bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bridging the genomic data gap in Africa: implications for global disease burdens
Authors: Omotoso Olabode Ebenezer , Teibo John Oluwafemi , Atiba Festus Adebayo , Oladimeji Tolulope , Adebesin Ayomide Oluwadarasimi , Babalghith Ahmad O. 
Published: December 2022

AbstractThis paper highlights the gap in the use of genomic data of Africans for global research efforts for disease cures. Genomic data represents an important tool used in disease research for understanding how diseases affect several populations and how these differences can be harnessed for the development of effective cures especially vaccines that have an impact at the genetic level e.g., RNA vaccines.This paper then provides a review of global genomic data status where three continents are reported to be the major contributor of genomic data to repositories used for disease research and the development of vaccines and medicines around the world.We reviewed the most recently published information about genetic data inclusiveness of populations, explaining how genomic data of Africans is lacking in global research efforts that cater towards the eradication of pandemics via the development of vaccines and other cures. We also discuss the implication of this non-inclusiveness for global disease burdens and indicate where changes need to be made in the last part of the paper.Lastly, the entire centers on some general policy recommendations to fully include African genomic data in such global genetic repositories. These recommendations can be implemented in African countries to improve genetic data collection, storage, and usage policies.
Patient-centered consultations for persons with musculoskeletal conditions
Authors: Belton Joletta , Birkinshaw Hollie , Pincus Tamar 
Published: December 2022

AbstractConsultations between practitioners and patients are more than a hypothesis-chasing exploration, especially when uncertainty about etiology and prognosis are high. In this article we describe a single individual's account of their lived experience of pain and long journey of consultations. This personal account includes challenges as well as opportunities, and ultimately led to self-awareness, clarity, and living well with pain. We follow each section of this narrative with a short description of the emerging scientific evidence informing on specific aspects of the consultation. Using this novel structure, we portray a framework for understanding consultations for persistent musculoskeletal pain from a position of patient-centered research to inform practice.
IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction
Authors: De Saeger Jonas , Park Jihae , Thoris Kai , De Bruyn Charlotte , Chung Hoo Sun , Inzé Dirk , Depuydt Stephen 
Published: December 2022

Abstract
Background
Copy number determination is one of the first steps in the characterization of transgenic plant lines. The classical approach to this, Southern blotting, is time-consuming, expensive and requires massive amounts of high-quality genomic DNA. Other PCR-based techniques are either inaccurate, laborious, or expensive.

Results
Here, we propose a new technique, IMPLANT (Insertion of competitive PCR calibrator for copy number estimation), a competitive PCR-based technique in which the competitor (based on an endogenous gene) is also incorporated in the T-DNA, which then gets integrated in the genome together with the gene of interest. As the number of integrated competitor molecules directly corresponds to the number of transgene copies, the transgene copy number can be determined by a single PCR reaction. We demonstrate that the results of this technique closely correspond with those obtained by segregation analysis in Arabidopsis and digital PCR In rice, indicating that it is a powerful alternative for other techniques for copy number determination.

Conclusions
We show that this technique is not only reliable, but is also faster, easier, and cheaper as compared with other techniques. Accurate results are obtained in both Arabidopsis and rice, but this technique can be easily extended to other organisms and as such can be widely adopted in the field of biotechnology.
Hybrid surgery for blunt aortic injury with rupture: a case report
Authors: Maruhashi Takaaki , Maruki Hideo , Mishima Toshiaki , Kitamura Tadashi , Kurihara Yutaro , Oi Marina , Kataoka Yuichi , Miyaji Kagami , Asari Yasushi 
Published: December 2022

Abstract
Background
Blunt thoracic aortic injury is one of the most lethal traumatic injuries. Ruptured cases often result in cardiac arrest before arrival at the hospital, and survival is rare.
Case presentation: A female patient in her 30 s was struck by an automobile while she was walking across an intersection. She was in a state of shock when emergency services arrived and was in cardiac arrest shortly after arriving at the hospital. A left anterolateral thoracotomy revealed a massive hemothorax secondary to thoracic aortic rupture. In addition, the patient had multiple traumas, including maxillary, pelvic, and lumbar burst fractures. We attempted to directly suture the aortic lesion; however, the increasing blood pressure caused the suture to break. We used a thoracic stent graft while ensuring permissive hypotension. Her postoperative prognosis was positive, and she was transferred to another hospital 85 days later.

