bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nothing in biology begins when you think it does
Authors: Johnson Norman 
Published: December 2020

AbstractNeil Shubin has written an excellent, accessible book explaining how innovations in biology evolve. The key insight—one provided by Darwin but fleshed out by biologists over the subsequent century and a half—is that the precursors of traits involved in innovations usually were present in the ancestors but had a different function. In this book, Shubin also provides rich biographical detail of the scientists involved in the discoveries.
Rhythms and prognosis of patients with cardiac arrest, emphasis on pseudo-pulseless electrical activity: another reason to use ultrasound in emergency rooms in Colombia
Authors: Devia Jaramillo German , Navarrete Aldana Norberto , Rojas Ortiz Zaira 
Published: December 2020

Abstract
Background
The cardiac arrest is still an emergency with a bad prognosis. The growing adoption of bedside ultrasound allowed to classify PEA in two groups: the true PEA and the pseudo-PEA. pPEA is used to describe a patient who has a supposed PEA in the absence of pulse, with evidence of some cardiac activity on the bedside ultrasound.

Objective
This work aims to assess the bedside ultrasound use as a predictor for ROSC and survival at discharge in cardiac arrest patients and compare the pseudo-pulseless electrical activity to other cardiac arrest rhythms, including shockable rhythms.

Materials and methods
This is an observational, historic cohort study carried out in the emergency room of the University Hospital Mayor Méderi. Data were collected from all the adult patients treated for cardiac arrest from June 2018 to 2019. An ultrasound was performed to every cardiac arrest patient.

Results
Of a total of 108 patients, the median of the age was 71 years, 65.8% were male subjects, and the most frequent cause for cardiac arrest was the cardiogenic shock (32.4%). ROSC was observed in 41 cases (37.9%) and survival at discharge was 18 cases (16.7%). VF/VT and pPEA were the two rhythms that showed the highest ROSC and survival at discharge. For the pPEA group, we were able to conclude that the cardiac activity type is related to ROSC.

Conclusion
There is a significant difference for ROSC and survival at discharge prognosis among the cardiac arrest rhythms, with better outcomes for VF/VT and pPEA. Among patients with PEA, a routine ultrasound assessment is recommended. The type of cardiac activity recorded during the ultrasound of the cardiac arrest patient might be related to the ROSC and survival at discharge prognosis.
A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2
Authors: Gohl Daryl M. , Garbe John , Grady Patrick , Daniel Jerry , Watson Ray H. B. , Auch Benjamin , Nelson Andrew , Yohe Sophia , Beckman Kenneth B. 
Published: December 2020

AbstractBackgroundThe global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and viral tracking. Next generation sequencing technologies have enabled large-scale genomic surveillance of SARS-CoV-2 as thousands of isolates are being sequenced around the world and deposited in public data repositories. A number of methods using both short- and long-read technologies are currently being applied for SARS-CoV-2 sequencing, including amplicon approaches, metagenomic methods, and sequence capture or enrichment methods. Given the small genome size, the ability to sequence SARS-CoV-2 at scale is limited by the cost and labor associated with making sequencing libraries.ResultsHere we describe a low-cost, streamlined, all amplicon-based method for sequencing SARS-CoV-2, which bypasses costly and time-consuming library preparation steps. We benchmark this tailed amplicon method against both the ARTIC amplicon protocol and sequence capture approaches and show that an optimized tailed amplicon approach achieves comparable amplicon balance, coverage metrics, and variant calls to the ARTIC v3 approach.ConclusionsThe tailed amplicon method we describe represents a cost-effective and highly scalable method for SARS-CoV-2 sequencing.
Development of a risk scoring system for prognostication in HIV-related toxoplasma encephalitis
Authors: Li Yao , Zeng Yan-Ming , Liu Min , Lu Yan-Qiu , Liu Xue-Yan , Zhang Yu-Lin , Jiang Zhong-Sheng , Yang Tong-Tong , Sun Yan , Lan Ke , Chen Yao-Kai 
Published: December 2020

Abstract
Background
This study aims to evaluate specific risk factors influencing prognosis of HIV-infected patients with toxoplasma encephalitis (TE) in order to develop a prognostic risk scoring system for them.

