bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raciolinguistic Ideologies and Second Language Spanish: Case Study of an Interracial Couple
Authors: Menard-Warwick Julia 
Published: January 2021

Abstract
The theoretical framework of raciolinguistics examines connections between language ideologies and racialization, but few studies have analyzed the adult learning of languages other than English. This case study is based on life history interviews with a married couple, a Black male journalist and a White female nurse, who learned Spanish as adults. Both grew up as monolingual English speakers, in multilingual US communities where Spanish was widely spoken, and both studied the language in school, but only began using it in US settings as adults in professional contexts. Their Spanish use expanded during three years of volunteer service in Bolivia, where I interviewed them twice, a year apart, as part of a larger interview study on bilingual identities. In this article, I employ a Bakhtinian lens to explore this couple’s perspectives on their encounters with raciolinguistic ideologies; the contexts in which their Spanish use was ratified or not; and their eventual establishment of (somewhat limited) Spanish-speaking voices through the affordances of their intersectional identities.
Female and male plumage color is linked to parental quality, pairing, and extrapair mating in a tropical passerine
Authors: Leitão Ana V , Hall Michelle L , Mulder Raoul A 
Published: January 2021

AbstractSexual selection has been proposed to drive the evolution of elaborate phenotypic traits in males, which often confer success in competition or mating. However, in many species, both males and females display such traits. Studies examining how selection acts on both sexes are scarce. In this study, we investigated whether plumage ornamentation is sexually selected in females and males lovely fairy-wren Malurus amabilis, a cooperatively breeding songbird. We found that female and male plumage color was correlated with parental quality but not with individual quality or survival. We also found evidence of positive assortative mating based on plumage color. Microsatellite analyses of paternity indicated that the lovely fairy-wren has high levels of extrapair paternity (EPP), with 53% of offspring (in 58% of broods of 57% of females) resulting from extrapair (EP) mating. Female and male plumage color did not predict reproductive success or the proportion of EP offspring in their own nest, but less colorful males obtained higher EPP when paired with more colorful females and gained overall higher total paternity (own nest and other nests). We argue that plumage color may be under sex-specific selection, highlighting the importance of looking at both sexes in studies of sexual selection and ornament evolution. The current findings together with the previous study suggest that plumage color in female and male lovely fairy-wrens appears to be an honest signal relevant in both intrasexual and intersexual competition contexts.
PrInCE: an R/Bioconductor package for protein–protein interaction network inference from co-fractionation mass spectrometry data
Authors: Skinnider Michael A. , Cai Charley , Stacey R. Greg , Foster Leonard J. 
Published: January 2021

Abstract

Summary
We present PrInCE, an R/Bioconductor package that employs a machine-learning approach to infer protein–protein interaction networks from co-fractionation mass spectrometry (CF-MS) data. Previously distributed as a collection of Matlab scripts, our ground-up rewrite of this software package in an open-source language dramatically improves runtime and memory requirements. We describe several new features in the R implementation, including a test for the detection of co-eluting protein complexes and a method for differential network analysis. PrInCE is extensively documented and fully compatible with Bioconductor classes, ensuring it can fit seamlessly into existing proteomics workflows.

Availability and implementation
PrInCE is available from Bioconductor (https://www.bioconductor.org/packages/devel/bioc/html/PrInCE.html). Source code is freely available from GitHub under the MIT license (https://github.com/fosterlab/PrInCE). Support is provided via the GitHub issues tracker (https://github.com/fosterlab/PrInCE/issues).

Supplementary information
Supplementary data are available at Bioinformatics online.
Measurement of 45 cytokine, chemokine and growth factors in established cell culture supernatants and autologous serum from advanced melanoma patients
Authors: Montoyo-Pujol Yoel Genaro , Wang Xu , Bermúdez-Sánchez Sandra , Martin Aurelio , Almazan Francisco , López-Nevot Miguel Ángel 
Published: January 2021

