bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation energy prediction of neutral single-atom impurities in 2D materials using tree-based machine learning
Authors: Kesorn Aniwat , Hunkao Rutchapon , Na Talang Cheewawut , Cholsuk Chanaprom , Sinsarp Asawin , Vogl Tobias , Suwanna Sujin , Yuma Suraphong 
Published: July 2024

Abstract
We applied tree-based machine learning algorithms to predict the formation energy of impurities in 2D materials, where adsorbates and interstitial defects are investigated. Regression models based on random forest, gradient boosting regression, histogram-based gradient-boosting regression, and light gradient-boosting machine algorithms are employed for training, testing, cross validation, and blind testing. We utilized chemical features from fundamental properties of atoms and supplemented them with structural features from the interaction of the added chemical element with its neighboring host atoms via the Jacobi–Legendre (JL) polynomials. Overall, the prediction accuracy yields optimal

MAE
≈
0.518

,

RMSE
≈
1.14

, and

R
2

≈
0.855

. When trained separately, we obtained lower residual errors RMSE and MAE, and higher R
2 value for predicting the formation energy in the adsorbates than in the interstitial defects. In both cases, the inclusion of the structural features via the JL polynomials improves the prediction accuracy of the formation energy in terms of decreasing RMSE and MAE, and increasing R
2. This work demonstrates the potential and application of physically meaningful features to obtain physical properties of impurities in 2D materials that otherwise would require higher computational cost.
Cloud-based introduction to BASH programming for biologists
Authors: Wilkins Owen M , Campbell Ross , Yosufzai Zelaikha , Doe Valena , Soucy Shannon M 
Published: July 2024

Abstract
This manuscript describes the development of a resource module that is part of a learning platform named ‘NIGMS Sandbox for Cloud-based Learning’, https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial authored by National Institute of General Medical Sciences: NIGMS Sandbox: A Learning Platform toward Democratizing Cloud Computing for Biomedical Research at the beginning of this supplement. This module delivers learning materials introducing the utility of the BASH (Bourne Again Shell) programming language for genomic data analysis in an interactive format that uses appropriate cloud resources for data access and analyses. The next-generation sequencing revolution has generated massive amounts of novel biological data from a multitude of platforms that survey an ever-growing list of genomic modalities. These data require significant downstream computational and statistical analyses to glean meaningful biological insights. However, the skill sets required to generate these data are vastly different from the skills required to analyze these data. Bench scientists that generate next-generation data often lack the training required to perform analysis of these datasets and require support from bioinformatics specialists. Dedicated computational training is required to empower biologists in the area of genomic data analysis, however, learning to efficiently leverage a command line interface is a significant barrier in learning how to leverage common analytical tools. Cloud platforms have the potential to democratize access to the technical tools and computational resources necessary to work with modern sequencing data, providing an effective framework for bioinformatics education. This module aims to provide an interactive platform that slowly builds technical skills and knowledge needed to interact with genomics data on the command line in the Cloud. The sandbox format of this module enables users to move through the material at their own pace and test their grasp of the material with knowledge self-checks before building on that material in the next sub-module.
This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.
Association of resilience and psychological flexibility with surgeons’ mental wellbeing
Authors: Greville-Harris Maddy , Withers Catherine , Wezyk Agata , Thomas Kevin , Bolderston Helen , Kane Amy , McDougall Sine , Turner Kevin J 
Published: July 2024

Abstract

Background
Existing research highlights the link between certain personality traits and mental health in surgeons. However, little research has explored the important role of psychological skills and qualities in potentially explaining this link. A cross-sectional survey of UK-based surgeons was used to examine whether two such skills (psychological flexibility and resilience) helped to explain why certain personality traits might be linked to mental health in surgeons.

Method
An online survey comprising measures of personality (neuroticism, extraversion and conscientiousness), psychological skills/qualities (psychological flexibility and resilience) and mental health (depression, anxiety, stress and burnout) was sent to surgeons practising in the UK. Mediation analyses were used to examine the potential mediating role of psychological flexibility and resilience in explaining the relationship between personality factors and mental health.

