bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liver Cancer Gene Discovery Using Gene Targeting, Sleeping Beauty, and CRISPR/Cas9
Authors: Kieckhaefer Julia , Maina Flavio , Wells Rebecca , Wangensteen Kirk 
Published: March 2019

AbstractHepatocellular carcinoma (HCC) is a devastating and prevalent cancer with limited treatment options. Technological advances have enabled genetic screens to be employed in HCC model systems to characterize genes regulating tumor initiation and growth. Relative to traditional methods for studying cancer biology, such as candidate gene approaches or expression analysis, genetic screens have several advantages: they are unbiased, with no a priori selection; can directly annotate gene function; and can uncover gene–gene interactions. In HCC, three main types of screens have been conducted and are reviewed here: (1) transposon-based mutagenesis screens, (2) knockdown screens using RNA interference (RNAi) or the CRISPR/Cas9 system, and (3) overexpression screens using CRISPR activation (CRISPRa) or cDNAs. These methods will be valuable in future genetic screens to delineate the mechanisms underlying drug resistance and to identify new treatments for HCC.
Healthcare Effectiveness Data and Information Set (HEDIS) Measures of Alcohol and Drug Treatment Initiation and Engagement among People Living with the Human Immunodeficiency Virus (HIV) and Patients without an Hiv Diagnosis
Authors: Hechter Rulin C. , Horberg Michael A. , Weisner Constance , Campbell Cynthia I. , Contreras Richard , Chen Lie-Hong , Yarborough Bobbi Jo H. , Lapham Gwen T. , Haller Irina V. , Ahmedani Brian K. , Binswanger Ingrid A. , Kline-Simon Andrea H. , Satre Derek D. 
Published: March 2019

Background Problematic use of alcohol and other drugs (AOD) is highly prevalent among people living with the human immunodeficiency virus (PLWH), and untreated AOD use disorders have particularly detrimental effects on human immunodeficiency virus (HIV) outcomes. The Healthcare Effectiveness Data and Information Set (HEDIS) measures of treatment initiation and engagement are important benchmarks for access to AOD use disorder treatment. To inform improved patient care, we compared HEDIS measures of AOD use disorder treatment initiation and engagement and health care utilization among PLWH and patients without an HIV diagnosis. Methods Patients with a new AOD use disorder diagnosis documented between October 1, 2014, and August 15, 2015, were identified using electronic health records (EHR) and insurance claims data from 7 health care systems in the United States. Demographic characteristics, clinical diagnoses, and health care utilization data were also obtained. AOD use disorder treatment initiation and engagement rates were calculated using HEDIS measure criteria. Factors associated with treatment initiation and engagement were examined using multivariable logistic regression models. Results There were 469 PLWH (93% male) and 86,096 patients without an HIV diagnosis (60% male) in the study cohort. AOD use disorder treatment initiation was similar in PLWH and patients without an HIV diagnosis (10% vs. 11%, respectively). Among those who initiated treatment, few engaged in treatment in both groups (9% PLWH vs. 12% patients without an HIV diagnosis). In multivariable analysis, HIV status was not significantly associated with either AOD use disorder treatment initiation or engagement. Conclusions AOD use disorder treatment initiation and engagement rates were low in both PLWH and patients without an HIV diagnosis. Future studies need to focus on developing strategies to efficiently integrate AOD use disorder treatment with medical care for HIV.
Allometric equations for aboveground biomass estimation of
Diospyros abyssinica
(Hiern) F. White tree species
Authors: Daba Damena Edae , Soromessa Teshome 
Published: March 2019

ABSTRACT

Introduction
: Quantifying forest biomass requires the application of allometric equations which is a fundamental step. Generalized allometric equations have been applied to quantify aboveground biomass (AGB) of forests. But, adopting generalized allometric equations to quantify AGB of different forests creates uncertainty. Therefore, developing species- and site-specific allometric equations is essential to accurately quantify the biomass. The study was aimed to develop species-specific allometric equations for
Diospyros abyssinica
(Hiern) F. White in Yayu Coffee Forest Biosphere Reserve using the Semi-destructive method. The vegetation types of Yayu Coffee Forest Biosphere Reserve is categorized to Moist Evergreen Montane Rainforest of Ethiopia.