Methods
This is a six-center retrospective study of hospitalized HIV/TE patients. Data including six-week mortality after diagnosis, baseline characteristics, clinical features, laboratory tests and radiological characteristics of eligible patients were assimilated for risk model establishing.

Results
In this study, the six-week mortality among 94 retrospective cases was 11.7% (11/94). Seven specific risk factors, viz. time from symptom onset to presentation, fever, dizziness, CD4+ T-cell counts, memory deficits, patchy brain lesions, and disorders of consciousness were calculated to be statistically associated with mortality. A criterion value of ‘9’ was selected as the optimal cut-off value of the established model. The AUC of the ROC curve of this scoring model was 0.976 (p < 0.001). The sensitivity and specificity of the risk scoring model was 100.0 and 86.9%, respectively, which were 81.8 and 94.1% of this scoring model in the verification cohort, respectively.

Conclusions
The developed scoring system was established with simple risk factors, which also allows expeditious implementation of accurate prognostication, and appropriate therapeutic interventions in HIV-infected patients with TE.
Predictors and one-year outcomes of patients with delayed graft function after deceased donor kidney transplantation
Authors: Chen Rao , Wang Haifeng , Song Lei , Hou Jianfei , Peng Jiawei , Dai Helong , Peng Longkai 
Published: December 2020

AbstractBackgroundDelayed graft function (DGF) is closely associated with the use of marginal donated kidneys due to deficits during transplantation and in recipients. We aimed to predict the incidence of DGF and evaluate its effect on graft survival.MethodsThis retrospective study on kidney transplantation was conducted from January 1, 2018, to December 31, 2019, at the Second Xiangya Hospital of Central South University. We classified recipients whose operations were performed in different years into training and validation cohorts and used data from the training cohort to analyze predictors of DGF. A nomogram was then constructed to predict the likelihood of DGF based on these predictors.ResultsThe incidence rate of DGF was 16.92%. Binary logistic regression analysis showed correlations between the incidence of DGF and cold ischemic time (CIT), warm ischemic time (WIT), terminal serum creatine (Scr) concentration, duration of pretransplant dialysis, primary cause of donor death, and usage of LifePort. The internal accuracy of the nomogram was 83.12%. One-year graft survival rates were 93.59 and 99.74%, respectively, for the groups with and without DGF (P < 0.05).ConclusionThe nomogram established in this study showed good accuracy in predicting DGF after deceased donor kidney transplantation; additionally, DGF decreased one-year graft survival.
CSE/H2S system alleviates uremic accelerated atherosclerosis by regulating TGF-β/Smad3 pathway in 5/6 nephrectomy ApoE−/− mice
Authors: Lu Xiangxue , Wang Shixiang , Feng Sujuan , Li Han 
Published: December 2020

AbstractBackgroundHydrogen sulfide (H2S) has been shown to inhibit the atherosclerosis development and progression. It is produced by cystathionine γ-lyase (CSE) in the cardiovascular system. In our previous study, it has been shown that CSE/H2S system plays a significant role in the changes of uremic accelerated atherosclerosis (UAAS), but the mechanism is not known clearly.MethodsIn this study, we explored the antagonism of CSE/H2S system in UAAS and identified its possible signaling molecules in ApoE−/−mice with 5/6 nephrectomy and fed with atherogenic diet. Mice were divided into sham operation group (sham group), UAAS group, sodium hydrosulfide group (UAAS+NaHS group) and propargylglycine group (UAAS+PPG group). Serum creatinine, urea nitrogen, lipid levels and lesion size of atherosclerotic plaque in the aortic roots were analyzed. Meanwhile, the expression of CSE, TGF-β and phosphorylation of Smad3 were detected.ResultsCompared with sham group, the aortic root of ApoE−/−mice in the UAAS group developed early atherosclerosis, the levels of total cholesterol, triglyceride, low-density lipoprotein-cholesterol, serum creatinine and urea nitrogen were also higher than that in the sham group. NaHS administration can inhibit the development of atherosclerosis, but PPG administration can accelerate the atherosclerosis development. Meanwhile, the protein expression levels of CSE and TGF-β and phosphorylation of Smad3 significantly decreased in the UAAS mice. Treatment of UAAS mice with NaHS inhibited TGF-β protein expression and Smad3 phosphorylation decrease, but PPG treatment had the opposite effect.ConclusionsThe CSE/H2S system is of great importance for treating atherosclerosis in patients with chronic kidney disease, and it may protect the vascular from atherosclerosis through the TGF-β/Smad pathway.
Relationship between leukocyte counts and large vessel occlusion in acute ischemic stroke
Authors: Tarkanyi Gabor , Karadi Zsofia Nozomi , Szabo Zsofia , Szegedi Istvan , Csiba Laszlo , Szapary Laszlo 
Published: December 2020

