bluuebunny/crossref_metadata_2025_split huggingface dataset:
SimSpliceEvol: alternative splicing-aware simulation of biological sequence evolution
Authors: Kuitche Esaie , Jammali Safa , Ouangraoua Aïda 
Published: December 2019

AbstractBackgroundIt is now well established that eukaryotic coding genes have the ability to produce more than one type of transcript thanks to the mechanisms of alternative splicing and alternative transcription. Because of the lack of gold standard real data on alternative splicing, simulated data constitute a good option for evaluating the accuracy and the efficiency of methods developed for splice-aware sequence analysis. However, existing sequence evolution simulation methods do not model alternative splicing, and so they can not be used to test spliced sequence analysis methods.ResultsWe propose a new method called SimSpliceEvol for simulating the evolution of sets of alternative transcripts along the branches of an input gene tree. In addition to traditional sequence evolution events, the simulation also includes gene exon-intron structure evolution events and alternative splicing events that modify the sets of transcripts produced from genes. SimSpliceEvol was implemented in Python. The source code is freely available athttps://github.com/UdeS-CoBIUS/SimSpliceEvol.ConclusionsData generated using SimSpliceEvol are useful for testing spliced RNA sequence analysis methods such as methods for spliced alignment of cDNA and genomic sequences, multiple cDNA alignment, orthologous exons identification, splicing orthology inference, transcript phylogeny inference, which requires to know the real evolutionary relationships between the sequences.
The direct healthcare costs attributable to West Nile virus illness in Ontario, Canada: a population-based cohort study using laboratory and health administrative data
Authors: Shing Emily , Wang John , Nelder Mark P. , Parpia Camilla , Gubbay Jonathan B. , Loeb Mark , Kristjanson Erik , Marchand-Austin Alex , Moore Stephen , Russell Curtis , Sider Doug , Sander Beate 
Published: December 2019

Abstract
Background
West Nile virus (WNV) is a mosquito-borne flavivirus, first detected in the Western Hemisphere in 1999 and spread across North America over the next decade. Though endemic in the most populous areas of North America, few studies have estimated the healthcare costs associated with WNV. The objective of this study was to determine direct healthcare costs attributable to WNV illness in Ontario, Canada.

Methods
We conducted a cost-of-illness study on incident laboratory confirmed and probable WNV infected subjects identified from the provincial laboratory database from Jan 1, 2002 through Dec 31, 2012. Infected subjects were linked to health administrative data and matched to uninfected subjects. We used phase-of-care methods to calculate costs for 3 phases of illness: acute infection, continuing care, and final care prior to death. Mean 10-day attributable costs were reported in 2014 Canadian dollars, per capita. Sensitivity analysis was conducted to test the impact of WNV neurologic syndromes on healthcare costs.

Results
One thousand five hundred fifty-one laboratory confirmed and probable WNV infected subjects were ascertained; 1540 (99.3%) were matched to uninfected subjects. Mean age of WNV infected subjects was 49.1 ± 18.4 years, 50.5% were female. Mean costs attributable to WNV were $1177 (95% CI: $1001, $1352) for acute infection, $180 (95% CI: $122, $238) for continuing care, $11,614 (95% CI: $5916, $17,313) for final care - acute death, and $3199 (95% CI: $1770, $4627) for final care - late death. Expected 1-year costs were $13,648, adjusted for survival. Three hundred seventeen infected subjects were diagnosed with at least one neurologic syndrome and greatest healthcare costs in acute infection were associated with encephalitis ($4710, 95% CI: $3770, $5650).

Conclusions
WNV is associated with increased healthcare resource utilization across all phases of care. High-quality studies are needed to understand the health system impact of vector-borne diseases and evaluate the cost effectiveness of novel WNV interventions.
Diagnostic accuracy of multi-slice computed tomography in children with Abernethy malformation
Authors: Guo Chen , Zhong Yu-Min , Wang Qian , Hu Li-Wei , Gu Xiao-Hong , Shao Hong , Wu Wei , Cao Jian-Feng , Qiu Hai-Sheng 
Published: December 2019

Abstract
Background
Abernethy malformation is a rare congenital abnormality. Imaging examination is an important method for the diagnosis. The purpose of this study was to demonstrate manifestations of multi-slice computed tomography (MSCT) in Abernethy malformation and its diagnostic accuracy.