Results
A total of 348 surgeons completed the survey. In all 12 mediation models, psychological flexibility and/or resilience played a significant role in explaining the relationship between personality traits (neuroticism, extraversion and conscientiousness) and mental health (depression, anxiety and burnout).

Conclusion
Findings suggest that it is not only a surgeon’s personality that is associated with their mental health, but the extent to which a surgeon demonstrates specific psychological qualities and skills (psychological flexibility and resilience). This has important implications for improving surgeons’ mental wellbeing, because psychological flexibility and resilience are malleable, and can be successfully targeted with interventions in a way that personality traits cannot.
Robot-assisted minimally invasive oesophagectomy versus thoracoscopic approach: multi-institutional study on short-term outcomes
Authors: Chao Yin-Kai , Lee Jui-Ying , Huang Wen-Chien , Lee Jang-Ming , Tseng Yau-Lin , Lu Hung-I 
Published: July 2024

Abstract

Background
Robot-assisted minimally invasive oesophagectomy and conventional minimally invasive oesophagectomy are superior to open techniques. However, few studies have directly compared the outcomes of the two minimally invasive approaches.

Methods
A retrospective study of patients from six medical centres with oesophageal squamous cell carcinoma who underwent minimally invasive oesophagectomy between 2015 and 2022. Perioperative outcomes were compared after applying inverse probability of treatment weighting.

Results
The study included 577 patients (robot-assisted minimally invasive oesophagectomy: 206; conventional minimally invasive oesophagectomy: 371). After applying inverse probability of treatment weighting, robot-assisted minimally invasive oesophagectomy was found to yield a higher number of mediastinal nodes compared with conventional minimally invasive oesophagectomy (14.86 versus 12.66, P = 0.017). Robot-assisted minimally invasive oesophagectomy was notably effective in retrieving upper mediastinal left recurrent laryngeal nerve nodes, averaging 1.97 nodes versus 1.14 nodes harvested by conventional minimally invasive oesophagectomy (P &lt; 0.001). This was coupled by a significant decrease in nerve palsy rates (13.9% versus 22.8%, P = 0.020). A significantly larger percentage of patients in the robot-assisted minimally invasive oesophagectomy group had an uncomplicated postoperative course (51.8% versus 34%, P &lt; 0.001). Robot-assisted minimally invasive oesophagectomy also led to a reduction in pneumonia rates (8.6% versus 15.2%, P = 0.041) and was linked to a shorter length of stay (length of stay; 16.64 versus 21.14 days, P = 0.007). The advantage of robot-assisted minimally invasive oesophagectomy in reducing the length of stay was especially pronounced in patients with a high Charlson co-morbidity index (≥2, mean difference 8.46 days; P = 0.0069) and those who underwent neoadjuvant therapy (mean difference 5.63 days; P &lt; 0.001).

Conclusion
In oesophageal squamous cell carcinoma, the use of robot-assisted minimally invasive oesophagectomy led to fewer cases of pneumonia and faster recovery compared with conventional minimally invasive oesophagectomy. Additionally, robot-assisted minimally invasive oesophagectomy significantly improved the feasibility and safety of performing lymph node dissection along the recurrent laryngeal nerve.
Takotsubo syndrome in a cancer patient treated with a combination of anti-cancer drugs including immune checkpoint inhibitors: a case report
Authors: Yamada Keita , Ida-Ichikawa Mizuki , Fujimoto Naoki , Ishida Masaki , Dohi Kaoru 
Published: July 2024

Abstract

Background
Takotsubo syndrome (TTS) is characterized by transient regional left ventricular (LV) dysfunction occurring in individuals exposed to physical or emotional stress. Various stressors are triggers for TTS in cancer patients, and anti-cancer drugs have recently been proposed as a trigger. Therefore, further studies are needed to clarify these triggers and avoid the unnecessary interruption of anti-cancer treatment.

