bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large‐scale analysis of BAP1 expression reveals novel associations with clinical and molecular features of malignant pleural mesothelioma
Authors: De Rienzo Assunta , Chirieac Lucian R , Hung Yin P , Severson David T , Freyaldenhoven Samuel , Gustafson Corinne E , Dao Nhien T , Meyerovitz Claire V , Oster Michela E , Jensen Roderick V , Yeap Beow Y , Bueno Raphael , Richards William G 
Published: September 2020

AbstractBRCA1‐associated protein‐1 (BAP1) expression is commonly lost in several tumors including malignant pleural mesothelioma (MPM). Presence or absence of immunohistochemical BAP1 nuclear staining in tumor cells is currently used for differential diagnosis of MPM. In this study, a large cohort of 596 MPM tumors with available clinical data was analyzed to examine associations of BAP1 staining pattern with clinical and molecular features that may reflect the impact of BAP1 mutation on MPM biology. Cases were classified according to the BAP1 staining pattern of tumor cells. Exome and RNA‐sequencing data were available for subsets of cases. Levels of mRNA encoding claudin 15 (CLDN15) and vimentin (VIM) were determined using RT‐qPCR on 483 cases to estimate the relative proportions of epithelial‐like and mesenchymal‐like components in each tumor. Four BAP1 staining patterns were observed: single‐pattern nuclear staining (36%), single‐pattern cytoplasmic staining (25%), single‐pattern absent staining (12%), and combinations of these staining patterns (27%). This study confirmed prior reports that nuclear BAP1 is more frequently associated with wild‐type BAP1 and sarcomatoid histology. However, no associations between BAP1 staining pattern(s) and mutations in specific protein domains and/or mutation type were observed. BAP1 staining patterns were significantly associated (p < 0.001) with BAP1 gene expression, MPM histologic subtypes, molecular clusters, and markers of epithelial‐to‐mesenchymal transition. Frequent observation of combinations of BAP1 staining patterns in MPM tumors indicated intra‐tumoral heterogeneity of BAP1 status. Cytoplasmic BAP1 staining was identified as a putative indicator of favorable prognosis in non‐epithelioid MPM. In conclusion, novel significant associations among different BAP1 staining patterns and subgroups of MPM tumors were observed, suggesting that the role of BAP1 in tumor progression may be more complex than its presumed tumor suppressor function. Cytoplasmic staining was identified as a putative indicator of favorable prognosis in non‐epithelioid MPM, potentially addressing a critical need in clinical decision‐making in this disease. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
Effect of processing method on cellulose nanocrystal/polyethylene‐co‐vinyl alcohol composites
Authors: Orr Matthew P. , Sonekan Amidat , Shofner Meisha L. 
Published: September 2020

AbstractCellulose nanocrystals (CNCs) have emerged as fillers of interest to the polymer nanocomposite community due to their inherent properties and renewable precursors. However, challenges persist to incorporate CNCs into polymer matrices due to component incompatibility and/or thermal stability limitations of the nanoparticles. Therefore, the objective of this research is to examine the efficacy of different processing methods in producing CNC/polymer composites. In this work, CNCs were incorporated into polyethylene‐co‐vinyl alcohol (EVOH) using either a solution casting method or a multi‐step method involving the same solution casting method followed by a melt mixing step. The resulting neat EVOH and composite materials were characterized to understand how the viscoelastic character and mechanical properties were influenced by CNC loading and processing method. The results of characterization experiments and micromechanical modeling suggested that the nanoparticle networks produced by each method were different and that a combined solution‐melt processing method is beneficial in producing composites with improved properties, particularly at higher CNC loadings. This processing strategy may be more broadly applied to other nanocomposites.
Optimization of antimicrobials in the treatment of cystic fibrosis pulmonary exacerbations:  II. Therapies for allergic bronchopulmonary aspergillosis
Authors: Epps Quovadis J. , Epps Kevin L. , Zobell Jeffery T. , Young David C. 
Published: September 2020

