bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advanced cardiovascular risk prediction in the emergency department: updating a clinical prediction model – a large database study protocol
Authors: Reynard Charles , Martin Glen P. , Kontopantelis Evangelos , Jenkins David A. , Heagerty Anthony , McMillan Brian , Jafar Anisa , Garlapati Rajendar , Body Richard 
Published: October 2021

Abstract
Background
Patients presenting with chest pain represent a large proportion of attendances to emergency departments. In these patients clinicians often consider the diagnosis of acute myocardial infarction (AMI), the timely recognition and treatment of which is clinically important. Clinical prediction models (CPMs) have been used to enhance early diagnosis of AMI. The Troponin-only Manchester Acute Coronary Syndromes (T-MACS) decision aid is currently in clinical use across Greater Manchester. CPMs have been shown to deteriorate over time through calibration drift. We aim to assess potential calibration drift with T-MACS and compare methods for updating the model.

Methods
We will use routinely collected electronic data from patients who were treated using TMACS at two large NHS hospitals. This is estimated to include approximately 14,000 patient episodes spanning June 2016 to October 2020. The primary outcome of acute myocardial infarction will be sourced from NHS Digital’s admitted patient care dataset. We will assess the calibration drift of the existing model and the benefit of updating the CPM by model recalibration, model extension and dynamic updating. These models will be validated by bootstrapping and one step ahead prequential testing. We will evaluate predictive performance using calibrations plots and c-statistics. We will also examine the reclassification of predicted probability with the updated TMACS model.

Discussion
CPMs are widely used in modern medicine, but are vulnerable to deteriorating calibration over time. Ongoing refinement using routinely collected electronic data will inevitably be more efficient than deriving and validating new models. In this analysis we will seek to exemplify methods for updating CPMs to protect the initial investment of time and effort. If successful, the updating methods could be used to continually refine the algorithm used within TMACS, maintaining or even improving predictive performance over time.

Trial registration
ISRCTN number: ISRCTN41008456
Direct numerical simulation of hypersonic boundary layer transition over a lifting-body model HyTRV
Authors: Qi Han , Li Xinliang , Yu Changping , Tong Fulin 
Published: October 2021

AbstractDirect numerical simulation (DNS) of transition over a hypersonic lifting body model HyTRV developed by China Aerodynamics Research and Development Center is performed. The free-stream parameters are: the free-stream Mach number is 6, the unit Reynolds number is 10000/mm, the free-stream temperature is 79 K, the angle of attack is 0, and the wall temperature is 300 K. Weak random blowing-and-suction perturbations in the leading range are used to trigger the transition. A high order finite-difference code OpenCFD developed by the authors is used for the simulation, and grid convergence test shows that the transition locations are grid-convergence. DNS results show that transition occurs in central area of the lower surface and the concaved region of the upper surface, and the transition regions are also the streamline convergence regions. The transition mechanisms in different regions are investigated by using the spectrum and POD analysis.
The utility of the standardized uptake value, metabolic tumor volume and total lesion glycolysis as predictive markers of recurrent breast cancer
Authors: Fathinul Fikri A. S. , Chong E. Y. , Syafrina A. H. 
Published: October 2021

Abstract
Background
Breast cancer is the second leading cancer killer of women globally. An early measure utilizing a noninvasive molecular marker for predicting cancer aggressiveness is important to better manage the patient and to avert early disease progression. We aimed to determine whether metabolic tumor volume (MTV) and total lesion glycolysis (TLG) are able to predict risk in high TNM tumor staging and the need for the appropriate treatment in breast cancer patients. This is a retrospective study of confirmed breast cancer patients who underwent neoadjuvant, local and adjuvant treatment and follow-up. The 18F-FDG PET/CT study for initial staging was performed, and metabolic parameters (MTV, TLG, SUVmax mean) were analyzed. Spearman correlation was used to assess correlations between metabolic parameters and clinicopathological factors with TNM staging and treatment intention. SUVmean, wbMTV and wbTLG were analyzed to predict the dichotomization of patient endpoint for low (stage I and II) and high (stage III and IV) TNM stage.

