bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vitro Activity Assays to Quantitatively Assess the Endogenous Reversible Oxidation State of Protein Tyrosine Phosphatases in Cells
Authors: Londhe Avinash D. , Rizvi Syed H. M. , Boivin Benoit 
Published: August 2020

AbstractThe reversible oxidation of protein tyrosine phosphatases (PTPs) impairs their ability to dephosphorylate substrates in vivo. This transient inactivation of PTPs occurs as their conserved catalytic cysteine residue reacts with cellular oxidants thereby abolishing the ability of this reactive cysteine to attack the phosphate of the target substrate. Hence, in vivo, the inhibition of specific PTPs in response to regulated and localized rises in cellular oxidants enables phospho‐dependent signaling. We present assays that measure the endogenous activity of specific PTPs that become transiently inactivated in cells exposed to growth factors. Here, we describe the methods and highlight the pitfalls to avoid post‐lysis oxidation of PTPs in order to assess the inactivation and the reactivation of PTPs targeted by cellular oxidants in signal transduction. © 2020 Wiley Periodicals LLC.Basic Protocol 1: Cell transfection (optional)Support Protocol: Preparation of degassed lysis buffersBasic Protocol 2: Cellular extraction in anaerobic conditionsBasic Protocol 3: Enrichment and activity assay of specific PTPsAlternate Protocol: Measurement of active PTPs via direct cysteinyl labeling
Understanding the use of message passing interface in exascale proxy applications
Authors: Sultana Nawrin , Rüfenacht Martin , Skjellum Anthony , Bangalore Purushotham , Laguna Ignacio , Mohror Kathryn 
Published: August 2020

SummaryThe Exascale Computing Project (ECP) focuses on the development of future exascale‐capable applications. Most ECP applications use the message passing interface (MPI) as their parallel programming model with mini‐apps serving as proxies. This paper explores the explicit usage of MPI in such ECP proxy applications. We empirically analyze 14 proxy applications from the ECP Proxy Apps Suite. We use the MPI profiling interface (PMPI) to collect MPI usage patterns in ECP proxy apps. Our analysis shows that a small subset of features from MPI is commonly used in the proxies of exascale‐capable applications, even when they reference third‐party libraries. This study is intended to provide a better understanding of the use of MPI in current exascale applications. The findings can help focus software investments made for exascale systems in the MPI middleware including optimization, fault‐tolerance, tuning, and hardware‐offload.
A rare sporadic pancreatic desmoid fibromatosis diagnosed by endoscopic ultrasound‐guided fine‐needle aspiration: Case report and literature review
Authors: Stone Andrew B. , Mallery J. Shawn , Stewart Jimmie , Amin Khalid 
Published: August 2020

AbstractIntra‐abdominal desmoid fibromatosis (also known as desmoid tumor) is a rare benign but often locally aggressive infiltrative fibrous proliferation. Pancreatic desmoid fibromatosis is even rarer, with only 31 cases previously reported in the English‐language literature. These tumors present a distinct diagnostic challenge due to their rarity and non‐specific image findings and presentation, with most cases diagnosed as desmoid fibromatosis only after surgical resection. This report presents a rare case of pancreatic desmoid fibromatosis in a 72 year old man, who on a follow‐up CT for a previously diagnosed angiomyolipoma of the kidney was found to have a 4.0 cm pancreatic tail mass. This was sampled pre‐operatively by endoscopic ultrasound (EUS)‐guided fine‐needle aspiration (FNA). Examination of the cytology material showed a low‐grade spindle cell lesion. Immunohistochemistry (IHC) performed on FNA cell block showed the lesional cells to be positive for beta‐catenin, consistent with fibromatosis. Additional mutational analysis on cell block material revealed the characteristic CTNNB1 gene mutation (T41A), confirming the diagnosis. The mass was then surgically resected and again confirmed to be desmoid fibromatosis on histopathologic examination. On review of previously published cases of pancreatic desmoid fibromatosis, most were initially suspected to be some type of pancreatic neoplasm and were not biopsied prior to surgical resection. This case suggests a potential key role for fine‐needle aspiration cytology in the preoperative diagnosis of pancreatic and other intra‐abdominal desmoid tumors, particularly as evidence emerges that non‐surgical treatment may be a viable first option for some cases.
Cytological diagnosis of Xp11 translocation renal cell carcinoma: An unusual suspect in bone metastases from unknown primary malignancies
Authors: Montella Marco , Franco Renato , Aquino Gabriella , Ronchi Andrea , Zito Marino Federica , Di Napoli Marilena , Pignata Sandro , Cozzolino Immacolata 
Published: August 2020

