bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Virus-like Features and Intrinsically Disordered Regions in Retrotransposon-derived Mammalian Genes
Authors: Cagliani Rachele , Forni Diego , Mozzi Alessandra , Fuchs Rotem , Tussia-Cohen Dafna , Arrigoni Federica , Pozzoli Uberto , De Gioia Luca , Hagai Tzachi , Sironi Manuela 
Published: August 2024

Abstract
Several mammalian genes have originated from the domestication of retrotransposons, selfish mobile elements related to retroviruses. Some of the proteins encoded by these genes have maintained virus-like features; including self-processing, capsid structure formation, and the generation of different isoforms through −1 programmed ribosomal frameshifting. Using quantitative approaches in molecular evolution and biophysical analyses, we studied 28 retrotransposon-derived genes, with a focus on the evolution of virus-like features. By analyzing the rate of synonymous substitutions, we show that the −1 programmed ribosomal frameshifting mechanism in three of these genes (PEG10, PNMA3, and PNMA5) is conserved across mammals and originates alternative proteins. These genes were targets of positive selection in primates, and one of the positively selected sites affects a B-cell epitope on the spike domain of the PNMA5 capsid, a finding reminiscent of observations in infectious viruses. More generally, we found that retrotransposon-derived proteins vary in their intrinsically disordered region content and this is directly associated with their evolutionary rates. Most positively selected sites in these proteins are located in intrinsically disordered regions and some of them impact protein posttranslational modifications, such as autocleavage and phosphorylation. Detailed analyses of the biophysical properties of intrinsically disordered regions showed that positive selection preferentially targeted regions with lower conformational entropy. Furthermore, positive selection introduces variation in binary sequence patterns across orthologues, as well as in chain compaction. Our results shed light on the evolutionary trajectories of a unique class of mammalian genes and suggest a novel approach to study how intrinsically disordered region biophysical characteristics are affected by evolution.
Human Immunodeficiency Virus–Induced Interferon-Stimulated Gene Expression Is Associated With Monocyte Activation and Predicts Viral Load
Authors: van Pul Lisa , van Dort Karel A , Girigorie Arginell F , Maurer Irma , Harskamp Agnes M , Kootstra Neeltje A 
Published: August 2024

Abstract

Background
Chronic immune activation is one of the hallmarks of human immunodeficiency virus (HIV) pathogenesis. Persistent upregulation of interferons (IFNs) and interferon-stimulated genes (ISGs) has previously been associated with chronic immune activation and HIV progression. Here a longitudinal analysis of the IFN and ISG response during HIV infection was performed to gain insights into the ongoing immune activation during HIV infection.

Methods
IFN and ISG levels were determined using quantitative polymerase chain reaction in peripheral blood mononuclear cells of people with HIV at pre-seroconversion, during acute and chronic HIV infection, and during suppressive antiretroviral therapy (ART).

Results
HIV infection induced the expression of a set of 4 ISGs—RSAD2, ISG15, IFI44L, and IFI27—which remained upregulated during chronic infection. This set of ISGs showed no clear correlations with T-cell activation as determined by co-expression of CD38 and HLA-DR. However, a strong correlation with monocyte activation marker soluble CD163 in serum was found. Furthermore, the expression of this ISG cluster was predictive of viral load before ART initiation and, on ART, expression levels normalized to pre-seroconversion levels.

Conclusions
The results presented here suggests that ISG expression is linked to monocyte activation, possibly driven by viral replication.
Facial recognition for disease diagnosis using a deep learning convolutional neural network: a systematic review and meta-analysis
Authors: Kong Xinru , Wang Ziyue , Sun Jie , Qi Xianghua , Qiu Qianhui , Ding Xiao 
Published: August 2024

Abstract

Background
With the rapid advancement of deep learning network technology, the application of facial recognition technology in the medical field has received increasing attention.

Objective
This study aims to systematically review the literature of the past decade on facial recognition technology based on deep learning networks in the diagnosis of rare dysmorphic diseases and facial paralysis, among other conditions, to determine the effectiveness and applicability of this technology in disease identification.