Conclusions
We successfully performed a hybrid surgery combining thoracotomy and endovascular repair for this emergency case of blunt thoracic aortic injury with rupture.
Clinical and genetic characteristics of Chinese patients with congenital cranial dysinnervation disorders
Authors: Jia Hongyan , Ma Qian , Liang Yi , Wang Dan , Chang Qinglin , Zhao Bo , Zhang Zongrui , Liang Jing , Song Jing , Wang Yidi , Zhang Ranran , Tu Zhanhan , Jiao Yonghong 
Published: December 2022

Abstract
Background
Congenital cranial dysinnervation disorders (CCDDs) are a group of diseases with high clinical and genetic heterogeneity. Clinical examinations combined with Magnetic resonance imaging (MRI) and whole exome sequencing (WES) were performed to reveal the phenotypic and genotypic characteristics in a cohort of Chinese CCDDs patients.

Results
A total of 122 CCDDs patients from 96 families were enrolled. All patients showed restrictive eye movements, and 46 patients from 46 families (47.9%, 46/96) were accompanied by multiple congenital malformations. Multi-positional high-resolution MRI was performed in 94 patients from 88 families, of which, all patients had hypoplasia of the cranial nerves except HGPPS patients and 15 patients from 15 families (17.0%,15/88) were accompanied by other craniocerebral malformations. WES was performed in 122 CCDDs patients. Ten pathogenic variants were detected in KIF21A, TUBB3, and CHN1 genes in 43 families. Three variants were unreported, including KIF21A (c.1064T > C, p.F355S), TUBB3 (c.232T > A, p.S78T) and CHN1 (c.650A > G, p.H217R). Of the 43 probands harboring pathogenic variants, 42 were diagnosed with Congenital Fibrosis of Extraocular Muscles (CFEOM) and one was Duane Retraction Syndrome (DRS). No definite pathogenic variants in known candidate genes of CCDDs were found in sporadic DRS, Möbius Syndrome (MBS) and Horizontal Gaze Palsy with Progressive Scoliosis (HGPPS) patients. The CFEOM patients harboring R380C, E410K and R262H variants in TUBB3 gene and F355S variant in KIF21A gene exhibited syndromic phenotypes.

Conclusions
This study broadened the phenotypic and genotypic spectrums of CCDDs, and it was the largest clinical and genetic investigation for CCDDs patients from China. KIF21A and TUBB3 were the common pathogenic genes in Chinese CFEOM. MRI coupled with WES can provide a supportive diagnosis in patients with clinically suspected CCDDs.
The emerging role of epigenetic regulation in the progression of silicosis
Authors: Yin Haoyu , Xie Yujia , Gu Pei , Li Wei , Zhang Yingdie , Yao Yuxin , Chen Weihong , Ma Jixuan 
Published: December 2022

AbstractSilicosis is one of the most severe occupational diseases worldwide and is characterized by silicon nodules and diffuse pulmonary fibrosis. However, specific treatments for silicosis are still lacking at present. Therefore, elucidating the pathogenesis of silicosis plays a significant guiding role for its treatment and prevention. The occurrence and development of silicosis are accompanied by many regulatory mechanisms, including epigenetic regulation. The main epigenetic regulatory mechanisms of silicosis include DNA methylation, non-coding RNA (ncRNA), and histone modifications. In recent years, the expression and regulation of genes related to silicosis have been explored at epigenetic level to reveal its pathogenesis further, and the identification of aberrant epigenetic markers provides new biomarkers for prediction and diagnosis of silicosis. Here, we summarize the studies on the role of epigenetic changes in the pathogenesis of silicosis to give some clues for finding specific therapeutic targets for silicosis.
AI in breast screening mammography: breast screening readers' perspectives
Authors: de Vries Clarisse Florence , Colosimo Samantha J. , Boyle Moragh , Lip Gerald , Anderson Lesley A. , Staff Roger T. ,   the iCAIRD Radiology Collaboration, Harrison D. , Black C. , Murray A. , Wilde K. , Blackwood J. D. , Butterly C. , Zurowski J. , Eilbeck J. , McSkimming C. 
Published: December 2022

Abstract
Objectives
This study surveyed the views of breast screening readers in the UK on how to incorporate Artificial Intelligence (AI) technology into breast screening mammography.