Abstract
Background
Neuroinflammation plays an important role in the pathogenesis of acute ischemic stroke (AIS) and peripheral leukocyte counts have proved to be independent predictors of stroke severity and outcomes. Clinical significance of large vessel occlusion (LVO) in AIS is increasing, as these patients are potential candidates for endovascular thrombectomy and likely to have worse outcomes if not treated urgently. The aim of our study was to assess the relationship between on admission leukocyte counts and the presence of LVO in the early phase of AIS.

Methods
We have conducted a cross-sectional, observational study based on a registry of consecutive AIS patients admitted up to 4.5 h after stroke onset. Blood samples were taken at admission and leukocyte counts were measured immediately. The presence of LVO was verified based on the computed tomography angiography scan on admission.

Results
Total white blood cell (WBC) and neutrophil counts were significantly higher in patients with LVO than those without LVO (P < 0.001 respectively). After adjustment for potential confounders total WBC counts (adjusted OR: 1.405 per 1 × 109/L increase, 95% CI: 1.209 to 1.632) and neutrophil counts (adjusted OR: 1.344 per 1 × 109/L increase, 95% CI: 1.155 to 1.564) were found to have the strongest associations with the presence of LVO. Total WBC and neutrophil counts had moderate ability to discriminate an LVO in AIS (AUC: 0.667 and 0.655 respectively). No differences were recorded in leukocyte counts according to the size of the occluded vessel and the status of collateral circulation in the anterior vascular territory. However, total WBC and neutrophil counts tended to be higher in patients with LVO in the posterior circulation (p = 0.005 and 0.010 respectively).

Conclusion
Higher admission total WBC and neutrophil counts are strongly associated with the presence of LVO and has moderate ability to discriminate an LVO in AIS. Detailed evaluation of stroke-evoked inflammatory mechanisms and changes according to the presence of LVO demands further investigation.
An effective combination of codon optimization, gene dosage, and process optimization for high-level production of fibrinolytic enzyme in Komagataella phaffii (Pichia pastoris)
Authors: Che Zhiqun , Cao Xiaoyan , Chen Guiguang , Liang Zhiqun 
Published: December 2020

Abstract
Background
As a main drug for diseased thrombus, some clinically used thrombolytic agents have various disadvantages, safer novel thrombolytic agents are of great demand. This study aimed to achieve high and efficient production of a fibrinolytic enzyme with superior enzymatic properties, by a combination strategy of codon optimization, gene dosage and process optimization in Komagataella phaffii (K. phaffii).

Results
After codon optimization, the fibase from a marine Bacillus subtilis was expressed and secreted in K. phaffii GS115. Recombinant strains harboring different copies of the fib gene (fib-nc) were successfully obtained via Geneticin (0.25–4 mg/ml) screening on minimal dextrose selection plates and assessment via real-time quantitative PCR. The respective levels of fibase produced by strains expressing fib-5.4c, fib-6c, fib-8c, fib-9c, and fib-12c were 4428, 5781, 7323, 7930, and 2472 U/ml. Levels increased as the copy number increased from 4 to 9, but decreased dramatically at copy number 12. After high cell density fermentation optimization, the highest fibase activity of the strain expressing fib-9c was 7930 U/ml in a shake flask and increased to 12,690 U/ml after 3 days of continuous culture in a 5-L fermenter, which is one of the highest levels of production reported. The recombinant fibase was maximally active at pH 9.0 and 45 °C, and was remarkably stable at pH levels ranging from 5 to 10 and temperatures up to 50 °C. As a metal-dependent serine protease, fibase did not cause hemolysis in vitro and preferentially degraded fibrin directly.

