bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paper review: An overview on microarray technologies
Authors: Fajriyah Rohmatul 
Published: April 2021

Bioinformatics is a branch in Statistics which is still unpopular among statistics students in Indonesia. Bioinformatics research used microarray technology, because data is available through to microarray experiment on tissue sample at hand. Microarray technology has been widely used to provide data for bioinformatics research, since it was first introduced in late 1990, particularly in life sciences and biotechnology research. The emergence and development of the Covid-19 disease further reinforces the need to understand bioinformatics and its technology. There are two of the most advance platforms in microarray technology, namely, are the Affymetrix GeneChip and Illumina BeadArray. This paper aims to give an overview about microarray technology on the two platforms and the advantage of using them on bioinformatics research.
Lower extremity arterial interventions in England
Authors: Staniszewska A , Gimzewska M , Onida S , Lane T , Davies AH 
Published: April 2021

Introduction The increasing prevalence of diabetes mellitus and advances in endovascular therapies continue to have an impact on the epidemiology and management of lower extremity arterial disease. This study describes trends in lower extremity revascularisation and major lower limb amputation in NHS England over the past two decades (2000–2019). Methods Numbers of lower extremity endovascular interventions, open surgical procedures and major lower limb amputations performed in NHS England between 2000 and 2019 were extracted from publicly available hospital admitted patient care activity reports. Trends in intervention were assessed with linear regression models and chi-square tests for trend. Results Over this period, 527,131 revascularisations and 92,053 amputations were performed. The mean age of patients was 67.5 years (standard deviation 1.6 years) and 65.3% were male. The number of lower limb revascularisation procedures increased by 402.4 units/year (95% confidence interval, CI, 290.1–514.6, p < 0.001). The number of endovascular interventions rose by 43.5% (10,912 in 2000 vs 15,657 in 2019; β = 359.5.0, 95% CI 279.3–439.8, p < 0.001) compared with no significant increase in the number of open surgical procedures (8,483 in 2000 vs 7,872 in 2019; β = 42.8, 95% CI −8.3 to 94.0, p = 0.095). The number of major lower limb amputations has decreased by 9.4% (5,418 in 2000 vs 4,907 in 2019; β = −31.0; 95% CI −49.6 to −12.5, R2 = 0.42, p = 0.003). Conclusions There has been a significant increase in the rate of lower limb revascularisation procedures associated with decreased numbers of major lower limb amputations over the past two decades. These changes in overall trends may affect both service provision and vascular surgery training planning.
Waterlow score for risk assessment in surgical patients: a systematic review
Authors: Nayar SK , Li D , Ijaiya B , Barakat A , Lloyd D , Bharathan R 
Published: April 2021

Introduction The Waterlow score (WS) is used routinely in clinical practice to assess risk of pressure sore development. Recent studies have also suggested its use in preoperative risk stratification. The primary aim of this systematic review was to evaluate the current evidence on the WS in predicting morbidity and mortality in surgical patients. Methods A systematic review was carried out in accordance with PRISMA and SWiM guidelines. A search strategy was conducted on the MEDLINE and EMBASE databases. Quality was assessed using the Newcastle–Ottawa scale. Findings Overall, 72 papers were identified, of which 7 met inclusion criteria for full text review, and 4 were included for analysis. All studies were cohort in nature and published between 2013 and 2016, encompassing a total of 505 surgical patients. The studies included general, vascular, transplant and orthopaedic surgery. A high WS was demonstrated to have statistically significant association with increased morbidity and mortality as well as need for intensive care unit admission and length of stay. Furthermore, this was a more accurate predictor compared with the P-POSSUM and ASA scoring systems used currently in routine practice. Conclusions The WS is a promising tool for risk stratification of surgical patients. It is already collected routinely by nursing staff throughout hospitals in the UK and would therefore be easy to implement. However, further large prospective studies are required in order to validate these findings prior to its establishment for this role in everyday surgical practice.
The safety and efficacy of day-case total joint arthroplasty
Authors: Dey S , Gadde R , Sobti A , Macdonald N , Jacob J , Unnithan A 
Published: April 2021