Methods
An online questionnaire was circulated to the UK breast screening readers. Questions included their degree of approval of four AI implementation scenarios: AI as triage, AI as a companion reader/reader aid, AI replacing one of the initial two readers, and AI replacing all readers. They were also asked to rank five AI representation options (discrete opinion; mammographic scoring; percentage score with 100% indicating malignancy; region of suspicion; heat map) and indicate which evidence they considered necessary to support the implementation of AI into their practice among six options offered.

Results
The survey had 87 nationally accredited respondents across the UK; 73 completed the survey in full. Respondents approved of AI replacing one of the initial two human readers and objected to AI replacing all human readers. Participants were divided on AI as triage and AI as a reader companion. A region of suspicion superimposed on the image was the preferred AI representation option. Most screen readers considered national guidelines (77%), studies using a nationally representative dataset (65%) and independent prospective studies (60%) as essential evidence. Participants’ free-text comments highlighted concerns and the need for additional validation.

Conclusions
Overall, screen readers supported the introduction of AI as a partial replacement of human readers and preferred a graphical indication of the suspected tumour area, with further evidence and national guidelines considered crucial prior to implementation.
Predictive performance of radiomic models based on features extracted from pretrained deep networks
Authors: Demircioğlu Aydin 
Published: December 2022

Abstract
Objectives
In radiomics, generic texture and morphological features are often used for modeling. Recently, features extracted from pretrained deep networks have been used as an alternative. However, extracting deep features involves several decisions, and it is unclear how these affect the resulting models. Therefore, in this study, we considered the influence of such choices on the predictive performance.

Methods
On ten publicly available radiomic datasets, models were trained using feature sets that differed in terms of the utilized network architecture, the layer of feature extraction, the used set of slices, the use of segmentation, and the aggregation method. The influence of these choices on the predictive performance was measured using a linear mixed model. In addition, models with generic features were trained and compared in terms of predictive performance and correlation.

Results
No single choice consistently led to the best-performing models. In the mixed model, the choice of architecture (AUC + 0.016; p < 0.001), the level of feature extraction (AUC + 0.016; p < 0.001), and using all slices (AUC + 0.023; p < 0.001) were highly significant; using the segmentation had a lower influence (AUC + 0.011; p = 0.023), while the aggregation method was insignificant (p = 0.774). Models based on deep features were not significantly better than those based on generic features (p > 0.05 on all datasets). Deep feature sets correlated moderately with each other (r = 0.4), in contrast to generic feature sets (r = 0.89).

Conclusions
Different choices have a significant effect on the predictive performance of the resulting models; however, for the highest performance, these choices should be optimized during cross-validation.
Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder
Authors: Kim Hwanhee , Ko Soohyun , Kim Byung Ju , Ryu Sung Jin , Ahn Jaegyoon 
Published: December 2022

AbstractIn this paper, a reinforcement learning model is proposed that can maximize the predicted binding affinity between a generated molecule and target proteins. The model used to generate molecules in the proposed model was the Stacked Conditional Variation AutoEncoder (Stack-CVAE), which acts as an agent in reinforcement learning so that the resulting chemical formulas have the desired chemical properties and show high binding affinity with specific target proteins. We generated 1000 chemical formulas using the chemical properties of sorafenib and the three target kinases of sorafenib. Then, we confirmed that Stack-CVAE generates more of the valid and unique chemical compounds that have the desired chemical properties and predicted binding affinity better than other generative models. More detailed analysis for 100 of the top scoring molecules show that they are novel ones not found in existing chemical databases. Moreover, they reveal significantly higher predicted binding affinity score for Raf kinases than for other kinases. Furthermore, they are highly druggable and synthesizable.
Male guanine-rich RNA sequence binding factor 1 knockout mice (Grsf1−/−) gain less body weight during adolescence and adulthood
Authors: Dumoulin Bernhard , Heydeck Dagmar , Jähn Desiree , Lassé Moritz , Sofi Sajad , Ufer Christoph , Kuhn Hartmut 
Published: December 2022

