bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy benchmark of the GeneMind GenoLab M sequencing platform for WGS and WES analysis
Authors: Li Chaoyang , Fan Xue , Guo Xin , Liu Yongfeng , Wang Miao , Zhao Xiaochao , Wu Ping , Yan Qin , Sun Lei 
Published: March 2022

Abstract
Background: GenoLab M is a recently developed next-generation sequencing (NGS) platform from GeneMind Biosciences. To establish the performance of GenoLab M, we present the first report to benchmark and compare the WGS and WES sequencing data of the GenoLab M sequencer to NovaSeq 6000 and NextSeq 550 platform in various types of analysis. 30-fold sequencing from Illumina NovaSeq platform and processed by GATK pipeline is currently considered as the golden standard of WGS. Thus this dataset is generated as a benchmark reference in this study.Results: GenoLab M showed an average of 94.62% of Q20 percentage for base quality, while the NovaSeq was slightly higher at 96.97%. However, GenoLab M outperformed NovaSeq or NextSeq at a duplication rate, suggesting more usable data after deduplication. For WGS short variant calling, GenoLab M showed significant accuracy improvement over the same depth dataset from NovaSeq, and reached similar accuracy to NovaSeq 33X dataset with 22x depth. For 100X WES, the F-score and Precision in GenoLab M were higher than NovaSeq or NextSeq, especially for InDel calling.Conclusions: GenoLab M is a promising NGS platform for high-performance WGS and WES applications. For WGS, 22X depth in the GenoLab M sequencing platform offers a cost-effective alternative to the current mainstream 33X depth on Illumina.
Quarantine preparedness – the missing factor in COVID-19 behaviour change? Qualitative insights from Australia
Authors: Davis Angela , Munari Stephanie , Doyle Joseph , Sutton Brett , Cheng Allen , Hellard Margaret , Gibbs Lisa 
Published: March 2022

Abstract
BackgroundA key feature of the global public health response to contain and slow the spread of COVID-19 has been community-based quarantine and self-isolation. As part of The Optimise Study, this research sought to understand the factors that influence people’s ability to undertake home-based quarantine and isolation to contain the spread of COVID-19. MethodsSemi-structured qualitative phone interviews (n=25) were conducted by telephone with people who participated in community-based quarantine in Australia before 31 March 2020. The Capability Opportunity Motivation Behaviour model was used to conduct a thematic analysis.ResultsParticipants required clear, accessible and trusted information to guide them in home-based quarantine and isolation. A sense of social responsibility and belief in the efficacy of the restrictions to reduce viral transmission aided their motivation. Access to essential needs, supportive living environments, and emotional support were required to adhere to restrictions, but few were prepared. ConclusionsFindings demonstrate that in addition to having the capability and motivation to adhere to restrictions, it is vital that people are also encouraged to prepare for the challenge to ensure access to physical, social and emotional support. Findings also illustrate the importance of engaging communities in planning and preparedness for quarantine and self-isolation public health responses.
Identification Of A Novel Homozygous Intron 3 Splice Site (A&gt;T) Mutation In The ARG1 Gene In Cerebral Palsy Pediatric Cases From Odisha, India
Authors: Behera Chinmay Kumar , Rup Amit Ranjan , Samal Sagnika , Das Biswadeep 
Published: March 2022

Abstract
Background: Arginases are essential for the completion of the last step of the urea cycle. In hyperarginemia, an autosomal recessive disorder of the urea cycle, a regression of development occurs after the first year of life, followed by gradually progressive atonic cerebral palsy, spastic quadriplegia, and mental decline. ARG1 mutations have been reported in hyperarginemia in the Western population because they obliterated or partially damaged arginase activity. Hence, it is important to assess the ARG1 mutations in such cases of cerebral palsy with hyperarginemia in different populations. Methods and Results: Two pediatric patients of two East Indian families presented with a range of manifestations including hypotonia of all limbs, mental retardation, and multiple episodes of seizure. The onset of the disease ranged from 1 to 3 years of age. Hyperammonemia (> 250 micromoles) and serum hyperarginemia (> 350 micromoles) were observed in both patients. Whole-genome sequencing, followed by Sanger sequencing analysis of both patients confirmed the presence of a homozygous 3' splice site variation in intron 3 of the ARG1 gene (chr6: g.131902357A>T) that affects the invariant AG acceptor splice site of exon 4 (c.330-2A>T; ENST00000356962.2). Conclusion: The study reports the presence of a novel ARG1 mutation in two different pediatric cases from Odisha, India associated with hyperarginemia. The pathogenicity of the mutation was robustly supported by the clinical phenotype, complete co-segregation with the disease, and biochemical observations.
Comprehensive Optimization Model for Open Channel Design
Authors: Salem Aly Khaled Aly , Imam Yehya Emad , Ghanem Ashraf Hassan , Bazaraa Abdallah Sadik 
Published: March 2022