Results
Twenty-six patients (4 low stage, 22 high stage) with a mean age of 51.8 ± 11.8 years with confirmed breast cancer underwent 18FFDG PET/CT. The MTV and TLG parameters in the tumor (T) were significantly correlated with the TNM stage (P < 0.050); the SUVmax mean (4.18 ± 1.68 g/dl), wbMTV mean (404.68 ± 558.02 cm3) and wbTLG (1756.55 ± 2432.11 g) differed significantly in the high versus low TNM staging with the best predictive cut-off value of SUVmax mean (3.55 g/ml, p < 0.05), wbMTV (20 cm3, p < 0.05) and wbTLG (130 g, p < 0.05) when these values were exceeded. Only wbTLG (130 g, p < 0.05) showed significance difference in treatment intention.

Conclusions
In this study, the metabolic parameters SUVmax mean, MTV and TLG showed potential good relationships with TNM staging. TLG was the only marker that influenced the treatment intention in predicting breast cancer aggressiveness.
COVITALE 2020 from eastern Indian population: imageologists perspective, a learning curve
Authors: Kumar Sen Kamal , Dubey Roopak , Goyal Mayank , Sethi Humsheer , Sharawat Ajay , Arora Rohit 
Published: October 2021

AbstractBackgroundHigh-resolution computed tomography (HRCT) chest becomes a valuable diagnostic tool for identifying patients infected with Coronavirus Disease 2019 (COVID-19) in the early stage, where patients may be asymptomatic or with non-specific pulmonary symptoms. An early diagnosis of COVID-19 is of utmost importance, so that patients can be isolated and treated in time, eventually preventing spread of the disease, improving the prognosis and reducing the mortality. In this paper, we have highlighted our radiological experience of dealing with the pandemic crisis of 2020 through the study of HRCT thorax, lung ultrasonography, chest X-rays and artificial intelligence (AI).ResultsResults of CT thorax analysis have been given in detail. We had also compared CT severity score (CTSS) with clinical and laboratory parameters. Correlation of CTSS with SpO2 values and comorbidities was also studied. We also analysed manual CTSS with the CTSS scored calculated by the AI software.ConclusionsCTSS and use of COVID-19 Reporting and Data System (CORADS) result in accuracy and uniform percolation of information among the clinicians. Bed-side X-rays and ultrasonography have played a role where the patients could not be shifted for CT scan. The possibility of predicting impending or progression of hypoxia was not possible when SpO2 mapping was correlated with the CTSS. AI was alternatively tried with available software (CT pneumonia analysis) which was not so appropriate considering the imaging patterns in the bulk ofatypical category.
Centralized colorectal cancer screening outreach and patient navigation for vulnerable populations in North Carolina: study protocol for the SCORE randomized controlled trial
Authors: Malo Teri L. , Correa Sara Y. , Moore Alexis A. , Ferrari Renée M. , Leeman Jennifer , Brenner Alison T. , Wheeler Stephanie B. , Tan Xianming , Reuland Daniel S. ,   on behalf of the Scaling Colorectal Cancer Screening Through Outreach, Referral, and Engagement (SCORE) Study Protocol Consortium, Ratner Shana , Frerichs Leah , Lich Kristen Hassmiller , Crockett Seth , Rohweder Catherine , Farr Deeonna E. , Richardson Claudia , Erhard Cory , Beasley Evan , Hogsed Michelle , Bland Ashley 
Published: October 2021

Abstract
Background
Although colorectal cancer (CRC) screening is effective in reducing CRC mortality, screening rates in vulnerable populations served by community health centers (CHCs) remain below national targets. CHCs in North Carolina are challenged to reach CRC screening targets as they tend to be under-resourced, have limited capacity to implement and sustain population health interventions, and typically operate independently from one another and from regional colonoscopy providers. The Scaling Colorectal Cancer Screening Through Outreach, Referral, and Engagement (SCORE) project is designed to address barriers to CRC screening in partnership with CHCs by implementing a multilevel intervention that includes centralized support infrastructure for mailed fecal immunochemical test (FIT) outreach and patient navigation to follow-up colonoscopy. This paper describes protocols for the SCORE implementation trial.

Methods
We will conduct a type 2 hybrid effectiveness-implementation trial that will assess effectiveness at increasing CRC screening and follow-up rates while also assessing implementation outcomes. The planned trial sample will include 4000 CHC patients who are at average CRC risk and due for screening. Participants will be randomized 1:1 to receive either usual care or a multilevel intervention that includes mailed FIT outreach and patient navigation support to follow-up colonoscopy for those with abnormal FIT. The primary effectiveness outcome is completion of any CRC screening test at six months after randomization. We will also conduct a multilevel assessment of implementation outcomes and determinants.

