bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research trends and areas of focus on cryoablation and oncology: A bibliometric analysis from 2001 to 2020
Authors: Liu Hang , Song Changen , Zhang Bingzhe , Luo Rong , Yang Jijin 
Published: December 2022

Background:
Cryoablation is an interdisciplinary, widely used treatment approach for several types of solid tumors, making it difficult to obtain a comprehensive picture of its current status and popular research topics. This study aimed to use a bibliometric approach to understand important research themes and trends in cryoablation and oncology.

Methods:
Literature studies on cryoablation and oncology from 2001 to 2020 were extracted from the Web of Science. A bibliometric analysis was performed based on the annual publication volume, several journal articles and local citation score, and distribution of keywords and trends in the literature using tools such as COOC version 9.94, VOSviewer version 1.6.17, and the bibliometrix version 3.1.3 R package.

Results:
This study included 2793 publications. Total yearly publications have plateaued over the last 20 years. Five research themes were presented in the keyword network, including clinical applications of cryoablation in liver, lung, kidney, prostate, and skin cancers and comparison of cryoablation with other energy ablations. After 2012, 2 new research topics emerged: synergy between cryoablation and immunotherapy in tumors and cryoablation of Barrett esophagus. The high cited literatures are dominated by studies related to cryoablation for renal and prostate cancer treatment, but they also reflect the recent increasing interest in immunotherapy and bone metastases. Twenty important journals were identified, with Cryobiology publishing the most articles.

Conclusion:
Bibliometric analysis of studies related to tumor cryoablation can help researchers rapidly comprehend popular topics and determine future trends, guiding future research directions.
A typical multisite invasive infection caused by hvKP: A case report and literature review
Authors: Liu Jia , Dai Mingying , Sun Qiang , Fang Wei 
Published: December 2022

Rationale:
Hypervirulent K. pneumoniae (hvKP) is a new variant of K. pneumoniae that can caused metastatic spreading by blood, including Splenic abscess, endogenous endophthalmitis, purulent meningitis. This report described a case of A typical multisite invasive infection caused by hvKP and carry out a historical review of the literature.

Patient concerns:
A 55-year-old man was referred to our hospital due to liver abscess. Diabetes was found during this hospitalization. Because of glycemic was uncontrolled, splenic abscess, endogenous endophthalmitis and purulent meningitis occurred during subsequent treatment.

Diagnoses:
We made s diagnosis of liver abscess and invasive K. pneumoniae liver abscess syndrome through generation sequencing and imaging features.

Interventions and outcomes:
The patient recovered and was subsequently discharged after mechanical ventilation, continuous renal replacement therapy, laparoscopic exploration and various antimicrobials.

Lessons:
HvKP are very aggressive and can disseminate to multiple sites, especially in patient who have diabetes, which is a treatment challenge for clinician.
Effects of the Orthognathic Surgery on the Voice Characteristics of Skeletal Class III Patients
Authors: Sahin Serife , Sen Yilmaz Berza 
Published: December 2022

Objectives:
To analyze the effects of the bimaxillary orthognathic surgery on the voice characteristics of skeletal Class III cases, and to evaluate correlations between acoustic and skeletal changes.

Method:
Skeletal Class III adult patients (7 male, 18 female) were asked to pronounce the sounds “[a], [ɛ], [ɯ], [i], [ɔ], [œ], [u], [y]” for 3 seconds. Voice records and lateral cephalometric x-rays were taken before the surgery (T0) and 6 months after (T1). Voice records were taken for the control group with 6 months of interval (n=20). The formant frequencies (F0, F1, F2, and F3), Shimmer, Jitter and Noise to Harmonic Ratio (NHR) parameters were considered with Praat version 6.0.43.