Methods
Fourteen children with Abernethy malformation were admitted to our center in China between July 2011 and January 2018. All 14 patients (eight males and six females) received MSCT and digital subtraction angiography (DSA) while eight patients also received ultrasound. The patients’ age ranged from 1 to 14 (median age 8 years old). The clinical records of the patients were retrospectively reviewed. MSCT raw data were transferred to an Advantage Windows 4.2 or 4.6 workstation (General Electric Medical Systems, Waukesha, WI). We compared the findings of MSCT with DSA and surgical results in order to ascertain diagnostic accuracy.

Results
Three cases had type Ib Abernethy malformation and eleven cases had type II. Two cases of type II Abernethy malformation were misdiagnosed as type Ib using MSCT. Comparing the findings of MSCT with DSA and surgical results, the accuracy of MSCT was 85.7% (12/14), in which 100.0% (3/3) were type Ib and 81.8% (9/11) were type II. Clinical information included congenital heart disease, pulmonary hypertension, diffuse pulmonary arteriovenous fistula, abnormal liver function, hepatic nodules, elevated blood ammonia, and hepatic encephalopathy. Eleven cases were treated after diagnosis. One patient with Abernethy malformation type Ib (1/3) underwent liver transplantation. Seven patients with Abernethy malformation type II (7/11) were treated by shunt occlusion, received laparoscopy, or were treated with open surgical ligation. Another three patients (3/11) with Abernethy malformation type II were treated by interventional portocaval shunt occlusion under DSA.

Conclusion
MSCT attains excellent capability in diagnosing type II Abernethy malformation and further shows the location of the portocaval shunt. DSA can help when it is hard to determine diagnosis between Abernethy type Ib and II using MSCT.
Association between lifestyle and musculoskeletal pain: cross-sectional study among 10,000 adults from the general working population
Authors: Kirsch Micheletti Jéssica , Bláfoss Rúni , Sundstrup Emil , Bay Hans , Pastre Carlos Marcelo , Andersen Lars Louis 
Published: December 2019

AbstractBackgroundWork-related musculoskeletal pain is a major cause of work disability and sickness absence. While pain is a multifactorial phenomenon being influenced by work as well as lifestyle, less is known about the association between specific lifestyle factors and the type of musculoskeletal pain. The aim of the study was to investigate if a dose-response association existed between lifestyle factors and musculoskeletal pain intensity in the low back and neck-shoulder.MethodsCurrently employed wage earners (N = 10,427) replied in 2010 to questions about work environment, lifestyle and health. Logistic regression analyses adjusted for various confounders tested the association of alcohol intake, physical activity, fruit and vegetable intake, and smoking (explanatory variables) with low back pain and neck-shoulder pain intensity (outcomes variables, scale 0–9, where ≥4 is high pain).ResultsThe minimally adjusted model found that physical activity and fruit and vegetable intake were associated with lower risk of musculoskeletal pain, while smoking was associated with higher risk of musculoskeletal pain. In the fully adjusted model, physical activity ≥5 h per week was associated with lower risk of low back pain and neck-shoulder pain with risk ratios (RR) of 0.95 (95% CI 0.90–1.00) and 0.90 (95% CI 0.82–0.99), respectively. No association was found between alcohol intake and pain.ConclusionBeing physically active associated with lower risk of having musculoskeletal pain, while smoking habits and healthy eating were associated with higher pain when adjusting for age and gender. Considering the continuously increasing retirement age in many societies, initiatives to promote healthy habits should still be a political priority to help the workers to stay healthy and cope to their work.
Should intraoperative nerve monitoring be used routinely in primary thyroid surgeries?
Authors: Akıcı Murat , Çilekar Murat , Yılmaz Sezgin , Arıkan Yüksel 
Published: December 2019

