bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection
Authors: Lázaro-Perona Fernando , Rodriguez-Antolín Carlos , Alguacil-Guillén Marina , Gutiérrez-Arroyo Almudena , Mingorance Jesús , García-Rodriguez Julio ,   on behalf of the SARS-CoV-2 Working Group
Published: February 2021

BackgroundTwo automatable in-house protocols for high-troughput RNA extraction from nasopharyngeal swabs for SARS-CoV-2 detection have been evaluated.MethodsOne hundred forty one SARS-CoV-2 positive samples were collected during a period of 10-days. In-house protocols were based on extraction with magnetic beads and designed to be used with either the Opentrons OT-2 (OT-2in-house) liquid handling robot or the MagMAXTMExpress-96 system (MMin-house). Both protocols were tested in parallel with a commercial kit that uses the MagMAXTMsystem (MMkit). Nucleic acid extraction efficiencies were calculated from a SARS-CoV-2 DNA positive control.ResultsNo significant differences were found between both in-house protocols and the commercial kit in their performance to detect positive samples. The MMkitwas the most efficient although the MMin-housepresented, in average, lower Cts than the other two. In-house protocols allowed to save between 350€ and 400€ for every 96 extracted samples compared to the commercial kit.ConclusionThe protocols described harness the use of easily available reagents and an open-source liquid handling system and are suitable for SARS-CoV-2 detection in high throughput facilities.
Decreasing trends in cholangiocarcinoma incidence and relative survival in Khon Kaen, Thailand: An updated, inclusive, population-based cancer registry analysis for 1989–2018
Authors: Kamsa-ard Supot , Santong Chalongpon , Kamsa-ard Siriporn , Luvira Vor , Luvira Varisara , Suwanrungruang Krittika , Bhudhisawasdi Vajarabhongsa 
Published: February 2021

Background
Cholangiocarcinoma (CCA) is a leading cause of cancer death in northeastern Thailand. We reported on the incidence of CCA using only one method. In the current study, we used three different statistical methods to forecast future trends and estimate relative survival.

Methods
We reviewed the CCA cases diagnosed between 1989 and 2018 recorded in the population-based Khon Kaen Cancer Registry (KKCR). Annual percent change (APC) was calculated to quantify the incidence rate trends using Joinpoint regression. Age-period-cohort models (APC model) were used to examine the temporal trends of CCA by age, calendar year, and birth cohort. We projected the incidence of CCA up to 2028 using three independent approaches: the Joinpoint, Age-period-cohort, and Nordpred models. Survival assessments were based on relative survival (RS).

Results
The respective APC in males and females decreased significantly (-3.1%; 95%CI: -4.0 to -2.1 and -2.4%; 95%CI: -3.6 to -1.2). The APC model—AC-P for male CCA—decreased according to a birth-cohort. The CCA incidence for males born in 1998 was 0.09 times higher than for those born in 1966 (Incidence rate ratios, IRR = 0.09; 95%CI: 0.07 to 0.12). The relative incidence for female CCA similarly decreased according to a birth-cohort (IRR = 0.11; 95%CI: 0.07 to 0.17). The respective projection for the age-standardized rate for males and females for 2028 will be 7.6 per 100,000 (102 patients) and 3.6 per 100,000 (140 patients). The five-year RS for CCA was 10.9% (95%CI: 10.3 to 11.6).

Conclusion
The incidence rate of CCA has decreased. The projection for 2028 is that the incidence will continue to decline. Nevertheless, the survival of patients with CCA remains poor.
Cardiac autonomic dysfunction is associated with hypothalamic damage in patients with childhood-onset craniopharyngioma
Authors: Jung Hae Woon , Kim Hwa Young , Kim Ji Young , Cheon Jung-Eun , Kim In-One , Kim Seung-Ki , Shin Choong Ho , Yang Sei Won , Lee Young Ah 
Published: February 2021

Background
Autonomic nervous system dysfunction is implicated in the development of hypothalamic obesity. We investigated the relationship between hypothalamic involvement (HI), central obesity, and cardiac autonomic dysfunction by assessing heart rate variability (HRV) indices in patients with childhood-onset craniopharyngioma.

Methods
A cross-sectional study of 48 patients (28 males, 10–30 years old) with hypothalamic damage after childhood-onset craniopharyngioma was performed. Postoperative HI was graded as mild (n = 19) or extensive (n = 29) on magnetic resonance imaging. Anthropometry, body composition and HRV indices including the standard deviation of all normal R-R intervals (SDNN) and total power (TP) as overall variability markers, root-mean square differences of successive R-R intervals (RMSSD) and high frequency (HF) as parasympathetic modulation markers, and low frequency (LF) as a sympathetic/sympathovagal modulation marker were measured.