Results:
In the surgery group, significant differences were observed in the F1 of [e], F2 and Shimmer of [ɯ] and F1 and F2 of [œ] and F1 of [y] sound, the post-surgery values were lower. F3 of [u] sound was higher. In comparison with the control group, ΔF3 of the [ɔ], ΔF3 of the [u] and ΔF1 of the [y] sound, ΔShimmer of [ɛ], [ɯ], [i], [ɔ], [u] and [y], and the ΔNHR of [ɔ] sound significantly changed. The Pearson correlation analysis proved some correlations; ΔF2 between ΔSNA for [ɯ] and [œ] sounds, ΔF1 between ΔHBV for [y] sound.

Conclusion:
Bimaxillary orthognathic surgery changed some voice parameters in skeletal Class III patients. Some correlations were found between skeletal and acoustic parameters. We advise clinicians to consider these findings and inform their patients.
Large Vertex Encephaloceles: Management and Outcomes
Authors: Schneider Hoa , Cappitelli Alex , Langa Olivia C. , Goobie Susan M. , Meara John G. , Proctor Mark , Ganske Ingrid M. 
Published: December 2022

Background:Complex vertex and posterior encephaloceles containing brain tissue have uncertain prognosis and high operative risk. Patients may not be offered operative intervention depending on local and regional specialist expertise. The authors present their experience treating 5 such pediatric patients.Methods:This is a retrospective review of the surgical assessment, planning, and technique of cranial repairs, as well as surgical outcomes and developmental follow-up regarding adaptive functioning for patients presenting for second opinion for encephalocele of the cranial vertex after having been deemed too high risk at another institution.Results:Five consecutive patients presented between January 2014 and June 2016. One patient was not offered repair. Of 4 patients who underwent reconstruction, average age at time of repair was 2.7 months (range, 0.9–6.7). One presented with ruptured encephalocele, whereas the remaining 3 underwent drainage of the encephalocele (average volume of 1200 mL) at time of surgical resection. Operative time averaged 3.7 hours (range, 2.2–5.3). There were no deaths. One patient had a single seizure postoperatively. Two patients required placement of permanent shunt for hydrocephalus. Two patients completed developmental evaluations, both of whom exhibited delays in adaptive functioning relative to same-aged peers.Conclusions:Patients with large, complex encephalocele warrant evaluation by an experienced high-volume tertiary care pediatric craniofacial center. The decision to proceed with surgical management should include an interdisciplinary team of surgeons, anesthesiologists, neurologists, and social work. Further study of developmental outcomes in both operated and unoperated patients is necessary to better understand risks and benefits of reconstruction.
Simulation-Based Education in US Undergraduate Medical Education
Authors: Campbell Krystle K. , Wong Kristen E. , Kerchberger Anne Marie , Lysikowski Jerzy , Scott Daniel J. , Sulistio Melanie S. 
Published: December 2022

Purpose
Simulation-based education (SBE) provides experiential learning, improvement in quality of care, and reduction in errors. In 2011, the Association of American Medical Colleges described adoption of SBE in 68.0% of medical schools and 25.0% of teaching hospitals. We sought to examine current trends of SBE integration in American undergraduate medical education since previous publications.

Methods
From 2016 to 2019, University of Texas Southwestern Medical Center postgraduate year 1 residents were invited to participate in a survey assessing medical school simulation experience with 26 clinical tasks from three categories: procedural, communication, and other. Deidentified results were analyzed to assess demographics including sex, specialty, residency program type, allopathic versus osteopathic medical school, and medical school region.

Results
Nine hundred sixty-seven of 1047 (92.3%) responses were obtained, representing 139 US medical schools, 91% from allopathic training. Of procedural tasks, most simulated was suturing (n = 848, 89.6%) and least simulated was thoracentesis (n = 737, 80.9%). Of communication tasks, most simulated was taking a history (n = 475, 51.1% reporting simulation >30) and least simulated (never or ≤1) were obtaining a consent (n = 669, 73.2%) and disclosing a medical error (n = 666, 72.4%). Of other tasks, most simulated was chest compressions (n = 898, 96.0%) and least simulated was operating a defibrillator (n = 206, 22.1%). Results were similar regardless of procedural or nonprocedural program. There was no significant difference in SBE exposure between allopathic and osteopathic students (P = 0.89). Two participants (0.002%) reported no simulation exposure.

