bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sparse least trimmed squares regression with compositional covariates for high-dimensional data
Authors: Monti Gianna Serafina , Filzmoser Peter 
Published: August 2021

AbstractMotivationHigh-throughput sequencing technologies generate a huge amount of data, permitting the quantification of microbiome compositions. The obtained data are essentially sparse compositional data vectors, namely vectors of bacterial gene proportions which compose the microbiome. Subsequently, the need for statistical and computational methods that consider the special nature of microbiome data has increased. A critical aspect in microbiome research is to identify microbes associated with a clinical outcome. Another crucial aspect with high-dimensional data is the detection of outlying observations, whose presence affects seriously the prediction accuracy.ResultsIn this article, we connect robustness and sparsity in the context of variable selection in regression with compositional covariates with a continuous response. The compositional character of the covariates is taken into account by a linear log-contrast model, and elastic-net regularization achieves sparsity in the regression coefficient estimates. Robustness is obtained by performing trimming in the objective function of the estimator. A reweighting step increases the efficiency of the estimator, and it also allows for diagnostics in terms of outlier identification. The numerical performance of the proposed method is evaluated via simulation studies, and its usefulness is illustrated by an application to a microbiome study with the aim to predict caffeine intake based on the human gut microbiome composition.Availability and implementationThe R-package ‘RobZS’ can be downloaded at https://github.com/giannamonti/RobZS.Supplementary informationSupplementary data are available at Bioinformatics online.
Prognostic implications of histological organ involvement in retroperitoneal sarcoma
Authors: Tyler R , Lee M , Ierodiakonou V , Hodson J , Taniere P , Almond M , Ford S , Desai A 
Published: August 2021

Abstract

Background
The prognostic significance of histological organ involvement by retroperitoneal sarcoma subtype is unknown. The present study aimed to describe organ involvement across the subtypes, and the implications for survival.

Methods
Patients undergoing surgery for primary retroperitoneal sarcoma at the Queen Elizabeth Hospital, Birmingham from April 2005 to September 2018 were identified retrospectively. Histological organ involvement was classed as pushing, infiltrative or neither. Univariable and multivariable Cox regression models were produced to analyse the association between histological organ involvement and both overall (OS) and recurrence-free (RFS) survival for the cohort as a whole, and by histological subtype.

Results
Data were available for a total of 197 patients, of whom 171 (86.8 per cent) had at least one organ resected. Infiltrative organ behaviour was seen in 37 patients (18.8 per cent), and pushing behaviour in 67 (34.0 per cent). For the cohort as a whole, infiltration (hazard ratio (HR) 4.32, 95 per cent c.i. 2.35 to 7.93; P &lt; 0.001), but not pushing (HR 1.62, 0.90 to 2.92; P = 0.106), was associated with significantly shorter OS, in comparisons with a group with neither of these behaviours. However, this effect was found to differ significantly by histological subtype (P = 0.009). For patients with dedifferentiated liposarcoma, there was no significant association between tumour behaviour and either OS (P = 0.508) or RFS (P = 0.313). However, in leiomyosarcoma, infiltrative behaviour was associated with shorter OS (P = 0.002), and both infiltrative (P &lt; 0.001) and pushing (P = 0.010) behaviours were associated with shorter RFS, compared with tumours with neither behaviour. Multivariable analyses of both OS and RFS returned similar results.

Conclusion
The prognostic implications of organ involvement in retroperitoneal sarcoma vary by histological subtype.
Is radiomic MRI a feasible alternative to OncotypeDX® recurrence score testing? A systematic review and meta-analysis
Authors: Davey M G , Davey M S , Ryan É J , Boland M R , McAnena P F , Lowery A J , Kerin M J 
Published: August 2021

Abstract

Background
OncotypeDX® recurrence score (RS) aids therapeutic decision-making in oestrogen-receptor-positive (ER+) breast cancer. Radiomics is an evolving field that aims to examine the relationship between radiological features and the underlying genomic landscape of disease processes. The aim of this study was to perform a systematic review of current evidence evaluating the comparability of radiomics and RS.