Results
Patients with extensive HI had increased means of body mass index, waist circumference, and fat mass than those with mild HI (P < 0.05, for all). Centrally obese patients had a lower mean HF, a parasympathetic modulation marker, than centrally non-obese patients (P < 0.05). The extensive HI group had lower means of overall variability (SDNN and TP), parasympathetic modulation (HF), and sympathetic/sympathovagal modulation (LF) than the mild HI group (P < 0.05, for all). The interaction effect of HI and central obesity on HRV indices was not significant. In models adjusted for age, sex, and family history of cardiometabolic disease, the means of the overall variability indices (P < 0.05 for both SDNN and TP) and a sympathetic/sympathovagal modulation index (P < 0.05 for LF) were lower with extensive HI, without differences according to central obesity.

Conclusions
The reduced HRV indices with extensive HI suggests that hypothalamic damage may contribute to cardiac autonomic dysfunction, underscoring the importance of minimizing hypothalamic damage in patients with childhood-onset craniopharyngioma.
30-day mortality after hip fracture surgery: Influence of postoperative factors
Authors: Blanco Juan F. , da Casa Carmen , Pablos-Hernández Carmen , González-Ramírez Alfonso , Julián-Enríquez José Miguel , Díaz-Álvarez Agustín 
Published: February 2021

Purpose
The 30-day mortality rate after hip fracture surgery has been considered as an indirect indicator of the quality of care. The aim of this work is to analyse preoperative and postoperative factors potentially related to early 30-day mortality in patients over 65 undergoing hip fracture surgery.

Methods
Prospective cohort study including all consecutive primary hip fracture patients over 65 admitted to Trauma and Orthopaedics department from January 1, 2018 to December 31, 2019. Bed-ridden, non- surgically treated patients, and high energy trauma or tumoral aetiology fractures were excluded. A total of 943 patients were eligible (attrition rate: 2.1%). Follow-up included 30-days after discharge. We noted the 30-day mortality after hip fracture surgery, analysing 130 potentially related variables including biodemographic, fracture-related, preoperative, and postoperative clinical factors. Qualitative variables were assessed by χ2, and quantitative variables by non-parametric tests. Odds ratio determined by binary logistic regression. We selected preventable candidate variables for multivariate risk assessment by logistic regression.

Results
A total of 923 patients were enrolled (mean age 86.22±6.8, 72.9% women). The 30-day mortality rate was 6.0%. We noted significant increased mortality on men (OR = 2.381[1.371–4.136], p = 0.002), ageing patients (ORyear = 1.073[1.025–1.122], p = 0.002), and longer time to surgery (ORday = 1.183[1.039–1146], p<0.001), on other 20 preoperative clinical variables, like lymphopenia (lymphocyte count <103/μl, OR = 1.842[1.063–3.191], p = 0.029), hypoalbuminemia (≤3.5g/dl, OR = 2.474[1.316–4.643], p = 0.005), and oral anticoagulant intake (OR = 2.499[1.415–4.415], p = 0.002), and on 25 postoperative clinical variables, like arrhythmia (OR = 13.937[6.263–31.017], p<0.001), respiratory insufficiency (OR = 7.002[3.947–12.419], p<0.001), hyperkalaemia (OR = 10.378[3.909–27.555], p<0.001), nutritional supply requirement (OR = 3.576[1.894–6.752], p = 0.021), or early arthroplasty dislocation (OR = 6.557[1.206–35.640], p = 0.029). We developed a predictive model for early mortality after hip fracture surgery based on postoperative factors with 96.0% sensitivity and 60.7% specificity (AUC = 0.863).

Conclusion
We revealed that not only preoperative, but also postoperative factors have a great impact after hip fracture surgery. The influence of post-operative factors on 30-day mortality has a logical basis, albeit so far they have not been identified or quantified before. Our results provide an advantageous picture of the 30-day mortality after hip fracture surgery.
The basic reproduction number can be accurately estimated within 14 days after societal lockdown: The early stage of the COVID-19 epidemic in Denmark
Authors: Valentin Jan Brink , Møller Henrik , Johnsen Søren Paaske 
Published: February 2021

Objective
Early identification of the basic reproduction number (BRN) is imperative to political decision making during an epidemic. In this study, we estimated the BRN 7, 14, 21 and 28 days after societal lockdown of Denmark during the early stage of the COVID-19 epidemic.

Method
We implemented the SEIR dynamical system for disease spread without vital dynamics. The BRN was modulated using a sigmoid function. Model parameters were estimated on number of admitted patients, number of patients in intensive care and cumulative number of deaths using the simulated annealing Monte Carlo algorithm. Results are presented with 95% prediction intervals (PI).

