bluuebunny/crossref_metadata_2025_split huggingface dataset:
MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus
Authors: Krishnan Karthic , Katneni Vinaya Kumar , Prabhudas Sudheesh K. , Kaikkolante Nimisha , Jangam Ashok Kumar , Katneni Upendra Kumar , Hauton Chris , Peruzza Luca , Mudagandur Shashi Shekhar , Koyadan Vijayan K. , Poochirian Jithendran Karingalakkandy , Jena Joykrushna 
Published: April 2023

Abstract
Background
The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature.

Methods
We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes.

Results
We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases.

Conclusions
Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes.
Synchronous thyroid cancer and malignant struma ovarii: concordant mutations and microRNA profile, discordant loss of heterozygosity loci
Authors: Seo Gabriella T. , Minkowitz Jeremy , Kapustin Danielle A. , Fan Jun , Minkowitz Gerald , Minkowitz Miriam , Dowling Eric , Matloob Ammar , Asti Divya , Dhar Meekoo , Shutty Christopher , Brickman Alan , Urken Mark L. , Brandwein-Weber Margaret , Finkelstein Sydney D. 
Published: April 2023

Abstract
Background
Struma ovarii is an unusual ovarian teratoma containing predominantly thyroid tissue. Less than 10% of cases undergo malignant transformation in the thyroid tissue and are considered malignant struma ovarii (MSO). MSO have been reported with concurrent thyroid lesions, but molecular data is lacking.

Case presentation
A 42-year-old female developed MSO and synchronous multifocal subcentimeter papillary thyroid carcinoma (PTC). The patient underwent a salpingo-oophrectomy, thyroidectomy, and low-dose radioactive iodine ablation. Both the thyroid subcentimeter PTC and MSO were positive for BRAF V600E mutation, and microRNA expression profiles were similar across all tumor deposits. However, only the malignant component demonstrated extensive loss of heterozygosity (LOH) involving multiple tumor suppressor gene (TSG) chromosomal loci.

Conclusions
We present the first reported case of MSO with synchronous multifocal subcentimeter PTC in the thyroid containing concordant BRAF V600E mutations and resulting with discordant LOH findings. This data suggests that loss of expression in tumor suppressor gene(s) may be an important contributor to phenotypic expression of malignancy.
Diacerein versus non-steroidal anti-inflammatory drugs in the treatment of knee osteoarthritis: a meta-analysis
Authors: Zeng Fan , Wang Kang , Duan Hang , Xu Xiao-tong , Kuang Gao-yan , Lu Min 
Published: April 2023

Abstract
Background
Knee osteoarthritis (KOA) is a common musculoskeletal condition affecting millions of people worldwide and posing a significant challenge to clinicians and researchers. Emerging evidence suggests that the multifaceted symptomatology of KOA may be alleviated by diacerein. With this in mind, we conducted a systematic review and meta-analysis to evaluate the efficacy and safety of diacerein in patients with KOA.

Methods
We systematically searched Embase, PubMed, Cochrane Library, Web of Science, Chinese Biomedical Literature Database (CBM), Wanfang Database (WanFang), China National Knowledge Infrastructure (CNKI), and China Science and Technology Journal Database (VIP) from their inception to August 2022 for randomized controlled trials (RCTs) of diacerein intervention on patients with KOA. Two reviewers independently performed the selection of eligible studies and the extraction of relevant data. The meta-analysis was performed using RevMan 5.4 and R 4.1.3 software tools. Depending on the type of outcome indicator selected, summary measures were expressed as mean differences (MD), standardized mean differences (SMD), or odds ratio (OR) with 95% confidence intervals (CI).

Results
Twelve RCTs with 1732 patients were included. The results revealed that diacerein had comparable efficacy to non-steroidal anti-inflammatory drugs (NSAIDs) in reducing pain indicators such as Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) (SMD = 0.09, 95% CI [−0.10, 0.28], P = 0.34) and visual analogue scale (VAS) (SMD = −0.19, 95% CI [−0.65, 0.27], P = 0.42). However, diacerein outperformed NSAIDs in terms of global efficacy assessment by both patients and investigators (patients: 1.97, 95% CI [1.18, 3.29], P = 0.01; investigator: 2.18, 95% CI [0.99, 4.81], P = 0.05) at the end of treatment and sustained effectiveness in reducing WOMAC score and VAS score at four weeks after treatment. Moreover, there was no significant difference in adverse events incidence between the diacerein and NSAID groups. However, the GRADE evaluation indicated that the majority of the evidence quality was low.