Conclusions
Our study is the first to describe a high prevalence of SBE adoption in medical schools nationwide since the Association of American Medical Colleges' 2011 publication, with overall equal exposure for students regardless of residency type and allopathic or osteopathic medical school. Despite widespread adoption of simulation, opportunities remain to expand SBE use to teach critically important communication skills.
A First in Human Trial to Evaluate the Safety and Immunogenicity of a G Protein Based Recombinant Respiratory Syncytial Virus Vaccine in Healthy Adults 18-45 Years
Authors: Cheng Xin , Zhao Gan , Dong Aihua , He Zhonghuai , Wang Jiarong , Jiang Brian , Wang Bo , Wang Miaomiao , Huai Xuefen , Zhang Shijie , Feng Shuangshuang , Qin Hong , Wang Bin 
Published: December 2022

AbstractBackgroundWith enormous morbidity and mortality induced by respiratory syncytial virus (RSV) infection among infants and the elderly, vaccines against RSV infection are in huge market demand.MethodsWe conducted a First-in-human (FIH), randomized, double-blind, placebo-controlled dose escalation study to evaluate the safety and immunogenicity response of the rRSV vaccine (BARS13) in healthy adults aged 18-45. A total of 60 eligible participants were randomized in a 4:1 ratio to receive one of four dose levels or vaccination regimens of BARS13 or placebo.ResultsNo serious adverse event (SAE) was experienced by any study participant. The geometric mean fold increase (GMFI) from baseline in all participants post-administration indicated that compared with single dose regimens, the IgG antibody level from baseline in participants received repeat dose regimens at Day 60 has increased over a 3-fold.ConclusionsBARS13 has a generally good safety and tolerability profile, and no significant difference in terms of adverse reaction severity or frequency has been observed between different dose groups. The immune response in repeat dose recipients shows more potential in further study and has guiding significance for the dose selection of subsequent studies.
Clinical Validation of Optical Genome Mapping for the Detection of Structural Variations in Hematological Malignancies
Authors: Pang Andy Wing Chun , Kosco Karena , Sahajpal Nikhil , Sridhar Arthi , Hauenstein Jen , Clifford Benjamin , Estabrook Joey , Chitsazan Alex , Sahoo Trilochan , Iqbal Anwar , Kolhe Ravindra , Raca Gordana , Hastie Alex R. , Chaubey Alka 
Published: December 2022

AbstractStructural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescencein situhybridization (FISH), employed globally for the past three decades have significant limitations in the resolution or the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS) based technologies are now widely used to detect clinically significant sequence variants but are limited in their ability to accurately detect SVs. Optical genome mapping (OGM) is an emerging technology enabling the genome-wide detection of all classes of SVs at a significantly higher resolution than karyotyping and FISH. OGM neither requires cultured cells nor amplification of DNA and hence addresses the limitations of culture and amplification biases. This study reports the clinical validation of OGM as a laboratory developed test (LDT), according to CLIA guidelines, for genome-wide SV detection in different hematological malignancies. In total, 68 cases with hematological malignancies (of various subtypes), 27 controls and two cancer cell lines were used for this study. Ultra-high molecular weight DNA was extracted from the samples, fluorescently labeled, and run on the Bionano Genomics Saphyr system. A total of 207 datasets, including replicates, were generated and 100% could be analyzed successfully. Sample data were then analyzed using either disease specific or pan-cancer specific BED files to prioritize calls that are known to be diagnostically or prognostically relevant. Accuracy, precision, PPV and NPV were all 100% against standard of care results. Sensitivity, specificity, and reproducibility were 100%, 100% and 96%, respectively. Following the validation, 11 cases were run and analyzed using OGM at three additional sites. OGM found more clinically relevant SVs compared to SOC testing due to its ability to detect all classes of SVs at much higher resolution. The results of this validation study demonstrate OGM’s superiority over traditional SOC methods for the detection of SVs for the accurate diagnosis of various hematological malignancies.
Putting on academic armor: How Black physicians and trainees take stances to make racism visible amidst publishing constraints
Authors: Johnson M. , Maggio L.A. , Konopasky A. 
Published: December 2022