AbstractThis review is the second article in the State‐of‐the‐Art series and aims to evaluate medications used in the treatment of allergic bronchopulmonary aspergillosis (ABPA) in pediatric and adult patients with cystic fibrosis (CF). ABPA is one of several organisms that are found in the airways of CF patients. This review provides an evidence‐based summary of pharmacokinetic (PK)/pharmacodynamic (PD), tolerability, and efficacy studies of medications including corticosteroids, amphotericin B, azole antifungals (isavuconazole, itraconazole, posaconazole, and voriconazole), and a monoclonal antibody omalizumab in the treatment of ABPA and identifies areas where further study is warranted.
Exposure‐Safety Analyses Identify Predictors of Change in Bone Mineral Density and Support Elagolix Labeling for Endometriosis‐Associated Pain
Authors: Abbas Suleiman Ahmed , Nader Ahmed , Winzenborg Insa , Beck Denise , Polepally Akshanth R. , Ng Juki , Noertersheuser Peter , Mostafa Nael M. 
Published: September 2020

Elagolix is a novel oral gonadotropin releasing hormone receptor antagonist, that can suppress estradiol in a dose‐dependent manner. It is indicated for management of moderate‐to‐severe pain associated with endometriosis. A population exposure‐response model describing the relationship between elagolix exposure and changes in bone mineral density (BMD) was developed using data from four phase III studies in premenopausal women with endometriosis‐associated pain. Elagolix pharmacokinetic exposure‐dependent changes in BMD were described by an indirect‐response maximum effect (Emax) model through stimulation of bone resorption. African American race, higher body mass index (BMI), and lower type‐I collagen C‐telopeptide concentrations were significantly associated with higher baseline BMD. Higher BMI was significantly associated with higher bone formation rates. Simulations using the final model demonstrated that elagolix 150 mg q.d. dosing for 24 months is predicted to result in −1.45% (−2.04 to −0.814) decrease from baseline in BMD and were used to support corresponding dosing recommendations in the label.
Urological and sexual function after robotic and laparoscopic surgery for rectal cancer: A systematic review, meta‐analysis and meta‐regression
Authors: Wee Ian Jun Yan , Kuo Li‐Jen , Ngu James Chi‐Yong 
Published: September 2020

AbstractBackgroundThis systematic review sought to compare the urogenital functions after laparoscopic (LAP) and robotic (ROB) surgery for rectal cancer.MethodsThis study conformed to the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses guidelines.ResultsTwenty‐six studies (n = 2709 for ROB, n = 2720 for LAP) were included. There was a lower risk of 30‐day urinary retention in the ROB group (risk ratios 0.78, 95% confidence interval [CI] 0.61–0.99), but the long‐term risk was comparable (p = 0.460). Meta‐regression showed a small, positive relationship between age and risk of 30‐day urinary retention in both the ROB (p = 0.034) and LAP groups (p = 0.004). The International Prostate Symptom Score was better in the ROB group at 3 months (mean difference [MD] −1.58, 95% CI −3.10 to −0.05). The International Index of Erectile Function score was better in the ROB group at 6 months (MD 4.06, 95% CI 2.38 – 5.74).ConclusionWhile robotics may improve urogenital function after rectal surgery, the quality of evidence is low based on the Grading of Recommendations, Assessment, Development and Evaluation approach.
Robust control for state constrained systems based on composite barrier Lyapunov functions
Authors: Llorente‐Vidrio Dusthon , Mera Manuel , Salgado Ivan , Chairez Isaac 
Published: September 2020

SummaryThis study aims to design a robust state feedback controller for uncertain and perturbed linear systems with state constraints described by a polytope. This novel design incorporates the use of a composite barrier Lyapunov function (CBLF) and the convex hull of a set of ellipsoids inscribed in the given polytopic constraint set. The CBLF is used to ensure that this convex hull is an invariant set for the perturbed system states. Then, an optimization scheme is implemented to maximize the size of this invariant set to use it as a safe set. This is a set of initial conditions ensuring that the system solutions conform to the constraints for any subsequent time instant. Additionally, a minimal ultimate bound for the states is calculated to ensure asymptotic convergence to a region as close to the origin as possible. This region is characterized by a second convex hull of ellipsoids using the well‐known attractive ellipsoid method and the CBLF. Numerical simulations illustrate and compare the obtained results against a similar approach, considering the classical quadratic Lyapunov function, instead of the CBLF.
Information frictions and entrepreneurship
Authors: Hegde Deepak , Tumlinson Justin 
Published: September 2020

