bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broad-range and effective detection of human noroviruses by colloidal gold immunochromatographic assay based on the shell domain of the major capsid protein
Authors: Xu Meng , Lu Feifeng , Lyu Chenang , Wu Qingping , Zhang Jumei , Tian Peng , Xue Liang , Xu Ting , Wang Dapeng 
Published: January 2021

Abstract
Background
Human noroviruses (HuNoVs) are a major cause of nonbacterial gastroenteritis in all age groups worldwide. HuNoVs can be detected in vitro using molecular assays such as RT-PCR and RT-qPCR. However, these molecular-based techniques require special equipment, unique reagents, experienced personnel, and extended time to obtain results. Besides, the diversity of viral genotypes is high. Therefore, methods that are rapid, broad-range and effective in the detection of HuNoVs are desiderated for screening the feces or vomit of infected people during outbreaks.

Results
In this study, a colloidal-gold-based immunochromatographic assay (ICA) was developed for effective detection of HuNoVs in clinical samples. Monoclonal antibodies (MAbs) against the shell (S) domain in the major capsid protein of HuNoVs were used in the ICA. The limitations of detection for HuNoVs in clinical samples were 1.2 × 106 genomic copies per gram of stool sample (gc/g) and 4.4 × 105 gc/g for genogroup I and II (GI and GII) HuNoVs, respectively. A total of 122 clinical samples were tested for HuNoVs by ICA and compared against RT-qPCR. The relative sensitivity, specificity and agreement of ICA was 84.2% (95% CI: 83.6–84.8%), 100.0% (95% CI: 98.5–100.0%) and 87.7% (95% CI: 85.6–89.8%), respectively. No cross-reaction with other common enteric viruses or bacteria was observed. The ICA detected a broad range of genotypes, including GI.1, GI.3, GI.4, GI.6, GI.14, GII.2, GII.3, GII.4, GII.6, GII.13, and GII.17 HuNoVs.

Conclusions
This study demonstrates that ICA targeting the S domain of VP1 is a promising candidate for effectively identifying the different genotypes of HuNoVs in clinical samples with high sensitivity and specificity.
Transgenic chickpea (Cicer arietinum L.) harbouring AtDREB1a are physiologically better adapted to water deficit
Authors: Das Alok , Basu Partha Sarathi , Kumar Manoj , Ansari Jamal , Shukla Alok , Thakur Shallu , Singh Parul , Datta Subhojit , Chaturvedi Sushil Kumar , Sheshshayee M S , Bansal Kailash Chandra , Singh Narendra Pratap 
Published: January 2021

AbstractBackgroundChickpea (Cicer arietinumL.) is the second most widely grown pulse and drought (limiting water) is one of the major constraints leading to about 40–50% yield losses annually. Dehydration responsive element binding proteins (DREBs) are important plant transcription factors that regulate the expression of many stress-inducible genes and play a critical role in improving the abiotic stress tolerance. Transgenic chickpea lines harbouring transcription factor, Dehydration Responsive Element-Binding protein 1A fromArabidopsis thaliana(AtDREB1agene) driven by stress inducible promoterrd29awere developed, with the intent of enhancing drought tolerance in chickpea.Performance of the progenies of one transgenic event and control were assessed based on key physiological traits imparting drought tolerance such as plant water relation characteristics, chlorophyll retention, photosynthesis, membrane stability and water use efficiency under water stressed conditions.ResultsFour transgenic chickpea lines harbouring stress inducibleAtDREB1awere generated with transformation efficiency of 0.1%. The integration, transmission and regulated expression were confirmed by Polymerase Chain Reaction (PCR), Southern Blot hybridization and Reverse Transcriptase polymerase chain reaction (RT-PCR), respectively. Transgenic chickpea lines exhibitedhigherrelative water content,longerchlorophyll retention capacity andhigherosmotic adjustment under severe drought stress (stress level 4), as compared to control. The enhanced drought tolerance in transgenic chickpea lines were also manifested by undeterred photosynthesis involving enhanced quantum yield of PSII, electron transport rate at saturated irradiance levels and maintaining higher relative water content in leaves under relatively severe soil water deficit. Further, lower values of carbon isotope discrimination in some transgenic chickpea lines indicated higher water use efficiency. Transgenic chickpea lines exhibiting better OA resulted in higher seed yield, with progressive increase in water stress, as compared to control.ConclusionsBased on precise phenotyping, involving non-invasive chlorophyll fluorescence imaging, carbon isotope discrimination, osmotic adjustment, higher chlorophyll retention and membrane stability index, it can be concluded thatAtDREB1atransgenic chickpea lines were better adapted to water deficit by modifying important physiological traits. The selected transgenic chickpea event would be a valuable resource that can be used in pre-breeding or directly in varietal development programs for enhanced drought tolerance under parched conditions.
The safety of early administration of oral fluid following general anesthesia in children undergoing tonsillectomy: a prospective randomized controlled trial
Authors: Wu Meng-Hang , Liu Chang-qing , Zeng Xiao-qi , Jia An-na , Yin Xiao-rong 
Published: January 2021