Case summary
A 66-year-old woman presented with dyspnoea 10 days after the initiation of atezolizumab in combination with bevacizumab. She had previously received osimertinib as first-line therapy for recurrent lung cancer after primary resection and atezolizumab in combination with bevacizumab, paclitaxel, and carboplatin as second-line therapy. She was admitted due to electrocardiography abnormalities and elevated troponin I and brain natriuretic peptide levels. Echocardiography revealed circumferential severe LV hypokinesis at the mid-ventricular level, with preserved wall motion at the base and apex. Cardiac catheterization performed after the attenuation of symptoms with 20 mg of intravenous furosemide showed normal coronary arteries. Cardiac magnetic resonance imaging on Day 4 revealed increases in T1 and T2 values and extracellular volume fraction; however, neither myocardial infiltration of inflammatory cells or myocardial necrosis was observed in endomyocardial samples obtained on the day of her arrival. Atypical TTS was suspected, and she was treated with perindopril, bisoprolol, and spironolactone. Magnetic resonance imaging 1.5 months after the onset of TTS showed improvements in LV contractility, T1 and T2 values, and the extracellular volume fraction.

Discussion
A more detailed understanding of the relationship between anti-cancer drugs and TTS is crucial for preventing interruptions to anti-cancer therapy.
Kirchhoff prestack time migration of crooked-line seismic data
Authors: Chen Xiangzhong , Yue Yubo , Xie Yu , Li Wei 
Published: July 2024

Abstract
The crooked-line seismic survey has been widely used in oil and gas exploration in complex areas of western China. However, due to the unconventional acquisition geometry, current migration methods cannot fully account for the characteristics of crooked-line seismic data and may lead to poorly resolved images with inaccurate kinematics. To mitigate this problem, we present in this paper a modified Kirchhoff prestack time migration well adapted to such seismic data. We first carry out a theoretical analysis on the propagation geometry of crooked-line seismic data and demonstrate problems associated with conventional 3D traveltime-based migration. Then, we present a modified 2D migration scheme based on the projection between the actual imaging trace within the vertical plane of seismic reflections and the output imaging trace. Compared with the 3D traveltime-based migration, our method not only ensures the accuracy of imaging depth, but also improves the focusing and continuity of the migrated image. We use both synthetic and real data tests to validate the correctness and effectiveness of the proposed method.
Safety and efficacy of antibiotic-impregnated absorbable calcium sulfate beads (Stimulan) in cranioplasty
Authors: Evans Alexander R , Kimmell Marianne E , Kharbat Abdurrahman F , Shakir Hakeem J 
Published: July 2024

Abstract
Cranioplasty is a common neurosurgical procedure that follows hemicraniectomy in the setting of neoplasm resection or increased intracranial pressure. Although standardized practices aim at minimizing infection risk, infection of the surgical site has been reported in 6.6%–8.4% of patients. In this work, we document the novel use of synthetic dissolvable antibiotic-impregnated calcium sulfate beads (STIMULANⓇ Rapid Cure, Biocomposites Ltd, Wilmington, NC, USA) in five cases of cranioplasty at our institution. Four patients experienced wound healing as expected with no complications related to the use of Stimulan beads. One patient’s clinical course was complicated by pseudomeningocele with superficial wound infection occurring 74 days following cranioplasty. Of note, this patient had suffered an avulsion injury and subgaleal hematoma of the scalp ipsilateral to the cranial incision, predisposing to infection due to incompetent scalp vasculature. No complications could be directly attributed to the use of STIMULANⓇ beads.
Forgotten and ignored: making digital health work for migrant population in Africa
Authors: Adigun Taofeekat , Opone Esther , Baidoo Bettina , Mathenge Moses , Avoka Cephas , Awosiku Olutola 
Published: July 2024

Abstract
The African continent has experienced an alarming increase in forcibly displaced individuals, driven by socio-political conflict, economic instability and climate-induced calamities. The urgent need for contextualized and adaptable health solutions in the face of ongoing conflicts and crises underscores the importance of harnessing digital health innovations while ensuring inclusivity and equity for all. This commentary explores the potential of digital health to address healthcare disparities among migrant populations, examining the barriers to adoption and providing recommendations for policymakers and stakeholders to promote inclusivity and improve healthcare access. While digital health emerged as a promising avenue for improving healthcare access, there is also a greater necessity for tailoring these innovations to the specific needs and vulnerabilities of the target populations.
A genetic mouse model mimicking MET related human osteofibrous dysplasia is characterized by delays in fracture repair and defective osteogenesis
Authors: Hong Guoju , Xie William , Ahmed Kashif , Oborn Connor , Soltys Carrie‐lynn , Kannu Peter 
Published: July 2024

