bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent indefinite for dysplasia in Barrett’s esophagus is a risk factor for dysplastic progression to low-grade dysplasia
Authors: Henn Andrew J , Song Kevin Y , Gravely Amy A , Mesa Hector , Sultan Shahnaz , Shaheen Nicholas J , Shaukat Aasma , Hanson Brian J 
Published: May 2020

SummaryPatients with Barrett’s esophagus (BE) are at increased risk of esophageal adenocarcinoma (EAC). The risk is largely based on the degree of dysplasia. Dysplasia cannot always be differentiated from inflammatory changes, and therefore may be classified as indefinite for dysplasia (IND). The risk of progressive dysplasia in patients with IND is unclear. Our aim is to characterize the risk of progression in US veterans with BE-IND. We performed a single-center retrospective cohort study of patients with BE-IND between 2006 and 2016. All IND was diagnosed by consensus conference with an expert gastrointestinal (GI) pathologist or review by an expert GI pathologist and persistence was defined as IND present on subsequent endoscopic biopsy. The primary outcome was the incidence rate of high-grade dysplasia (HGD)/EAC. Secondary outcomes included any progression including incident low-grade dysplasia (LGD), any prevalent dysplasia and risk factors for dysplastic progression, namely persistent IND. Risk factors for progression were assessed using univariate and multivariate analysis with logistic regression. Among 107 patients with BE-IND, there were no incident cases of HGD/EAC. Twenty patients (18.7%) developed incident LGD during a median follow-up of 2.39 years (interquartile range, 1.13–5.17). The annual rate of progression to LGD was 5.95 per 100 patient-years (95% CI, 3.73–9.02). Prevalent dysplasia was common (9.3%). Eight patients had prevalent LGD, one patient had prevalent HGD and one patient had prevalent EAC. Twenty-eight patients (30.1%) were found to have persistent IND. Among those with persistent IND, 10 (36%) patients progressed to LGD (none to HGD/EAC). The progression rate to LGD for patients with persistent IND was 7.86 (95% CI, 3.99–14.02) cases per 100 patient-years versus 4.78 (95% CI, 2.48–8.52) for nonpersistent IND (P = 0.036). The odds ratio for progression to LGD in persistent IND was 3.06 (95% CI, 1.08–8.64). In multivariate analysis adjusting for age, smoking history, presence of hiatal hernia and BMI &gt; 30, persistent IND remained significant (OR 3.23; 95% CI, 1.04–9.98). Regression to nondysplastic BE was very common. Seventy-one (61%) patients developed complete and sustained regression of all dysplastic changes at last follow-up. Persistent IND, present in one-third of patients with IND, is an independent risk factor for progression to LGD. Although no patients in this cohort developed HGD/EAC, prevalent dysplasia was common (9.3%). Taken together, patients with IND should receive close surveillance for both prevalent and incident dysplasia especially if IND is persistent.
Intra-population strain variation in phosphorus storage strategies of the freshwater cyanobacterium Raphidiopsis raciborskii
Authors: Xiao Man , Hamilton David P , Chuang Ann , Burford Michele A 
Published: May 2020

ABSTRACTSeveral cyanobacteria, including diazotrophic Raphidiopsis raciborskii, can form harmful blooms when dissolved inorganic phosphorus concentrations are very low. We hypothesized that R. raciborskii strains would vary in phosphorus (P) allocations to cell growth and storage, providing resilience of populations to continuously low or variable P supplies. We tested this hypothesis using six toxic strains (producing cylindrospermopsins) isolated from a field population using batch monocultures with and without P and dissolved inorganic nitrogen (DIN). Treatments replete with DIN, irrespective of P addition, had similar exponential growth rates for individual strains. P storage capacity varied 4-fold among strains and was significantly higher in DIN-free treatments than in replete treatments. P was stored by all R. raciborskii strains, in preference to allocation to increase growth rates. P stores decreased with increased growth rate across strains, but weeere not related to the time to P starvation in P-free treatments. The storage capacity of R. raciborskii, combined with strategies to efficiently uptake P, means that P controls may not control R. raciborskii populations in the short term. Intra-population strain variation in P storage capacity will need to be reflected in process-based models to predict blooms of R. raciborskii and other cyanobacteria adapted to low-P conditions.
Androgen receptor variants: RNA-based mechanisms and therapeutic targets
Authors: Tietz Kiel T , Dehm Scott M 
Published: May 2020