Objective: This study presents the effects of intraoperative nerve monitoring on RLN injuries in patients who underwent primary surgery for benign thyroid pathology.
Methods: We retrospectively evaluated the data of 273 patients who had primary thyroidectomy due to benign thyroid pathology between January 2012 and July 2017. The patients were classified into two groups. Group-1 consists of patients whose nerves were monitored. We separated the patients whose nerves were not monitored into Group-2.
Results: There were 140 and 133 patients in Groups 1 and 2, respectively. Regarding the age, gender and surgical indication between the groups, statistically significant difference was not found (P > 0.05). In Group-1, transient paralysis developed in four patients (2.9%). The permanent paralysis developed in one patient (0.7%). In Group-2, transient paralysis developed in nine patients (6.8%). The permanent paralysis developed in four patients (3%). When the groups were evaluated, there was statistically significant difference in terms of transient and permanent paralysis (P=0.01, P =0.001, respectively).
Conclusions: In view of the negative effects of RLN injury on the patient, we think that intraoperative nerve monitoring should be used routinely in benign thyroid surgeries.
doi: https://doi.org/10.12669/pjms.36.2.1054
How to cite this:Akici M, Cilekar M, Yilmaz S, Arikan Y. Should intraoperative nerve monitoring be used routinely in primary thyroid surgeries? Pak J Med Sci. 2020;36(2):276-280. doi: https://doi.org/10.12669/pjms.36.2.1054
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.
Association of anti-HCV sero-prevalence with blood transfusion and practice of haemodialysis from multiple centres in patients on maintenance haemodialysis
Authors: Amjad Umbreen , Ahmad Saqib Qayyum , Mir Saima , Ayub Moazam 
Published: December 2019

Objectives: To determine the frequency of anti-HCV in patients on maintenance haemodialysis (HD) and its association with history of blood transfusion and with the practice of HD from more than one center.
Methods: All the patients on maintenance HD at Bahria International hospital (BIH) Rawalpindi from March 2019 to May 2019 were included. Demographic details, history of blood transfusions and history of HD from any other center in addition to BIH, were recorded. Anti-HCV was done by chemiluminescent assay. Chi-square was used to compare the categorical variables. Odds ratio (OR) and relative risk (RR) for the groups exposed to risk were calculated.
Results: Of 96 patients, 40 (41.6%) were anti-HCV positive. Sixty–two (64.6%) had transfusion history. Thirty-one (50%) of these 62 were anti–HCV positive as compared to 9 (26.5%) of 34 with no history of transfusion (p=0.025); OR=2.78 (p=0.0278), RR=1.89 (p=0.0420). Among 66(68.7%) of 96 who had HD from other centres in addition to ours, 33(50%) were anti-HCV positive as compared to 7(23.3%) of 23 who had HD from BIH only (p=0.014); OR=3.29 (p=0.0167), RR=2.14 (p=0.0309).
Conclusion: There was a high prevalence (41.6%) of anti-HCV in our HD patients and anti-HCV positivity had significant association with history of blood transfusion as well as with history of HD from multiple centres.
doi: https://doi.org/10.12669/pjms.36.2.1343
How to cite this:Amjad U, Ahmad SQ, Mir S, Ayub M. Association of anti-HCV sero-prevalence with blood transfusion and practice of haemodialysis from multiple centres in patients on maintenance haemodialysis. Pak J Med Sci. 2020;36(2):286-289. doi: https://doi.org/10.12669/pjms.36.2.1343
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.
Keele asend eesti palatalisatsioonis
Authors: Malmi Anton , Lippus Pärtel 
Published: December 2019

Artiklis uuritakse palatalisatsiooni mõju konsonandi ja talle eelneva vokaali häälduskohale ja kestusele. Katse viidi läbi elektromagnetartikulograafi abil, mis mõõdab katseisiku artikulaatoritele liimitud sensorite liikumist kolmemõõtmelises ruumis. Tulemused näitasid, et palataliseerimisega kaasnes konsonandi ja talle eelneva vokaali hääldamisel keele kõrgem ja eespoolsem asend. Keele eesosa kõrgus oli vähesel määral palatalisatsioonist mõjutatud, kuid kõrguse muutumine ei olnud süsteemne. Tulemused ei näidanud palatalisatsiooni süstemaatilist efekti ka konsonandi ja talle eelneva vokaali kestusele. Ainult üksikutel juhtudel pikenes hääliku kestus palataliseeritud kontekstis olulisel määral.
Abstract. Anton Malmi and Pärtel Lippus: The position of the tongue in Estonian palatalization. This article analyses the effect of secondary palatalization of alveolar consonants on the place of articulation and the segmental duration in Estonian CVC words. The study was carried out with 21 test subjects using a Carstens AG501 electromagnetic articulograph. The results show that the place of articulation of palatalized consonants was always higher and more anterior than that of non-palatalized consonants. The back of the tongue was raised towards the hard palate, but the height of the apical part of the tongue was not systematically affected by palatalization. With few exceptions, the duration of the vowels and consonants were not affected by palatalization.
Keywords: articulatory phonetics, experimental phonetics, articulation, palatalization, Estonian, duration, Carstens AG501
Universos lúdico-conceituais como uma intervenção pedagógica: dando suporte à aprendizagem e ao desenvolvimento da criança pré-escolar em contextos lúdicos
Authors: Fleer Marilyn 
Published: December 2019