Conclusions
The results of this study suggest that diacerein could potentially be considered as a pharmacological agent with significant efficacy for the treatment of patients suffering from KOA, offering a potential alternative treatment strategy for those patients contraindicated to NSAIDs. However, further high-quality studies with longer follow-up are needed to make more informed decisions about its efficacy in the treatment of KOA.
Craniofacial growth and function in achondroplasia: a multimodal 3D study on 15 patients
Authors: Morice Anne , Taverne Maxime , Eché Sophie , Griffon Lucie , Fauroux Brigitte , Leboulanger Nicolas , Couloigner Vincent , Baujat Geneviève , Cormier-Daire Valérie , Picard Arnaud , Legeai-Mallet Laurence , Kadlub Natacha , Khonsari Roman Hossein 
Published: April 2023

Abstract
Background
Achondroplasia is the most frequent FGFR3-related chondrodysplasia, leading to rhizomelic dwarfism, craniofacial anomalies, stenosis of the foramen magnum, and sleep apnea. Craniofacial growth and its correlation with obstructive sleep apnea syndrome has not been assessed in achondroplasia. In this study, we provide a multimodal analysis of craniofacial growth and anatomo-functional correlations between craniofacial features and the severity of obstructive sleep apnea syndrome.

Methods
A multimodal study was performed based on a paediatric cohort of 15 achondroplasia patients (mean age, 7.8 ± 3.3 years), including clinical and sleep study data, 2D cephalometrics, and 3D geometric morphometry analyses, based on CT-scans (mean age at CT-scan: patients, 4.9 ± 4.9 years; controls, 3.7 ± 4.2 years).

Results
Craniofacial phenotype was characterized by maxillo-zygomatic retrusion, deep nasal root, and prominent forehead. 2D cephalometric studies showed constant maxillo-mandibular retrusion, with excessive vertical dimensions of the lower third of the face, and modifications of cranial base angles. All patients with available CT-scan had premature fusion of skull base synchondroses. 3D morphometric analyses showed more severe craniofacial phenotypes associated with increasing patient age, predominantly regarding the midface—with increased maxillary retrusion in older patients—and the skull base—with closure of the spheno-occipital angle. At the mandibular level, both the corpus and ramus showed shape modifications with age, with shortened anteroposterior mandibular length, as well as ramus and condylar region lengths. We report a significant correlation between the severity of maxillo-mandibular retrusion and obstructive sleep apnea syndrome (p < 0.01).

Conclusions
Our study shows more severe craniofacial phenotypes at older ages, with increased maxillomandibular retrusion, and demonstrates a significant anatomo-functional correlation between the severity of midface and mandible craniofacial features and obstructive sleep apnea syndrome.
Cross-sectional survey in Central African Republic finds mortality 4-times higher than UN statistics: how can we not know the Central African Republic is in such an acute humanitarian crisis?
Authors: Gang Karume Baderha Augustin , O’Keeffe Jennifer , Anonymous  , Roberts Les 
Published: April 2023

Abstract
Background
CAR is one of the poorest countries in the world. While UN statistics suggest that there is no health emergency in the country, two recently published mortality surveys contradict this. Moreover, recent accusations of massive scale human rights abuses by mercenaries suggested the need for a nationwide mortality survey.

Methods
Two stage cluster surveys were conducted in two different strata: one in the roughly half of the country within the Government’s control, and one in the areas mostly outside of the Government’s control. We randomly selected 40 clusters of 10 households in each stratum. The survey included questions on vital events with open-ended questions about health and household challenges at the beginning and end of each interview.

Results
70 of 80 selected clusters were successfully visited. We interviewed 699 households, containing 5070 people. 11 households (1.6%) refused to be interviewed and approximately 18.3% of households were absent at the time of visitation, mainly in the safer Government controlled areas. Interviewed households had a birth rate of 42.6 /1000 / year (95%CI 35.4–59.7) and a crude mortality rate (CMR) of 1.57 /10,000/day (95%CI: 1.36–1.78). The birth rate was lower and the death rate markedly higher in the strata outside of Government control. Families described malaria or fever, and diarrhea as the primary reported causes of death with violence accounting for 6% of all deaths.

Conclusions
CAR is experiencing a severe health emergency, with the highest measured nationwide mortality in the world to our knowledge. UN published death rate estimates appear to be less than one fourth of reality. There is a desperate need for food aid in the form of general distributions in CAR, along with the accompanying work programs, seed and tool distributions needed to restart local economies. This is of particular importance in rural areas outside of the Government control. While some humanitarian actors are doing their best to respond, the crisis level mortality rate suggests that the needs in CAR are being largely unmet.
Evaluation of errors related to surgical pathology specimens of different hospital departments with a patient safety approach: a case study in Iran
Authors: Tabatabaee Seyed Saeed , Ghavami Vahid , Kalhor Rohollah , Amerzadeh Mohammad , Zomorrodi-Niat Hadi 
Published: April 2023

Abstract
Background
Most surgical specimen errors occur in the pre-analysis stage, which can be prevented. This study aims to identify errors related to surgical pathology specimens in one of the most comprehensive healthcare centers in Northeast Iran.