Methods
A systematic review was performed as per PRISMA guidelines. Studies comparing radiomic MRI tumour analyses and RS were identified. Sensitivity, specificity and area under curve (AUC) delineating low risk (RS less than 18) versus intermediate–high risk (equal to or greater than 18) and low–intermediate risk (RS less than 30) and high risk (RS greater than 30) were recorded. Log rate ratios (lnRR) and standard error were determined from AUC and 95 per cent confidence intervals.

Results
Nine studies including 1216 patients met inclusion criteria; the mean age at diagnosis was 52.9 years. Mean RS was 16 (range 0–75); 401 patients with RS less than 18, 287 patients with RS 18–30 and 100 patients with RS greater than 30. Radiomic analysis and RS were comparable for differentiating RS less than 18 versus RS 18 or greater (RR 0.93 (95 per cent c.i. 0.85 to 1.01); P = 0.010, heterogeneity (I2)=0%) as well as RS less than 30 versus RS 30 or greater (RR 0.76 (95 per cent c.i. 0.70 to 0.83); P &lt; 0.001, I2=0%). MRI sensitivity and specificity for RS less than 18 versus 18 or greater was 0.89 (95 per cent c.i. 0.85 to 0.93) and 0.72 (95 per cent c.i. 0.66 to 0.78) respectively, and 0.79 (95 per cent c.i. 0.72 to 0.86) and 0.74 (95 per cent c.i. 0.68 to 0.80) for RS less than 30 versus 30 or greater.

Conclusion
Radiomic tumour analysis is comparable to RS in differentiating patients into clinically relevant subgroups. For patients requiring MRI, radiomics may complement and enhance RS for prognostication and therapeutic decision making in ER+ breast cancer.
The frozen elephant trunk technique: impact of proximalization and the four-sites perfusion technique
Authors: Tsagakis Konstantinos , Osswald Anja , Weymann Alexander , Demircioglu Aydin , Schmack Bastian , Wendt Daniel , Jakob Heinz , Ruhparwar Arjang 
Published: August 2021

Abstract

OBJECTIVES
To improve organ protection with the frozen elephant trunk (FET) procedure, a so-called four-sites perfusion in combination with proximalization for the distal aortic anastomosis was performed. The impact of these techniques on patient outcome is reported.

METHODS
Between February 2005 and April 2020, a total of 357 patients underwent the FET procedure for acute (54%) or chronic (22%) aortic dissection or aneurysmal disease (24%). The level of the distal FET anastomosis was defined according to aortic arch zones 0–3. Patients were divided into 3 groups according to the intraoperative perfusion strategy: (i) selective antegrade cerebral perfusion (SACP) alone (N = 96, 2 sites); (ii) SACP plus left subclavian artery or distal aorta (N = 84, 3 sites) and (iii) SACP plus left subclavian artery plus distal aorta (N = 177, 4 sites). Early outcome was addressed by a composite end point: occurrence of either a disabling stroke, a disabling spinal cord injury, extracorporeal circulatory support, kidney dialysis or death within 90 days.

RESULTS
Preoperative characteristics were similar among the groups. Surgery in group C was characterized by FET proximalization in arch zone ≤2, moderate hypothermia at 28°C and shorter periods of extracorporeal circulation, SACP, hypothermic circulatory arrest and cardioplegic arrest (P &lt; 0.001, respectively). Occurrence of the composite end point was reduced in group C (P = 0.008). The combination of FET proximalization and four-sites perfusion was a protective factor for the composite outcome in multivariable analysis (P = 0.009). The 5-year survival was improved in patients who underwent FET proximalization in zone ≤2 (hazard ratio 0.7, 95% confidence interval 0.4–1.0; P = 0.036).

CONCLUSIONS
FET proximalization in combination with four-sites perfusion has the potential to improve patient outcomes in terms of survival and major events.