AbstractThe guanine-rich RNA sequence binding factor 1 (GRSF1) is an RNA-binding protein of the heterogenous nuclear ribonucleoprotein H/F (hnRNP H/F) family that binds to guanine-rich RNA sequences forming G-quadruplex structures. In mice and humans there are single copy GRSF1 genes, but multiple transcripts have been reported. GRSF1 has been implicated in a number of physiological processes (e.g. embryogenesis, erythropoiesis, redox homeostasis, RNA metabolism) but also in the pathogenesis of viral infections and hyperproliferative diseases. These postulated biological functions of GRSF1 originate from in vitro studies rather than complex in vivo systems. To assess the in vivo relevance of these findings, we created systemic Grsf1−/− knockout mice lacking exons 4 and 5 of the Grsf1 gene and compared the basic functional characteristics of these animals with those of wildtype controls. We found that Grsf1-deficient mice are viable, reproduce normally and have fully functional hematopoietic systems. Up to an age of 15 weeks they develop normally but when male individuals grow older, they gain significantly less body weight than wildtype controls in a gender-specific manner. Profiling Grsf1 mRNA expression in different mouse tissues we observed high concentrations in testis. Comparison of the testicular transcriptomes of Grsf1−/− mice and wildtype controls confirmed near complete knock-out of Grsf1 but otherwise subtle differences in transcript regulations. Comparative testicular proteome analyses suggested perturbed mitochondrial respiration in Grsf1−/− mice which may be related to compromised expression of complex I proteins. Here we present, for the first time, an in vivo complete Grsf1 knock-out mouse with comprehensive physiological, transcriptomic and proteomic characterization to improve our understanding of the GRSF1 beyond in vitro cell culture models.
Wastewater-based surveillance in Italy leading to the first detection of mcr-10-positive Klebsiella quasipneumoniae
Authors: Formenti Nicoletta , Guarneri Flavia , Bertasio Cristina , Parisio Giovanni , Romeo Claudia , Scali Federico , Birbes Laura , Boniotti Maria Beatrice , Diegoli Giuseppe , Candela Loredana , Romeo Gianluca Antonio , Pasquali Paolo , Alborali Giovanni Loris 
Published: December 2022

AbstractWastewater-based surveillance enabled the first detection of the mobile colistin resistance genemcr-10in Italy. This plasmid-borne resistance gene was found in strains ofKlebsiella quasipneumoniaeisolated from samples of human raw sewage collected over several months. Although the isolates were phenotypically susceptible to colistin, the emergence ofmcr-10is concerning due to the highly variable expression of the gene and the potential for horizontal transfer to other species. In addition, the strains also carried an extended-spectrum β-lactamase gene and were phenotypically resistant to several beta-lactams. This study highlights the value of wastewater-based surveillance as an effective tool to monitor the emergence of antimicrobial resistance in strains circulating in the community and the environment.
Mid-term outcomes after total hip arthroplasty in 106 Crowe II/III hips: different hip center positions
Authors: Jia Cheng-Qi , Pan Hong-Fa , Wu Yu-Jie , You Yong-Gang , Cao Shi-Qi , Zhang Xue-Song 
Published: December 2022

Abstract
Background
Under the obvious acetabular superolateral bone defect of Crowe II/III hips, this study aimed to investigate the difference in surgical technique of different hip center positions from the surgical data and clinical outcomes.