Abstract
Prostate cancer is the second leading cause of male cancer death in the United States. The androgen receptor (AR) transcription factor is a master regulator of normal glandular homeostasis in the prostate, as well as growth and survival of prostate cancer cells. Therefore, AR-targeted therapies are effective for improving overall survival of patients with advanced prostate cancer that is incurable by surgery or radiation. However, prostate cancer will inevitably progress on AR-targeted therapies to a castration-resistant prostate cancer (CRPC) phenotype that accounts for virtually all prostate cancer-specific death. mRNA transcript variants of the AR gene are expressed in CRPC cells and can be translated to produce AR variant (AR-V) proteins that function as ligand-independent, constitutively active transcription factors. AR-Vs are able to support growth of CRPC cells by promoting expression of AR target genes that are normally suppressed by AR-targeted therapies. Knowledge of mechanisms that govern expression of AR-Vs is incomplete. Studies have shown genomic rearrangements of the AR gene underlie expression of diverse AR-Vs in certain CRPC tumors, but post-transcriptional processes represent a broader regulatory mechanism for expression of AR-Vs in CRPC. This review focuses on alternative splicing, 3′ end processing, miRNA-mediated mRNA repression, of AR and AR-V expression and the potential these mechanisms hold as therapeutic targets for CRPC.
On a Search for a Neurogenomics of Cognitive Processes Supporting Avian Migration and Navigation
Authors: Bingman Verner P , Ewry Emily M 
Published: May 2020

Synopsis
The migratory behavioral profile of birds is characterized by considerable variation in migratory phenotype, and a number of distinct orientation and navigational mechanisms supports avian migration and homing. As such, bird navigation potentially offers a unique opportunity to investigate the neurogenomics of an often spectacular, naturally occurring spatial cognition. However, a number of factors may impede realization of this potential. First, aspects of the migratory behavior displayed by birds, including some navigational-support mechanisms, are under innate/genetic influence as, for example, young birds on their first migration display appropriate migratory orientation and timing without any prior experience and even when held in captivity from the time of birth. Second, many of the genes with an allelic variation that co-varies with migratory phenotype are genes that regulate processes unrelated to cognition. Where cognition and navigation clearly converge is in the familiar landmark/landscape navigation best studied in homing pigeons and known to be dependent on the hippocampus. Encouraging here are differences in the hippocampal organization among different breeds of domestic pigeons and a different allelic profile in the LRP8 gene of homing pigeons. A focus on the hippocampus also suggests that differences in developmentally active genes that promote hippocampal differentiation might also be genes where allelic or epigenetic variation could explain the control of or comparison-group differences in a cognition of navigation. Sobering, however, is just how little has been learned about the neurogenomics of cognition (“intelligence”) in humans despite the vast resources and research activity invested; resources that would be unimaginable for any avian study investigating bird navigation.
Recurrent left ventricular pseudoaneurysm with an ominous presentation
Authors: Seabra Daniel , Moreno Nuno , Pissarra Diana , Amorim Mário 
Published: May 2020

Abstract
We present a case of a 58-year-old male with a recurrent left ventricular pseudoaneurysm. Two years before, the patient underwent repair of an apical aneurysm with a thrombus, which was very likely infected and complicated by huge pseudoaneurysm. The dramatic presentation of the recurrent pseudoaneurysm, as it invaded the left chest wall tissue and protruded into the skin through an intercostal space, and the complexity of the procedures are well documented by surgical and accompanying technical images.
The role of overweight in the association between the Mediterranean diet and the risk of type 2 diabetes mellitus: a mediation analysis among 21 585 UK biobank participants
Authors: André Perrine , Proctor Gordon , Driollet Bénédicte , Garcia-Esquinas Esther , Lopez-Garcia Esther , Gomez-Cabrero David , Neyraud Eric , Rodriguez-Artalejo Fernando , Morzel Martine , Féart Catherine 
Published: May 2020