Conclusions
The combination of codon optimization, gene dosage, and process optimization described herein could be used for the expression of other therapeutic proteins difficult to express. The characteristics of the recombinant fibase suggest that it has potential applications for thrombosis prevention and therapy.
An evaluation of Alberta retina health service delivery in an office setting: a cross-sectional survey of patient experience
Authors: Henry Tyler , Palakkamanil Mathew , Al Hamarneh Yazid N. , Tennant Matthew T. S. 
Published: December 2020

Abstract
Background
Retina sub-specialists provide much of the retina related eye care across Canada. In the province of Alberta, 18 retina sub-specialists work across six different offices. The purpose of this study was to assess the quality of care provided by Alberta retina sub-specialists in an office setting by administering a patient satisfaction survey. The results of this survey were provided to the same retina specialists to promote improvements in patient-centered health care delivery.

Methods
A cross sectional patient satisfaction survey was performed using a thirty-part questionnaire developed in collaboration with the Physician Learning Program at the University of Alberta. The survey was modelled after other similar patient satisfaction surveys used in other areas of medicine. Patients from ten of the eighteen retina practices in Alberta participated in this survey. Topics of the survey included pre-appointment experience, physician-patient interactions and quality, comments/ feedback and patient demographics.

Results
214 randomly sampled patients completed the survey from three geographically separate office locations in Calgary and Edmonton. 90% of patients responded that their retina sub-specialist listened adequately and provided quality care in a timely manner. Patients felt that there could be improvements to accessibility to the clinic and reduced wait times, as well as in the pre-operative consent process. Including a more complete explanation of the procedure as well as the potential risks and benefits. Only 51% of patients felt that the risks of a potential surgery had been adequately explained to them. There was a statistically significant association found between overall satisfaction and lower wait times, understanding of procedural risks and time with, listening to and involving the patient in care. There were no correlations found with other demographics such as ethnicity, sex, distance traveled or age.

Conclusions
This patient satisfaction survey provided valuable patient care feedback to the retina sub-specialists of Alberta. The survey results will assist this group to improve the consent process and thereby improve patient centered health care delivery. We would recommend the distribution of this survey or other similar patient satisfaction questionnaire by retina sub-specialists to their patients to improve patient centered care in their clinics.
The associations between social, built and geophysical environment and age-specific dementia mortality among older adults in a high-density Asian city
Authors: Ho Hung Chak , Fong Kenneth N. K. , Chan Ta-Chien , Shi Yuan 
Published: December 2020

Abstract
Background
Although socio-environmental factors which may affect dementia have widely been studied, the mortality of dementia and socio-environmental relationships among older adults have seldom been discussed.

Method
A retrospective, observational study based on territory-wide register-based data was conducted to evaluate the relationships of four individual-level social measures, two community-level social measures, six short-term (temporally varying) environmental measures, and four long-term (spatially varying) environmental measures with dementia mortality among older adults in a high-density Asian city (Hong Kong), for the following decedents: (1) all deaths: age >= 65, (2) “old-old”: age > = 85, (3) “mid-old”: aged 75–84, and (4) “young-old”: aged 65–74.

Results
This study identified 5438 deaths (3771 old-old; 1439 mid-old; 228 young-old) from dementia out of 228,600 all-cause deaths among older adults in Hong Kong between 2007 and 2014. Generally, regional air pollution, being unmarried or female, older age, and daily O3 were associated with higher dementia mortality, while more urban compactness and greenness were linked to lower dementia mortality among older adults. Specifically, being unmarried and the age effect were associated with higher dementia mortality among the “old-old”, “mid-old” and “young-old”. Regional air pollution was linked to increased dementia mortality, while urban compactness and greenness were associated with lower dementia mortality among the “old-old” and “mid-old”. Higher daily O3 had higher dementia mortality, while districts with a greater percentage of residents whose native language is not Cantonese were linked to lower dementia mortality among the “old-old”. Economic inactivity was associated with increased dementia mortality among the “young-old”. Gender effect varied by age.