Abstract
Background
The feasibility and safety of administrating a small amount of oral fluid to children in the early recovery period following tonsillectomy under general anesthesia to reduce the thirst and its associated restlessness remain unknown.

Methods
This study was approved by the institutional ethics committee and adhered to the CONSORT guidelines. Pediatric patients undergoing tonsillectomy who met the inclusion and exclusion criteria of our study were randomized into the study and control groups. In the study group, patients were given a small amount of water instantly after recovering from general anesthesia, which included the recovery of the cough and deglutition reflex, and attaining grade V of muscle strength. The control group was given a small amount of water at 4 to 6 h after the operation. The incidence of nausea and vomiting and the degree of thirst relief were measured and compared between the two groups.

Results
Three hundred patients were randomized into each group. There was no significant difference in the incidence of nausea and vomiting at 20 min after drinking water between the two groups (P > 0.05). The thirst score of children over 5 years old in the study group was significantly lower than that of the control group (P < 0.05).

Conclusion
Early administration of a small amount of oral fluid to children following tonsillectomy and recovering from general anesthesia is not only safe but also effective in reducing postoperative thirst.

Trial registration
Current Controlled Trials ChiCTR1800020058, 12-12-2018.
McGRATH MAC video laryngoscope assistance during transesophageal echocardiography may reduce the risk of complications: a manikin study
Authors: Kumamoto Taisuke , Tashima Koichiro , Hiraoka Chieko , Ikuta Yoshihiro , Yamamoto Tatsuo 
Published: January 2021

Abstract
Background
Although transesophageal echocardiography (TEE) is considered a relatively safe diagnostic monitoring method, blind probe insertion is associated with pharyngeal trauma. Through visual observation of the esophageal inlet with the McGRATH video laryngoscope, it may be possible to insert the TEE probe at an appropriate angle and prevent pharyngeal trauma. We conducted a manikin study to investigate whether the use of the McGRATH video laryngoscope for TEE probe insertion reduced the pressure on the posterior pharyngeal wall.

Methods
Twenty-seven junior (inexperienced group) and 10 senior (experienced group) anesthesiologists participated in this study. The TEE probe was inserted into an airway manikin in a blind fashion (blind group) or under visualization with the McGRATH (McGRATH group) video laryngoscope (three times each). A sealed bag filled with normal saline was placed on the back of the posterior pharyngeal wall of the manikin and connected to a patient monitoring system via a pressure transducer. We measured the internal bag pressure and approximated this value to the pressure on the posterior pharyngeal wall.

Results
The pressure on the posterior pharyngeal wall was significantly lower in the McGRATH group than in the blind group (p < 0.001) and was significantly reduced when the McGRATH was employed in both the inexperienced (p < 0.001) and experienced (p < 0.001) groups.