AbstractBackgroundThere is growing evidence that the Mediterranean (Medi) diet may lower the risk of type 2 diabetes mellitus (T2DM). Whether this association is due to the Medi diet by itself or is mediated by a diet-associated lower rate of overweight is uncertain. Our aim was to disentangle these relationships among UK adults.MethodsBased on 21 585 participants from the UK Biobank cohort, the adherence to the Medi diet (high fruits, vegetables, legumes, cereals, fish, olive oil; low meat, dairy products; and intermediate alcohol intakes) was assessed (range 0–18). Data on diabetes were self-reported, and overweight was defined as a body mass index (BMI) ≥ 25 kg/m². A mediation analysis was implemented to disentangle the role of overweight in the Medi diet-T2DM relationship.ResultsThe average baseline Medi diet score was 8.8 [standard deviation (SD) 2.6]. During a mean follow-up of 6.1 years, 473 individuals developed T2DM. A higher adherence to a Medi diet (+1 point) was associated with 14% decreased risk of T2DM [hazard ratio (HR): 0.86, 95% confidence interval (CI): 0.82–0.90]. This association split into an indirect effect of 10%, mediated by lower odds of overweight (HR: 0.90, 95% CI: 0.87–0.92), and a direct effect of the Medi diet of 4% (HR: 0.96, 95% CI: 0.93–0.99), regardless of the effect mediated by overweight.ConclusionsConsidered as a single mediator, reduced overweight mainly contributes to the association between greater Medi diet adherence and lower risk of T2DM on this British subsample. However, the direct effect of the diet on the risk of T2DM, even weaker, should not be overlooked.
Fourier Frames for Surface-Carried Measures
Authors: Iosevich Alex , Lai Chun-Kit , Liu Bochen , Wyman Emmett 
Published: May 2020

Abstract
In this paper, we show that the surface measure on the boundary of a convex body of everywhere positive Gaussian curvature does not admit a Fourier frame. This answers a question proposed by Lev and provides the 1st example of a uniformly distributed measure supported on a set of Lebesgue measure zero that does not admit a Fourier frame. In contrast, we show that the surface measure on the boundary of a polytope always admits a Fourier frame. We also explore orthogonal bases and frames adopted to sets under consideration. More precisely, given a compact manifold $M$ without a boundary and $D \subset M$, we ask whether $L^2(D)$ possesses an orthogonal basis of eigenfunctions. The non-abelian nature of this problem, in general, puts it outside the realm of the previously explored questions about the existence of bases of characters for subsets of locally compact abelian groups. This paper is dedicated to Alexander Olevskii on the occasion of his birthday. Olevskii’s mathematical depth and personal kindness serve as a major source of inspiration for us and many others in the field of mathematics.
The Domestic Impact of International Standards
Authors: Perlman Rebecca L 
Published: May 2020

Abstract
Regulation is no longer purely a domestic affair. International standards now exist across a broad range of regulatory arenas, touching on issues that may be central to domestic values, such as the regulation of health, safety, and the environment. Although a number of studies have looked at the domestic impact of globalization more generally, few scholars have evaluated the effects of international standards, specifically. This paper investigates that issue, with an empirical focus on agrochemicals. Using original data on changes to US agrochemical regulations between 1996 and 2015, I evaluate whether and how domestic rules have changed in response to international standards. Contrary to common fears, I find little evidence that international standards primarily act as a ceiling, thereby undermining domestic regulations. Instead, international standards seem to serve as focal points, pulling nations toward leniency as well as toward stringency. These findings not only contribute to the broader literature on the domestic effects of globalization, but they also allay concerns that international standards could act as a regulatory cap, encouraging nations to sacrifice caution for economic gain.
Current status and prospects of cryopreservation in aquatic crustaceans and other invertebrates
Authors: Guo Jun-Ho , Weng Ching-Feng 
Published: May 2020

