, traditional methods typically involve intricate and time-consuming procedures, including assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple sequence alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive data sets. In this study, we develop PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as a reference for phylogenetic and evolutionary analyses. Through testing with simulated data sets of species spanning the tree of life, PhyloAln demonstrates consistently robust performance compared with other reference-based tools across different data types, sequencing technologies, coverages, and species, with percent completeness and identity at least 50 percentage points higher in the alignments. Additionally, we validate the efficacy of PhyloAln in removing a minimum of 90% foreign and 70% cross-contamination issues, which are prevalent in sequencing data but often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments (completeness mostly larger than 80%, identity larger than 90%) and reconstructing robust phylogenies using real data sets of transcriptomes of ladybird beetles, plastid genes of peppers, or ultraconserved elements of turtles. With these advantages, PhyloAln is expected to facilitate phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.
Enhanced surveillance for the detection of psoriatic arthritis in a UK primary care psoriasis population: results from the TUDOR trial
Authors: McHugh Neil , Tillett William , Helliwell Philip , Packham Jonathan , Collier Howard , Davies Claire , Ransom Myka , Coates Laura , Brown Sarah T ,   PROMPT study group
Published: July 2024

Abstract

Background
Our objective was to determine whether early detection of undiagnosed psoriatic arthritis (PsA) in a primary care psoriasis population improves outcome in physical function at 24 months post-registration.

Methods
A multicentre, prospective, parallel group cluster randomised controlled trial in patients with psoriasis was conducted. Participants with suspected inflammatory arthritis on screening were referred for an assessment of PsA (enhanced surveillance (ES) arm: at baseline, 12 and 24 months; standard care (SC) arm: at 24 months). The primary outcome measure was the Health Assessment Questionnaire Disability Index (HAQ-DI) at 24 months post registration in participants diagnosed with PsA.

Results
A total of 2225 participants across 135 GP practices registered: 1123 allocated to ES and 1102 to SC. The primary analysis population consisted of 87 participants with a positive diagnosis of PsA: 64 in ES, 23 in SC. The adjusted odds ratio (OR) for achieving a HAQ-DI score of 0 at 24 months post registration in ES compared with SC was 0.64 (95% CI (0.17, 2.38)), and the adjusted OR of achieving a higher (non-zero) HAQ-DI score at 24 months post registration in ES relative to SC arm was 1.12 (95% CI: 0.67, 1.86), indicating no evidence of a difference between the two treatment groups (p= 0.66).

Conclusion
The trial was underpowered for demonstrating the prespecified treatment effect; in patients with psoriasis there was no evidence that early diagnosis of PsA by ES in primary care changes physical function at 24 months compared with SC.

Clinical Trial Registration
The TUDOR trial is registered as ISRCTN38877516.
The effect of academic outcomes, equity, and student demographics on parental preferences for schools: evidence from a survey experiment
Authors: Thompson Marissa E 
Published: July 2024

Abstract
How does competition for school resources, along with racial and socioeconomic biases, shape parental preferences for schools? In this article, I investigate how school attributes affect preferences and choice, which sheds light on the processes that maintain school segregation. To do so, I conduct a survey experiment that explores parental preferences and the tradeoffs inherent in the process of school selection using school profiles that resemble those available on widely used education data platforms. I find that parents hold the strongest positive preferences for learning opportunities and overall school achievement compared to other attributes, including school racial and socioeconomic composition. Additionally, though parents prefer schools that have higher equity rankings, highly equitable schools are less desirable to parents than schools with more status and learning opportunities. However, parents also hold independent racial and socioeconomic preferences and —on average—avoid schools with more students of color and low-income students. Furthermore, results suggest they are largely unwilling to make tradeoffs that would result in schools with higher fractions of students of color or low-income students. Taken together, this study links prior studies on the segregating effects of educational data with literatures on school segregation by illustrating the specific dimensions that drive school choice.
Morin attenuates arsenic-induced toxicity in 3T3 embryonic fibroblast cells by suppressing oxidative stress, inflammation, and apoptosis: In vitro and silico evaluations
Authors: Unsal Velid , Cicek Mustafa , Aktepe Necmettin , Oner Erkan 
Published: July 2024