Conclusions
These findings suggest that TEE probe insertion under the assistance of the McGRATH video laryngoscope can reduce the pressure on the posterior pharyngeal wall, regardless of the clinician’s experience, and may inform clinical practice with the potential to reduce probe insertion-associated complication rates.
Short-term real-time prediction of total number of reported COVID-19 cases and deaths in South Africa: a data driven approach
Authors: Reddy Tarylee , Shkedy Ziv , Janse van Rensburg Charl , Mwambi Henry , Debba Pravesh , Zuma Khangelani , Manda Samuel 
Published: January 2021

Abstract
Background
The rising burden of the ongoing COVID-19 epidemic in South Africa has motivated the application of modeling strategies to predict the COVID-19 cases and deaths. Reliable and accurate short and long-term forecasts of COVID-19 cases and deaths, both at the national and provincial level, are a key aspect of the strategy to handle the COVID-19 epidemic in the country.

Methods
In this paper we apply the previously validated approach of phenomenological models, fitting several non-linear growth curves (Richards, 3 and 4 parameter logistic, Weibull and Gompertz), to produce short term forecasts of COVID-19 cases and deaths at the national level as well as the provincial level. Using publicly available daily reported cumulative case and death data up until 22 June 2020, we report 5, 10, 15, 20, 25 and 30-day ahead forecasts of cumulative cases and deaths. All predictions are compared to the actual observed values in the forecasting period.

Results
We observed that all models for cases provided accurate and similar short-term forecasts for a period of 5 days ahead at the national level, and that the three and four parameter logistic growth models provided more accurate forecasts than that obtained from the Richards model 10 days ahead. However, beyond 10 days all models underestimated the cumulative cases. Our forecasts across the models predict an additional 23,551–26,702 cases in 5 days and an additional 47,449–57,358 cases in 10 days. While the three parameter logistic growth model provided the most accurate forecasts of cumulative deaths within the 10 day period, the Gompertz model was able to better capture the changes in cumulative deaths beyond this period. Our forecasts across the models predict an additional 145–437 COVID-19 deaths in 5 days and an additional 243–947 deaths in 10 days.

Conclusions
By comparing both the predictions of deaths and cases to the observed data in the forecasting period, we found that this modeling approach provides reliable and accurate forecasts for a maximum period of 10 days ahead.
Fitting a shared frailty illness-death model to left-truncated semi-competing risks data to examine the impact of education level on incident dementia
Authors: Lee Catherine , Gilsanz Paola , Haneuse Sebastien 
Published: January 2021

AbstractBackgroundSemi-competing risks arise when interest lies in the time-to-event for some non-terminal event, the observation of which is subject to some terminal event. One approach to assessing the impact of covariates on semi-competing risks data is through the illness-death model with shared frailty, where hazard regression models are used to model the effect of covariates on the endpoints. The shared frailty term, which can be viewed as an individual-specific random effect, acknowledges dependence between the events that is not accounted for by covariates. Although methods exist for fitting such a model to right-censored semi-competing risks data, there is currently a gap in the literature for fitting such models when a flexible baseline hazard specification is desired and the data are left-truncated, for example when time is on the age scale. We provide a modeling framework and openly available code for implementation.MethodsWe specified the model and the likelihood function that accounts for left-truncated data, and provided an approach to estimation and inference via maximum likelihood. Our model was fully parametric, specifying baseline hazards via Weibull or B-splines. Using simulated data we examined the operating characteristics of the implementation in terms of bias and coverage. We applied our methods to a dataset of 33,117 Kaiser Permanente Northern California members aged 65 or older examining the relationship between educational level (categorized as: high school or less; trade school, some college or college graduate; post-graduate) and incident dementia and death.ResultsA simulation study showed that our implementation provided regression parameter estimates with negligible bias and good coverage. In our data application, we found higher levels of education are associated with a lower risk of incident dementia, after adjusting for sex and race/ethnicity.ConclusionsAs illustrated by our analysis of Kaiser data, our proposed modeling framework allows the analyst to assess the impact of covariates on semi-competing risks data, such as incident dementia and death, while accounting for dependence between the outcomes when data are left-truncated, as is common in studies of aging and dementia.
Missed opportunities for HIV testing in patients newly diagnosed with HIV in Morocco
Authors: Marih Latifa , Sawras Victoire , Pavie Juliette , Sodqi Mustapha , Malmoussi Mourad , Tassi Noura , Bensghir Rajaa , Nani Samira , Lahsen Ahd Oulad , Laureillard Didier , El Filali Kamal Marhoum , Champenois Karen , Weiss Laurence 
Published: January 2021