AbstractOsteofibrous dysplasia (OFD) is a rare, benign, fibro‐osseous lesion that occurs most commonly in the tibia of children. Tibial involvement leads to bowing and predisposes to the development of a fracture which exhibit significantly delayed healing processes, leading to prolonged morbidity. We previously identified gain‐of‐function mutations in the MET gene as a cause for OFD. In our present study, we test the hypothesis that gain‐of‐function MET mutations impair bone repair due to reduced osteoblast differentiation. A heterozygous Met exon 15 skipping (MetΔ15‐HET) mouse was created to imitate the human OFD mutation. The mutation results in aberrant and dysregulation of MET‐related signaling determined by RNA‐seq in the murine osteoblasts extracted from the wide‐type and genetic mice. Although no gross skeletal defects were identified in the mice, fracture repair was delayed in MetΔ15‐HET mice, with decreased bone formation observed 2‐week postfracture. Our data are consistent with a novel role for MET‐mediated signaling regulating osteogenesis.
Metagenomic next‐generation sequencing of cerebrospinal fluid reveals etiological and microbiological features in patients with various central nervous system infections
Authors: Wang Xiaojuan , Xu Huan , Qin Lingzhi , Wang Huimin , Jiang Yushu , Liu Huiqin , Zhang Milan , Pang Rui , Wu Wencai , Li Wei 
Published: July 2024

AbstractThe application of metagenomic next‐generation sequencing (mNGS) in pathogens detection of cerebrospinal fluid (CSF) is limited because clinical, microbiological, and biological information are not well connected. We analyzed the 428 enrolled patients' clinical features, pathogens diagnostic efficiency of mNGS in CSF, microbial community structure and composition in CSF, and correlation of microbial and clinical biomarkers in CSF. General characteristics were unspecific but helpful in formulating a differential diagnosis. CSF mNGS has a higher detection rate (34.6%) compared to traditional methods (5.4%). mNGS detection rate was higher when the time from onset to CSF collection was ≤20 days, the CSF leukocytes count was >200 × 106/L, the CSF protein concentration was >1.3 g/L, or CSF glucose concentration was ≤2.5 mmol/L in non‐postoperative bacterial CNS infections (CNSi). CSF was not strictly a sterile environment, and the potential pathogens may contribute to the dysbiosis of CSF microbiome. Furthermore, clinical biomarkers were significantly relevant to CNS pathogens. Clinical data are helpful in choosing a proper opportunity to obtain an accurate result of mNGS, and can speculate whether the mNGS results are correct or not. Our study is a pioneering study exploring the CSF microbiome in different CNSIs.
Qualitative Exploration of the #MeTooMedicine Online Discourse: “Holding Beacons of Light to Shine in the Corners They Are Hoping to Keep Dark”
Authors: LaDonna Kori A. , Field Emily , Cowley Lindsay , Ginsburg Shiphra , Watling Chris , Pack Rachael 
Published: July 2024

Abstract

Purpose
The MeToo movement forced a social reckoning, spurring women in medicine to engage in the #MeTooMedicine online discourse. Given the risks of reporting sexual violence, discrimination, or harassment, it is important to understand how women in medicine use platforms like Twitter to publicly discuss their experiences. With such knowledge, the profession can use the public documentation of women in medicine for transformative change.

Method
Using reflexive thematic analysis, 7,983 tweets (posted between November 2017 and January 2020) associated with #WomenInMedicine, #MeTooMedicine, and #TimesUpHC were systematically analyzed in 2020–2022, iteratively moving from describing their content, to identifying thematic patterns, to conceptualizing the purpose the tweets appeared to serve.

Results
The Twitter engagement of women in medicine was likened to “holding beacons of light to shine in the corners [harassers] are hoping to keep dark,” both reinforcing the message that “gender bias is alive and well” and calling for a “complete transformation in how we approach” the problem. The tweets of women in medicine primarily seemed aimed at disrupting complacency; encouraging bystanders to become allies; challenging stereotypes about women in medicine; championing individual women leaders, peers, and trainees; and advocating for reporting mechanisms and policies to ensure safety and accountability across medical workplaces.