Abstract
Open channels are one of the most used water conveyance systems to deliver water for diﬀerent purposes. Existing models for the design of open channels mainly assume uniform ﬂow, focus on cross-section sizing, and generally decouple cross-section sizing from the selection of channel alignment and proﬁle. This study developed an optimization model for a comprehensive design of conveyance channels. The model minimizes the sum of costs for earthwork, lining, water losses, and land acquisition; accounts for non-uniform, mixed-regime ﬂow; and considers multiple geometric and hydraulic constraints. The model was validated using several idealized scenarios. The model potential in minimizing the cost of real open channel projects was demonstrated through application to an existing irrigation water transmission canal in Egypt (the Sheikh Zayed Canal). The results of validation scenarios matched the anticipated outcomes for channel proﬁle and alignment and reproduced analytical solutions given in the literature for channel cross-section design. Application of the model to the Sheikh Zayed Canal gave a more optimal design; the OCCD model produced a design alternative with ~27% less cost than the constructed alternative.
The Prevalence and Natural History of Hepatic Cysts Examined by Ultrasound: A Health Checkup Population Retrospective Cohort Study
Authors: Tsuruya Kota , Nishizaki Yasuhiro , Tatemichi Masayuki , Mishima Yusuke , Shimma Yoshimasa , Arase Yoshitaka , Hirose Shunji , Shiraishi Koichi , Kagawa Tatehiro 
Published: March 2022

Abstract
The prevalence of hepatic cysts in the general population and their natural history are largely unknown. This study aimed to assess the prevalence and natural history of hepatic cysts by investigating health checkup participants. Ultrasonographic data of health checkup participants (n = 38,842) were retrospectively evaluated to calculate its prevalence. In addition, we assessed the changes in the size and characteristics of hepatic cysts over 10 years (n = 7,709). We found the prevalence of hepatic cysts was 21.9%. Older age, female sex, and presence of kidney cysts or pancreatic cysts were associated with the occurrence of hepatic cysts. Younger age, female sex, and the existence of multiple hepatic cysts were associated with cyst enlargement. Among 126 individuals who had hepatic cysts with a diameter of 30 mm or larger at the first visit, two (1.6%) required treatment. Remain 124 cases showed four patterns: 44 cases with enlargement, 47 stable, 11 regression after enlargement, and 22 regression. Hyperechoic fluid inside the cysts was observed in 54.5% (18 of 33), which was significantly higher than 6.6% (6 of 91) of the non-regression (OR = 17.0). The appearance of intracystic hyperechoic fluid by ultrasound may predict subsequent regression of the hepatic cyst.
High Prevalence of Clinical Jaundice Associated with Poor Adherence Among Adults on Boosted Atazanavir Antiretroviral Therapy Regimen at the Infectious Disease Institute HIV/AIDS Clinic in Kampala, Uganda
Authors: Nabakooza Angella Kigongo , Nakamanya Sharon Kitibwakye , Laker Eva , Katana Elizabeth , Owarwo Noela , Lwanga Isaac , Castelnuovo Barbara , Lamorde Mohammed , Kitutu Freddy Eric 
Published: March 2022