Discussion
This hybrid effectiveness-implementation trial will evaluate the effectiveness and implementation of an intervention that provides centralized infrastructure for mailed FIT screening and patient navigation for CHCs that operate independently of other healthcare facilities. Findings from this research will enhance understanding of the effectiveness of a centralized approach and factors that determine successful implementation in vulnerable patient populations.

Trial registration
The trial was registered on May 28, 2020, at ClinicalTrials.gov (identifier NCT04406714).
Aptitude of endophytic microbes for production of novel biocontrol agents and industrial enzymes towards agro-industrial sustainability
Authors: Falade Ayodeji O. , Adewole Kayode E. , Ekundayo Temitope C. 
Published: October 2021

AbstractBackgroundEndophytes have continued to receive increased attention worldwide, probably, due to the enormous biotechnological potentials spanning through various industrial sectors. This paper outlines the biotechnological potentials of endophytes in biocontrol and industrial enzyme production, and the possible contribution towards achieving agro-industrial sustainability using published articles on endophytes in both Web of Science and Scopus (1990–2020).Main body of the abstractThis review discusses the potential of endophytes to produce novel secondary metabolites with effective biocontrol activity against insect pests and plant pathogens. More so, the aptitude of endophytes for production of a wide range of enzymes with potential applications in agriculture, energy and health is discussed in this review. Furthermore, this review highlights the emerging potentials of endophytes in the production of exopolysaccharide and fatty acids. This paper also advocates the need for bioprospecting endophytes for novel biocontrol agents against termites, which are known for causing significant damage to forest and stored products.Short conclusionExploration of endophytes for biocontrol and production of biomolecules of industrial significance could contribute significantly towards agricultural and industrial sustainability.
Evolution of RNA viruses from SARS to SARS-CoV-2 and diagnostic techniques for COVID-19: a review
Authors: Khan Johra , Asoom Lubna Ibrahim Al , Khan Maryam , Chakrabartty Ishani , Dandoti Sayequa , Rudrapal Mithun , Zothantluanga James H. 
Published: October 2021

AbstractBackgroundFrom the start of the twenty-first century up to the year 2021, RNA viruses are the main causative agents of the majority of the disease outbreaks the world has confronted. Recently published reviews on SARS-CoV-2 have mainly focused on its structure, development of the outbreak, relevant precautions, management trials and available therapies. However, in this review, we aim to explore the history, evolution of all coronaviruses and the associated viral outbreaks along with the diagnostics for COVID-19 in the twenty-first century.Main bodyWe have focused on different RNA viruses’ viz. SARS-CoV, MERS-CoV, and SARS-CoV-2, their classification, and the various disease outbreaks caused by them. In the subsequent section, the comparison of different RNA viruses affecting humans has been made based on the viral genome, structure, time of the outbreak, mode of spread, virulence, causative agents, and transmission. Due to the current mayhem caused by the rapidly emerging virus, special attention is given to SARS-CoV-2, its genome updates, and infectivity. Finally, the current diagnostic techniques such as nucleic acid testing (real time-polymerase chain reaction and loop-mediated isothermal amplification), CRISPR-based diagnostics (CRISPR based DETECTR assay, CRISPR based SHERLOCK test, AIOD-CRISPR, FELUDA, CREST), chest radiographs (computed tomography, X-ray), and serological tests (Lateral flow assay, enzyme-linked immunosorbent assay, chemiluminescent immunoassay, neutralization assay, nano-sensors, blood test, viral sequencing) with their pros and cons, and future diagnostic prospective have been described.ConclusionsThe present gloomy scenario mandates clinical manifestations, contact tracing, and laboratory tests as important parameters that need to be taken into consideration to make the final diagnosis.
Interplay between the genetics of personality traits, severe psychiatric disorders and COVID-19 host genetics in the susceptibility to SARS-CoV-2 infection
Authors: Heilbronner Urs , Streit Fabian , Vogl Thomas , Senner Fanny , Schaupp Sabrina K. , Reich-Erkelenz Daniela , Papiol Sergi , Oraki Kohshour Mojtaba , Klöhn-Saghatolislam Farahnaz , Kalman Janos L. , Heilbronner Maria , Gade Katrin , Comes Ashley L. , Budde Monika , Andlauer Till F. M. , Anderson-Schmidt Heike , Adorjan Kristina , Stürmer Til , Loerbroks Adrian , Amelang Manfred , Poisel Eric , Foo Jerome , Heilmann-Heimbach Stefanie , Forstner Andreas J. , Degenhardt Franziska , Zimmermann Jörg , Wiltfang Jens , von Hagen Martin , Spitzer Carsten , Schmauss Max , Reininghaus Eva , Reimer Jens , Konrad Carsten , Juckel Georg , Lang Fabian U. , Jäger Markus , Figge Christian , Fallgatter Andreas J. , Dietrich Detlef E. , Dannlowski Udo , Baune Bernhardt T. , Arolt Volker , Anghelescu Ion-George , Nöthen Markus M. , Witt Stephanie H. , Andreassen Ole A. , Chen Chi-Hua , Falkai Peter , Rietschel Marcella , Schulze Thomas G. , Schulte Eva C. 
Published: October 2021