Introduction The popularity of day-case arthroplasty has been fuelled by focus on its cost effectiveness for the healthcare system. Safety concerns still remain. The aim of this review was to compare readmission rates after total joint arthroplasty for patients undergoing day-case surgery and for inpatients. Methods A comprehensive online search of databases was performed for all published articles in the English language evaluating readmission rates after total hip arthroplasty (THA) and total knee arthroplasty (TKA). Seventeen studies were deemed eligible and included in the meta-analysis. Results All studies included in the meta-analysis described readmission rates following THA/TKA. The readmission rate for day-case patients was 1.9% (n=124) whereas for inpatients, it was 2.0% (n=12,399). Compared with inpatient arthroplasty, day-case arthroplasty was associated with lower total readmission rates (odds ratio [OR]: 0.77, 95% confidence interval [CI]: 0.63–0.94, p=0.01). Furthermore, day-case surgery conferred a decrease in readmission rates for both THA (1.3% vs 7.0%) and TKA (2.7% vs 4.3%). Moreover, day-case THA and TKA were both associated with a decreased chance of readmission (OR: 0.27, 95% CI: 0.17–0.42, p<0.00001; and OR: 0.55, 95% CI: 0.42–0.72, p<0.00001 respectively). Conclusions This review emphasises that with a thoughtful, designated protocol and with careful patient selection, day-case arthroplasty is a safe and effective option.
Ultrashort pulse written fiber Bragg gratings as narrowband filters in multicore fibers
Authors: Goebel T. A. , Nold J. , Hupel C. , Kuhn S. , Haarlammert N. , Schreiber T. , Matzdorf C. , Imogore T. O. , Krämer R. G. , Richter D. , Tünnermann A. , Nolte S. 
Published: April 2021

We present the inscription of narrow-linewidth fiber Bragg gratings (FBGs) into different types of multicore fibers (MCFs) using ultrashort laser pulses and the phase mask technique, which can act as notch filters. Such filters are required, e.g., to suppress light emitted by hydroxyl in the Earth’s upper atmosphere, which disturbs ground-based observation of extraterrestrial objects in the near infrared. However, the inscription into a commercially available seven-core fiber showed a quite large core-to-core deviation of the resonance wavelength of up to 0.45 nm. Two options are presented to overcome this: first, we present the photo-treatment of the FBGs to tune the resonance wavelength, which allows for sufficient resonance shifts. Second, adapted MCFs containing 12 cores, arranged on a circle, are fabricated. For this, two different fabrication procedures were investigated, namely, the mechanical drilling of the preform for a rod-in-tube version as well as a stack-and-draw approach. Both adapted MCFs yielded significant improvements with core-to-core wavelength variations of the FBGs of only about 0.18 nm and 0.11 nm, respectively, sufficient to fulfill the requirements for astronomical filter applications as discussed above.
CMOS-foundry-based blue and violet photonics
Authors: Morin Theodore J. , Chang Lin , Jin Warren , Li Chenlei , Guo Joel , Park Hyundai , Tran Minh A. , Komljenovic Tin , Bowers John E. 
Published: April 2021

We demonstrate a CMOS-foundry-based

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Polyester nasal swabs collected in a dry tube are a robust and inexpensive, minimal self-collection kit for SARS-CoV-2 testing
Authors: Padgett Leah R. , Kennington Lauren A. , Ahls Charlotte L. , Samarasinghe Delini K. , Tu Yuan-Po , Wallander Michelle L. , Cooper Shawna D. , Elliott James S. , Rains Douglas 
Published: April 2021

Background
In order to identify an inexpensive yet highly stable SARS-CoV-2 collection device as an alternative to foam swabs stored in transport media, both contrived (“surrogate”) CoV-positive and patient-collected spun polyester swabs stored in dry tubes were evaluated for time- and temperature-stability using qPCR.