AbstractBackgroundRenal cell carcinoma (RCC) constitutes 3% of all cancers, with a higher incidence in patients with age between 60 and 70 years. RCC frequently present as a metastatic tumor at diagnosis, and bones represent one of the most frequent sites. Many cases, mainly in young patients, includes the Xp11 translocation RCC. The cytological diagnosis of Xp11 translocation RCC in adult population it is rarely performed, likely for the morphological overlap with other adult renal cell carcinoma subtypes.MethodsWe retrospectively analyze a series of 92 adult patients with metastatic bone tumors, diagnosed on fine‐needle aspiration cytology (FNAC) samples, focusing mainly on the cytological, immunophenotypic and molecular features of Xp11 translocation RCC.ResultsIn our series 6 of 92 (6.5%) cases were metastatic RCC (mRCC), among them 2 cases were metastasis from Xp11translocation RCC. Those cases showed a bloody background, with several groups of atypical cells arranged in syncytial groups or in papillary groups composed by atypical cells with abundant cytoplasm, with scattered clear cells. TFE3 was positive on immunocytochemical analysis and specific translocation t(Xp11.23) was detected by FISH analysis.ConclusionsIn adult patients with mRCC, it is necessary to consider also Xp11 translocation RCC among the diagnostic hypotheses. FNAC represents a valid tool to investigate bone lesions but cytological features of Xp11 translocation RCC are still poorly described and must necessarily be better defined.
Honey bee colony performance affected by crop diversity and farmland structure: a modeling framework
Authors: Horn Juliane , Becher Matthias A. , Johst Karin , Kennedy Peter J. , Osborne Juliet L. , Radchuk Viktoriia , Grimm Volker 
Published: August 2020

AbstractForage availability has been suggested as one driver of the observed decline in honey bees. However, little is known about the effects of its spatiotemporal variation on colony success. We present a modeling framework for assessing honey bee colony viability in cropping systems. Based on two real farmland structures, we developed a landscape generator to design cropping systems varying in crop species identity, diversity, and relative abundance. The landscape scenarios generated were evaluated using the existing honey bee colony model BEEHAVE, which links foraging to in‐hive dynamics. We thereby explored how different cropping systems determine spatiotemporal forage availability and, in turn, honey bee colony viability (e.g., time to extinction, TTE) and resilience (indicated by, e.g., brood mortality). To assess overall colony viability, we developed metrics, PH and PP, which quantified how much nectar and pollen provided by a cropping system per year was converted into a colony's adult worker population. Both crop species identity and diversity determined the temporal continuity in nectar and pollen supply and thus colony viability. Overall farmland structure and relative crop abundance were less important, but details mattered. For monocultures and for four‐crop species systems composed of cereals, oilseed rape, maize, and sunflower, PH and PP were below the viability threshold. Such cropping systems showed frequent, badly timed, and prolonged forage gaps leading to detrimental cascading effects on life stages and in‐hive work force, which critically reduced colony resilience. Four‐crop systems composed of rye‐grass–dandelion pasture, trefoil–grass pasture, sunflower, and phacelia ensured continuous nectar and pollen supply resulting in TTE > 5 yr, and PH (269.5 kg) and PP (108 kg) being above viability thresholds for 5 yr. Overall, trefoil–grass pasture, oilseed rape, buckwheat, and phacelia improved the temporal continuity in forage supply and colony's viability. Our results are hypothetical as they are obtained from simplified landscape settings, but they nevertheless match empirical observations, in particular the viability threshold. Our framework can be used to assess the effects of cropping systems on honey bee viability and to develop land‐use strategies that help maintain pollination services by avoiding prolonged and badly timed forage gaps.
Where identities converge: The importance of intersectionality in eating disorders research
Authors: Burke Natasha L. , Schaefer Lauren M. , Hazzard Vivienne M. , Rodgers Rachel F. 
Published: August 2020