Methods
The present study is descriptive and analytical research conducted cross-sectionally in 2021 at Ghaem healthcare center in the Mashhad University of Medical Sciences on the basis of a census sampling. We used a standard checklist to collect information. Professors and pathologists evaluated the validity and reliability of the checklist using Cronbach’s alpha calculation method of 0.89. We analyzed the results using statistical indices, SPSS 21 software, and the chi-square test.

Results
Out of 5617 pathology specimens studied, we detected 646 errors. The highest number of errors is the mismatch of the specimen with the label (219 cases; 3.9%) and the non-compliance of the patient’s profile in the specimen sent with the label (129 cases; 2.3%), and the lowest errors are the inappropriate volume of the fixator(24 cases; 0.4%), and they accounted for insufficient sample size (25 cases; 0.4%). Based on Fisher’s exact test results, there was a significant difference between the proportion of errors in different departments and months.

Conclusion
Considering the frequency of labeling errors in the stage before the analysis in the pathology department, the use of barcode imprinted in specimen containers, the removal of the paper request for pathology, the use of radio frequency chip technology, the use of the rechecking system and improving communication in different departments can be effective in reducing these errors.
LINC00240 in the 6p22.1 risk locus promotes gastric cancer progression through USP10-mediated DDX21 stabilization
Authors: Zhang Nasha , Wang Bowen , Ma Chi , Zeng Jiajia , Wang Teng , Han Linyu , Yang Ming 
Published: April 2023

Abstract
Background
Gastric cancer remains the leading cause of cancer death in the world. It is increasingly evident that long non-coding RNAs (lncRNAs) transcribed from the genome-wide association studies (GWAS)-identified gastric cancer risk loci act as a key mode of cancer development and disease progression. However, the biological significance of lncRNAs at most cancer risk loci remain poorly understood.

Methods
The biological functions of LINC00240 in gastric cancer were investigated through a series of biochemical assays. Clinical implications of LINC00240 were examined in tissues from gastric cancer patients.

Results
In the present study, we identified LINC00240, which is transcribed from the 6p22.1 gastric cancer risk locus, functioning as a novel oncogene. LINC00240 exhibits the noticeably higher expression in gastric cancer specimens compared with normal tissues and its high expression levels are associated with worse survival of patients. Consistently, LINC00240 promotes malignant proliferation, migration and metastasis of gastric cancer cells in vitro and in vivo. Importantly, LINC00240 could interact and stabilize oncoprotein DDX21 via eliminating its ubiquitination by its novel deubiquitinating enzyme USP10, which, thereby, promote gastric cancer progression.

Conclusions
Taken together, our data uncovered a new paradigm on how lncRNAs control protein deubiquitylation via intensifying interactions between the target protein and its deubiquitinase. These findings highlight the potentials of lncRNAs as innovative therapeutic targets and thus lay the ground work for clinical translation.
Extracorporeal cardiopulmonary resuscitation dissemination and integration with organ preservation in the USA: ethical and logistical considerations
Authors: Schiff Tamar , Koziatek Christian , Pomerantz Erin , Bosson Nichole , Montgomery Robert , Parent Brendan , Wall Stephen P. 
Published: April 2023