Abstract
This study aims to investigate the curative effects of Morin, a flavonoid, against arsenic toxicity in 3T3 embryonic fibroblast cells and its effect on the molecular mechanisms of cells. The cytotoxicity and viability of the cells were measured by MTT and LDH tests. Arsenic (0.74 μM) was used to trigger toxicity and Morin (50 μM) was used for treatment. The levels of oxidative stress biomarkers and the activities of antioxidant enzymes were measured by spectrophotometric method, and inflammatory markers were measured by ELISA method. While mRNA expression levels of Bax, Bcl-2 levels, and Caspase-3 activity were measured by qRT-PCR technique, TUNEL staining was performed to detect DNA breaks and DAPI staining to visualize nuclear changes. Protein structures were retrieved from the protein data bank. OpenBabel and Autodock programs were used for the molecular docking study. Morin rescued the 3T3 embryonic fibroblast cells exposed to arsenic. However, Arsenic decreased the activities of antioxidant enzymes in cells and significantly increased oxidative stress, inflammation, and apoptosis. Morin treatment reduced oxidative damage and TNF-α and IL-1β levels. Arsenic-induced Caspase-3 mRNA expression level and Bax protein mRNA expression level were significantly increased, while Bcl-2 mRNA expression level was significantly decreased. While Caspase-3 mRNA expression level and Bax protein mRNA expression level decreased with morin treatment, Bcl-2 mRNA expression level increased significantly. Molecular docking study results showed good binding affinity of morin in SOD, GSH-Px, Bax, Bcl-2, Caspase-3, TNF-α, and IL-1β structures. Morin showed antioxidant, anti-inflammatory, and anti-apoptotic effects against Arsenic-induced cellular toxicity.
The Development of Spinal Endoscopic Ultrasonic Imaging System With an Automated Tissue Recognition Algorithm
Authors: Jiang Chang , Xiang Yiwei , Zhang Zhiyang , Cao Yuanwu , Xu Nixi , Chen Yinglun , Yao Jiaqi , Jiang Xiaoxing , Ding Fang , Zheng Rui , Chen Zixian 
Published: July 2024

Study Design:
Preclinical experimental study.

Objective:
To develop an intraoperative ultrasound-assisted imaging device, which could be placed at the surgical site through an endoscopic working channel and which could help surgeons recognition of different tissue types during endoscopic spinal surgery (ESS).

Summary of Background Data:
ESS remains a challenging task for spinal surgeons. Great proficiency and experience are needed to perform procedures such as intervertebral discectomy and neural decompression within a narrow channel. The limited surgical view poses a risk of damaging important structures, such as nerve roots.

Methods:
We constructed a spinal endoscopic ultrasound system, using a 4-mm custom ultrasound probe, which can be easily inserted through the ESS working channel, allowing up to 10 mm depth detection. This system was applied to ovine lumbar spine samples to obtain ultrasound images. Subsequently, we proposed a 2-stage classification algorithm, based on a pretrained DenseNet architecture for automated tissue recognition. The recognition algorithm was evaluated for accuracy and consistency.

Results:
The probe can be easily used in the ESS working channel and produces clear and characteristic ultrasound images. We collected 367 images for training and testing of the recognition algorithm, including images of the spinal cord, nucleus pulposus, adipose tissue, bone, annulus fibrosis, and nerve roots. The algorithm achieved over 90% accuracy in recognizing all types of tissues with a Kappa value of 0.875. The recognition times were under 0.1 s using the current configuration.

Conclusion:
Our system was able to be used in existing ESS working channels and identify at-risk spinal structures in vitro. The trained algorithms could identify 6 intraspinal tissue types accurately and quickly. The concept and innovative application of intraoperative ultrasound in ESS may shorten the learning curve of ESS and improve surgical efficiency and safety.
Modeling Plutonium Decorporation in a Female Nuclear Worker Treated with Ca-DTPA after Inhalation Intake
Authors: Dumit Sara , Avtandilashvili Maia , McComish Stacey L. , Miller Guthrie , Swanson Jasen , Tolmachev Sergey Y. 
Published: July 2024

Abstract
The present work models plutonium (Pu) biokinetics in a female former nuclear worker. Her bioassay measurements are available at the US Transuranium and Uranium Registries. The worker was internally exposed to a plutonium-americium mixture via acute inhalation at a nuclear weapons facility. She was medically treated with injections of 1 g Ca-DTPA on days 0, 5, and 14 after the intake. Between days 0 and 20, fecal and urine samples were collected and analyzed for 239Pu and 241Am. Subsequently, she was followed up for bioassay monitoring over 14 y, with additional post-treatment urine samples collected and analyzed for 239Pu. The uniqueness of this dataset is due to the availability of: (1) both early and long-term bioassay data from a female with plutonium intake; (2) data on chelation therapy for a female; and (3) fecal measurement results. Chelation therapy with Ca- and/or Zn-salts of DTPA is known to aid in reducing the internal radiation dose by enhancing the excretion of plutonium and americium from the body. Such enhancement affects plutonium biokinetics in the human body, posing a challenge to the internal dose assessment. The current radiation dose assessment practice is to exclude the data affected by Ca-DTPA from the analysis. The present analysis is the first to explicitly model the chelation-affected bioassay data in a female by using a newly developed chelation model. Thus, the bioassay data collected during and after the Ca-DTPA administrations were used for biokinetic modeling and dose assessment. The Markov Chain Monte Carlo method was used to investigate model parameter uncertainty, based on the bioassay data and assumed prior probability distributions. A χ
2/nData (number of data points) ≈ 1 was observed in this study, which indicates self-consistency of the data with the model. Results of this study show that the worker’s 239Pu intake was 12 Bq, with a committed effective dose to the whole-body of 1.2 mSv and a committed equivalent dose to the bone surfaces, liver, and lungs of 37.8, 9.1, and 0.8 mSv, respectively. This study also discusses the worker’s dose reduction due to chelation treatment.
Implementation and Evaluation of Clinical Decision Support for Apixaban Dosing in a Community Teaching Hospital
Authors: Cope Rebecca , Sarsour Maram , Sasson Evan , Badran Hasan , Kim Ka Yeun , Quinn Rachel 
Published: July 2024

Objectives
This study aimed to describe and evaluate the transition from a specialty service-based prospective order approval system to a computerized clinical decision support (CCDS) tool for apixaban dosing at a community teaching hospital. The primary objective was to assess the impact of the transition on the appropriateness of apixaban prescribing.