AbstractDisparities in eating disorder (ED) risk, diagnosis, and treatment for those who occupy multiple marginalized social identities (e.g., combined racial/ethnic and sexual minority statuses), underscore the need for advancing multicultural research in the ED field. In this article, we argue that intersectionality‐informed approaches, which examine the ways in which one's multiple social identities interact to inform risk for ED outcomes, offer an established framework for identifying frequently underserved individuals who may be at greatest risk for EDs. We highlight preliminary intersectional research in EDs and offer suggestions for further progression. In particular, we encourage future intersectionality‐informed research to incorporate a broader range of social identities (e.g., age, ability status), consider the ways in which these identities may be dimensional and fluid, and embrace strengths‐based approaches to illuminate dimensions of identity that may serve as protective factors. To support such research, we describe quantitative and qualitative methods for pursuing questions of intersectionality in ED investigations. Given the success of intersectionality‐informed research in other areas of psychopathology and its relevance to ED as suggested by initial research, the continued pursuit of these approaches in EDs has high potential to improve identification and treatment for patients who have too often been overlooked.
Persistence of microbial extracellular enzymes in soils under different temperatures and water availabilities
Authors: Gómez Enrique J. , Delgado Jose A. , González Juan M. 
Published: August 2020

AbstractMicrobial extracellular enzyme activity (EEA) is critical for the decomposition of organic matter in soils. Generally, EEA represents the limiting step governing soil organic matter mineralization. The high complexity of soil microbial communities and the heterogeneity of soils suggest potentially complex interactions between microorganisms (and their extracellular enzymes), organic matter, and physicochemical factors. Previous studies have reported the existence of maximum soil EEA at high temperatures although microorganisms thriving at high temperature represent a minority of soil microbial communities. To solve this paradox, we attempt to evaluate if soil extracellular enzymes from thermophiles could accumulate in soils. Methodology at this respect is scarce and an adapted protocol is proposed. Herein, the approach is to analyze the persistence of soil microbial extracellular enzymes at different temperatures and under a broad range of water availability. Results suggest that soil high‐temperature EEA presented longer persistence than enzymes with optimum activity at moderate temperature. Water availability influenced enzyme persistence, generally preserving for longer time the extracellular enzymes. These results suggest that high‐temperature extracellular enzymes could be naturally accumulated in soils. Thus, soils could contain a reservoir of enzymes allowing a quick response by soil microorganisms to changing conditions. This study suggests the existence of novel mechanisms of interaction among microorganisms, their enzymes and the soil environment with relevance at local and global levels.
Links between soil microbial communities, functioning, and plant nutrition under altered rainfall in Australian grassland
Authors: Ochoa‐Hueso Raúl , Arca Valentina , Delgado‐Baquerizo Manuel , Hamonts Kelly , Piñeiro Juan , Serrano‐Grijalva Lilia , Shawyer Julien , Power Sally A. 
Published: August 2020

AbstractThe size, frequency, and timing of precipitation events are predicted to become more variable worldwide. Despite these predictions, the importance of changes in precipitation in driving multiple above‐ and belowground ecosystem attributes simultaneously remains largely underexplored. Here, we carried out 3 yr of rainfall manipulations at the DRI‐Grass facility, located in a mesic grassland in eastern Australia. Treatments were implemented through automated water reapplication and included +50% and −50% amount, reduced frequency of events, and an extreme summer drought. We evaluated the spatiotemporal responses of multiple ecosystem attributes including microbial biomass, community composition and activity, soil nutrient content and availability, and plant nutritional status to altered rainfall regimes. We found that changing precipitation patterns resulted in multiple direct and indirect changes in microbial communities and soil and plant nutrient content. Main results included greater availability of soil macronutrients and reduced availability of micronutrients under drought, and taxon‐specific changes in the composition of soil microbial communities in response to altered rainfall. Moreover, using structural equation modeling, we showed that, in summer 2015, plant macronutrient contents, a widely used ecological indicator of pasture quality, were simultaneously explained by greater soil nutrient availability and the structure of soil microbial communities, and significantly reduced by lower rainfall. Plant micronutrients were also reduced by lower rainfall and explained by changes in microbial attributes. Despite treatment effects on many of the soil, microbial, and plant variables analyzed across the 3 yr of study, many of these ecosystem attributes varied greatly across sampling events. This resulted in many significant interactions between the rainfall treatments and experimental duration, suggesting complex system‐level responses to changing rainfall in our grassland, and a high natural buffering capacity of the ecosystem to varying rainfall conditions. Some interactions manifested as changes in the coefficient of variation of ecosystem attributes, particularly in response to changes in the timing of precipitation events and the extreme summer drought. Finally, we posit that a detailed understanding of plant–soil–microbial interactions, and the role of climate in modifying these linkages, will be key for adapting the sustainability of grasslands to a future that will be shaped by climate change.
Scaling up biodiversity–ecosystem function relationships across space and over time
Authors: Qiu Jiangxiao , Cardinale Bradley J. 
Published: August 2020