AbstractResearch SummaryWhy do individuals become entrepreneurs? Why do some succeed? We propose two theories in which information frictions play a central role in answering these questions. Empirical analysis of longitudinal samples from the United States and the United Kingdom reveals the following patterns: (a) entrepreneurs have higher cognitive ability than employees with comparable education, (b) employees have better education than equally able entrepreneurs, and (c) entrepreneurs' earnings are higher and exhibit greater variance than employees with similar education. These and other empirical tests support our asymmetric information theory of entrepreneurship that when information frictions cause firms to undervalue workers lacking traditional credentials, workers' quest to maximize their private returns drives the most able into successful entrepreneurship.Managerial SummarySteve Jobs, Bill Gates, Mark Zuckerberg, Rachael Ray, and Oprah Winfrey are all entrepreneurs whose educational qualifications belie their extraordinary success. Are they outliers or do their examples reveal a link between education and success in entrepreneurship? We argue that employers assess potential workers based on their educational qualifications, especially early in their careers when there is little direct information on work accomplishments and productivity. This leads those who correctly believe that they are better than their résumés show to become successful entrepreneurs. Evidence from two nationally representative samples of workers (from the United States and the United Kingdom) supports our theory, which applies to equally to the immigrant food vendor lacking a high school diploma as well as the PhD founder of a science‐based startup.
Exploration and Investigation of Periodic Elements for Electrocatalytic Nitrogen Reduction
Authors: Patil Shivaraj B. , Wang Di‐Yan 
Published: September 2020

AbstractHigh demand for green ecosystems has urged the human community to reconsider and revamp the traditional way of synthesis of several compounds. Ammonia (NH3) is one such compound whose applications have been extended from fertilizers to explosives and is still being synthesized using the high energy inhaling Haber‐Bosch process. Carbon free electrocatalytic nitrogen reduction reaction (NRR) is considered as a potential replacement for the Haber‐Bosch method. However, it has few limitations such as low N2 adsorption, selectivity (competitive HER reactions), low yield rate etc. Since it is at the early stage, tremendous efforts have been devoted in understanding the reaction mechanism and screening of the electrocatalysts and electrolytes. In this review, the electrocatalysts are classified based on the periodic table with heat maps of Faraday efficiency and yield rate of NH3 in NRR and their electrocatalytic properties toward NRR are discussed. Also, the activity of each element is discussed and short tables and concise graphs are provided to enable the researchers to understand recent progress on each element. At the end, a perspective is provided on countering the current challenges in NRR. This review may act as handbook for basic NRR understandings, recent progress in NRR, and the design and development of advanced electrocatalysts and systems.
Seasonal Variation in Trophic Diversity and Relative Importance of Basal Resources Supporting Tropical River Fish Assemblages in Chiapas, Mexico
Authors: Pease Allison A. , Soria‐Barreto Miriam , González‐Díaz Alfonso A. , Rodiles‐Hernández Rocío 
Published: September 2020

AbstractEnvironmental changes caused by hydrological shifts between wet and dry seasons in the tropics drive variation in resource availability and feeding interactions for riverine fish assemblages, but studies of trophic structure typically take place over short time scales that do not adequately capture this variation. In this study, we used analysis of stable isotopes (δ13C and δ15N) to assess seasonal changes in the diversity and relative importance of production sources supporting fish assemblages in La Venta River, the largest tributary of Netzahualcoyotl Reservoir on the Grijalva River in Chiapas, Mexico. Based on established river ecosystem theories, we expected the relative importance of carbon sources supporting fishes to shift seasonally, with greater use of instream resources during low‐water periods and an increasing contribution from terrestrial sources during high‐water periods. Abundant, low‐trophic‐level food resources (i.e., plants and invertebrates) were expected to support most fish species in the wet season, whereas piscivory was predicted to increase as habitat volume declined and fish density increased in the dry season. Somewhat surprisingly, we found that terrestrial energy sources were assimilated more during low‐water conditions at some sites, and ranges of δ13C were higher in the dry season. Terrestrial carbon supporting fish production in low‐water periods likely came from riparian plant detritus that remained in the river after flows receded and/or leaf litter that accumulated in the dry season. Ranges of δ15N were similar across seasons, with no apparent increase in piscivory during the dry season. Higher trophic redundancy was observed in the wet season, likely due to fish taking advantage of the same readily available food items (e.g., pulses of arthropod prey) during high flows. Documenting seasonal use of trophic resources provides critical information as expanding hydroelectric dam construction threatens the natural variability of energy pathways that support fisheries resources in tropical rivers.
A high‐quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes
Authors: Song Zhenqiao , Lin Caicai , Xing Piyi , Fen Yuanyuan , Jin Hua , Zhou Changhao , Gu Yong Q. , Wang Jianhua , Li Xingfeng 
Published: September 2020