Background
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with its impact on our way of life, is affecting our experiences and mental health. Notably, individuals with mental disorders have been reported to have a higher risk of contracting SARS-CoV-2. Personality traits could represent an important determinant of preventative health behaviour and, therefore, the risk of contracting the virus.

Aims
We examined overlapping genetic underpinnings between major psychiatric disorders, personality traits and susceptibility to SARS-CoV-2 infection.

Method
Linkage disequilibrium score regression was used to explore the genetic correlations of coronavirus disease 2019 (COVID-19) susceptibility with psychiatric disorders and personality traits based on data from the largest available respective genome-wide association studies (GWAS). In two cohorts (the PsyCourse (n = 1346) and the HeiDE (n = 3266) study), polygenic risk scores were used to analyse if a genetic association between, psychiatric disorders, personality traits and COVID-19 susceptibility exists in individual-level data.

Results
We observed no significant genetic correlations of COVID-19 susceptibility with psychiatric disorders. For personality traits, there was a significant genetic correlation for COVID-19 susceptibility with extraversion (P = 1.47 × 10−5; genetic correlation 0.284). Yet, this was not reflected in individual-level data from the PsyCourse and HeiDE studies.

Conclusions
We identified no significant correlation between genetic risk factors for severe psychiatric disorders and genetic risk for COVID-19 susceptibility. Among the personality traits, extraversion showed evidence for a positive genetic association with COVID-19 susceptibility, in one but not in another setting. Overall, these findings highlight a complex contribution of genetic and non-genetic components in the interaction between COVID-19 susceptibility and personality traits or mental disorders.
Effectiveness of Sofosbuvir and Daclatasvir in treatment of Hepatitis-C: An experience of tertiary care hospital in Karachi
Authors: Butt Nazish , Saleem Anoshia , Khan Muhammad Ali , Akbar Ali 
Published: October 2021

Objective: To assess the effectiveness of Sofosbuvir (SOF) and Daclatasvir (DCV) in patients with chronic hepatitis C (CHC), compensated cirrhosis (CC) and decompensated cirrhosis (DCLD) either treatment naïve or experienced.
Methods: This was a prospective, observational study, conducted from January 2017 to December 2018 at Jinnah Postgraduate Medical Centre, Karachi. All patients above 12 years of age with detectable HCV RNA PCR were included. Patients were divided into three groups: CHC, CC and DCLD. SOF and DCV for 12 or 24 weeks were given. Ribavirin (RBV) was given to treatment experienced and cirrhotic patients. Primary outcome was End of Treatment Response (ETR) and secondary outcome was Sustained Virological Response (SVR) at post treatment week 12 or 24.
Results: Total 300 patients with mean age of 40.49 ± 13.86 were enrolled. Majority were females 174 (58%). CHC were 200 (66.6%) while cirrhotic were 100 (33.4%). Treatment naïve patients were 267 (89%) and 33 (11%) patients were experienced. Most common genotype was 3 (83%). ETR was achieved in 292 (97.33%) and SVR in 265 (88.33%) patients respectively.
Conclusion: SOF plus DCV with or without RBV is a highly effective treatment for chronic HCV and is still used in many centers of Pakistan. This regimen has excellent results for GT-3. The outcomes are mainly influenced by the presence or absence of cirrhosis.
doi: https://doi.org/10.12669/pjms.37.7.4627
How to cite this:Butt N, Anoshia, Khan MA, Akbar A. Effectiveness of Sofosbuvir and Daclatasvir in treatment of Hepatitis-C: An experience of tertiary care hospital in Karachi. Pak J Med Sci. 2021;37(7):2014-2019. doi: https://doi.org/10.12669/pjms.37.7.4627
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Screening for postoperative vital signs abnormalities, and particularly hemodynamic ones, by continuous monitoring: protocol for the Biobeat-Postop cohort study
Authors: Paternot Alexis , Aegerter Philippe , Martin Aurélie , Ouattara Jonathan , Ma Sabrina , Adjavon Sherifa , Trillat Bernard , Alfonsi Pascal , Fischler Marc , Le Guen Morgan 
Published: October 2021