Methods
This study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines for literature search and retrieved relevant literature from multiple databases, including PubMed, on 31 December 2023. The search keywords included deep learning convolutional neural networks, facial recognition, and disease recognition. A total of 208 articles on facial recognition technology based on deep learning networks in disease diagnosis over the past 10 years were screened, and 22 articles were selected for analysis. The meta-analysis was conducted using Stata 14.0 software.

Results
The study collected 22 articles with a total sample size of 57 539 cases, of which 43 301 were samples with various diseases. The meta-analysis results indicated that the accuracy of deep learning in facial recognition for disease diagnosis was 91.0% [95% CI (87.0%, 95.0%)].

Conclusion
The study results suggested that facial recognition technology based on deep learning networks has high accuracy in disease diagnosis, providing a reference for further development and application of this technology.
‘We’ve Been Left Out’: women’s refuges in Northern Ireland, 1974–2008
Authors: McKimm Alice 
Published: August 2024

Abstract
With histories of late-twentieth-century Northern Ireland1 consumed with political violence, and studies of the contemporary women’s movements in Britain only recently shifting their focus beyond London, Northern Irish women’s refuges have been obscured from historical view. This article proposes that re-situating women’s refuges in the context of the Troubles can enrich our understanding of the refuge movements, and wider women’s activism, across the UK at the turn of the twenty-first century. Drawing from archived and original interviews as well as documentary sources, the article traces the development of the Northern Irish refuge movement over four key periods: early years (1974–83), cross-community organizing (1983–93), development (1993–8), and efforts for diversity and inclusion (1998–2008). Such a chronology challenges the perception of the 1980s as an era of division and decline for UK feminism, and highlights the value of moving away from overarching chronologies of women’s activism towards more localized timelines. Furthermore, re-contextualizing women’s refuges in the battleground of the Troubles offers new evidence of their efforts to reduce domestic abuse, bring together women from opposing communities, and rebuild a democratic society. These activities contributed to the ‘vernacular’ peace process taking place in Northern Ireland’s voluntary sector, and suggest that refuges across the UK were similarly engaged in a peace process addressing violence in the home.
Exploring the therapeutic potential of urine‐derived stem cell exosomes in temporomandibular joint osteoarthritis
Authors: Zhou Jian‐Ping , Peng Si‐Si , Xu Jie , Cheng Xing‐Wang , Wang Xiao‐Hui , Tao Jun‐Li , Dai Hong‐Wei , Cao Xin 
Published: August 2024

AbstractTemporomandibular joint osteoarthritis (TMJOA) is a degenerative ailment that causes slow cartilage degeneration, aberrant bone remodeling, and persistent discomfort, leading to a considerable reduction in the patient's life quality. Current treatment options for TMJOA have limited efficacy. This investigation aimed to explore a potential strategy for halting or reversing the progression of TMJOA through the utilization of exosomes (EXOs) derived from urine‐derived stem cells (USCs). The USC‐EXOs were obtained through microfiltration and ultrafiltration techniques, followed by their characterization using particle size analysis, electron microscopy, and immunoblotting. Subsequently, an in vivo model of TMJOA induced by mechanical force was established. To assess the changes in the cartilage of TMJOA treated with USC‐EXOs, we performed histology analysis using hematoxylin–eosin staining, immunohistochemistry, and histological scoring. Our findings indicate that the utilization of USC‐EXOs yields substantial reductions in TMJOA, while concurrently enhancing the structural integrity and smoothness of the compromised condylar cartilage surface. Additionally, USC‐EXOs exhibit inhibitory effects on osteoclastogenic activity within the subchondral bone layer of the condylar cartilage, as well as attenuated apoptosis in the rat TMJ in response to mechanical injury. In conclusion, USC‐EXOs hold considerable promise as a potential therapeutic intervention for TMJOA.
Preventing Hypothermia in Newborns With Congenital Anomalies in the Delivery Room
Authors: Heimall Lauren , Barrila-Yetman Michele , McCray Kia R. , Cestare Danielle , Duran Melissa , Wild K. Taylor , Ades Anne 
Published: August 2024

Background:
Thermoregulation interventions in the delivery room have historically focused on preterm infants and studies often exclude term infants or those infants with known congenital anomalies.