AbstractSalvia miltiorrhiza Bunge, also known as red sage or Danshen, is an important traditional Chinese medicine (TCM) that has been used for thousands of years to treat cardiovascular and other diseases. It is also considered an important model TCM plant. Here, a high‐quality reference genome of S. miltiorrhiza was generated by combining PacBio long‐read sequencing and chromatin interaction mapping (Hi‐C) technologies, resulting in the chromosome‐scale assembly of a 594.75‐Mb genome sequence with a contig N50 of 2.70 Mb. This assembly shows the highest level of continuity for a Danshen genome generated thus far. The S. miltiorrhiza genome contained 32,483 protein‐coding genes, with a repetitive DNA content of approximately 64.84%. The high percentage of young LTRs suggests that multiple TE transposition bursts occurred recently in S. miltiorrhiza. Genes unique to secondary metabolism pathways were expanded in the S. miltiorrhiza genome. A new CYP450 gene cluster was identified in the phloem of red roots where active components were synthesized. This reference genome sequence will facilitate future studies aimed at the elucidation of the secondary metabolism synthesis pathway and the genetic improvement of S. miltiorrhiza.
A comprehensive phenotypic and genomic characterization of Ethiopian sorghum germplasm defines core collection and reveals rich genetic potential in adaptive traits
Authors: Girma Gezahegn , Nida Habte , Tirfessa Alemu , Lule Dagnachew , Bejiga Tamirat , Seyoum Amare , Mekonen Moges , Nega Amare , Dessalegn Kebede , Birhanu Chemeda , Bekele Alemnesh , Gebreyohannes Adane , Ayana Getachew , Tesso Tesfaye , Ejeta Gebisa , Mengiste Tesfaye 
Published: September 2020

AbstractUnderstanding population genetic structure and diversity of a crop is essential in designing selection strategies in plant breeding. About 2010 Ethiopian sorghum accessions were phenotyped for different traits at multiple locations. A subset of the collection, 1628 accessions, predominantly landraces, some improved varieties, and inbred lines were genotyped by sequencing. Phenotypic data revealed association of important traits with different sorghum growing agro‐climatic regions, high genetic diversity and the presence of rare natural variation in the Ethiopian sorghum germplasm. Subsequent genotypic analysis determined optimum number of sub‐populations, distinct cluster groups and ancestries of each sorghum accessions. To improve utilization of germplasm, a core subset of 387 lines were selected following posteriori grouping of genotypes based on cluster groups obtained through GBS analysis followed by stratified random sampling using quantitative traits. In order to evaluate how well this new sorghum and millet innovation lab (SMIL) collection from Ethiopia is represented within the largest world sorghum collection at United States Department of Agriculture ‐ National Plant Germplasm System (USDA‐NPGS) and the sorghum association panel (SAP), comparisons were conducted based on SNP data. The SMIL collection displayed high genetic diversity with some redundancy with the USDA‐NPGS germplasm but SAP showed clear distinction. Furthermore, genome‐environment association analysis identified candidate genes associated with adaptation to abiotic factors, that will be important for exploitation of adaptive potential to different environments. In summary, our results described the diversity and relationship of sorghum collections, representativeness of developed core and provide novel insights into candidate genes associated to abiotic stress tolerance.
The oxidative degradation of Caffeine in UV/Fe(II)/persulfate system—Reaction kinetics and decay pathways
Authors: Rao Yongfang , Long Huimin , Hao Jingchen 
Published: September 2020