Abstract
Melanoma is one of the most aggressive forms of human cancer and its incidence has significantly increased worldwide over the last decades. This neoplasia has been characterized by the release of a wide variety of soluble factors, which could stimulate tumor cell proliferation and survival in an autocrine and paracrine manner. Consequently, we sought to evaluate the pattern of soluble factors produced by pre-metastatic and metastatic melanoma established cultures, and to determine whether these factors can be detected in the autologous serum of malignant melanoma patients. Our results showed that both melanoma cultures had a common profile of 27 soluble factors mainly characterized by the high expression of VEGF-A, IL-6, MCP-1, IL-8, and SDF-1. In addition, when we compared supernatants, we observed significant differences in VEGF-A, BDNF, FGF-2, and NGF-β concentrations. As we found in melanoma cultures, serum samples also had their specific production pattern composed by 21 soluble factors. Surprisingly, PDGF-BB and EGF were only found in serum, whereas IL-2, IL-4, IL-8, IL31, FGF2, and GRO-α were only expressed in the supernatant. Significant differences in PDGF-BB, MIP-1β, HGF, PIGF-1, BDNF, EGF, Eotaxin, and IP-10 were also found after comparing autologous serum with healthy controls. According to this, no correlation was found between culture supernatants and autologous serum samples, which suggests that some factors may act locally, and others systemically. Nonetheless, after validation of our results in an independent cohort of patients, we concluded that PDGF-BB, VEGF-A, and IP-10 serum levels could be used to monitor different melanoma stages.
A New Application of PARAFAC Model to UPLC Dataset for the Quantitative Resolution of a Tri-Component Drug Mixture
Authors: Güzel Remziye , Ertekin Zehra Ceren , Dinç Erdal 
Published: January 2021

Abstract
In the presented work, a three-way analysis of ultra-performance liquid chromatography-photodiode array (UPLC-PDA) dataset was performed by parallel factor analysis (PARAFAC) for quantitatively resolving a ternary mixture containing paracetamol and methocarbamol with indapamide selected as an internal standard in their co-eluted chromatographic conditions. Paracetamol and methocarbamol were quantified in the working range between 3–24 and 5–50 μg/mL by applying PARAFAC decomposition to UPLC-PDA data array obtained under unresolved chromatographic peak conditions. To compare the experimental results provided by co-eluted UPLC-PARAFAC method, an ordinary UPLC method was developed ensuring proper separation of the peaks. The performance of both PARAFAC and ordinary UPLC methods were assessed by quantifying independent test samples, intra- and inter-day samples and spiked samples of pharmaceutical preparations. Then, both methods were applied for quantitative estimation of the related drugs in a commercial pharmaceutical preparation. In this study, PARAFAC method was proved to be a very powerful alternative for the quality control of pharmaceutical preparations containing paracetamol and methocarbamol even in their co-eluted chromatograms with high precision and accuracy in a short chromatographic runtime of 1.2 min.
Emergence and Transmission of Daptomycin and Vancomycin-Resistant Enterococci Between Patients and Hospital Rooms
Authors: El Haddad Lynn , Hanson Blake M , Arias Cesar A , Ghantoji Shashank S , Harb Cynthia P , Stibich Mark , Chemaly Roy F 
Published: January 2021

Abstract

Background
Vancomycin-resistant enterococci (VRE) are a major cause of morbidity and mortality in immunocompromised patients. Tracking the dissemination of VRE strains is crucial to understand the dynamics of emergence and spread of VRE in the hospital setting.

Methods
Whole genome sequencing (WGS) and phylogenetic analyses were performed to identify dominant VRE strains and potential transmission networks between 35 patients with VRE-positive rectal swabs and their rooms (main rooms and bathrooms) on the leukemia (LKM) and the hematopoietic cell transplant (HCT) floors. Sequence types (STs), drug resistance genes, and patients’ outcomes were also determined.

Results
A total of 89 VRE strains grouped into 10 different STs, of which newly described STs were isolated from both floors (ST736, ST494, ST772, and ST1516). We observed highly genetically related strains transmitted between rooms, floors, and time periods in an average period of 39 days (ranging from 3 to 90 days). Of 5 VRE bacteremia events, 3 strains were lacking the pili operon fms14–17–13 (ST203) and the remaining 2 were resistant to daptomycin (DAP; ST736, ST664). Of 10 patients harboring DAP-resistant strains, only 2 were exposed to DAP within 4 months before strain recovery.