Subject collection
120; 161.
The robotic surgery learning curve of a surgeon experienced in video-assisted thoracoscopic surgery compared with his own video-assisted thoracoscopic surgery learning curve for anatomical lung resections
Authors: Gómez-Hernández María Teresa , Fuentes Marta G , Novoa Nuria M , Rodríguez Israel , Varela Gonzalo , Jiménez Marcelo F 
Published: August 2021

Abstract

OBJECTIVES
Robotic surgery, although it shares some technical features with video-assisted thoracoscopic surgery (VATS), offers some advantages, such as ergonomic design and a 3-dimensional view. Thus, the learning curve for robotic lung resection could be expected to be shorter than that of VATS for surgeons who are proficient in VATS. The goal of this study was to analyse the robotic learning curve of a VATS experienced surgeon and to compare it to his own VATS learning curve for anatomical lung resections.

METHODS
We conducted a retrospective observational study based on the prospectively recorded data of the first 150 anatomical lung resections performed with VATS (75 cases) and with the robotic (75 cases) approach by the same surgeon in our centre. Learning curves were analysed using the cumulative sum method to assess the trends for total operating time and surgical failure (intraoperative complications, conversion, technical postoperative complications and reintervention) across case sequences. Subsequently, using adequate statistical tests, we compared the postoperative outcomes in both groups.

RESULTS
The median operating time was similar for both approaches (P = 0.401). Surgical failure rate was higher for the robotic cases (21.3% vs 12%; P = 0.125). Based on cumulative sum analyses, operating time decreased starting with case 34 in the VATS group and with case 32 in the robotic cohort. Surgical failure tended to decline starting with case 28 in the VATS group and with case 32 in the robotic group. Perioperative results were similar in both groups.

CONCLUSIONS
When we compared robotic and VATS learning curves for anatomical lung resection, we did not find any differences. Postoperative outcomes were also similar with both approaches.
The hobby course: towards a languaging curriculum
Authors: Watson Todd Richard , Rangsarittikun Ronnakrit 
Published: August 2021

Abstract
The English as a lingua franca (ELF) and languaging research areas have challenged the norm that the goal of ELT is to teach a standardized language. This article reports on a course following the principles of ELF and languaging where the goal is to support students to use and grow their existing repertoire of resources to do things in English. The course was taught at a Thai university and was organized around each student learning a hobby of their choice. Focusing on strategies for using language, the course provided support for students to learn about their hobby, to interact with others through social media, and to create videos. Students’ reflections on their learning show substantial developments in their ability to do things in English and preliminary changes in attitude. The shift from teaching linguistic features to exploring strategies for exploiting existing learning resources provides a new paradigm in ELT.
Stability study of metronidazole cream, extemporaneously made in pharmacy
Authors: Dambrauskas Andrius 
Published: August 2021

Abstract

Background
Rosacea is a chronic recurrent disease, characterized by facial redness, dilated blood vessels, inflammatory rash elements on the face. The pharmacy produces 2% metronidazole cream extemporaneously for the treatment of the disease, as there is no such cream concentration on the market. The treatment of the disease is usually long, so the shelf life of the cream is very important for the patient, especially for those who do not have the opportunity to reach the manufacturing pharmacy. The aim of this investigation was to determine the stability and shelf life of metronidazole cream.

Methods
Long-term stability study of metronidazole cream was applied at 25 ± 2° C, 60 ± 5% relative humidity; accelerated stability test at 40 ± 2 °C, 75 ± 5% relative humidity. The influence of stress conditions were evaluated on the stability of metronidazole cream. It was determined metronidazole cream texture and microbiological examination was applied.

Results
It was found that color (white), odor (odorless), integrity (homogeneous), pH (6.8) did not change during storage of metronidazole (6 months). Mechanical properties of the metronidazole cream: firmness, shear, consistency and cohesion throughout the study remained stable. High performance liquid chromatography in the full stability study showed that metronidazole concentrations did not fluctuate within ± 5%. Stress factors such as acid media, alkaline media, hydrogen peroxide, daylight and heat did not affect the stability of the cream. A microbiological examination of the metronidazole cream suited European Pharmacopoeia requirements.