AbstractIn this study, the degradation of caffeine was investigated by UV/Fe2+/persulfate (PS) process. Caffeine (CAF) degradation in sole‐UV, UV/Fe2+, UV/PS, and Fe2+/PS systems was also conducted to examine the contribution of isolated processes to CAF degradation. The effects of pH levels, the concentration of Fe2+ and PS, inorganic anions, and initial concentration of CAF on the performance of UV/Fe2+/PS process were evaluated. Radical competitive reactions indicated both hydroxyl radicals and sulfate radicals played important roles in CAF degradation in UV/Fe2+/PS system. Nine intermediates, among which three were detected for the first time, were identified by ultra‐performance liquid chromatography/electrospray‐time‐of‐flight mass spectrometry (UPLC/ESI‐TOF‐MS) and SPME (solid‐phase microextraction)/GC/MS. The possible degradation pathways of CAF were proposed, among which demethylation, hydroxylation, the oxidation of olefinic double bond, and the cleavage of pyrimidine ring and imidazole ring were involved in the degradation of CAF in UV/Fe2+/PS system.Practitioner points

Caffeine degradation by UV/Fe2+/PS process was investigated.

Caffeine degradation did not follow a simple pseudo‐first order kinetics

Chloride ions promoted CAF degradation.

The anions NO3−, SO42−, and H2PO4− exerted a negative influence on caffeine degradation.

Nine intermediates were detected, and decay pathways were proposed.
Herbicide Exposure and Toxicity to Aquatic Primary Producers
Authors: Vonk J. Arie , Kraak Michiel H. S. 
Published: September 2020

AbstractThe aim of the present review was to give an overview of the current state of science concerning herbicide exposure and toxicity to aquatic primary producers. To this end we assessed the open literature, revealing the widespread presence of (mixtures of) herbicides, inevitably leading to the exposure of non-target primary producers. Yet, herbicide concentrations show strong temporal and spatial variations. Concerning herbicide toxicity, it was concluded that the most sensitive as well as the least sensitive species differed per herbicide and that the observed effect concentrations for some herbicides were rather independent from the exposure time. More extensive ecotoxicity testing is required, especially considering macrophytes and marine herbicide toxicity. Hence, it was concluded that the largest knowledge gap concerns the effects of sediment-associated herbicides on primary producers in the marine/estuarine environment. Generally, there is no actual risk of waterborne herbicides to aquatic primary producers. Still, median concentrations of atrazine and especially of diuron measured in China, the USA and Europe represented moderate risks for primary producers. Maximum concentrations due to misuse and accidents may even cause the exceedance of almost 60% of the effect concentrations plotted in SSDs. Using bioassays to determine the effect of contaminated water and sediment and to identify the herbicides of concern is a promising addition to chemical analysis, especially for the photosynthesis-inhibiting herbicides using photosynthesis as endpoint in the bioassays. This review concluded that to come to a reliable herbicide hazard and risk assessment, an extensive catch-up must be made concerning macrophytes, the marine environment and especially sediment as overlooked and understudied environmental compartments.
Matching and running sensitivity in non-renormalizable inflationary models
Authors: Fumagalli Jacopo , Postma Marieke , van den Bout Melvin 
Published: September 2020

AbstractMost of the inflationary models that are in agreement with the Planck data rely on the presence of non-renormalizable operators. If the connection to low energy particle physics is made, the renormalization group (RG) introduces a sensitivity to ultraviolet (UV) physics that can be crucial in determining the inflationary predictions. We analyse this effect for the Standard Model (SM) augmented with non-minimal derivative couplings to gravity. Our set-up reduces to the SM for small values of the Higgs field, and allows for inflation in the opposite large field regime. The one-loop beta functions in the inflationary region are calculated using a covariant approach that properly accounts for the non-trivial structure of the field space manifold. We run the SM parameters from the electroweak to the inflationary scale, matching the couplings of the different effective field theories at the boundary between the two regimes, where we also include threshold corrections that parametrize effects from UV physics. We then compute the spectral index and tensor-to-scalar ratio and find that RG flow corrections can be determinant: a scenario that is ruled out at tree level can be resurrected and vice versa.