Conclusions
Our comparisons of VRE strains derived from the environment and immunocompromised patients confirmed horizontal transfer of highly related genetic lineages of multidrug-resistant (particularly to DAP) VRE strains between HCT and LKM patients and their room environment. Implementing WGS can be useful in distinguishing VRE reservoirs where interventions can be targeted to prevent and control the spread of highly resistant organisms.
Outcomes after kidney transplantation, let’s focus on the patients’ perspectives
Authors: Wang Yiman , Snoep Jaapjan D , Hemmelder Marc H , van der Bogt Koen E A , Bos Willem Jan W , van der Boog Paul J M , Dekker Friedo W , de Vries Aiko P J , Meuleman Yvette 
Published: January 2021

Abstract
Graft function and patient survival are traditionally the most used parameters to assess the objective benefits of kidney transplantation. Monitoring graft function, along with therapeutic drug concentrations and transplant complications, comprises the essence of outpatient management in kidney transplant recipients (KTRs). However, the patient’s perspective is not always included in this process. Patients’ perspectives on their health after kidney transplantation, albeit subjective, are increasingly acknowledged as valuable healthcare outcomes and should be considered in order to provide patient-centred healthcare. Such outcomes are known as patient-reported outcomes (PROs; e.g. health-related quality of life and symptom burden) and are captured using PRO measures (PROMs). So far, PROMs have not been routinely used in clinical care for KTRs. In this review we will introduce PROMs and their potential application and value in the field of kidney transplantation, describe commonly used PROMs in KTRs and discuss structural PROMs implementation into kidney transplantation care.
Dietary Intake Pattern is Associated with Occurrence of Flares in IBD Patients
Authors: Peters Vera , Spooren Corinne E G M , Pierik Marie J , Weersma Rinse K , van Dullemen Hendrik M , Festen Eleonora A M , Visschedijk Marijn C , Masclee Adriaan A M , Hendrix Evelien M B , Almeida Rui Jorge , Perenboom Corine W M , Feskens Edith J M , Dijkstra Gerard , Campmans-Kuijpers Marjo J E , Jonkers Daisy M A E 
Published: January 2021

Abstract

Background
Diet is associated with the onset of inflammatory bowel disease [IBD]. Up to half of IBD patients believe that diet contributes to flares. However, studies on this topic are sparse and merely focus on specific nutrients, food items or food groups. We aimed to analyse the association between dietary patterns and flare occurrence in two geographically distinct Dutch cohorts.

Methods
In this longitudinal study, 724 IBD patients [Northern cohort: n = 486, Southern cohort: n = 238] were included and followed for 2 years. Habitual dietary intake was obtained via semi-quantitative food frequency questionnaires at baseline. Principal component analysis [PCA] was conducted on 22 food groups to identify dietary patterns. Flare occurrence was analysed in 427 patients in remission at baseline, using multivariable Cox proportional hazards.

Results
Compared to the Southern cohort, patients in the Northern cohort were younger at diagnosis, comprised more females, and had lower overall energy intakes [all p &lt; 0.05]. PCA revealed three dietary patterns explaining 28.8% of the total variance. The most pronounced pattern [explaining 11.6%] was characterized by intake of grain products, oils, potatoes, processed meat, red meat, condiments and sauces, and sugar, cakes and confectionery. Of the 427 patients, 106 [24.8%] developed an exacerbation during follow-up. The above dietary pattern was associated with flare occurrence (hazard ratio [HR]: 1.51, 95% confidence interval [CI]: 1.04–2.18, p = 0.029), as was female sex [HR: 1.63, 95% CI 1.04–2.55, p = 0.032].

Conclusions
A dietary pattern, which can be seen as a ‘traditional [Dutch]’ or “Western’ pattern was associated with flare occurrence. Confirmation in prospective studies is needed.
Real-world safety and efficacy of direct oral anticoagulants in atrial fibrillation: a systematic review and meta-analysis of 605 771 patients
Authors: Menichelli Danilo , Del Sole Francesco , Di Rocco Arianna , Farcomeni Alessio , Vestri Annarita , Violi Francesco , Pignatelli Pasquale , Lip Gregory Y H , Pastori Daniele 
Published: January 2021

Abstract

Aims
To analyse the safety and efficacy of direct oral anticoagulants (DOACs) in real-world studies including atrial fibrillation (AF) patients.