AbstractIntroductionWhile there are a growing number of empirical studies of Black physicians’ and trainees’ experiences of racism, there are still few accounts from a first-person perspective. These personal commentaries or editorials require taking a delicate stance, balancing the professional, social, and individual. Black authors in the medical publishing space, who already experience microaggressions and racial trauma in their work spaces, must put on their academic armor to further experience them in publishing spaces. Medicine and medical education interpellate each of us, including the authors and readers of this piece, as a particular kind of subject. Beginning with a narrative grounding in the authors’ personal stances, this study seeks to understand the stances Black physicians and trainees take as they share their personal experiences of racism while protecting the institution of medicine from racism’s irreparable harms.MethodsThe authors searched four databases identifying 29 articles authored by Black physicians and trainees describing their experiences. During initial analysis, the authors identified three sets of discursive strategies:identification(introducing and tracking themselves throughout the article);intertextuality(dialoguing and drawing on other “texts” beyond the focus of the articles); andspace-time(social constructions of space and time linked to a network of social practices). The authors used a Google form to capture these strategies and direct quotes from the articles. Throughout the study, the authors reflected on theirownstances in relation to the experience of conducting the study and its findings.ResultsAuthors engaged in stance taking, which aligned with the concept of donning academic armor, by evaluating and positioning themselves with respect to racism and the norms of academic discourse in response to ongoing conversations both within medicine and in the broader US culture. They did this by (a) positioning themselves as being Black and, therefore, qualified to notice and name personal racist experiences while also aligning themselves with the reader through shared professional experiences and goals, (b) intertextual connections to other related events, people, and institutions that they–and their readers–value and (c) aligning themselves with a hoped-for future rather than a racist present.DiscussionBecause the discourses of medicine and medical publishing interpellate Black authors as Others they must carefully consider the stances they take, particularly when naming racism. The academic armor they put on must not only be able to defend them from attack, but help them slip unseen through institutional bodies replete with mechanisms to eject them. In addition to analyzing their own personal stance, authors leave readers with thought provoking questions regarding this armor as they return to narrative grounding.
Alternative Polyadenylation alters UBASH3B-ZNF652 competition to involve in Triple-Negative Breast Cancer
Authors: Wu Sijia , Hu Changbao , Wu Xiaoming , Zhou Xiaobo , Huang Liyu 
Published: December 2022

ABSTRACTAlternative polyadenylation (APA) is an RNA-processing mechanism which may affect gene expression. Its involvements in cancers including the triple-negative breast cancer (TNBC) have been demonstrated in previous studies. Given the lack of biomarkers for TNBC, in this study, we were committed to finding novel biomarkers related to TNBC prognosis from the perspective of APA-mediated microRNA regulation. For this goal, raw bulk RNA sequencing data was collected for the identification of nine survival-related APA events by multivariate Cox regression analysis and forward-selected Likelihood Ratio Test. They showed good prognosis ability on TNBC risk. Of them, the APA event inUBASH3Bwas proposed as a novel potential biomarker. This event disturbed microRNA regulation on its host gene and other competing tumor genes to possibly involve in the pathogenesis of TNBC.
A new framework for metabolic connectivity mapping using bolus [18F]FDG PET and kinetic modelling
Authors: Volpi Tommaso , Vallini Giulia , Silvestri Erica , De Francisci Mattia , Durbin Tony , Corbetta Maurizio , Lee John J. , Vlassenko Andrei G. , Goyal Manu S. , Bertoldo Alessandra 
Published: December 2022