Methods
Surrogate specimens were prepared by combining multiple, residual SARS-CoV-2-positive clinical specimens and diluting to near-LOD levels in either porcine or human mucus (“matrix”), inoculating foam or polyester nasal swabs, and sealing in dry tubes. Swabs were then subjected to one of three temperature excursions: (1) 4°C for up to 72 hours; (2) 40°C for 12 hours, followed by 32°C for up to 60 hours; or (3) multiple freeze-thaw cycles (-20°C). The stability of extracted SARS-CoV-2 RNA for each condition was evaluated by qPCR. Separate usability studies for the dry polyester swab-based HealthPulse@home COVID-19 Specimen Collection Kit were later conducted in both adult and pediatric populations.

Results
Polyester swabs stored dry demonstrated equivalent performance to foam swabs for detection of low and moderate SARS-CoV-2 viral loads. Mimicking warm- and cold- climate shipment, surrogate specimens were stable following either 72 hours of a high-temperature excursion or two freeze-thaw cycles. In addition, usability studies comprised of self-collected patient specimens yielded sufficient material for molecular testing, as demonstrated by RNase P detection.

Conclusions
Polyester nasal swabs stored in dry collection tubes offer a robust and inexpensive self-collection method for SARS-CoV-2 viral load testing, as viral RNA remains stable under conditions required for home collection and shipment to the laboratory.
Firearms and violence in Europe–A systematic review
Authors: Krüsselmann Katharina , Aarten Pauline , Liem Marieke 
Published: April 2021

Background
Higher availability of firearms has been connected to higher rates of interpersonal violence in previous studies. Yet, those studies have focused mainly on the United States, or used aggregated international data to study firearm violence. Whether those aggregated findings are applicable to understanding the phenomenon in continental Europe specifically remains unclear. The aim of this systematic review is to bring together all studies that exclusively use European data.

Methods
Nine databases were searched, resulting in more than 1900 individual studies. These studies were assessed on relevance and eligibility for this study, based on their title, abstract and full text. Information on study characteristics, operationalizations of main concepts and study results were extracted from the six eligible studies.

Results
Four studies assessed the impact of firearm restrictive regulations on the rate of firearm homicides. Two other studies correlated rates of firearm availability and -violence. Results vary: some studies show a clear decline once availability of firearms is restricted, while others indicate a limited effect on only a very specific subgroup, such as female victims, or national guards with weapons at home. Moreover, studies used various operationalizations for firearm availability, thereby decreasing the comparability of findings.

Conclusion
Empirical research exclusively using European data is still lacking. To increase comparability of future studies, methodological inconsistencies and regional gaps need to be overcome. Assessing how firearm availability can be measured with reliable and valid proxies across countries will be a crucial first step to improve future research on the link between firearms and firearm violence.
Mapping expanded prostate cancer index composite to EQ5D utilities to inform economic evaluations in prostate cancer: Secondary analysis of NRG/RTOG 0415
Authors: Khairnar Rahul , Pugh Stephanie L. , Sandler Howard M. , Lee W. Robert , Villalonga Olives Ester , Mullins C. Daniel , Palumbo Francis B. , Bruner Deborah W. , Shaya Fadia T. , Bentzen Soren M. , Shah Amit B. , Malone Shawn C. , Michalski Jeff M. , Dayes Ian S. , Seaward Samantha A. , Albert Michele , Currey Adam D. , Pisansky Thomas M. , Chen Yuhchyau , Horwitz Eric M. , DeNittis Albert S. , Feng Felix Y. , Mishra Mark V. 
Published: April 2021

Purpose
The Expanded Prostate Cancer Index Composite (EPIC) is the most commonly used patient reported outcome (PRO) tool in prostate cancer (PC) clinical trials, but health utilities associated with the different health states assessed with this tool are unknown, limiting our ability to perform cost-utility analyses. This study aimed to map EPIC tool to EuroQoL-5D-3L (EQ5D) to generate EQ5D health utilities.

Methods and materials
This is a secondary analysis of a prospective, randomized non-inferiority clinical trial, conducted between 04/2006 and 12/2009 at cancer centers across the United States, Canada, and Switzerland. Eligible patients included men >18 years with a known diagnosis of low-risk PC. Patient HRQoL data were collected using EPIC and health utilities were obtained using EQ5D. Data were divided into an estimation sample (n = 765, 70%) and a validation sample (n = 327, 30%). The mapping algorithms that capture the relationship between the instruments were estimated using ordinary least squares (OLS), Tobit, and two-part models. Five-fold cross-validation (in-sample) was used to compare the predictive performance of the estimated models. Final models were selected based on root mean square error (RMSE).