Methods
From July 2007 to December 2016, 87 patients (106 Crowe II/III hips) consecutively received total hip arthroplasty (THA). The minimum follow-up time was 5 years. The mean limb length discrepancy was 1.97 ± 1.81 cm. Twenty-four hips had surgical histories. The patients were divided into three groups according to the acetabular prosthesis positions, depending on the Crowe classification, respectively, group 1 (Crowe I), group 2 (Crowe II) and group 3 (Crowe III). The surgical data and clinical results were used to evaluate the outcome of different surgical techniques of different hip center positions, including surgical time, blood loss, blood transfusion, number of osteotomy hips, osteotomy length, the distribution of prothesis, postoperative inpatient days, Harris hip scores, Visual Analogue Scale (VAS), Back Pain Function Scale (BPFS) and complications.

Results
The mean follow-up time was 8.93 ± 2.55 years. Nineteen hips performed intraoperative osteotomy. From group 1 to group 3, the mean osteotomy length were 0.53 ± 1.11 cm, 0.05 ± 0.22 cm, and 0.00 ± 0.00 cm, respectively (p = 0.083); the surgical time were 142.57 ± 57.94 min, 118.4 ± 41.22 min, and 120.00 ± 84.85 min, respectively (p = 0.324); the blood loss were 498.21 ± 368.53 mL, 333.33 ± 167.62 mL, and 350.00 ± 212.13 mL, respectively (p = 0.255); the blood transfusion were 288.48 ± 381.68 mL, 128.00 ± 235.17 mL, and 385.00 ± 219.20 mL, respectively (p = 0.199); the postoperative inpatient days were 7.95 ± 4.42 d, 7.47 ± 4.29 d, and 6.50 ± 0.71 d, respectively (p = 0.831). Among the groups, the distribution of acetabular prosthesis, acetabular liner, acetabular prosthesis sizes, femoral head sizes and femoral prothesis distal sizes were not significantly different (p > 0.05). Only the distribution of femoral prosthesis was significantly different (p = 0.046); the Harris, VAS, BPFS, and the distribution of complications were not significantly different (p > 0.05).

Conclusions
We provided a framework to guide decision-making in Crowe II/III hips for surgeons: the surgical technique of different hip center positions was stable and had good outcomes, but the acetabular prothesis position and femoral prothesis should be determined according to the intraoperative situation.

Level of evidence
Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.
Carbon storages and sequestration potentials in remnant forests of different patch sizes in northern Ethiopia: an implication for climate change mitigation
Authors: Muluneh Melese Genete , Worku Belachew Bogale 
Published: December 2022

Abstract
Background
Forests provide various ecosystem services. They are natural capitals that enhance nature to regulate itself via carbon sinks. However, anthropogenic and natural factors have altered their CO2 sequestration and carbon storage potentials. This study is aimed for examining the effect of patch size and biomass extraction on carbon stocks in northern Ethiopia. A total of 61 sample plots measuring 20 m × 20 m size each (0.04 ha) had been systematically assigned on patches classified into three size categories. However, the numbers of plots taken per patch were different with their sizes. Moreover, stump density has been computed at each plot to estimate the difference in the level of disturbance among patches. Carbon stocks had been estimated via models previously developed. One-way ANOVA was used to examine a variation in carbon stocks and sequestration potentials. Besides, a linear regression analysis was discretely done to examine the relationship between patch sizes, disturbance level, and carbon stocks.

Results
The overall aboveground biomass (ton ha−1) for the studied patches was 2059.13. There was a statistically significant variation in carbon stocks (ton ha−1) among patch size categories. The mean levels of disturbance ranges from 10.83% ± 1.30 to 30.8% ± 4.04. However, statistically significant difference in the level of disturbance was observed between large and small patch size categories, respectively (p < 0.05). Besides, a regression analysis confirmed a significant and negative relationship between patch size and patch disturbances (R2 = 0.65, p < 0.05). However, significant positive relation between carbon stocks (ton ha−1) and patch size (R2 = 0.53, p < 0.05) had observed.

Conclusions
In general, patch size and biomass extinction significantly influenced carbon stocks and CO2 sequestration potentials of forests. Consequently, with the pressing need to mitigate the effects of rising atmospheric CO2, maximizing carbon storage in the forest ecosystem is increasingly considered a viable management strategy. Therefore, disturbed land restoration, increasing forest patch size, sustainable management, and conservation of the existing remnant forest patch is needed to enhance carbon stocks and CO2 sequestration potentials.