Abstract
Background
In Morocco, of the estimated 29,000 people living with HIV in 2011, only 20% were aware of their HIV status. More than half of diagnoses were at the AIDS stage. We assumed that people who were unaware of their infection had contacts with the healthcare system for HIV indicators that might prompt the healthcare provider to offer a test. The aim was to assess missed opportunities for HIV testing in patients newly diagnosed with HIV who accessed care in Morocco.

Methods
A cross-sectional study was conducted in 2012–2013 in six Moroccan HIV centers. Participants were aged ≥18, and had sought care within 6 months after their HIV diagnosis. A standardized questionnaire administered during a face-to-face interview collected the patient’s characteristics at HIV diagnosis, HIV testing and medical history. Contacts with care and the occurrence of clinical conditions were assessed during the 3 years prior to HIV diagnosis. Over this period, we assessed whether healthcare providers had offered HIV testing to patients with HIV-related clinical or behavioral conditions.

Results
We enrolled 650 newly HIV-diagnosed patients (median age: 35, women: 55%, heterosexuals: 81%, diagnosed with AIDS or CD4 < 200 cells/mm3: 63%). During the 3 years prior to the HIV diagnosis, 71% (n = 463) of participants had ≥1 contact with the healthcare system. Of 323 people with HIV-related clinical conditions, 22% did not seek care for them and 9% sought care and were offered an HIV test by a healthcare provider. The remaining 69% were not offered a test and were considered as missed opportunities for HIV testing. Of men who have sex with men, 83% did not address their sexual behavior with their healthcare provider, 11% were not offered HIV testing, while 6% were offered HIV testing after reporting their sexual behavior to their provider.

Conclusions
Among people who actually sought care during the period of probable infection, many opportunities for HIV testing, based on at-risk behaviors or clinical signs, were missed. This highlights the need to improve the recognition of HIV clinical indicators by physicians, further expand community-based HIV testing by lay providers, and implement self-testing to increase accessibility and privacy.
The transition to Xpert MTB/RIF ultra: diagnostic accuracy for pulmonary tuberculosis in Kampala, Uganda
Authors: Andama A. , Jaganath D. , Crowder R. , Asege L. , Nakaye M. , Katumba D. , Mukwatamundu J. , Mwebe S. , Semitala C. F. , Worodria W. , Joloba M. , Mohanty S. , Somoskovi A. , Cattamanchi A. 
Published: January 2021

AbstractBackgroundThe World Health Organization (WHO) has endorsed the next-generation Xpert MTB/RIF Ultra (Ultra) cartridge, and Uganda is currently transitioning from the older generation Xpert MTB/RIF (Xpert) cartridge to Ultra as the initial diagnostic test for pulmonary tuberculosis (TB). We assessed the diagnostic accuracy of Ultra for pulmonary TB among adults in Kampala, Uganda.MethodsWe sampled adults referred for Xpert testing at two hospitals and a health center over a 12-month period. We enrolled adults with positive Xpert and a random 1:1 sample with negative Xpert results. Expectorated sputum was collected for Ultra, and for solid and liquid culture testing for Xpert-negative patients. We measured sensitivity and specificity of Ultra overall and by HIV status, prior history of TB, and hospitalization, in reference to Xpert and culture results. We also assessed how classification of results in the new “trace” category affects Ultra accuracy.ResultsAmong 698 participants included, 211 (30%) were HIV-positive and 336 (48%) had TB. The sensitivity of Ultra was 90.5% (95% CI 86.8–93.4) and specificity was 98.1% (95% CI 96.1–99.2). There were no significant differences in sensitivity and specificity by HIV status, prior history of TB or hospitalization. Xpert and Ultra results were concordant in 670 (96%) participants, with Ultra having a small reduction in specificity (difference 1.9, 95% CI 0.2 to 3.6,p=0.01). When “trace” results were considered positive for all patients, sensitivity increased by 2.1% (95% CI 0.3 to 3.9,p=0.01) without a significant reduction in specificity (− 0.8, 95% CI − 0.3 to 2.0,p=0.08).ConclusionsAfter 1 year of implementation, Ultra had similar performance to Xpert. Considering “trace” results to be positive in all patients increased case detection without significant loss of specificity. Longitudinal studies are needed to compare the benefit of greater diagnoses to the cost of overtreatment.
A deep learning model for diagnosing dystrophinopathies on thigh muscle MRI images
Authors: Yang Mei , Zheng Yiming , Xie Zhiying , Wang Zhaoxia , Xiao Jiangxi , Zhang Jue , Yuan Yun 
Published: January 2021