Abstract
BackgroundBoosted atazanavir (ATV/r)-based Antiretroviral Therapy (ART) regimen is recommended by the World Health Organization (WHO) as second line treatment for HIV/AIDS. ATV/r is known to cause clinical jaundice, which may lead to non-adherence to treatment and the attendant treatment failure and drug resistance. We sought to determine the prevalence of clinical jaundice and explore its effect on adherence to the ART regimen. MethodsWe conducted a cross-sectional study among 236 adult patients taking ATV/r-based ART regimens attending the Infectious Disease Institute (IDI) HIV/AIDS clinic in Kampala, Uganda from April to May 2019. We assessed the study participants by self-report for existing or previous experience of clinical jaundice after their start on ATV/r-based ART regimen. Adherence to the ATV/r-based ART was determined using the 8-item Morisky scale; score <3 and >3 was interpreted as good and poor adherence to ART, respectively. Logistic regression was used to explore the effect of clinical jaundice and other sociodemographic factors on adherence to ART regimen.ResultsOf the 236 participants, majority were female (66.5%) with a mean age of 39.9 (SD 10.8) years and had been on ART for 10 to 13 years (42.8%). Most (69%) were on TDF/3TC backbone and 24% on AZT/3TC backbone. The period and point prevalence of clinical jaundice was 31.8% (95% confidence interval [CI]: 26.1% – 38.1%) and 21.1% (95% CI: 14.9% – 37.5%) respectively. Up to 8.5% (95% CI: 5.5 – 12.8) had poor adherence (> 3). At multivariable analysis, clinical jaundice was the only predictor of poor adherence (adjusted odds ratio= 2.9, 95% CI: 1.15 – 7.34, p=0.024). Sex, alcohol use, and stigma and discrimination did not achieve statistical significance.Conclusion Our study indicates a high prevalence of clinical jaundice among patients on ATV/r ART regimen and there is association between experiencing clinical jaundice and poor adherence. For patients whose ART adherence is affected by the presence of clinical jaundice; they should be switched to another second-line ART alternative.
Structural Basis For The Simultaneous Recognition Of NEMO And Acceptor Ubiquitin By The HOIP NZF1 Domain
Authors: Rahighi Simin , Iyer Mamta , Oveisi Hamid , Nasser Sammy , Duong Vincent 
Published: March 2022

Abstract
Ubiquitination of NEMO by the linear ubiquitin chain assembly complex (LUBAC) is essential for activating the canonical NF-κB signaling pathway. While the NZF1 domain of the HOIP subunit of LUBAC recognizes the NEMO substrate, it is unclear how it cooperates with the catalytic domains in the ubiquitination process. Here, we report a crystal structure of NEMO in complex with HOIP NZF1 and linear diubiquitin chains, in which the two proteins bind to distinct sites on NEMO. Moreover, the NZF1 domain simultaneously interacts with NEMO and Ile44 surface of a proximal ubiquitin from a linear diubiquitin chain, where the C-term tail of the ubiquitin is in the proximity of the NEMO ubiquitination site (Lys285). We further propose a model for the linear ubiquitination of NEMO by HOIP. In the model, NZF1 binds the monoubiquitinated NEMO and recruits the catalytic domains to the ubiquitination site, thereby ensuring site-specific ubiquitination of NEMO.
Optimal 1,5-anhydroglucitol cut-off points for diagnosing diabetes based on prevalence of retinopathy in Chinese population
Authors: CHEN Cheng , QIU Shanhu , DU Ziwei , GUO Haijian , WANG Bei , SUN Zilin , Wang Yao 
Published: March 2022

Abstract
Background: A new glycemic index, 1,5-anhydroglucitol (1,5-AG), can reflect glucose fluctuation over 3–7 days. The aim of this study was to evaluate the possibility of 1,5-AG in diagnosing diabetes based on the prevalence of diabetic retinopathy in the Chinese population.Method: The study enrolled 3579 adults aged 20–70 years. Values for 1,5-AG, fasting plasma glucose (FPG), 2-hour postprandial glucose (2hPG), and glycated haemoglobin(HbA1c) were measured. Retinal photographs were taken, and diabetic retinopathy was assessed and graded according to the Early Treatment Diabetic Retinopathy Study (ETDRS). Retinopathy with an ETDRS level≥21 was defined as diabetic retinopathy, with level≥31 as “diabetic-specific retinopathy.” A receiver operating characteristic curve was used to determine the optimal cut-off point.Results: Serum 1,5-AG was negatively correlated with FPG, 2hPG, and HbA1c. The 1,5-AG level was significantly lower in the diabetic retinopathy group. The optimal cut-off point of 1,5-AG was 13.05μg/m. At this point, the sensitivity and specificity were 74.1% and 91.2%, respectively, and the area under the receiver operating characteristic curve was 0.846. The optimal cut-off point remained unchanged after excluding participants on hypoglycemic medication. Combining 1,5-AG with FPG or HbA1c could raise the specificity in diagnosis.Conclusion: Our data found that 1,5-AG at 13.05μg/mL had a good specificity for diagnosing diabetes in the Chinese population. In combination with FPG or HbA1c, 1,5-AG was a good tool for detecting diabetes without symptoms.
Assessing the SAfety and FEasibility of Bedside Portable Low-Field Brain Magnetic Resonance Imaging in Patients on ECMO (SAFE-MRI ECMO study) – Study Protocol and First Case Series Experience
Authors: Cho Sung-Min , Wilcox Christopher , Keller Steven , Acton Matthew , Rando Hannah , Etchill Eric , Bush Errol L. , Sair Haris I. , Pitts John , Kim Bo Soo , Whitman Glenn , Giuliano Kate 
Published: March 2022