Results
We were unable to determine any reliable estimate of the BRN at 7 days following lockdown. The BRN had stabilised at day 14 throughout day 28, with the estimate ranging from 0.95 (95% PI: 0.92–0.98) at day 7 to 0.92 (95% PI: 0.92–0.93) at day 28. We estimated the BRN prior to lockdown to be 3.32 (95% PI: 3.31–3.33). The effect of the lockdown was occurring over a period of a few days centred at March 18th (95% PI: 17th-18th) 2020.

Conclusion
We believe our model provides a valuable tool for decision makers to reliably estimate the effect of a politically determined lockdown during an epidemic.
Albumin and the fibrinogen-to-albumin ratio: Biomarkers for the acute phase response following total knee arthroplasty
Authors: Amaro Emilie , Moore-Lotridge Stephanie N. , Wessinger Bronson , Benvenuti Michael A. , An Thomas J. , Oelsner William K. , Polkowski Gregory G. , Schoenecker Jonathan G. 
Published: February 2021

Purpose
Complications following total knee arthroplasty (TKA) lead to patient morbidity and cost. While acute phase reactants, such as c-reactive protein (CRP) and fibrinogen, have been used to predict complications following TKA, the extent and duration of changes in albumin levels following TKA are unknown. It is hypothesized that like CRP and fibrinogen, albumin, and the fibrinogen/albumin ratio (FAR) represent useful measures of the acute phase response (APR) following TKA. The purpose of this study was to describe the longitudinal course of albumin and FAR in healthy patients following TKA, relative to established biomarkers, and examine if the variance in albumin or FAR correlates with patient comorbidities.

Methods
This retrospective cohort study of patients undergoing TKA at a tertiary medical center. CRP, fibrinogen, and albumin values were collected pre- and post-operatively. An age-adjusted Charlson comorbidity index (CCI) was utilized as a measure of patient comorbidity status.

Results
The median preoperative albumin value was 4.3 g/dL, which dropped to 3.6 g/dL on postoperative day 1 following TKA. The albumin value returned to 93% of the baseline by postoperative week 2. The course of albumin inversely mirrored the course of CRP (r = -0.41). Median preoperative FAR was 0.087 g/L, which rose to 0.130 g/L by postoperative week 2 and returned to baseline by postoperative week 6. While preoperative FAR strongly correlated with postoperative week 2 values (r = 0.74), there was a weak positive correlation between age-adjusted CCI and pre-operative FAR (r = 0.24) in patients undergoing primary TKA.

Conclusion
Albumin levels follow a predictable postoperative decline that inversely correlates with CRP in healthy patients following TKA. Given the low cost and abundance of laboratories offering albumin levels, direct albumin levels and/or albumin ratios such as FAR may be underutilized biomarkers for monitoring the APR following TKA.
Role of ivermectin in the prevention of SARS-CoV-2 infection among healthcare workers in India: A matched case-control study
Authors: Behera Priyamadhaba , Patro Binod Kumar , Singh Arvind Kumar , Chandanshive Pradnya Dilip , S. R. Ravikumar , Pradhan Somen Kumar , Pentapati Siva Santosh Kumar , Batmanabane Gitanjali , Mohapatra Prasanta Raghab , Padhy Biswa Mohan , Bal Shakti Kumar , Singh Sudipta Ranjan , Mohanty Rashmi Ranjan 
Published: February 2021

Background
Ivermectin is one among several potential drugs explored for its therapeutic and preventive role in SARS-CoV-2 infection. The study was aimed to explore the association between ivermectin prophylaxis and the development of SARS-CoV-2 infection among healthcare workers.

Methods
A hospital-based matched case-control study was conducted among healthcare workers of AIIMS Bhubaneswar, India, from September to October 2020. Profession, gender, age and date of diagnosis were matched for 186 case-control pairs. Cases and controls were healthcare workers who tested positive and negative, respectively, for COVID-19 by RT-PCR. Exposure was defined as the intake of ivermectin and/or hydroxychloroquine and/or vitamin-C and/or other prophylaxis for COVID-19. Data collection and entry was done in Epicollect5, and analysis was performed using STATA version 13. Conditional logistic regression models were used to describe the associated factors for SARS-CoV-2 infection.