Purpose:
The purpose of this quality improvement project was to reduce the rate of admission hypothermia in neonates of all gestational ages born with congenital anomalies and admitted to the intensive care unit (ICU).

Methods:
Utilizing the Institute for Healthcare Improvement model for improvement, implementation of plan, do study, act cycles focused on standardizing temperatures of the delivery room and resuscitation bed, recommendations for temperature monitoring, trialing polyethylene lined hats, and implementing a delivery room thermoregulation checklist.

Results:
Overall, the mean rate of neonates admitted to the ICU hypothermic (<36.5°C) decreased from 27% to 9% over an 8-month period.

Implications for Practice and Research:
The interventions significantly reduced the number of neonates admitted to the ICU with hypothermia. Implementation of thermoregulation bundles should apply to all neonates with congenital anomalies to decrease risks associated with hypothermia.
Infant Cervical Vestibular Evoked Myogenic Potentials: A Scoping Review
Authors: Bassett Alaina M. , Suresh Chandan 
Published: August 2024

Objectives:
Children diagnosed with hearing loss typically demonstrate increased rates of vestibular loss as compared with their peers, with hearing within normal limits. Decreased vestibular function is linked with delays in gross motor development, acquisition of gross motor skills, and academic challenges. Timely development of sitting and walking gross motor skills aids in the progress of environmental exploratory activities, which have been tied to cognitive, language, and vocabulary development. Considering the time-sensitive development of gross motor skills and cognitive, language, and vocabulary development, identifying vestibular loss in infancy can support early intervention. This scoping review analyzes stimulus, recording, and participant factors relevant to assessing cervical vestibular evoked myogenic potentials (cVEMPs) in the infant population.

Design:
The scoping literature review was conducted on literature published between 2000 and 2023, focusing on articles assessing cVEMPs in infants. Two authors independently followed Preferred Reporting Items for Systematic and Meta-Analysis guidelines for title and abstract screening, full-text review, data extraction, and quality assessments. Sixteen articles meeting the inclusion criteria were included in the analysis.

Results:
The existing literature lacks consensus regarding stimulus and recording parameters for measuring infant cVEMPs. In addition, the review reveals a decrease in cVEMP response occurrence rates with the severity of hearing loss, especially in cases of severe to profound hearing loss, compared with mild to moderate sensorineural hearing loss in infants.

Conclusions:
This scoping review demonstrates the increasing use of cVEMP as a reliable tool for objectively assessing infant vestibular function. The lack of consensus in stimulus and recording parameters emphasizes the need for systematic research to establish an evidence-based protocol for cVEMP measurements in infants. Such a protocol will ensure the reliable measurement of cVEMPs in infants and enhance the effectiveness of cVEMP as part of the infant vestibular test battery. In addition, there is a necessity for a comprehensive large-scale study to evaluate the practicality and feasibility of implementing vestibular screening protocols for infants diagnosed with sensorineural hearing loss in the United States.
Iatrogenic Intraoperative Fracture in Patients With Osteogenesis Imperfecta
Authors: Georgiadis Andrew G. , Pottinger Todd J. , Sigrist Emmalynn J. , Truong Walter H. 
Published: August 2024

Background:
Osteogenesis imperfecta (OI) is a genetic defect in collagen type I, phenotypically characterized by bony fragility and a propensity to high rates of childhood fracture. Fragility fractures in patients with OI have been reported with routine hospital care. In addition, there is a nonzero rate of iatrogenic fracture during orthopaedic surgery directly related to the technical steps of the procedure itself. The rate of this latter has never been explicitly investigated.

Methods:
A review of all patients at a single OI referral center was conducted, including all patients with a diagnosis of OI seen between 2013 and 2023, inclusive. All patients who underwent orthopaedic surgery of any kind were reviewed, and clinical and radiographic details of all procedures were extracted. Among the details examined were the OI subtype, surgery details, any implants used, intraoperative and hospital stay complications, modified Clavien-Dindo classification of complications, and ultimate outcome.