AbstractThe response of crustaceans and other aquatic invertebrates to low temperatures and the application on cryopreservation has been extensively studied experimentally, which has resulted in the development of techniques that have proven to be valuable. This review addresses cryopreservation protocols for cells such as the general freezing damage caused by pre-treatment, freezing, and thawing as well as important factors that affect the preservation of sperm and embryos of aquatic invertebrates. This review also addresses the short- and long-term effects of low temperature resulting from cryopreservation, as well as a review of the relevant literature on the subject. We discuss specific issues related to the effect of ice crystal formation and freezing time on the survival rates of aquatic species: freezing and thawing rates, toxicity of cryoprotectant concentrations on embryos, osmotic pressure effects on cells, the formation of ice crystals inside and outside of cells, the effects of cryopreservation on development, and the effects of different concentrations of antifreeze protectants.
Responsive and Adaptive Survey Design: Use of Bias Propensity During Data Collection to Reduce Nonresponse Bias
Authors: Peytchev Andy , Pratt Daniel , Duprey Michael 
Published: May 2020

Abstract
Reduction in nonresponse bias has been a key focus in responsive and adaptive survey designs, through multiple phases of data collection, each defined by a different protocol, and targeting interventions to a subset of sample elements. Key in this approach is the identification of nonrespondents who, if interviewed, can reduce nonresponse bias in survey estimates. From a design perspective, we need to identify an appropriate model to select targeted cases, in addition to an effective intervention (change in protocol). From an evaluation perspective, we need to compare estimates to a control condition that is often omitted from study designs, in addition to the need for benchmark estimates for key survey measures to provide estimates of nonresponse bias. We introduced a bias propensity approach for the selection of sample members to reduce nonresponse bias. Unlike a response propensity approach in which the objective is to maximize the prediction of nonresponse, this new approach deliberately excludes strong predictors of nonresponse that are uncorrelated with survey measures and uses covariates that are of substantive interest to the study. We also devised an analytic approach to simulate which sample members would have responded in a control condition. This study also provided a rare opportunity to estimate nonresponse bias, using rich sampling frame information, prior round survey data, and data from extensive nonresponse follow-up. The bias propensity model yielded reasonable fit despite the exclusion of the strongest predictors of nonresponse. The intervention was found to be effective in increasing participation among identified sample members. On average, the responsive and adaptive survey design reduced nonresponse bias by more than one-quarter—almost one percentage point—regardless of the choice of benchmark estimates. Effort under the control condition did not reduce nonresponse bias. While results are strongly encouraging, we argue for replication with varied populations and methods.
Integrating N signals and root growth: the role of nitrate transceptor NRT1.1 in auxin-mediated lateral root development
Authors: Lay-Pruitt Katerina S , Takahashi Hideki 
Published: May 2020

This article comments on:
Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A and Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany 71, 4480–4494.
CReSCENT: CanceR Single Cell ExpressioN Toolkit
Authors: Mohanraj Suluxan , Díaz-Mejía J Javier , Pham Martin D , Elrick Hillary , Husić Mia , Rashid Shaikh , Luo Ping , Bal Prabnur , Lu Kevin , Patel Samarth , Mahalanabis Alaina , Naidas Alaine , Christensen Erik , Croucher Danielle , Richards Laura M , Shooshtari Parisa , Brudno Michael , Ramani Arun K , Pugh Trevor J 
Published: May 2020

AbstractCReSCENT: CanceR Single Cell ExpressioN Toolkit (https://crescent.cloud), is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA sequencing (scRNA-seq) data. While scRNA-seq data for tumour specimens are readily generated, subsequent analysis requires high-performance computing infrastructure and user expertise to build analysis pipelines and tailor interpretation for cancer biology. CReSCENT uses public data sets and preconfigured pipelines that are accessible to computational biology non-experts and are user-editable to allow optimization, comparison, and reanalysis for specific experiments. Users can also upload their own scRNA-seq data for analysis and results can be kept private or shared with other users.
Survival After Surgery for Renal Cell Carcinoma Metastatic to the Spine: Impact of Modern Systemic Therapies on Outcomes
Authors: Shankar Ganesh M , Van Beaver Laura A , Choi Bryan D , Hadzipasic Muhamed , Sivaganesan Ahilan , Karhade Aditya V , Ferrone Marco L , Harris Mitchel B , Schoenfeld Andrew J , Sadow Peter M , Oh Kevin , Schwab Joseph H , Saylor Philip J , Shin John H 
Published: May 2020

Abstract

BACKGROUND
Modern medical management of metastatic renal cell carcinoma (RCC) includes therapies targeting tyrosine kinases, growth pathways (mammalian target of rapamycin (mTOR)), and immune checkpoints.