AbstractPurposeMetabolic connectivity (MC) has been previously proposed as the covariation of static [18F]FDG PET images across participants, which we callacross-individualMC (ai-MC). In few cases, MC has also been inferred from dynamic [18F]FDG signals, similarly to fMRI functional connectivity (FC), which we termwithin-individualMC (wi-MC). The validity and interpretability of both MC approaches is an important open issue.Here we reassess this topic, aiming to 1) develop a novel methodology for wi-MC estimation; 2) compare ai-MC maps obtained using different [18F]FDG parameters (K1, i.e. tracer transport rate,k3, i.e. phosphorylation rate,Ki, i.e. tracer uptake rate, and the standardized uptake value ratio,SUVR); 3) assess the interpretability of ai-MC and wi-MC in comparison to structural and functional connectivity (FC) measures.MethodsWe analyzed dynamic [18F]FDG data from 54 healthy adults using kinetic modelling to quantify the macro- and microparameters describing the tracer behavior (i.e.Ki,K1, k3). We also calculatedSUVR. From the across-individual correlation ofSUVR, Ki, K1, k3, we obtained four different ai-MC matrices. A new approach based on Euclidean distance was developed to calculate wi-MC from PET time-activity curves.ResultsWe identified Euclidean similarity as the most appropriate metric to calculate wi-MC. ai-MC networks changed with different [18F]FDG parameters (k3MC vs.SUVRMC, r = 0.44). We found that wi-MC and ai-MC matrices are dissimilar (maximum r = 0.37), and that the match with FC is higher for wi-MC (Dice similarity: 0.47-0.63) than for ai-MC (0.24-0.39).ConclusionOur data demonstrate that individual-level MC from dynamic [18F]FDG data using Euclidean similarity is feasible and yields interpretable matrices that bear similarity to resting-state fMRI FC measures.
Prop3D: A Flexible, Python-based Platform for Machine Learning with Protein Structural Properties and Biophysical Data
Authors: Draizen Eli J. , Readey John , Mura Cameron , Bourne Philip E. 
Published: December 2022

AbstractBackgroundMachine learning (ML) has a rich history in structural bioinformatics, and modern approaches, such as deep learning, are revolutionizing our knowledge of the subtle relationships between biomolecular sequence, structure, function, dynamics and evolution. As with any advance that rests upon statistical learning approaches, the recent progress in biomolecular sciences is enabled by the availability of vast volumes of sufficiently-variable data. To be useful, such data must be well-structured, machine-readable, intelligible and manipulable. These and related requirements pose challenges that become especially acute at the computational scales typical in ML. Furthermore, in structural bioinformatics such data generally relate to protein three-dimensional (3D) structures, which are inherently more complex than sequence-based data. A significant and recurring challenge concerns the creation of large, high-quality, openly-accessible datasets that can be used for specific training and benchmarking tasks in ML pipelines for predictive modeling projects, along with reproducible splits for training and testing.ResultsHere, we report ‘Prop3D’, a platform that allows for the creation, sharing and extensible reuse of libraries of protein domains, featurized with biophysical and evolutionary properties that can range from detailed, atomically-resolved physicochemical quantities (e.g., electrostatics) to coarser, residue-level features (e.g., phylogenetic conservation). As a community resource, we also supply a ‘Prop3D-20sf’ protein dataset, obtained by applying our approach to CATH. We have developed and deployed the Prop3D framework, both in the cloud and on local HPC resources, to systematically and reproducibly create comprehensive datasets via the Highly Scalable Data Service (HSDS). Our datasets are freely accessible via a public HSDS instance, or they can be used with accompanying Python wrappers for popular ML frameworks.ConclusionProp3D and its associated Prop3D-20sf dataset can be of broad utility in at least three ways. Firstly, the Prop3D workflow code can be customized and deployed on various cloud-based compute platforms, with scalability achieved largely by saving the results to distributed HDF5 files via HSDS. Secondly, the linked Prop3D-20sf dataset provides a hand-crafted, already-featurized dataset of protein domains for 20 highly-populated CATH families; importantly, provision of this pre-computed resource can aid the more efficient development (and reproducible deployment) of ML pipelines. Thirdly, Prop3D-20sf’s construction explicitly takes into account (in creating datasets and data-splits) the enigma of ‘data leakage’, stemming from the evolutionary relationships between proteins.