Methods
A CCDS tool for apixaban dosing was developed and implemented using interprofessional collaboration. A retrospective chart review was conducted for apixaban orders placed before (preimplementation) and after (postimplementation) the CCDS transition. The primary outcome was the percent change in inappropriate apixaban orders, with secondary outcomes exploring percent change of apixaban orders with inappropriate dosing in different patient groups and indications per package insert.

Results
Fifty orders were assessed in both arms, with 8% of orders preimplementation and 10% postimplementation deemed inappropriate. After accounting for questionable orders, overall appropriateness of prescribing was 88% preimplementation and 84% postimplementation (P = 0.7). Challenges with implementation of CCDS included working with available information technology resources and facilitating acceptance of a new ordering process.

Conclusions
The implementation of a CCDS tool for apixaban dosing at a community teaching hospital demonstrated comparable rates of appropriateness to the previous specialty service-based approval process. While the transition streamlined resources and improved efficiency, ongoing efforts are needed to address specific dosing challenges. Future research should explore the sustainability and generalizability of CCDS tools in diverse healthcare settings.
Driving in the Wrong Direction: Exploring the Unintended Consequences of an Early Discharge Program on Length of Stay in Hospital Setting
Authors: Hodges Paul , Linke Christopher A. , Bjorgaard Johannah D. , Edgerton Megan E. 
Published: July 2024

Background and Objectives:
Early discharge of patients has become standard work in acute care settings to reduce inpatient length of stay (LOS), improve patient flow, and reduce boarding in the emergency department (ED).

Retrospective analysis of outcomes from a “discharge by 11 am” program at an academic medical center from January 1, 2020, to June 30, 2022. The analysis addresses the effects of a discharge by 11 am goal on time from discharge order release to patient discharge, ED boarding, LOS, and observed-to-expected LOS.

Methods:
Patient-level electronic health record data included discharge order entry time, discharge time, LOS, and diagnosis-related group geometric LOS (GMLOS). Additional unit-level data for ED boarding volumes and hours were included. Analyses were conducted at the hospital and unit levels where indicated.

Results:
Patients with a discharge order by 9 am have longer mean hours from order to discharge than patients without a discharge order by 9 am (9.04 vs 2.48 hours, P < .001) ED boarding total (R
2 = 46.2%, P ≤ .001), percentage (R
2 = 50.4%, P ≤ .001), median minutes (R
2 = 24.6%, P = .005), and total minutes (R
2 = 40.8%, P ≤ .001) all increased as discharge by 11 am performance improved. The mean LOS is longer for the discharge by 11 am group than the non–discharge by 11 am group –1.67; 95% CI, –2.03 to −1.28, P < .001). Discharge by 11 am patients had a LOS/GMLOS ratio 21.9% higher than the non–discharge by 11 am cohort (difference –0.31; 95% CI, –0.36 to –0.26, P < .001).

Conclusions:
Discharge order entry and release by 9 am and patient physically discharged by 11 am initiatives demonstrate a statistical increase in time from discharge order to discharge time, ED boarding, LOS, and observed-to-expected LOS.
Roadmap for Research and Scholarship in General Surgery Residency Training
Authors: Hawn Mary T. , Matthews Jeff B. , Bumgardner Ginny L. , Economou James , Itani Kamal , Kelz Rachel , Tracy Thomas , Zeiger Martha A. 
Published: July 2024

Objective:
To review the current state of research training during surgical residency and make recommendations commensurate with current surgical training and academic environment.

Background:
Research training has been a mainstay of academic surgical programs, yet the scientific disciplines have evolved significantly from the traditional years of bench research. It is time to reconsider how research training should prepare surgeons for future academic practice and ensure the foundational knowledge of research evidence.

Methods:
As part of the Blue Ribbon Committee II, a research subcommittee was tasked to make recommendations on research training during surgical residency. Our 8-member panel brought diverse perspectives on the roles and goals of research training. We also sought input from a convenience sample of current and recent surgical residents on the impact of research training during their residency.

Results:
We identified a lack of a common framework and foundational research training for all surgical residents. Participation in dedicated years of scholarly activity helped trainees meet several professional and personal goals. The lack of an integrated, dedicated research track may dissuade some medical school graduates from pursuing surgery.

Conclusions:
We recommend incorporating a minimum standard for all trainees and flexibility in dedicated scholarly training to meet the needs of future academic surgeons.