Results
A total of 565 patients in the estimation sample had complete information on both EPIC and EQ5D questionnaires at baseline. Mean observed EQ5D utility was 0.90±0.13 (range: 0.28–1) with 55% of patients in full health. OLS models outperformed their counterpart Tobit and two-part models for all pre-determined model specifications. The best model fit was: “EQ5D utility = 0.248541 + 0.000748*(Urinary Function) + 0.001134*(Urinary Bother) + 0.000968*(Hormonal Function) + 0.004404*(Hormonal Bother)– 0.376487*(Zubrod) + 0.003562*(Urinary Function*Zubrod)”; RMSE was 0.10462.

Conclusions
This is the first study to identify a comprehensive set of mapping algorithms to generate EQ5D utilities from EPIC domain/ sub-domain scores. The study results will help estimate quality-adjusted life-years in PC economic evaluations.
Pressure gradient measurement to verify hemodynamic results of the chimney endovascular aortic repair (chEVAR) technique
Authors: Milnerowicz Artur Igor , Milnerowicz Aleksandra , Bańkowski Tomasz , Protasiewicz Marcin 
Published: April 2021

Purpose
The use of the pressure gradient measurements to assess the renal artery flow hemodynamics after chimney endovascular aortic repair (chEVAR).

Methods
The study was a prospective analysis of 37 chEVAR procedures performend in 24 patients with perirenal aortic aneurysm. In all patients the measurement of: distal renal artery pressure (Pd), aortic pressure (Pa), Pd/Pa ratio (Pd/Pa) and mean gradient (MG) between the aorta and the distal renal artery were performed. Measurements were taken with 0.014 inch pressure wire catheter before and after the chEVAR procedure. MG greater than 9 mmHg and Pd/Pa ratio below 0.90 were considered as the measures of a significant decrease in distal pressure that limited flow in renal arteries. The 6 month follow-up computed tomographic angiography (CTA) was performed in all patients to diagnose potential endoleak presence and to verify the patency of the chimney stent-grafts.

Results
All procedures were successful, and no periprocedural complications were observed in any of the patients. The mean gradient values before and after the chimney implantation did not change significantly (6,2±2,0 mmHg and 6,8±2,2 mmHg, respectively). Similarly, no significant change in Pd/Pa values was noted with the value of 0.9 observed both before and after the procedure. All chimney stents were patent on the control CTA. Type Ia endoleak was found in 4 (10.8%) patients.

Conclusions
The application of the described technique seems to be a safe method which allows a direct measurement of renal artery flow hemodynamics before and after chimney implantation during the chEVAR technique. The use of covered balloon expandable stents, ensures the proper blood flow in the renal arteries during the chEVAR technique.
Factors associated with unfavorable treatment outcomes in patients with rifampicin-resistant tuberculosis in Colombia 2013–2015: A retrospective cohort study
Authors: Chaves-Torres Ninfa Marlen , Fadul Santiago , Patiño Jesus , Netto Eduardo 
Published: April 2021

Background
Multidrug- and rifampicin (RMP)-resistant tuberculosis (MDR/RR-TB) requires prolonged and expensive treatment, which is difficult to sustain in the Colombian health system. This requires the joint action of different providers to provide timely health services to people with TB. Identifying factors associated with unfavorable treatment outcomes in patients with MDR/RR-TB who received drug therapy between 2013 and 2015 in Colombia can help guide the strengthening of the national TB control program.

Method
A retrospective cohort study was conducted with all patients who received treatment for MDR/RR-TB between January 2013 and December 2015 in Colombia who were registered and followed up by the national TB control program. A multivariate logistic regression model was used to estimate the associations between the exposure variables with the response variable (treatment outcome).