Conclusions
The extemporaneously made metronidazole cream were stable for 6 months.
SARS-CoV-2 laboratory diagnostic methods: a systematic review
Authors: Nunes Rúben , Melo Carolina , Martins Diana , Mendes Fernando 
Published: August 2021

Abstract

Background
The new SARS-CoV-2 is a single-stranded RNA β-coronavirus, and it is comprising by structural proteins (N), (S), (E) and (M). Timely and accurate detection is necessary for spread control of SARS-CoV-2 infection, avoiding inaccurate outcomes. Therefore, in this systematic review, it is purpose to evaluate a set of laboratory diagnostic techniques and methods, analyse their specificity, sensitivity, contributing to improve detection rates and reduce false negative and false positive diagnostic results.

Methods
In this review, we used literature available on the indexed search database ‘PubMed’, concerning the following keywords: ‘SARS-CoV-2’, ‘Specimen handling’, ‘Cell Culture Technique’, ‘Viral Antigen’, ‘Immunoassay’, ‘NAAT’ according to Medical Subject Headings Mesh and applying the Prisma Diagram methodology.

Results
DD-PCR and CRISPER had more promising results, but they are unconventional and expensive NAAT methods, the usage of the target RdRp/He gene has exhibited very encouraging results improving sensitivity and specificity. After the onset of symptoms, the sensitivity of the immunoassay varies considering of blood collection day. The antigen detection test showed the highest specificity reached, however is sensitivity is lower compared to NAAT assays.

Conclusions
In summary, RT-PCR still considered the gold standard and precisely detects the presence of virus RNA, although with some flaws in sensitivity, while the serological tests identify a previous infection by the virus, detecting antibodies, allowing the kinetic and immunological studies, not being able to use as a diagnostic method. The molecular point of care testing equipment’s revelled be the future in the rapid and accurately diagnosis of SARS-CoV-2.
Distress and coping in third year, 2020–2201 Portuguese medicine students
Authors: Santiago Luiz Miguel , Pinto Joana Catarina 
Published: August 2021

Abstract

Background
Medical students are often exposed to stressors, studies showing that one third of them suffers from depression, a larger figure then the general population and more vulnerable to stress comparing to other courses’ students. The use of coping strategies when medical students are in distress must be studied and then discussed with students.

Methods
Prospective cohort analytical study with two points in time evaluation, in a quasi-random sample, representative of the 3rd year students in the 2020/2021 school year. An epidemiological survey, Patient Health Questionnaire–4 (PHQ-4) and BRIEF-COPE were applied. In between evaluations results were presented two discussions and motivational interventions being made.

Results
In samples of n = 101 3rd year students in September, and n = 112 students in November students’ distress by PHQ-4 (P &lt; 0.001), was worst in November and ‘Expression of feelings’ (P = 0.004) was more used in November in Brief-Cope questionnaire use. Increased use of coping strategies ‘Expression of feelings’ (P = 0.004) and ‘Planning’ (P = 0.045) and a decrease of ‘Substances abuse’ (P = 0.020) were found from September to November. A significant distress increase was verified in such period of time (P &lt; 0.001). In November significant weak positive correlation, between the level of distress and the items in BRIEF-COPE, for the strategies ‘Use emotional support’, ‘Positive reinterpretation’, ‘Acceptance’, ‘Self-distraction’ and ‘Substance use’ and a significant negative correlation in the items ‘Plan’, ‘Self-blame’, ‘Behavioural divestment’ and ‘Humour’ were found.

Conclusions
A noteworthy rise in distress was found. Students significantly altered some coping tactics even though distress increased. These findings are troublesome and deserve further studies and attention.
Cross cultural adaptation and validation of the ‘9-item patient health questionaire’
Authors: Pacheco Elisabete , Santiago Luiz Miguel 
Published: August 2021

Abstract

Background
Quality of life must be studied as a determinant of health. Depressive state must be measured with culturally adapted and population-validated instruments specially in times of COVID19 pandemics in undergraduate health students to avoid future health damages. The European Quality of Life 5 Dimensions (EQ5-D-3L) is validated but the ‘9-Item Patient Health Questionaire’ (PHQ-9) still needed validation for university population, which this study intended to do.

Methods
With original authors authorization and after cross-cultural adaptation, a cross sectional, observational study, applying the PHQ-9 and EQ-5D-3L to Faculty of Medicine and Faculty Pharmacy of the University of Coimbra (FMUC and FFUC) students, along with an epidemiological survey in a convenience sample using student’s social networks in november 2020. Descriptive, inferential and correlational statistics were performed.