Existe um interesse crescente em encontrar melhores maneiras de apoiar o aprendizado de conceitos em programas educativos voltados à primeira infância baseados na brincadeira. A introdução de termos como 'eduplay' em Hong Kong, 'Brincadeira intencionada' em Cingapura e 'ensino intencional' em programas baseados em brincadeiras na Austrália sugerem que os educadores estão trabalhando de diferentes maneiras para construir novas práticas que tragam brincadeira e aprendizado em unidade para dar suporte ao desenvolvimento das crianças. Este artigo contribui para esse cenário de pesquisa ao introduzir uma intervenção pedagógica chamada Universos lúdico-conceituais (Conceptual playworlds). Esse modelo de prática é teorizado usando os conceitos vygotskianos de imaginação e brincadeira, e o modelo hedegaardiano de valores sociais, práticas institucionais e configurações de atividades como base para o estudo da aprendizagem de conceitos em contextos baseados em brincadeiras. O conteúdo deste artigo está situado no contexto curricular em mudança da primeira infância da região australiana, onde valores sociais para melhores resultados estão moldando práticas institucionais que criam novas demandas e condições diferentes para o desenvolvimento das crianças.
Una mirada desde el interior
Authors: Pantaleón Dr. Arq. Carlos 
Published: December 2019

Este trabajo de reflexión indaga el significado de la palabra paisaje y su valor en el quehacer arquitectónico. Se basa en la investigación realizada sobre distintos conceptos de paisaje definidos a partir de los procesos perceptivos del hombre, sobre los imaginarios que conforma como producto de esos procesos, la incidencia de esos imaginarios en su formación cultural y el comportamiento que desempeña en el mundo a partir de la incorporación de esos imaginarios.
En este caso, y con el objetivo de reflexionar sobre algunas de las nociones desde las cuales se diseña un edificio, se considera la obra de arquitectura como intermediaria entre el sujeto que la habita y el entorno que la contiene, concibiéndose como un dispositivo para provocar sensaciones a través de imágenes proyectadas por el arquitecto.
Prologa el trabajo una síntesis de la historia del paisajismo en Occidente y en Oriente que define el marco teórico de este trabajo, a la vez que expone y documenta los conceptos que aquí se manejan. A partir de estos conceptos y a modo de conclusión, se reflexiona sobre los aportes que hace la Iglesia en el Agua, proyectada y construida por el arquitecto japonés Tadao Ando, a este enfoque particular del tema.
BATALLAS OBRERAS EN CONTEXTOS DE RADICALIZACIÓN SOCIAL Y POLÍTICA EN LA AGROINDUSTRIA (GRAN ROSARIO, 1969- 1972)
Authors: SIMONASSI SILVIA , VOGELMANN VERÓNICA 
Published: December 2019

Este artículo se propone analizar las batallas obreras acontecidas en la industria de la alimentación en el Gran Rosario luego del “Cordobazo” (mayo de 1969) y de los “Rosariazos” (mayo y setiembre de 1969). Dichas luchas fueron escasamente exploradas por la historiografía hasta el momento desde la perspectiva propuesta. Se articulan transformaciones estructurales, luchas y organización en una escala regional/local sin perder de vista las dinámicas nacionales. Asimismo, se develan los límites y contradicciones del proceso de radicalización social y política en el marco de luchas defensivas, por la conservación de fuentes de trabajo frente a suspensiones, cesantías y cierres. Se utilizan fuentes diversas: entrevistas, prensa periódica, de organizaciones sindicales y políticas, y documentos de servicios de inteligencia.
Vpliv porodnih praks na porodno izkušnjo v institucionalni oskrbi
Authors: Prosen Mirko 
Published: December 2019