Abstract
BACKGROUND
To assess the safety and feasibility of imaging of the brain with a point-of-care (POC) magnetic resonance imaging (MRI) system in patients on extracorporeal membrane oxygenation (ECMO). Early detection of acute brain injury (ABI) is critical in improving survival for patients with ECMO support.
METHODS
Patients from a single tertiary academic ECMO center who underwent head CT (HCT), followed by POC brain MRI exams within 24 hours following HCT while on ECMO. Primary outcomes were safety and feasibility, defined as completion of MRI exam without serious adverse events (SAEs). Secondary outcome was the quality of MR images in assessing ABIs.
RESULTS
We report 3 consecutive adult patients (median age: 47 years; 67% male) with veno-arterial (n = 1) and veno-venous ECMO (n = 2) (VA- and VV-ECMO) support. All patients were imaged successfully without SAEs. Times to complete POC brain MRI exams were 34, 40, and 43 minutes. Two patients had ECMO suction events, resolved with fluid and repositioning. Two patients were found to have an unsuspected acute stroke, well visualized with MRI.
CONCLUSIONS
Adult patients with VA- or VV-ECMO support can be safely imaged with low-field POC brain MRI in the intensive care unit, allowing for the assessment of presence and timing of ABI.
Sacroiliac Pain And Tenesmus As A Rare Manifestation Of COVID-19: A Case Series
Authors: Khodabandeh Mahmoud , Memar Elmira Haji Esmaeil , Hasanzadeh Alireza , Nematian Hossein , Sadeghirad Parisa 
Published: March 2022

Abstract
Background: The clinical manifestations of the SARS-CoV-2 infection are mainly respiratory but the virus can cause a variety of symptoms. There is a big challenge in detecting COVID-19 from uncommon manifestations. This study is going to present patients with COVID-19 reinfection who had symptoms of disabling sacroiliac pain and also some other patients with new COVID-19 infection that came with tenesmus.Case presentation: In this case report, we describe a COVID-19 patient who presented with sacroiliac pain or tenesmus. Eight patients with COVID-19 reinfection came with symptoms of disabling sacroiliac pain in their second course of the disease. This symptom limited their movement. These patients did not have any fever or respiratory distress. Also, six COVID-19 patients came with tenesmus which they described as a severe and unrelenting desire to defecate. Conclusions: These cases highlight the difficulty in detecting COVID-19 from a rare but important manifestation.
Unilateral and Bilateral Aplasia of the Anterior Cerebral Artery in the Presence of Their Vascular Sources
Authors: Trandafilović Milena , Vasović Ljiljana , Vlajković Slobodan , Stojanović Borisav , Mladenović‒Todorović Marija , Drevenšek Martina 
Published: March 2022

Abstract
Purpose
In continuation of our previous studies of vascular components of the cerebral arterial circle, our goal was to investigate the cases of aplasia of the anterior cerebral artery (ACA).
Methods
The macro- and microdissection of the target human brain arteries was applied under the magnifying glass. Each case was photographed and diagramatically represented in the workbook. The length and the outer diameter of the corresponding arteries on the photos were measured using a computer software program.
Results
There were 2/388 cases of ACA aplasia―unilaterally in one case (0.25%), and bilaterally in the other (0.25%). These two cases belonged to a male and a female adult, autopsied due to the homicide and myocardial infarction, aged 68 and 80, respectively. Except for the variations of the posterior communicating artery on one or both sides, and several arteries of the vertebrobasilar system, the instance of cerebral pathology was not recorded in either of these cases. We compared the recent cases with similar literature cases obtained from a number of retrospective studies and single reports.
Conclusion
Summarizing available literature cases of unilateral ACA aplasia, and taking into account that the presented cases of unilateral and bilateral ACA aplasia were not accompanied with cerebral pathology, we can nevertheless to underline the appearance of an aneurysm of the opposite ACA in more than a quarter of the studied cases, more typically on the right side and in male gender. The recent case of bilateral ACA aplasia which has been the second case discovered so far, represents a true rarity.
Significant Muscle Loss After Stereotactic Body Radiotherapy Predicts Worse Survival in Patients with Hepatocellular Carcinoma
Authors: Yang Jen-Fu , Huang Wen-Yen , Lo Cheng-Hsiang , Lee Meei-Shyuan , Lin Chun-Shu , Shen Po-Chien , Dai Yang-Hong , Wang Ying-Fu , Chen Teng-Wei 
Published: March 2022