Conclusion
The difference in strengths of association of various factors with dementia mortality among different age groups implies the need for a comprehensive framework for community health planning. In particular, strategies for air quality control, usage of greenspace and social space, and activity engagement to reduce vulnerability at all ages are warranted.
Relationship between serum triglyceride to high-density lipoprotein cholesterol ratio and sarcopenia occurrence rate in community-dwelling Chinese adults
Authors: Wang Na , Chen Mengjun , Fang Danhong 
Published: December 2020

Abstract
Background
A study conducted on elderly Korean men showed that a high serum triglyceride to high-density lipoprotein cholesterol (TG/HDL-C) ratio was associated with a high risk of developing sarcopenia. We aimed to determine such an association in community-dwelling Chinese adults.

Methods
From May 2016 to August 2017, we conducted a cross-sectional study on Chinese adults at the First Affiliated Hospital of Wenzhou Medical University. Univariate and multivariate logistic regression analyses were applied to evaluate a possible relationship between TG/HDL-C ratio and sarcopenia occurrence.

Results
We included 2613 adults in this study, with 13.85% presenting with sarcopenia. The odds ratios (ORs) for TG and HDL-C were 0.67 (95% confidence interval [CI]: 0.51–0.87), and 1.97 (95% CI: 1.49–2.61), respectively. Moreover, TG/HDL-C ratio was independently associated with sarcopenia status (OR: 0.63; 95% CI: 0.49–0.81).

Conclusions
We found that TG and HDL-C were, respectively, negatively and positively associated with sarcopenia occurrence rate in community-dwelling Chinese adults. However, a negative association was found between sarcopenia occurrence rate and TG/HDL-C ratio.
Physical activity and sedentary time of youth in structured settings: a systematic review and meta-analysis
Authors: Tassitano Rafael M. , Weaver R. Glenn , Tenório Maria Cecília M. , Brazendale Keith , Beets Michael W. 
Published: December 2020

Abstract
Background
Structured settings, such as school, childcare, afterschool programs, summer camps, and physical activity/sport programs are crucial to promoting physical activity (PA) opportunities and reducing sedentary (ST) for children and adolescents. However, little is known about how much PA and ST children and adolescents accumulate in structured settings. The aim of this study is to conduct a systematic review and meta-analysis of the absolute amount of time youth spend physically active and sedentary in different structured settings (Prospero number: 42018111804).

Methods
Observational and experimental/quasi-experimental studies (baseline data only) with full-text available, written in English and published in a peer-reviewed journal, reporting the total amount of objectively measured PA (light, moderate, vigorous, and/or total physical activity) and/or time spent ST during structured settings among youth (3 to 18 years) were eligible. Adjusted meta-analysis was conducted to estimate the pooled mean of time spent in PA and ST, by settings and sex.

Results
A total of 187 studies (childcare n=60; school n=91; afterschool programs n=14; summer camp n=4; and Physical activity/ sport programs n=18) from 30 countries (47.9% United States), representing 74,870 youth (mean age 8.6 years old) were included. Overall, there was a high variation between studies in outcomes and settings. The meta-analyses revealed, on average, youth spend 221.8 minutes (36.7 min/hour) in ST and 32.1 minutes (5.1 min/hour) in MVPA during childcare hours, and 223.9 minutes (36.7min/hour) in ST and 27.8 min (4.4 min/hour) in MVPA at school. Relatively, youth are engaged in more MVPA in afterschool programs (11.7 min/hour), PA/ sport programs (20.9 min/hour), and summer camps (6.4 min/hour), when compared to childcare and school.

Conclusion
Total PA accumulated during childcare and MVPA accumulated during schools hours were close to recommendations, despite high proportion of ST. Afterschool programs, summer camp and PA/ sport programs are important settings that can contribute to daily PA and reduced ST. Ensuring all youth have access to these structured settings may be an important step forward for public health.