AbstractUse of extracorporeal membrane oxygenation (ECMO) in cardiopulmonary resuscitation, termed eCPR, offers the prospect of improving survival with good neurological function after cardiac arrest. After death, ECMO can also be used for enhanced preservation of abdominal and thoracic organs, designated normothermic regional perfusion (NRP), before organ recovery for transplantation. To optimize resuscitation and transplantation outcomes, healthcare networks in Portugal and Italy have developed cardiac arrest protocols that integrate use of eCPR with NRP. Similar dissemination of eCPR and its integration with NRP in the USA raise novel ethical issues due to a non-nationalized health system and an opt-in framework for organ donation, as well as other legal and cultural factors. Nonetheless, eCPR investigations are ongoing, and both eCPR and NRP are selectively employed in clinical practice. This paper delineates the most pressing relevant ethical considerations and proposes recommendations for implementation of protocols that aim to promote public trust and reduce conflicts of interest. Transparent policies should rely on protocols that separate lifesaving from organ preservation considerations; robust, centralized eCPR data to inform equitable and evidence-based allocations; uniform practices concerning clinical decision-making and resource utilization; and partnership with community stakeholders, allowing patients to make decisions about emergency care that align with their values. Proactively addressing these ethical and logistical challenges could enable eCPR dissemination and integration with NRP protocols in the USA, with the potential to maximize lives saved through both improved resuscitation with good neurological outcomes and increased organ donation opportunities when resuscitation is unsuccessful or not in accordance with individuals’ wishes.
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
Authors: Schreiber Jacob Matthew , Boix Carles A. , wook Lee Jin , Li Hongyang , Guan Yuanfang , Chang Chun-Chieh , Chang Jen-Chien , Hawkins-Hooker Alex , Schölkopf Bernhard , Schweikert Gabriele , Carulla Mateo Rojas , Canakoglu Arif , Guzzo Francesco , Nanni Luca , Masseroli Marco , Carman Mark James , Pinoli Pietro , Hong Chenyang , Yip Kevin Y. , Spence Jefrey P. , Batra Sanjit Singh , Song Yun S. , Mahony Shaun , Zhang Zheng , Tan Wuwei , Shen Yang , Sun Yuanfei , Shi Minyi , Adrian Jessika , Sandstrom Richard S. , Farrell Nina P. , Halow Jessica M. , Lee Kristen , Jiang Lixia , Yang Xinqiong , Epstein Charles B. , Strattan J. Seth , Bernstein Bradley E. , Snyder Michael P. , Kellis Manolis , Noble William S. , Kundaje Anshul Bharat ,   ENCODE Imputation Challenge Participants
Published: April 2023

Abstract
A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder. However, identifying the best imputation methods and what measures meaningfully evaluate performance are open questions. We address these questions by comprehensively analyzing 23 methods from the ENCODE Imputation Challenge. We find that imputation evaluations are challenging and confounded by distributional shifts from differences in data collection and processing over time, the amount of available data, and redundancy among performance measures. Our analyses suggest simple steps for overcoming these issues and promising directions for more robust research.
Atrial fibrillation gut syndrome: severe gastroparesis with pyloric spasm following radiofrequency catheter ablation of drug resistant symptomatic atrial fibrillation: a case report
Authors: Kannan Lakshmi , Fahim Anfal 
Published: April 2023

Abstract
Background
Atrial fibrillation is the most common cardiac arrhythmia, and cardiac ablation is one of the treatment modalities for persistent symptomatic atrial fibrillation. Gastroparesis is a rare complication of radiofrequency catheter ablation for atrial fibrillation, which may be associated with high morbidity.

Case presentation
We present a 44-year-old Caucasian male with persistent atrial fibrillation who presented with nausea, vomiting, bloating, and constipation after radiofrequency catheter ablation. He was found to have gastroparesis due to pyloric spasm that was treated with botulinum toxin injection.

Conclusion
This case signifies the importance of identifying gastric complications after radiofrequency catheter ablation atrial fibrillation, and the need for prompt diagnosis and treatment of gastroparesis with botulinum toxin injection.
Detection of microbial biofilms inside the lumen of ureteral stents: two case reports
Authors: Barajas-García Carolina C. , Guerrero-Barrera Alma L. , Arreola-Guerra José M. , Avelar-González Francisco J. , Ramírez-Castillo Flor Y. 
Published: April 2023

Abstract
Background
We report large biofilm structures that covered almost the entirety of the lumen and surface of double-J stents in two postrenal transplant patients, with no development of urinary tract infection. Biofilm bacteria of one patient were integrated by coccus in a net structure, whereas overlapping cells of bacilli were present in the other patient. To the best of our knowledge, this is the first time that high-quality images of the architecture of noncrystalline biofilms have been found inside double-J stents from long-term stenting in renal transplant recipients.

Case presentation
Two renal transplant recipients, a 34-year-old male and a 39-year-old female of Mexican-Mestizo origin, who underwent a first renal transplant and lost it due to allograft failure, had a second transplant. Two months after the surgical procedure, double-J stents were removed and analyzed using scanning electron microscopy (SEM). None of the patients had an antecedent of UTI, and none developed UTI after urinary device removal. There were no reports of injuries, encrustation, or discomfort caused by these devices.

Conclusion
The bacterial biofilm inside the J stent from long-term stenting in renal transplant recipients was mainly concentrated on unique bacteria. Biofilm structures from the outside and inside of stents do not have crystalline phases. Internal biofilms may represent a high number of bacteria in the double-J stent, in the absence of crystals.