Methods and results
Systematic review and meta-analysis of observational studies including AF patients on DOACs. Primary endpoints: any, major, gastrointestinal (GI), intracranial haemorrhage (ICH), and haemorrhagic stroke (HS). Secondary endpoints: ischaemic stroke (IS), systemic embolism (SE), myocardial infarction (MI), and all-cause of death. A set of pair-wise meta-analyses using a random effect model and a random effect network meta-analysis under a Bayesian framework were performed. Prospero registration number: CRD42019137111. We included 21 studies with 605 771 AF patients. Apixaban was associated with lower major and GI bleeding compared with Rivaroxaban [hazard ratio (HR) 2.0, 95% confidence interval (CI) 1.6–2.5] and Dabigatran (HR 1.6, 95% CI 1.3–2.1). The latter drug performed better than Rivaroxaban (HR 1.2, 95% CI 1.0–1.5). Dabigatran and Apixaban had a similar association with HS, but Apixaban performed better than Rivaroxaban (HR 1.8, 95% CI 1.1–3.0). Apixaban had a similar association with Rivaroxaban and Dabigatran for ICH, the latter drug performing better than Rivaroxaban (HR 1.3, 95% CI 1.0–1.7). Rankograms showed that Apixaban was likely to be the first-choice treatment in relation to any (65%) major (100%) and GI bleeding (100%) followed by Dabigatran (46%, 100%, 99%, respectively). Dabigatran and Apixaban had similar rank as first choice for ICH (44% and 55%) and HS (52% and 48%). DOACs showed similar association with IS/SE, MI, all-cause of death.

Conclusions
Analysis of real-world studies shows significant differences for safety among DOACs.
Treatment of infectious aortic disease with bovine pericardial tube grafts
Authors: Kreibich Maximilian , Siepe Matthias , Berger Tim , Pingpoh Clarence , Puiu Paul , Morlock Julia , Walter Tim , Kondov Stoyan , Beyersdorf Friedhelm , Rylski Bartosz , Czerny Martin 
Published: January 2021

Abstract

OBJECTIVES
Our aim was to evaluate the mid-term outcomes of bovine pericardial tube graft repair for infectious aortic disease in any aortic segment.

METHODS
Between May 2015 and July 2020, 45 patients were treated for infectious aortic disease of the native (n = 9) aorta or after (endo-)graft (n = 36) implantation with bovine pericardial tube grafts. Clinical, infectious details, outcomes and follow-up data were evaluated.

RESULTS
All aortic segments underwent pericardial tube graft or bifurcational replacement: the aortic root (n = 12, 27%), ascending aorta (n = 18, 40%), aortic arch (n = 7, 16%), descending aorta (n = 5, 11%), thoraco-abdominal aorta (n = 6, 13%) and abdominal aorta (n = 18, 40%) including the iliac arteries (n = 14, 31%). Organ fistulation (n = 15, 33%) was the most common underlying pathology. Seven patients (16%) expired in-hospital secondary to ongoing sepsis (n = 5, 11%), respiratory failure (n = 1, 2%) and unknown cause (n = 1, 2%). A fungal infection was predictive for in-hospital mortality (P = 0.026, odds ratio: 19.470). After a median follow-up of 11 [first quartile: 2, third quartile 26] months, 9 additional patients (20%) expired and 1 patient developed a postoperative spondylodiscitis at the level of the aortic tube graft. Hence, freedom from proven aortic graft re-infection was 98%.

CONCLUSIONS
Orthotopic aortic reconstruction using bovine pericardial tube grafts to treat infectious aortic disease is possible in any aortic segment. Organ fistulation is a frequently observed disease mechanism requiring concomitant treatment. Granted, the early attrition rate is substantial, but after the initial period, both survival and freedom from re-infection appear encouraging.
Five-year outcomes of patients supported with HeartMate 3: a single-centre experience
Authors: Schmitto Jan D , Mariani Silvia , Li Tong , Dogan Guenes , Hanke Jasmin S , Bara Christoph , Pya Yuriy , Zimpfer Daniel , Krabatsch Thomas , Garbade Jens , Rao Vivek , Morshuis Michiel , Beyersdorf Friedhelm , Marasco Silvana , Netuka Ivan , Bauersachs Johann , Haverich Axel 
Published: January 2021

Abstract

OBJECTIVES
The HeartMate 3 left ventricular assist device was first implanted in 2014 and received the Conformité Européenne mark in 2015. Since then, several trials demonstrated its high haemocompatibility associated with good survival and low adverse events rates. Herein, we report our institutional experience with patients supported with HeartMate 3 for 5 years.