Abstract
Background
Dystrophinopathies are the most common type of inherited muscular diseases. Muscle biopsy and genetic tests are effective to diagnose the disease but cost much more than primary hospitals can reach. The more available muscle MRI is promising but its diagnostic results highly depends on doctors’ experiences. This study intends to explore a way of deploying a deep learning model for muscle MRI images to diagnose dystrophinopathies.

Methods
This study collected 2536 T1WI images from 432 cases who had been diagnosed by genetic analysis and/or muscle biopsy, including 148 cases with dystrophinopathies and 284 cases with other diseases. The data was randomly divided into three sets: the data from 233 cases were used to train the CNN model, the data from 97 cases for the validation experiments, and the data from 102 cases for the test experiments. We also validated our models expertise at diagnosing by comparing the model’s results on the 102 cases with those of three skilled radiologists.

Results
The proposed model achieved 91% (95% CI: 0.88, 0.93) accuracy on the test set, higher than the best accuracy of 84% in radiologists. It also performed better than the skilled radiologists in sensitivity : sensitivities of the models and the doctors were 0.89 (95% CI: 0.85 0.93) versus 0.79 (95% CI:0.73, 0.84; p = 0.190).

Conclusions
The deep model achieved excellent accuracy and sensitivity in identifying cases with dystrophinopathies. The comparable performance of the model and skilled radiologists demonstrates the potential application of the model in diagnosing dystrophinopathies through MRI images.
Mild cognitive impairment in novel SPG11 mutation-related sporadic hereditary spastic paraplegia with thin corpus callosum: case series
Authors: Li Chuan , Yan Qi , Duan Feng-ju , Zhao Chao , Zhang Zhuo , Du Ying , Zhang Wei 
Published: January 2021

Abstract
Background
SPG11 mutation-related autosomal recessive hereditary spastic paraplegia with thin corpus callosum (HSP-TCC) is the most common cause in complicated forms of HSP, usually presenting comprehensive mental retardation on early-onset stage preceding spastic paraplegias in childhood. However, there are many instances of sporadic late-onset HSP-TCC cases with a negative family history, and potential mild cognitive deficits in multiple domains may be easily neglected and inaccurately described.

Methods
In this study, we performed next generation sequencing in four sporadic late-onset patients with HSP-TCC, and combined Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) to evaluate cognition of the patients.

Results
By evolutionary conservation and structural modeling analysis, we have revealed 4 novel pathogenic SPG11 mutations, and firstly confirmed mild cognitive impairment (MCI) with normal MMSE scores (≥27) and decreased MoCA scores (< 26) in these SPG11 mutation-related HSP-TCC patients, predominantly presenting impairment of executive function, delayed recall, abstraction and language.

Conclusions
The results expand the mutational spectrum of SPG11-associated HSP-TCC from sporadic cases, and confirm MCI with combination of decreased MoCA and normal MMSE assessment, suggesting that clinicians should consider doing a MoCA to detect MCI in patients with HSP, particularly those with HSP-TCC.