AbstractUnderstanding how to scale up effects of biological diversity on ecosystem functioning and services remains challenging. There is a general consensus that biodiversity loss alters ecosystem processes underpinning the goods and services upon which humanity depends. Yet most of that consensus stems from experiments performed at small spatial scales for short time frames, which limits transferability of conclusions to longer‐term, landscape‐scale conservation policies and management. Here we develop quantitative scaling relationships linking 374 experiments that tested plant diversity effects on biomass production across a range of scales. We show that biodiversity effects increase by factors of 1.68 and 1.10 for each 10‐fold increase in experiment temporal and spatial scales, respectively. Contrary to prior studies, our analyses suggest that the time scale of experiments, rather than their spatial scale, is the primary source of variation in biodiversity effects. But consistent with earlier research, our analyses reveal that complementarity effects, rather than selection effects, drive the positive space–time interactions for plant diversity effects. Importantly, we also demonstrate complex space–time interactions and nonlinear responses that emphasize how simple extrapolations from small‐scale experiments are likely to underestimate biodiversity effects in real‐world ecosystems. Quantitative scaling relationships from this research are a crucial step towards bridging controlled experiments that identify biological mechanisms across a range of scales. Predictions from scaling relationships like these could then be compared with observations for fine‐tuning the relationships and ultimately improving their capacities to predict consequences of biodiversity loss for ecosystem functioning and services over longer time frames across real‐world landscapes.
Diagnostic and interventional circulating biomarkers in nonalcoholic steatohepatitis
Authors: Tincopa Monica A. 
Published: August 2020

AbstractIntroductionIn the setting of the obesity epidemic, nonalcoholic fatty liver disease (NAFLD) has become one of the most prevalent forms of chronic liver disease worldwide. Approximately 25% of adults globally have NAFLD which includes those with NAFL, or simple steatosis, and individuals with nonalcoholic steatohepatitis (NASH) where inflammation, hepatocyte injury and potentially hepatic fibrosis are found in conjunction with steatosis. Individuals with NASH, particularly those with hepatic fibrosis, have higher rates of liver‐related and overall mortality, making this distinction of significant clinical importance. One of the core challenges in current clinical practice is identifying this subset of individuals with NASH without the use of liver biopsy, the gold standard for both diagnostics and staging disease severity. Identifying noninvasive biomarkers, an accurately measured and reproducible parameter, would aide in identifying patients eligible for NASH pharmacotherapy clinical trials and to help tailor intensity of monitoring required.Methods, Results and ConclusionsIn this review, we highlight both the currently available and novel diagnostic and interventional circulating biomarkers under investigation for NASH, underscoring their accuracy and limitations relevant to our patient population and current clinical practice.
Study on Cd2+ Determination Using Bud‐like Poly‐L‐Tyrosine/Bi Composite Film Modified Glassy Carbon Electrode Combined with Eliminating of Cu2+ Interference by Electrodeposition
Authors: Wang Yan‐Ru , Zhai Wen‐Ying , Liu You‐Qin 
Published: August 2020