Uvod: Nosečnost in porod sta naravna dogodka, čeprav ju danes – ob upoštevanju dejstva, da živimo v »družbi tveganja« – opredeljujemo skozi prizmo patologije in potencialnih nevarnosti. Cilj raziskave je bil razumeti izkušnje in doživljanja žensk, povezana z rojevanjem v porodnišnicah skozi prevladujoče porodne prakse, ki so po prepričanju žensk pomembno krojile njihovo porodno izkušnjo.Metode: Uporabljena je bila sekundarna analiza kvalitativnih podatkov. Primarni podatki so bili zbrani leta 2014 v okviru raziskave Medikalizacija nosečnosti in poroda kot družbena konstrukcija z narativno metodo. V vzorec sekundarne analize je bilo vključenih 18 transkriptov intervjujev z ženskami, ki so rodile v porodnišnici. Analiza kvalitativnih podatkov je bila izvedena s pomočjo računalniškega programa NVivo, verzija 12.Rezultati: V analizi so bile identificirane tri teme: (1) pomembnost podpore zdravstvenega osebja in avtonomija odločanja; (2) sprememba fokusa v dojemanju carskega reza kot naravnega načina rojevanja; (3) rutinizacija in tehnifikacija porodnih praks.Diskusija in zaključek: Rojevanje tako danes kot nekoč usmerjajo negativne in pozitivne porodne izkušnje. Poznati je treba oboje. Za ženske je prva porodna izkušnja poučna in obenem določujoča, saj na njeni podlagi presojajo prihodnje porodne izkušnje. Podpora zdravstvenega osebja ter avtonomija odločanja sta ključni za pozitivno porodno izkušnjo. K temu bi lahko v prihodnje pomembno prispevale tudi spremembe nekaterih utečenih porodnih praks, ki bi morale hitreje slediti praksi, utemeljeni z dokazi.
Migratory Species Show Distinct Patterns in Corticosterone Levels during Spring and Autumn Migrations
Authors: Tsvey Arseny , Loshchagina Julia , Naidenko Sergey 
Published: December 2019

AbstractTwice a year billions of birds migrate between breeding and wintering grounds. To facilitate migrations, birds develop migratory disposition, a complex suite of behavioral and physiological adjustments. Glucocorticoid hormone corticosterone is involved in the regulation of migratory behavior and physiology, however no consensus on its exact role in controlling avian migration exists. Using a large dataset on seven songbird species (long- and short-distance migrants) obtained during eleven consecutive migratory seasons on the Courish Spit of the Baltic Sea, we showed the general tendency of similar baseline corticosterone concentrations during both migrations, although stress-induced levels were generally much higher during spring. No difference between long- and short-distance migrants was found in either baseline or stress-induced levels, while there was substantial between-species variation, especially in baseline concentrations. The distinct patterns of corticosterone secretion during seasonal migrations even in ecologically similar species indicate that it is likely to be a species-specific trait. Thus, our study corroborates the inconsistency found in earlier studies and demonstrates how scientific understanding of the role of corticosterone during migration is still evolving. Rather low baseline corticosterone concentrations observed in this study emphasize that birds in both migratory seasons were not in a “stressed” state before capture.
Leukocyte profiles vary with breeding latitude and infection status in a seasonally sympatric songbird
Authors: Becker Daniel J. , Talbott Katherine M. , Smiley Tara M. , Clark Kerry L. , Sauer Peter E. , Ketterson Ellen D. 
Published: December 2019

AbstractBillions of animals migrate annually in pursuit of food, safety, and reproduction. Long-distance migration can be energetically expensive, which can force tradeoffs with investment in other physiological systems (e.g., suppressing immunity). Understanding the physiological impacts of migration is important to predict when and where such animals may be vulnerable to parasites and how changes to migration might affect infectious disease risks. To isolate relationships between migration and physiology from energetic tradeoffs and hormonal shifts associated with spring reproduction, we assessed differences in leukocyte profiles between seasonally sympatric resident and recently arrived fall migrant dark-eyed juncos (Junco hyemalis) in the Appalachian Mountains. When examining heterophil:lymphocyte (HL) ratios, which can elevate for long durations after even mild stressors, we found weak associations with migratory strategy (resident or migrant subspecies). In contrast, feather δ2H values showed that HL ratios were highest for juncos breeding at more northern latitudes, and this relationship was strongest for birds that arrived at the overwintering site infected with haemosporidian parasites (PlasmodiumandHaemoproteusspp.). These patterns were more pronounced and better indicated hematological responses to stressors when using multivariate analyses. Our findings suggest that short- and long-distance migration may be more energetically costly in the presence of infection and highlight how approximating breeding latitude and using multivariate analyses can help understand host physiology.