Conclusions
Women in medicine appeared to use Twitter for a host of reasons: for amplification, peer support, advocacy, and seeking accountability. By sharing their experiences publicly, women in medicine seemed to make a persuasive argument that time is up, providing would-be allies with supporting evidence of sexual violence, discrimination, and harassment. Their tweets suggest a roadmap for what is needed to achieve gender equity, ensure that lack of awareness is no longer an excuse, and ask bystanders to grapple with why women’s accounts continue to be overlooked, ignored, or dismissed and how they will support women moving forward.
Associations Between Gestational Residential Radon Exposure and Term Low Birthweight in Connecticut, USA
Authors: Heo Seulkee , Li Longxiang , Son Ji-Young , Koutrakis Petros , Bell Michelle L. 
Published: July 2024

Background:
Studies suggest biologic mechanisms for gestational exposure to radiation and impaired fetal development. We explored associations between gestational radon exposure and term low birthweight, for which evidence is limited.

Methods:
We examined data for 68,159 singleton full-term births in Connecticut, United States, 2016–2018. Using a radon spatiotemporal model, we estimated ZIP code-level basement and ground-level exposures during pregnancy and trimesters for each participant’s address at birth or delivery. We used logistic regression models, including confounders, to estimate odds ratios (ORs) for term low birth weight in four exposure quartiles (Q1–Q4) with the lowest exposure group (Q1) as the reference.

Results:
Exposure levels to basement radon throughout pregnancy (0.27–3.02 pCi/L) were below the guideline level set by the US Environmental Protection Agency (4 pCi/L). The ORs for term low birth weight in the second-highest (Q3; 1.01–1.33 pCi/L) exposure group compared with the reference (<0.79 pCi/L) group for basement radon during the first trimester was 1.22 (95% confidence interval [CI] = 1.02, 1.45). The OR in the highest (Q4; 1.34–4.43 pCi/L) quartile group compared with the reference group during the first trimester was 1.26 (95% CI = 1.05, 1.50). Risks from basement radon were higher for participants with lower income, lower maternal education levels, or living in urban regions.

Conclusion:
This study found increased term low birth weight risks for increases in basement radon. Results have implications for infants’ health for exposure to radon at levels below the current national guideline for indoor radon concentrations and building remediations.
The Effect of Art on Premenstrual Syndrome Symptoms
Authors: Çitil Elif Tuğçe , Canbay Funda Çitil 
Published: July 2024

Art-based interventions can serve as a complementary and alternative method in managing various illnesses. This study aimed to investigate the impact of art-based interventions on symptoms of Premenstrual Syndrome (PMS). This study was conducted between September and December 2022, involving 72 midwifery students with PMS (37 in the experimental group [EG] and 35 in the control group [CG]). Art-based interventions were applied to the EG weekly for 8 weeks, while the students in the CG continued with their usual coping habits. The data were collected using the Personal Information Form and the Premenstrual Syndrome Scale (PMSS). At the end of 8 weeks, both the EG and the CG were reassessed with the PMSS. The students who participated in the study were similar in terms of sociodemographic, obstetric, and medical characteristics (P > .05). Analysis of the difference between pre- and posttest measurements revealed that the PMSS scores of the EG significantly decreased (P = .000), whereas the PMSS scores of the CG did not improve (P = .000). The findings of the study demonstrate that art-based interventions had a therapeutic effect on PMS symptoms.
The Effect of Self-Acupressure on Sleep Quality and Fatigue in Nurses
Authors: Çavuşoğlu Esra , Gün Meral 
Published: July 2024

This study was conducted to determine the effects of self-acupressure on sleep quality and fatigue in nurses working in medical clinics. A total of 64 nurses (n = 32 acupressure, n = 32 sham acupressure) participated in this prospective, 2-arm (1:1) study with an experimental design. In the study, both groups used the pressure points they were taught while performing self-acupressure 3 times per week for 4 weeks. After the intervention, the total mean score average of the acupressure group on the Pittsburg Sleep Quality Index and Fatigue Severity Scale was significantly lower than that of the sham acupressure group (P < .05). Self-acupressure is a noninvasive, easy-to-use, safe, and efficient complementary and integrated technique that nurses can use to improve their sleep quality and manage fatigue.