OBJECTIVE
To test our hypothesis that patients with spinal metastases would benefit from postoperative systemic therapy despite presenting with disease that, in many cases, was resistant to prior systemic therapy.

METHODS
This is an Institutional Review Board-approved clinical retrospective cohort analysis. A sample of adult patients with RCC metastatic to the spine who underwent operative intervention between January 2010 and December 2017 at 2 large academic medical centers was used in this study.

RESULTS
We identified 78 patients with metastatic RCC in whom instrumented stabilization was performed in 79% and postoperative stereotactic radiosurgery was performed in 41% of patients. Of patients presenting with weakness or myelopathy, 93% noted postoperative improvement and 78% reported improvement in radicular and axial paraspinal pain severity. Increased overall survival (OS) (913 d (95% CI: 633-1975 d, n = 49) vs 222 d (95% CI: 143-1005 d, n = 29), P = .003) following surgery was noted in patients who received postoperative systemic therapy a median of 80 d (interquartile range 48-227 d) following the surgical intervention.

CONCLUSION
Postoperative outcomes and palliation of symptoms for metastatic RCC without targeted therapies in this cohort are similar to those reported in earlier series prior to the adoption of these systemic therapies. We observed a significantly longer OS among patients who received modern systemic therapies postoperatively. These findings have implications for the preoperative evaluation of patients with systemic disease who may have been deemed poor surgical candidates prior to the availability of these systemic therapies.
Quantifying the Gap Between Equilibrium and Optimum under Monopolistic Competition*
Authors: Behrens Kristian , Mion Giordano , Murata Yasusada , Suedekum Jens 
Published: May 2020

Abstract
Equilibria and optima generally differ in imperfectly competitive markets. Although this is well understood theoretically, it is unclear how large the welfare distortions are in the aggregate economy. Do they matter quantitatively? To answer this question, we develop a multisector monopolistic competition model with endogenous firm entry and selection, productivity, and markups. Using French and UK data, we quantify the gap between the equilibrium and optimal allocations. We find that inefficiencies in the labor allocation and entry between sectors, as well as inefficient selection and output per firm within sectors, generate welfare losses of about 6%–10% of GDP.
The GARDpotency Assay for Potency-Associated Subclassification of Chemical Skin Sensitizers—Rationale, Method Development, and Ring Trial Results of Predictive Performance and Reproducibility
Authors: Gradin Robin , Johansson Angelica , Forreryd Andy , Aaltonen Emil , Jerre Anders , Larne Olivia , Mattson Ulrika , Johansson Henrik 
Published: May 2020

Abstract
Proactive identification and characterization of hazards attributable to chemicals are central aspects of risk assessments. Current legislations and trends in predictive toxicology advocate a transition from in vivo methods to nonanimal alternatives. For skin sensitization assessment, several OECD validated alternatives exist for hazard identification, but nonanimal methods capable of accurately characterizing the risks associated with sensitizing potency are still lacking. The GARD (Genomic Allergen Rapid Detection) platform utilizes exposure-induced gene expression profiles of a dendritic-like cell line in combination with machine learning to provide hazard classifications for different immunotoxicity endpoints. Recently, a novel genomic biomarker signature displaying promising potency-associated discrimination between weak and strong skin sensitizers was proposed. Here, we present the adaptation of the defined biomarker signature on a gene expression analysis platform suited for routine acquisition, confirm the validity of the proposed biomarkers, and define the GARDpotency assay for prediction of skin sensitizer potency. The performance of GARDpotency was validated in a blinded ring trial, in accordance with OECD guidance documents. The cumulative accuracy was estimated to 88.0% across 3 laboratories and 9 independent experiments. The within-laboratory reproducibility measures ranged between 62.5% and 88.9%, and the between-laboratory reproducibility was estimated to 61.1%. Currently, no direct or systematic cause for the observed inconsistencies between the laboratories has been identified. Further investigations into the sources of introduced variability will potentially allow for increased reproducibility. In conclusion, the in vitro GARDpotency assay constitutes a step forward for development of nonanimal alternatives for hazard characterization of skin sensitizers.