Results and discussion
: Evaluating statistical relationships of AGB against predictor variables, eight allometric equations were formulated. AGB was regressed against trunk diameter (D), total height (H), and wood density (ρ) individually and in combination. Selection of allometric equations was employed using model performance statistics. Equations with a higher coefficient of determination (adjusted
R
2
), lower residual standard error, and Akaike information criterion (AIC) values were found best-fitted. Relationships of AGB and independent variables were found statistically significant (
p
< 0.000). Overall, formulating species- and site-specific allometric equations is significant for accurate estimation of forest biomass and carbon stock budget.
A novel detector system for KATRIN to search for keV-scale sterile neutrinos
Authors: Mertens Susanne , Alborini Antonio , Altenmüller Konrad , Bode Tobias , Bombelli Luca , Brunst Tim , Carminati Marco , Fink David , Fiorini Carlo , Houdy Thibaut , Huber Anton , Korzeczek Marc , Lasserre Thierry , Lechner Peter , Manotti Michele , Peric Ivan , Radford David C , Siegmann Daniel , Slezák Martin , Valerius Kathrin , Wolf Joachim , Wüstling Sascha 
Published: March 2019

Abstract
Sterile neutrinos appear in minimal extensions of the Standard Model of particle physics. If their mass is in the keV regime, they are viable dark matter candidates. One way to search for sterile neutrinos in a laboratory-based experiment is via the analysis of β-decay spectra, where the new neutrino mass eigenstate would manifest itself as a kink-like distortion of the β-decay spectrum. The objective of the TRISTAN project is to extend the KATRIN setup with a new multi-pixel silicon drift detector system to search for a keV-scale sterile neutrino signal. In this paper we describe the requirements of such a new detector, and present first characterization measurement results obtained with a 7 pixel prototype system.
Atomistic simulations of charge transport in photoswitchable organic-graphene hybrids
Authors: Tonnelé Claire , Pershin Anton , Gali Sai Manoj , Lherbier Aurélien , Charlier Jean-Christophe , Castet Frédéric , Muccioli Luca , Beljonne David 
Published: March 2019

Abstract
Photoswitchable self-assembled monolayers (SAMs) in contact with a conductive or semiconductive layer can be used to remotely trigger changes in electrical current using light. In this study, we apply full-atomistic simulations to assess the changes in electronic structure and charge-transport properties of a graphene sheet in contact with an amorphous silica dielectric decorated by an azobenzene SAM. The simulations explicitly account for the structural and electrostatic disorder sourced by the dielectric, which turns out to be weakly affected by photoisomerization and spatially correlated over a length scale of 4–5 nm. Most interestingly, by combining large-scale (tight binding) density functional theory with Kubo–Greenwood quantum transport calculations, we predict that the trans-cis isomerization should induce a shift in surface electrostatic potential by a few tenths of a volt, accompanied by a variation in conductivity by a factor of about 3.
Analytical Performance and Clinicopathologic Correlation of Four Fecal Calprotectin Methods
Authors: Pelkmans Leonie P J , de Groot Monique J M , Curvers Joyce 
Published: March 2019

Abstract

Objectives
Calprotectin is a noninvasive biomarker that can distinguish inflammatory bowel disease from irritable bowel syndrome. We investigated four automated fecal calprotectin methods on five different platforms for their preanalytical process, analytical performance, and clinicopathologic correlation.

Methods
Four calprotectin methods (Bühlmann, EliA CN, EliA CN2, and DiaSorin) were performed on five platforms (Cobas 8000 E502, Phadia Immunocap 100 and 250, and Liaison and Liaison XL) in two hospital laboratories.

Results
Overall variation for the different extraction devices was less than 19% when feces were of normal consistency. Freeze-thawing of samples resulted in comparable results compared with fresh samples. The different methods had a good analytic correlation (R = 0.83-0.95). Their clinicopathologic correlation was comparable, but the Bühlmann method showed significantly higher calprotectin values in every patient category.