Results:
Eleven of 60 patients experienced an unplanned, iatrogenic intraoperative fracture during orthopaedic surgery (11/60 = 18.3%). This comprised 15 fractures among 356 total orthopaedic surgical episodes (15/356 = 4.2%). All but one fracture occurred on the operative long bone segment, all were a direct result of surgical steps, and 11 of 15 fractures occurred in the femur. Most fractures were secondary to the removal, insertion, or exchange of intramedullary implants in the lower extremity (11 of 15 fractures), most often the femur. Thirteen of 15 injuries were classified as modified Clavien-Dindo II or III, requiring modification of postop rehabilitation, additional treatments, or surgical intervention (87%). Overall, iatrogenic fracture was the most common intraoperative complication experienced in the cohort.

Conclusions:
Iatrogenic fracture during orthopaedic surgery for patients with OI is not uncommon. A sizeable minority of patients with OI undergoing orthopaedic surgery will experience unplanned fractures, most commonly in the femur, and care is altered in most instances. The risk of intraoperative fracture can be discussed with families of children with OI as part of informed consent and shared decision-making.

Level of Evidence:
Level IV—retrospective cohort series.
Hip Displacement After Triradiate Closure in Ambulatory Cerebral Palsy: Who Needs Continued Surveillance?
Authors: Lindgren Amelia M. , Asma Ali , Rogers Kenneth J. , Miller Freeman , Shrader M. Wade , Howard Jason J. 
Published: August 2024

Background:
Hip surveillance in cerebral palsy (CP) is an accepted practice with evidence-based guidelines implemented. For the skeletally immature with open triradiate cartilage (TRC), recommendations for radiographic surveillance stemmed from population-based studies. For nonambulatory CP, progression of hip displacement after skeletal maturity has been reported; less is known for ambulatory CP. We aimed to determine the prevalence and risk factors associated with progressive hip displacement after TRC closure, a proxy for skeletal maturity, for ambulatory CP.

Methods:
This is a retrospective cohort study of patients with ambulatory CP (Gross Motor Function Classification System I-III), with unilateral or bilateral involvement, hypertonic motor type, regular hip surveillance (≥3 radiographs after age 10 yr, 1 before TRC closure, ≥1 after age 16 yr), and 2-year follow-up post-TRC closure. The primary outcome was migration percentage (MP). Other variables included previous preventative/reconstructive surgery, topographic pattern, sex, scoliosis, epilepsy, and ventriculoperitoneal shunt. An “unsuccessful hip” was defined by MP ≥30%, MP progression ≥10%, and/or requiring reconstructive surgery after TRC closure. Statistical analyses included chi-square and multivariate Cox regression. Kaplan-Meier survivorship curves were also determined. Receiver operating characteristic analysis was used to determine the MP threshold for progression to an “unsuccessful hip” after TRC closure.

Results:
Seventy-six patients (39.5% female) met the inclusion criteria, mean follow-up 4.7±2.1 years after TRC closure. Sixteen (21.1%) patients had an unsuccessful hip outcome. By chi-square analysis, diplegia (P=0.002) and epilepsy (P=0.04) were risk factors for an unsuccessful hip. By multivariate analysis, only first MP after TRC closure (P<0.001) was a significant risk factor for progression to an unsuccessful hip; MP ≥28% being the determined threshold (receiver operating characteristic curve analysis, area under curve: 0.845, P<0.02).

Conclusions:
The risk of MP progression after skeletal maturity is relatively high (21%), similar to nonambulatory CP. Annual hip surveillance radiographs after TRC closure should continue for Gross Motor Function Classification System I-III with an MP ≥28% after TRC closure, especially for bilateral CP and epilepsy.

Level of Evidence:
III
Transcriptomic profiling of intermediate cell carcinoma of the liver
Authors: Jang Byungchan , Kwon So Mee , Kim Jang Hyun , Kim Jung Mo , Chung Taek , Yoo Jeong Eun , Kim Haeryoung , Calderaro Julien , Woo Hyun Goo , Park Young Nyun 
Published: August 2024

Background:
Intermediate cell carcinoma (Int-CA) is a rare and enigmatic primary liver cancer characterized by uniform tumor cells exhibiting mixed features of both HCC and intrahepatic cholangiocarcinoma. Despite the unique pathological features of int-CA, its molecular characteristics remain unclear yet.