Results
A size representative sample of 126 participants was studied, of which 72 from FMUC (57.1%) and 54 from FFUC (42.9%). For PHQ-9 (reliability cronbach’s alfa of 0.815, and F test = 38 786, P &lt; 0.001) were found and global score FFUC students and females was higher, P = 0.014 and P = 0.034, respectively. Females also scored worse for item 5 of EQ5D, P &lt; 0.001. PHQ9 and EQ5D correlation of ρ = -0.588, P &lt; 0.001 and PHQ9 and question 5 of EQ5D-3L with PHQ9 of ρ = +0.484, P &lt; 0.001 were found.

Conclusions
The cultural adaptation and validation of the ‘9-Item Patient Health Questionaire’ (PHQ9) with the European Quality of Life 5 Dimensions (EQ5D-3L) scale, in FMUC and FFUC students population, verified that the PHQ-9 allows to adequately assess the existence of depressive symptoms and that male individuals were in better mental health.
Colorectal cancer prevention: strategies for promoting literacy
Authors: Gomes Tânia , Espírito-Santo Margarida , Nascimento Tânia 
Published: August 2021

Abstract

Background
Colorectal cancer (CRC) is the most frequent and deadly cancer in Portugal, prevention and early detection with screening are key factors for decreasing the incidence of CRC and improving survival rates. CRC screenings allow the detection of benign situations and their remotion, preventing the development of a malignant condition. Thus, this study aimed to identify strategies that could promote CRC literacy in order to also increase the number of screenings.

Methods
A systematic review (SR) was performed using PICOS methodology to define study goals and then PRISMA methodology to collect data for the review, including intervention studies published from 2010.

Results
A final number of 11 articles were included in this SR, which used several strategies to promote literacy. These studies included patients mostly within the age range of 50–75 years. The different strategies identified contained delivering pamphlets, seminars, using technological solutions, among others. All of these educational strategies led to the breaking down of some barriers that might exist about screening and bowel preparation, which conduced to an increase in adherence to CRC screening. Since most of the studies were performed in populations presenting low health literacy or belonging to ethnic minorities, strategies such as verbal information sessions showed better results.

Conclusions
Several strategies seems to be effective, since the results of different interventions have translated into increased CCR literacy and also the number of screenings. Portuguese pharmacy professionals, given easy access and user confidence can contribute directly, as a future perspective, in the education of patients with CCR.
P and Z ICPC2 classifications as reason for encounter for sex and age in central Portugal in 2016 and 2019
Authors: Valente Fábio , Santiago Luiz Miguel 
Published: August 2021

Abstract

Background
ICPC2 reasons for encounter classified in P (Psychological) and Z (Social) chapters are scarce in the medical literature. We aimed to verify the frequency of such reasons for encounter classified in P and Z ICPC-2 chapters, to perceive their association by sex and age in the post-economic 2011 to 2015 economic and financial Portuguese crisis, calculating its trends from 2016 to 2019.

Methods
Observational, cross-sectional study in 2020 comparing data from 2016 and 2019 using the application R of the software RStudio® version 1.3.1093, considering 100 random samples of 10.000 dimension random samples with replacement from the original one. Absolute and relative frequencies and classification trends of all items corresponding to the component signs and symptoms and Illnesses and diagnostics of chapters P and Z in total and by gender were calculated.

Results
Classified reasons for encounter in 2016 and 2019 presented statistically significant association by sex (P &lt; 0.001) and age (P &lt; 0.001) being more common in women (67.4% in 2016 and 66.8% in 2019) and in adulthood (51.6 years in 2016 and 51.5 years in 2019). P and Z of components 1 and 7 reasons for encounter decreased in both chapters (Δ = -7.3% in component 1 and Δ = -2.3% in component 7 of P; Δ = -0.9% in component 1 of Z) between 2016 and 2019.

Conclusions
The P and Z ICPC-2 chapters classified as reasons for encounter presented statistically significant association by sex and age and were more frequent near to the crisis years, in the female sex and in those older than 50 years.