Conclusions
The automated calprotectin methods showed a good performance and comparable clinicopathologic correlation. Due to lack of standardization, the numerical values differ for the various methods.
PD-L1 Expression Patterns in Microsatellite Instability-High Intestinal Adenocarcinoma Subtypes
Authors: Roberts Jordan , Salaria Safia N , Cates Justin , Wang Yang , Vnencak-Jones Cindy , Berlin Jordan , Shi Chanjuan 
Published: March 2019

Abstract

Objectives
To investigate patterns of programmed death protein-1 (PD-L1) expression in microsatellite instability (MSI)-high intestinal carcinomas and correlate them with pathologic and molecular features.

Methods
One hundred and fifteen MSI-high and 41 microsatellite stable carcinomas were included. Tumor sections were immunohistochemically labeled for PD-L1. The results were correlated with histologic subtypes, MSI, and BRAF status.

Results
As expected, MSI status was associated with PD-L1 expression. Among 115 MSI-high tumors, PD-L1 expression was observed on tumor cells in 28 tumors and on tumor-associated inflammatory cells in 77 tumors. Medullary carcinoma demonstrated more frequent PD-L1 expression on tumor cells than mucinous and typical adenocarcinoma. PD-L1 expression was more frequent in medullary and typical adenocarcinoma than in mucinous adenocarcinoma based on combined positive scores. Tumors with more nucleotide shifts by PCR-based MSI testing were more likely to express PD-L1.

Conclusions
Expression of PD-L1 is different among different histologic subtypes of MSI-high intestinal carcinomas.
The Exhaustion of Authenticity: Biopolitical Aural Regimes and American Popular Music
Authors: Moreno Jairo 
Published: March 2019

AbstractJeffrey T. Nealon proposes that “twenty-first-century American biopolitical subjectivity” has as its “overarching logic” an arrangement in which being for something signifies a content-less affirmation: “I’m not like everyone else.” For Nealon, this “excorporative” logic grows out of, coincides with, and exhausts rock music’s discourses of authenticity from the second half of the twentieth century. Today, an endlessly interconnected network emerges in which old forms of cultural “individualism” become ever-interchangeable modes of “hip commodity consumption,” indexing a neoliberal regime that renders “everybody” into “prosumers” (producers-consumers). This review-essay considers the extent and limits of this proposal, querying Nealon’s understanding of listening and aurality and indicating the challenges presented by bypassing the mesopolitical in an effort to outline the macropolitics of consumption and the micropolitics of individuality.
Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize
Authors: Scaglione Davide , Pinosio Sara , Marroni Fabio , Di Centa Eleonora , Fornasiero Alice , Magris Gabriele , Scalabrin Simone , Cattonaro Federica , Taylor Gail , Morgante Michele 
Published: March 2019

Abstract

Background and Aims
The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample the genetic diversity. Genotyping-by-sequencing has become a widely adopted method for cost-effective genotyping. It basically requires no initial investment for design as compared with array-based platforms which have been shown to offer very robust assays. The latter, however, has the drawback of being limited to analyse only the genetic diversity accounted during selection of a set of polymorphisms and design of the assay. In contrast, genotyping-by-sequencing with random sampling of genomic loci via restriction enzymes or random priming has been shown to be fast and convenient but lacks the ability to target specific regions of the genome and to maintain high reproducibility across laboratories.

Methods
Here we present a first adoption of single-primer enrichment technology (SPET) which provides a highly efficient and scalable system to obtain targeted sequence-based large genotyping data sets, bridging the gaps between array-based systems and traditional sequencing-based protocols. To fully explore SPET performance, we conducted a benchmark study in ten Zea mays lines and a large-scale study of a natural black poplar population of 540 individuals with the aim of discovering polymorphisms associated with biomass-related traits.

Key Results
Our results showed the ability of this technology to provide dense genotype information on a customized panel of selected polymorphisms, while yielding hundreds of thousands of untargeted variable sites. This provided an ideal resource for association analysis of natural populations harbouring unexplored allelic diversities and structure such as in black poplar.