METHODS
This prospective cohort study included patients receiving a HeartMate 3 implantation in 2014 as part of the HeartMate 3 Conformité Européenne Mark clinical trial. Patients had follow-up visits every 3 months while on left ventricular assist device support, and all patients completed the 5-year follow-up. The primary end point was survival at 5 years. Secondary end points included adverse events, health status and quality of life.

RESULTS
Eight patients (men: 75%) aged 59 years (min–max: 52–66 years) were enrolled. At 5 years, survival was 100%. Patients remained on support for a median time of 1825 days (min–max: 101–1825 days); 2 patients successfully received cardiac transplants. No right heart failure, haemolysis, pump thrombosis, pump malfunction or neurological events occurred in any patients. A driveline infection was observed in 6 patients (0.25 events/patient-year). Compared to baseline, a significant improvement in quality of life and in New York Heart Association functional class was noted after the implant and for the whole follow-up time. A slight decline in kidney function and in the 6-min walk test results occurred after 3 years.

CONCLUSIONS
This study reports the longest single-centre follow-up of the HeartMate 3, showing excellent haemocompatibility over time with high survival and low complication rates at 5 years.
Does family farming reduce rural unemployment?
Authors: Wuepper David , Wimmer Stefan , Sauer Johannes 
Published: January 2021

AbstractThis article investigates the causal relationship between family farming and rural labour markets. To this end, we combine farm accountancy data and public labour market statistics at the district level (NUTS-3) for the years 2008–2013. While cross-sectional regressions reveal a strong and robust negative correlation between the share of family farm labour and unemployment rate in a region, fixed-effects panel data regressions suggest this is not causal. Instead, we find evidence that cultural differences in work ethic spuriously connect family farming with unemployment. Thus, supporting family farming to fight rural unemployment is not an effective strategy in Germany.
Single-dose oral anti-arrhythmic drugs for cardioversion of recent-onset atrial fibrillation: a systematic review and network meta-analysis of randomized controlled trials
Authors: Ibrahim Omar A , Belley-Côté Emilie P , Um Kevin J , Baranchuk Adrian , Benz Alexander P , Dalmia Shreyash , Wang Chang N , Alhazzani Waleed , Conen David , Devereaux P J , Whitlock Richard P , Healey Jeff S , McIntyre William F 
Published: January 2021

Abstract

Aims
Single oral dose anti-arrhythmic drugs (AADs) are used to cardiovert recent-onset atrial fibrillation (AF); however, the optimal agent is uncertain.

Methods
We performed a systematic review and network meta-analysis of randomized trials testing single oral dose AADs vs. any comparator to cardiovert AF &lt;7 days duration. We searched MEDLINE, Embase, and CENTRAL to April 2020. The primary outcome was successful cardioversion at timepoint nearest 8 h after administration.

Results
From 12 712 citations, 22 trials (2320 patients) were included. Thirteen trials included patients with some degree of heart failure; 19 included patients with some degree of ischaemic heart disease vs. placebo or rate-control (32% success) at 8 h, flecainide [73%, network odds ratio (OR) 7.6, 95% credible interval (CrI) 4.4–14.0], propafenone (70%, OR 4.6, CrI 2.9–7.3), and pilsicainide (59%, OR 10.0, CrI 1.8–69.0), but not amiodarone (28%, OR 1.0, CrI 0.4–2.8) were superior. Flecainide (OR 7.5, CrI 2.6–24.0) and propafenone (OR 4.5, CrI 1.6–13.0) were superior to amiodarone; propafenone vs. flecainide did not statistically differ (OR 0.6, CrI 0.3–1.1). At longest follow-up, amiodarone was superior to placebo (OR 11.0, CrI 3.2–41.0), flecainide vs. amiodarone (OR 0.79, CrI 0.19–3.1), and propafenone vs. amiodarone (OR 0.36, CrI 0.092–1.4) were not statistically different, and flecainide was superior to propafenone (OR 2.2, CrI 1.1–4.8). Atrial and ventricular tachyarrhythmias, bradyarrhythmias, and hypotension were rare with PO AADs.

Conclusion
Single oral dose Class 1C AADs are effective and safe for cardioversion of recent-onset AF. Flecainide may be superior to propafenone. Amiodarone is a slower acting alternative.