Results
Ivermectin prophylaxis was taken by 76 controls and 41 cases. Two-dose ivermectin prophylaxis (AOR 0.27, 95% CI, 0.15–0.51) was associated with a 73% reduction of SARS-CoV-2 infection among healthcare workers for the following month. Those involved in physical activity (AOR 3.06 95% CI, 1.18–7.93) for more than an hour/day were more likely to contract SARS-CoV-2 infection. Type of household, COVID duty, single-dose ivermectin prophylaxis, vitamin-C prophylaxis and hydroxychloroquine prophylaxis were not associated with SARS-CoV-2 infection.

Conclusion
Two-dose ivermectin prophylaxis at a dose of 300 μg/kg with a gap of 72 hours was associated with a 73% reduction of SARS-CoV-2 infection among healthcare workers for the following month. Chemoprophylaxis has relevance in the containment of pandemic.
Quantum model of naturally rotating Machian cosmology and galactic applications of current cosmic angular velocity
Authors: V.S. Seshavatharam U. , Lakshminarayana S. 
Published: February 2021

We would like to emphasize that, extraordinary physical concepts like Big bang, Inflation, Dark energy and Superluminal expansion demand super-normal efforts and need observational support. Observational data is raising day-by-day non-conformity and demanding changes in the original concepts. It is very interesting to note that James Peebles, the famous cosmologist and 2019 Nobel laureate strongly believes that Big bang concept is inappropriate in understanding the universe. It is better to understand and develop models of cosmology based on well supported physical concepts rather than extraordinary physical hypothesis. Unification point of view, quantum cosmology must be given a priority and one should make a note that, Spin is a basic property of quantum physics and rotation is a very common experience. In this context, with reference to life cycle of living creatures and independent of red-shift data, we have developed a quantum model of cosmology associated with Machian universe having Planck scale origin, total dark matter, light speed expansion, light speed rotation, equality of gravitational self energy density and thermal energy density, radially decreasing internal acceleration and radially increasing anisotropy. We are working on understanding and correlating observed redshift data in a unified approach. In this letter, we present various galactic applications of current cosmic angular velocity.Â Â
Effect of stacked breathing exercise on reducing pulmonary infection and complications for patients with pleural effusion
Authors: Abd El-Nasser Mohamed Amal , Anwar Abd El-Aziz Mervat , Aly Mahgoup Asmaa , Zareh Hassan Zain El-abedeen 
Published: February 2021

Background: Chest expansion exercises are widely used for patients with pleural effusion. One of these exercises is stacked breathing exercise which has shown to be effective in mobilizing greater lung volumes and in achieving and sustaining deep inspiration. But it is not known whether it will have similar effects in patients with pleural effusion and if it has effect on reducing pulmonary infection and complications for these patients.Objective: Was to evaluate the effectiveness of stacked breathing exercise on reducing pulmonary infection and complications for patients with pleural effusion.Design: A randomized controlled experimental study was used in this study.Participants: sixty patients with pleural effusion were selected by convenience sample and randomly assigned into two groups; the intervention and control groups (30 patients each).Method: Three tools were used. Tool I was Pleural effusion assessment tool included demographic and medical history, hemodynamic parameters and assessment of respiratory system. Tool II is stacked breathing exercise tool used to assess the exercise done to the intervention group. Tool III was Patients' outcomes evaluation sheet used to assess the effect of stacked breathing exercise on pulmonary infection score and complications.Results: There were significant differences in pulmonary infection score and complications between the intervention and control groups. Pulmonary infection score in the intervention group was much lower, and their complications were lower than those in the control group.Conclusion: implementing stacked breathing exercise had significant effect in reducing pulmonary infection and complications in patients with pleural effusion than the routine hospital care.Â Â Â
Analysis of damage-plasticity model of concrete under uniaxial compression loading
Authors: Rafiqul Islam Mohammad , Ali Abbas , Jahir Bin Alam Md. , Ahmad Tanvir , Sakib Salman 
Published: February 2021

Concrete is a quasi-brittle material and shows different behavior in compression and tension. It shows elastic behavior at initial stage and damage-plasticity behavior beyond elastic limit. Therefore, development of material behavior model of concrete is a complex phenomenon. In this study, concrete damage plasticity theory has been described under experiment on concrete cylinder considering uni-axial compression loading and interpreted with analytical data calculated using CEB-FIP model code equation. The code has divided the stress-strain curve for concrete compression into three sections according to concreteâ€™s elastic and non-elastic behaviors. Those three sections have been considered to calculate analytical data. In experiment, concrete behavior has been observed in two phases. The damage value for different stresses at the various points on the stress strain curve has been calculated. According to analytical data, the concrete shows elastic behavior up to 8.3MPa stress point and no damage occur in the concrete within the limit. However, in experimental data, concrete shows elastic behavior up to only 2.28MPa and damage occurred beyond the stress. Finally, the percentage of damage of concrete due to compression obtained from analysis and experiment has been assessed and compared. Above 32 percent of concrete damage is found for 22.5 MPa in both cases.Â Â
Health risk assessment of levels of some toxic metals and polycyclic aromatic hydrocarbons of some commercial soft drinks commonly consumed among students of Nnamdi Azikiwe university, Awka, Anambra state, Nigeria
Authors: Ngozi Asomugha Rose , Emmanuel Igwe Chijoke , Ukamaka Nome Peace , Mary Uchendu Onyinye , Godson Nwamkwere 
Published: February 2021