Conclusion
The improvement of sequencing throughput and the development of efficient library preparation methods has made it feasible to carry out targeted genotyping-by-sequencing experiments cost-competitively with either random complexity reduction systems or traditional array-based platforms, while maintaining the key advantages of both technologies.
Competition, seed dispersal and hunting: what drives germination and seedling survival in an Afrotropical forest?
Authors: Olsson Ola , Nuñez-Iturri Gabriela , Smith Henrik G , Ottosson Ulf , Effiom Edu O 
Published: March 2019

Abstract
Disentangling the contributions of different processes that influence plant recruitment, such as competition and seed dispersal, is important given the increased human-mediated changes in tropical forest ecosystems. Previous studies have shown that seedling communities in an Afrotropical rainforest in southeastern Nigeria are strongly affected by the loss of important seed-dispersing primates, including Cross River gorillas (Gorilla gorilla diehli), chimpanzee (Pan troglodytes elioti) and drill (Mandrillus leucophaeus). Here we study how germination and survival of tree seedlings are affected by competition and reduced seed dispersal in three contiguous forest reserves, in southeastern Nigeria, with similar mature tree species composition and structure. We use an experimental design aimed at manipulating the effect of competition among seedlings in three protected and three hunted sites within the reserves. We use a total of sixty 5 × 5 m plots of three types: plots cleared of all seedlings, plots selectively cleared of all primate-dispersed seedlings and control plots. All seedlings were identified, measured, assigned to dispersal mode and tagged, and after 1 year we evaluated survival, mortality and new recruits. We found that in hunted sites germination of abiotically dispersed species was over four times higher in cleared plots compared to control plots, whereas germination of primate-dispersed species was the same, which indicated that dispersal limitation was the dominant force in seedling recruitment in hunted sites. This was supported by the fact that the germination of all dispersal modes in the selectively cleared plots in protected sites was similar to the control plots in the same sites, but germination of abiotically dispersed species was significantly lower than in cleared plots in hunted sites. Competition among seedlings was mostly evident from the fact that 75 % more seedlings of primate-dispersed species germinated in cleared compared to control plots in protected sites. We conclude that inter-seedling competition may be irrelevant to seedling recruitment in hunted sites, where dispersal limitation appears to be a much stronger force shaping the seedling plant community, and thus hunting indirectly reverses the importance of competition and dispersal limitation in structuring seedling communities.
Carotid intraplaque neovascularization predicts coronary artery disease and cardiovascular events
Authors: Mantella Laura E , Colledanchise Kayla N , Hétu Marie-France , Feinstein Steven B , Abunassar Joseph , Johri Amer M 
Published: March 2019

Abstract

Aims
It is thought that the majority of cardiovascular (CV) events are caused by vulnerable plaque. Such lesions are rupture prone, in part due to neovascularization. It is postulated that plaque vulnerability may be a systemic process and that vulnerable lesions may co-exist at multiple sites in the vascular bed. This study sought to examine whether carotid plaque vulnerability, characterized by contrast-enhanced ultrasound (CEUS)-assessed intraplaque neovascularization (IPN), was associated with significant coronary artery disease (CAD) and future CV events.

Methods and results
We investigated carotid IPN using carotid CEUS in 459 consecutive stable patients referred for coronary angiography. IPN was graded based on the presence and location of microbubbles within each plaque (0, not visible; 1, peri-adventitial; and 2, plaque core). The grades of each plaque were averaged to obtain an overall score per patient. Coronary plaque severity and complexity was also determined angiographically. Patients were followed for 30 days following their angiogram. This study found that a higher CEUS-assessed carotid IPN score was associated with significant CAD (≥50% stenosis) (1.8 ± 0.4 vs. 0.5 ± 0.6, P < 0.0001) and greater complexity of coronary lesions (1.7 ± 0.5 vs. 1.3 ± 0.8, P < 0.0001). Furthermore, an IPN score ≥1.25 could predict significant CAD with a high sensitivity (92%) and specificity (89%). The Kaplan–Meier analysis demonstrated a significantly higher proportion of participants having CV events with an IPN score ≥1.25 (P = 0.004).