Results
A total of 511 patients with MDR/RR-TB were registered and followed up by the national TB control program in Colombia, of whom 16 (3.1%) had extensive drug resistance, 364 (71.2%) had multidrug resistance, and 131 (25.6%) had RMP monoresistance. The mean age was 39.9 years (95% confidence interval (CI): 38.5–41.3), most patients were male 285 (64.6%), and 299 (67.8%) were eligible for subsidized health services. The rate of unfavorable treatment outcomes in the RR-TB cohort was 50.1%, with rates of 85.7% for patients with extensive drug resistance, 47.6% for patients with multidrug resistance, and 52.6% for patients with RMP monoresistance. The 511 MDR/RR-TB patients were included in bivariate and multivariate analyses, patients age ≥ 60 years (crude odds ratio (ORc) = 2.4, 95% CI 1.1–5.8; adjusted odds ratio (ORa) = 2.7, 95% CI 1.1–6.8) and subsidized health regime affiliation (ORc = 3.6, 95% CI 2.3–5.6; ORa = 3.4, 95% CI 2.0–6.0) were associated with unfavorable treatment outcomes.

Conclusion
More than 50% of the patients with MDR/RR-TB in Colombia experienced unfavorable treatment outcomes. The patients who were eligible for subsidized care were more likely to experience unfavorable treatment outcomes. Those who were older than 60 years were also more likely to experience unfavorable treatment outcomes.
Recent HIV infection among pregnant women in the 2017 antenatal sentinel cross–sectional survey, South Africa: Assay–based incidence measurement
Authors: Woldesenbet Selamawit , Kufa-Chakezha Tendesayi , Lombard Carl , Manda Samuel , Cheyip Mireille , Ayalew Kassahun , Chirombo Brian , Barron Peter , Diallo Karidia , Parekh Bharat , Puren Adrian 
Published: April 2021

Introduction
New HIV infection during pre-conception and pregnancy is a significant contributor of mother–to–child transmission of HIV in South Africa. This study estimated HIV incidence (defined as new infection within the last one year from the time of the survey which included both new infections occurred during pregnancy or just before pregnancy) among pregnant women and described the characteristics of recently infected pregnant women at national level.

Methods
Between 1 October and 15 November 2017, we conducted a national cross–sectional survey among pregnant women aged 15–49 years old attending antenatal care at 1,595 public facilities. Blood specimens were collected from pregnant women and tested for HIV in a centralised laboratory. Plasma viral load and Limiting Antigen Avidity Enzyme Immunosorbent Assay (LAg) tests were further performed on HIV positive specimens to differentiate between recent and long–term infections. Recent infection was defined as infection that occurred within one year from the date of collection of blood specimen for the survey. Data on age, age of partner, and marital status were collected through interviews. Women whose specimens were classified as recent by LAg assay and with viral loads >1,000 copies/mL were considered as recently infected. The calculated proportion of HIV positive women with recent infection was adjusted for assay–specific parameters to estimate annual incidence. Survey multinomial logistic regression was used to examine factors associated with being recently infected using HIV negative women as a reference group. Age–disparate relationship was defined as having a partner 5 or more years older.

Results
Of 10,049 HIV positive participants with LAg and viral load data, 1.4% (136) were identified as recently infected. The annual HIV incidence was 1.5% (95% confidence interval (CI): 1.2–1.7). In multivariable analyses, being single (adjusted odds ratio, aOR: 3.4, 95% CI: 1.8–6.2) or cohabiting (aOR: 3.8, 95% CI: 1.8–7.7), compared to being married as well as being in an age–disparate relationship among young women (aOR: 3.1, 95% CI: 2.0–4.7; reference group: young women (15–24years) whose partners were not 5 years or more older) were associated with higher odds of recent infection.

Conclusions
Compared to previous studies among pregnant women, the incidence estimated in this study was substantially lower. However, the UNAIDS target to reduce incidence by 75% by 2020 (which is equivalent to reducing incidence to <1%) has not been met. The implementation of HIV prevention and treatment interventions should be intensified, targeting young women engaged in age–disparate relationship and unmarried women to fast track progress towards the UNAIDS target.