AbstractA bud‐like poly‐L‐tyrosine/Bi modified glassy carbon electrode (p‐Tyr/Bi/GC) was prepared by CV and in situ Bi plating, whose conductivity and membrane morphology were characterized by CV, EIS and SEM, respectively. The p‐Tyr membrane can effectively promote the enrichment of Cd2+. The optimal Tyr concentration and scanning number for p‐Tyr/GC preparation were 2.0 mmol ⋅ L−1 and 35, while the optimal Bi3+ concentration, pH and Cd2+ accumulation potential in test medium were 3.0 μmol ⋅ L−1, 6.5 and −1.3 V, respectively. The linear equation of p‐Tyr/Bi/GC's response to Cd2+ (1.0 nmol ⋅ L−1 to 2.0 μmol ⋅ L−1) was ip (μA) = −0.6809 + 100.2c (μmol ⋅ L−1) (R2 = 0.9985) with a detection limit of 0.11 nmol ⋅ L−1 (3S/N). The elimination of interference caused by Cu2+ in sample was studied by electrodeposition. The p‐Tyr/Bi/GC electrode was successfully used for detecting Cd in rice samples with good reliability and accuracy. The developed Cd2+ sensor exhibits high sensitivity, wide linear range and low detection limit, especially the designed method of eliminating Cu2+ interference has the characteristics of high selectivity, simple operation and wide application range.
Comparative Study of a Sensing Platform via Functionalized Calix[4]resorcinarene Ionophores on QCM Resonator as Sensing Materials for Detection of Heavy Metal Ions in Aqueous Environments
Authors: Shaban Abdul , Eddaif Larbi 
Published: August 2020

AbstractA flow type quartz crystal microbalance with impedance analysis capability (QCM‐I) chemical sensor was tested for heavy metal (HM) ions detection in aqueous solutions. The sensor development is based upon the complexing ability of the functionalized AT‐cut quartz resonator gold surface, by calixresorcinarenes, towards the HM ions. These calixresorcinarenes coated QCM sensors were tested for selectively adsorbing HM ions, such as copper, lead, mercury, and cadmium, from solution over a wide range of concentration (5‐1000 ppm) through complexation with functional groups in the coating layers. QCM‐Calix based chemosensors, C‐dec‐9‐en‐1‐ylcalix[4]resorcinarene (ionophore I), C‐undecylcalix[4]resorcinarene (ionophore II), C‐dec‐9‐enylcalix[4]resorcinarene‐O‐(S‐)‐α‐methylbenzylamine (ionophore III) and C‐dec‐9‐enylcalix[4]resorcinarene‐O‐(R+)‐α‐methylbenzylamine (ionophore IV), were synthesized and immobilized to detect HM ions of Pb2+, Cd2+, Hg2+, and Cu2+ in aqueous solutions. Using the impedance analysis, which facilitates a complete description of the acoustic loading of the crystal surface, the full width at half maximum of the QCM resonance peak (FWHM) values are obtained from the impedance spectra. FWHM variations revealed the effectiveness of the proposed ionophores in detecting HM at different levels. Sensitivities and wide linear relationships between HM concentration and FWHM were interpreted. Detection limits of (0.32, 0.57, 0.37, 0.89 ppm) and (1.63, 0.18, 0.76, 0.2 ppm) were determined for ionophore I and II, for Cd2+, Cu2+, Hg2+ and Pb2+ ions, respectively. Ionophore (I) showed binding preferences towards Cd2+ ions where ionophore (II) produced similar selectivity toward Cu2+ and Pb2+ ions. Ionophores III and IV were used for the assessment of ▵FWHM values to comprehend the detection affinities of the ionophores toward HM ions.
Two‐dimensional CoOOH as a Highly Sensitive and Selective H2S, HCN and HF Gas Sensor: A Computational Investigation
Authors: Opoku Francis , Govender Penny P. 
Published: August 2020

AbstractUsing density functional theory, we have systematically investigate the room temperature gas‐sensing performance of two‐dimensional delafossite cobalt oxyhydroxide (CoOOH) sheets as H2S, HCN and HF detection. Our findings show that CoOOH is sensitive to H2S, HCN and HF gas by a physisorption interaction. The CoOOH sheets exhibit significant changes after the gas molecules adsorption, particularly its electrical conductivity. The suitable adsorption energy, which guarantees short recovery time, remarkable high sensitivity and selectivity, appreciable work function change and sharply enhanced electrical conductivity make CoOOH sheets as an effective nanosensor for toxic H2S, HCN and HF gases detection.