Conclusion
Carotid plaque neovascularization was found to be predictive of significant and complex CAD and future CV events. CEUS-assessed carotid IPN is a clinically useful tool for CV risk stratification in high-risk cardiac patients.
External applicability of the COMPASS trial: the Western Denmark Heart Registry
Authors: Würtz Morten , Olesen Kevin Kris Warnakula , Thim Troels , Kristensen Steen Dalby , Eikelboom John W , Maeng Michael 
Published: March 2019

Abstract

Aims
In the COMPASS trial, combined aspirin and rivaroxaban treatment reduced ischaemic events in patients with stable coronary artery disease (CAD) or peripheral artery disease (PAD). We estimated the proportion of COMPASS eligible patients among unselected patients undergoing coronary angiography (CAG) and compared outcome rates among COMPASS eligible and non-eligible patients.

Methods and results
We applied the COMPASS study criteria on patients undergoing CAG in Western Denmark (2004–11). Both COMPASS eligible and non-eligible patients had CAD/PAD and met no exclusion criteria, but only COMPASS eligible patients met the inclusion criteria. We assessed the COMPASS primary endpoint of cardiovascular death, ischaemic stroke, haemorrhagic stroke, or myocardial infarction (MI). We computed event rates and adjusted incidence rate ratios (aIRRs). Of 80 071 patients undergoing CAG, 27 939 did not have CAD or PAD and were not considered. Of the 52 132 patients remaining, 11 930 were COMPASS eligible. Rates of the primary endpoint were 4.8 (95% confidence interval 4.6–5.0) events per 100 person-years among COMPASS eligible patients and 2.3 (2.2–2.4) among COMPASS non-eligible patients [aIRR 1.7 (1.6–1.9)]. COMPASS eligible patients also had higher risks of cardiovascular death [aIRR 2.5 (2.1–3.0)], ischaemic stroke [aIRR 1.4 (1.2–1.6)], and MI [aIRR 1.9 (1.7–2.1)].

Conclusion
In this all-comers CAG cohort, 15% were eligible for combined aspirin and rivaroxaban treatment. COMPASS eligible patients had up to 2.5-fold higher rates of cardiovascular events than non-eligible patients. The higher incidence of ischaemic events in COMPASS eligible patients highlights an unmet need for additional preventive measures.
Early silent graft failure in off-pump coronary artery bypass grafting: a computed tomography analysis†
Authors: Zientara Alicja , Rings Laura , Bruijnen Hans , Dzemali Omer , Odavic Dragan , Häussler Achim , Gruszczynski Michal , Genoni Michele 
Published: March 2019

Abstract

OBJECTIVES
The purpose was to assess predictors of early silent graft failure prior to discharge by multislice computed tomography in patients after off-pump coronary artery bypass grafting.

METHODS
From January 2017 until April 2018, 192 computed tomographic scans of consecutive asymptomatic patients were performed (seventh postoperative day ± 4 days) and analysed retrospectively. In total, 359 arterial and 278 venous anastomoses were evaluated. Two patient groups (overall patent anastomoses versus at least 1 occluded anastomosis) were compared. Cardiovascular risk factors, collateralization according to Rentrop, grade of native vessel stenosis and intraoperative flow measurements were analysed. Inferential statistics were performed with the Mann–Whitney U-test. Nominal and categorical variables were tested with the Fisher–Freeman–Halton exact test.

RESULTS
In 33 patients, at least 1 occluded anastomosis could be identified, predominantly in women (P = 0.04). The patency of the arterial anastomoses was 96.4% and 88.9% for the venous anastomoses. In 14 patients with occluded anastomoses, a successful interventional revascularization was performed before discharge. There were significant differences in lower bypass flow [P = 0.02, odds ratio 3.2, 95% confidence interval (CI) 1.7–6.0] and higher pulsatility index (P < 0.001, odds ratio 4.5, 95% CI 2.4–8.5) in the occluded group. A calculated cut-off value identified an increased probability for graft occlusion at a flow under 23 ml/min and a pulsatility index greater than 2.3.

CONCLUSIONS
Early silent graft failure occurred predominantly in venous grafts, with a tendency to female gender. A lower flow rate and a higher pulsatility index were significantly associated with graft occlusion, whereas collateralization and the degree of native vessel stenosis seem to play a tangential role. Fourteen patients had a successful percutaneous revascularization before discharge.

Clinical trial registration number
NCT03657199.