Food Safety is of growing concern globally, and more so considering the relatively high proportion of soft drinks in the beverage market worldwide, and its rate of consumption especially amongst the youths. It is essential to evaluate the levels of toxic metals and Polycyclic Aromatic Hydrocarbons (PAHs) residues of which when present in soft drinks above the permissible limits could pose serious public health risk. The aim of this present study was to assess the levels of heavy metals (Pb, Hg, Cd ,As) and Polycyclic aromatic Hydrocarbons(PAHs) in 16 commercial soft drinks marketed in Awka, using Atomic Absorption Spectroscopy(AAS) and Flame Ionization detector (GC-FID), respectively. The carcinogenic and non-carcinogenic risk assessment were performed using the method established by United State Environmental Protection agency(USEPA).The data obtained were compared with the permissible limit set for drinking water by United State Environmental Protection Agency(USEPA),World Health Organization (WHO),Standard Organization of Nigeria(SON) and Federal Environmental Protection Agency(FEPA). The highest mean level of 0.6116 mg/l is related to Pb and the lowest of 0.0028mg/l related to Hg. The mean levels of the metals increased in this order: Hg<As<Cd<Pb. For the PAHs, using Benzo(a)pyrene as the benchmark for other PAHs congeners because of its strong carcinogenic potency, is not detected in this study, and thus pose no health risk. The target hazard quotient (THQ) of Hg in the studied samples is less than 1. Pb levels in75% the studied samples had THQ>1, and thus, pose a health risk. The hazard index, calculated as the combined risk of heavy metal toxicity is greater than unity (HI>1).The incremental lifetime cancer risk (ILCR) values estimated for Pb, As and Cd in the sample were 6.25%,31.25% and 25% ,respectively, representing higher than acceptable risk value of (10-6 -10-4) . The results raise a concern for the public exposed with respect to As and Cd carcinogenic risk values.Â Â
تحليل تطور الفكر القومي العنصري في المانيا ١٩٢٠-١٩٤٥
Authors: Nouman Nijiar N. , Waisy Karwan S. 
Published: February 2021

نمى الشعور القومي في أوربا بشكل عام و في المانيا بشكل خاص في النصف الثاني من القرنين التاسع عشر و العشرين وأدى نمو هذا الشعور بدوره إلى بروز و تنامي عاطفة أكثر حيوية وأكثر عمقا و ذات مكانة و تاثير وهي عاطفة التضامن بين أعضاء الأمة الواحدة والتي شكلت فيما بعد البؤرة الاساسية لروح التضامن المتطرف. ولكن مايثير حساسية النمو المفرط لعاطفة التضامن هي مسالة مرافقتها لنمو الشعور بالكرامة الوطنية والشرف القومي والحس بالمصير القومي للعرق أو الجنس أو الطائفة وغيرها من المسميات الأخرى المدرجة كبيرة وصلت إلى حد إنكار كافة حقوق الاخر-المختلف طبعا- سواء داخل حدود الوطن أو معاداة دولة محاددة جغرافيا على هذا الاساس الضيق من العنصرية المغلقة بمكونتها، وفي الوقت نفسه نمت الرغبة في فرض اأسبقية وأهلية الصفات القومية بدا من أبسط أشكال الاختلاف بين القوميات منها الشكل و الجنس مثلا إلى أعقد وأعمق أوجه الاختلافات الاخرى و التي تتعلق بعضها بالصفات الخارجة عن الاإرداة البشرية، وبدا مسالة التأكيد على أهمية الشعور القومي وفرضه على مرأى ومسمع من العناصر الأجنبية الأخرى الموجودة في نفس الدولة مما تسبب في ظهور أزمة تقبل الاخر أو الطرف المختلف قوميا. لقد اختفى معنى كلمة القومية مع الزمن ولم يتحدد أويظهر مرة اخرى حتى أيامنا هذه. وما ذلك إلا لاختلاف العقليات التي تنظر إلى مفهوم القومية. ولذا فالتعقيد والغموض والالتباس مازالت تجري تحت أقلام المفكرين و المهتمين بدراسة الأمة والعاطفة القومية.