Background: Postoperative hypotension associated with postoperative morbidity and early mortality has been studied previously. Hypertension and other hemodynamic, respiratory, and temperature abnormalities have comparatively understudied during the first postoperative days. Methods: This bi-centre observational cohort study will include 114 adult patients undergoing non-cardiac surgery hospitalized on an unmonitored general care floor and wearing a multi-signal wearable sensor, allowing remote monitoring (Biobeat Technologies Ltd, Petah Tikva, Israel). The study will cover the first 72 hours after discharge of the patient from the post-anaesthesia care unit. Several thresholds will be used for each variable (arterial pressure, heart rate, respiratory rate, oxygen saturation, and skin temperature). Data obtained using the sensor will be compared to data obtained during the routine nurse follow-up. The primary outcome is hemodynamic abnormality. The secondary outcomes are postoperative respiratory and temperature abnormalities, artefacts and blank/null outputs from the wearable device, postoperative complications, and finally, the ease of use of the device. We hypothesize that remote monitoring will detect abnormalities in vital signs more often or more quickly than the detection by nurses’ routine surveillance. Discussion: A demonstration of the ability of wireless sensors to outperform standard monitoring techniques paves the way for the creation of a loop which includes this monitoring mode, the automated creation of alerts, and the sending of these alerts to caregivers. Trial registration: ClinicalTrials.gov, NCT04585178. Registered on October 14, 2020
Improvement of Cardiac Fibrosis Biomarkers through Inflammation Inhibition by Green Tea and Decaffeinated Light Roasted Green Coffee Extract Combination Administration in Metabolic Syndrome Rat Model
Authors: Lukitasari Mifetika , Rohman Mohammad Saifur , Nugroho Dwi Adi , Wahyuni Nila Aisyah , Nur Kholis Mukhamad , Widodo Nashi 
Published: October 2021

Background: Metabolic syndrome is a significant risk factor for cardiovascular diseases. Green tea and green coffee extracts, antioxidant and anti-inflammatory agents may participate in metabolic syndrome-induced cardiac fibrosis alleviation. However, the effect of combination of those extracts still needs exploration. Therefore, this study investigated the effect of green tea and decaffeinated light roasted green coffee extracts and their combination in metabolic syndrome-induced cardiac fibrosis rats. Methods: Metabolic syndrome rat model was i1nduced through high-fat high sucrose diets feeding for 8 weeks and injection of low dose streptozotocin at the 2nd week. The metabolic syndrome rats were divided into 4 experimental groups metabolic syndrome rats (MS); metabolic syndrome rats treated with 300 mg/ kg b.w green tea extract (GT); metabolic syndrome rats treated with 200 mg/ kg b.w decaffeinated light roasted green coffee extract (GC); metabolic syndrome rats treated with the combination of the two extracts (CE); and a normal control (NC) group was added. Angiotensin 2 level was analyzed by ELISA method. Gene expression of NF-κB, TNF-α, IL-6, Tgf-β1, Rac-1, and α-sma were analyzed by touchdown polymerase chain reaction methods. Results: Metabolic syndrome rats treated with green tea and decaffeinated light roasted green coffee significantly decreased angiotensin-2 serum level and cardiac inflammation and fibrosis gene expression level (NF-κB, TNF-α, IL-6, Tgf-β1, Rac-1, and α-sma). More significant alleviation was observed in the combination group. Conclusion: This study suggested that combination of green tea and decaffeinated light roasted green coffee extracts showed better improvement in metabolic syndrome-induced cardiac fibrosis rat model compared to that of single extract administration through inflammation inhibition