Methods:
RNA sequencing and whole genome sequencing profiling were performed on int-CA tumors and compared with those of HCC and intrahepatic cholangiocarcinoma.

Results:
Int-CAs unveiled a distinct and intermediate transcriptomic feature that is strikingly different from both HCC and intrahepatic cholangiocarcinoma. The marked abundance of splicing events leading to intron retention emerged as a signature feature of int-CA, along with a prominent expression of Notch signaling. Further exploration revealed that METTL16 was suppressed within int-CA, showing a DNA copy number–dependent transcriptional deregulation. Notably, experimental investigations confirmed that METTL16 suppression facilitated invasive tumor characteristics through the activation of the Notch signaling cascade.

Conclusions:
Our results provide a molecular landscape of int-CA featured by METTL16 suppression and frequent intron retention events, which may play pivotal roles in the acquisition of the aggressive phenotype of Int-CA.
The role of patient and family advisory boards in promoting greater attention to patient social needs by U.S. acute care hospitals
Authors: Hearld Larry R. , Jennings J’Aime , Hubbard Demetria , Lee Seung-Yup , Hearld Kristine R. 
Published: August 2024

Background
There is growing attention to individual-level patient social needs such as unstable housing and food insecurity. Such considerations, however, have historically been the purview of public health and have not been a priority of more traditional health care delivery organizations, such as acute care hospitals.

Purpose
The purpose of this study was to examine whether the presence of patient and family advisory boards (PFABs) among acute care community hospitals was associated with screening for and programs to address patient social needs.

Methods
We used a secondary data set derived from the American Hospital Association’s 2020 and 2021 annual surveys, along with multinomial and negative binomial regression models to assess the relationship between the presence/absence of a PFAB and the likelihood of offering and the number of areas addressed by social needs screening programs.

Results
More than half (55.9%) of all responding hospitals reported having a PFAB in 2020 (55.9%) and 2021 (52.7%). The presence of a PFAB among hospitals was significantly associated with patient social needs screening, more areas addressed by programs, and more types of partners to address these needs.

Conclusions
Community hospitals with a PFAB have more robust programs and partnerships to address patient social needs.

Practice Implications
Hospital leaders should consider going beyond simply establishing programs to address social needs but also consider comprehensiveness of these programs to recognize the intersectionality of social needs. One way to do this is to formally establish a PFAB to help hospitals better identify and prioritize the needs in local communities and design social needs programs/solutions that are patient- and family-centric.
Clinical outcomes and short-term survival of neoadjuvant immunochemotherapy for resectable esophageal cancer: a multicenter retrospective cohort study
Authors: Lan Ke , Yan Xiaolong , Lei Jie , Guo Xufeng , Zhou Yongan , Wang Xiaoping , Liu Honggang , Tian Feng , Lu Qiang , Gu Zhongping , Sun Jianyong , Yang Ende , Zhong Daixing , Wang Tao , Huang Lijun , Wang Jian , Liu Xu , Ni Yunfeng , Jiang Tao , Zhao Jinbo 
Published: August 2024

Objective:
The present retrospective cohort study aims to evaluate the efficacy and safety of neoadjuvant immunochemotherapy for resectable esophageal cancer and report the preliminary short-term survival.

Methods:
A multicenter, retrospective study was conducted concerning patients who received neoadjuvant PD-1 agents plus platinum-based chemotherapy between January 2019 and January 2022. The primary endpoint was the tumor pathologic complete response (pCR) rate.

Results:
Two hundred and thirteen patients with initial stage cI-IVA esophageal cancer who received neoadjuvant immunochemotherapy were identified. The complete tumor resection(R0) rate was 99.1%. The pCR rate was 31.9%, and the overall major pathological response rate was 49.8%. The 2-year DFS rate was 78.9% (95% CI: 72.9–85.4%) and the 2-years OS rate was 80.9% (95% CI: 75.3–86.9%). The incidence of TRAEs and surgical complications rate were 68.5 and 35.2%, respectively.

Conclusion:
The PD-1 agents combined with chemotherapy in the neoadjuvant treatment for resectable stage I–IVA esophageal cancer had a high pCR rate as well as good short-term survival benefits and tolerable toxicity.