Abstract
Background: The relationship between sarcopenia and treatment outcomes, especially in patients with hepatocellular carcinoma (HCC) undergoing stereotactic body radiotherapy (SBRT) has not been well-explored. This study aimed to investigate the effects of sarcopenia on the survival and toxicity after SBRT in patients with HCC.Methods: We included 137 patients with HCC treated with SBRT between 2008 and 2018. Sarcopenia was defined as a skeletal muscle index (SMI) of < 49 cm2/m2 for men and < 31 cm2/m2 for women using computed tomography images at the mid-level of the third lumbar vertebra. The SMI change was presented as the change per 90 days. The Kaplan–Meier method was used for survival estimation, and the Cox regression was used to determine prognosticators. Results: Sarcopenia was present in 67 of 137 eligible patients. With the median follow-up of 14.1 months and 32.7 months in the entire cohort and in those alive, respectively, patients with pre-SBRT sarcopenia or SMI loss ≥ 7% after SBRT had worse overall survival than their counterparts. Significant survival predictors on multivariate analysis were SMI loss ≥ 7% after SBRT [hazard ratio (HR): 1.96, p = 0.013], presence of extrahepatic metastasis (HR: 3.47, p <0.001), neutrophil-to-lymphocyte ratio (HR: 1.79, p = 0.027), and multiple tumors (HR: 2.19, p = 0.003). Separate Cox models according to the absence and presence of pre-SBRT sarcopenia showed that SMI loss ≥ 7% remained a significant survival predictor in patients with sarcopenia (HR: 3.06, p = 0.017) compared with those without sarcopenia. SMI loss ≥ 7% is also a predictor of the Child-Pugh score increase by ≥ 2 points after SBRT.Conclusions: SMI loss ≥ 7% after SBRT is a significant prognostic factor for worse survival and is associated with liver toxicity compared with pre-SBRT sarcopenia.
The prognostic value of KRAS mutation in locally advanced rectal cancer.
Authors: Asawa Palash , Bakalov Veli , Kancharla Pragnan , Abel Stephen , Chahine Zena , Monga Dulabh K. , Kirichenko Alexander V. , Wegner Rodney E. 
Published: March 2022

Abstract
BackgroundThe prognostic value of the KRAS proto-oncogene mutation in colorectal cancer has been debated. Herein, we analyzed the National Cancer Database (NCDB) to assess the role of KRAS mutation as a prognostic marker in patients with locally advanced rectal cancer (LARC). MethodsWe identified LARC patients treated with neoadjuvant chemoradiation from 2004-2015 excluding those with stage I/IV disease and unknown KRAS status. Multivariable logistic regression identified variables associated with KRAS positivity. Propensity adjusted univariable and multivariable analyses identified predictors of survival. ResultsOf the 784 eligible patients, 506 were KRAS negative (KRAS-) and 278 were KRAS positive (KRAS+). Median survival was 63.6 months and 76.3 months for KRAS+ and KRAS- patients respectively, with propensity adjusted 3 and 5-year survival of 79.9% vs. 83.6% and 56.7% vs 61.9% respectively (HR 1.56, p 1.074-2.272). Male sex, no insurance, and KRAS+ disease was associated with poorer survival on unadjusted and propensity adjusted multivariable analyses. ConclusionsOur analysis of KRAS+ LARC suggest that KRAS+ disease is associated with poorer overall survival. Given the inherent limitations of retrospective data, prospective validation is warranted.
Bianchi Type I Model of Universe With Customized Scale Factors
Authors: Sarmah Pranjal , Goswami Umananda Dev 
Published: March 2022

Abstract
According to standard cosmology, the universe is homogeneous and isotropic at large scales. However, some anisotropies can be observed at the local scale in the universe through various ways. Here we have studied the Bianchi type I model with customizing the scale factors to understand the anisotropic nature of the universe. We have considered two cases with slight modifications of scale factors in different directions in the generalized Bianchi Type I metric equation, and compared the results with the ΛCDM model and also with available cosmological observational data. Through this study, we also want to predict the possible degree of anisotropy present in the early universe and its evolution to current time by calculating the value of density parameter for anisotropy (Ωσ) for both low and high redshift (z) along with the possible relative anisotropy that exist among different directions. It is found that there was a significant amount of anisotropy in the early universe and the anisotropic nature of the universe vanishes at the near past and the present epochs. Thus at near past and present stages of the universe there is no effective distinction between this anisotropic model and the standard ΛCDM model.