bluuebunny/crossref_metadata_2025_split huggingface dataset:
A locking-free P0 finite element method for linear elasticity equations on polytopal partitions
Authors: Liu Yujie , Wang Junping 
Published: June 2021

Abstract
This article presents a $P_0$ finite element method for boundary value problems for linear elasticity equations. The new method makes use of piecewise constant approximating functions on the boundary of each polytopal element and is devised by simplifying and modifying the weak Galerkin finite element method based on $P_1/P_0$ approximations for the displacement. This new scheme includes a tangential stability term on top of the simplified weak Galerkin to ensure the necessary stability due to the rigid motion. The new method involves a small number of unknowns on each element, it is user friendly in computer implementation and the element stiffness matrix can be easily computed for general polytopal elements. The numerical method is of second-order accurate, locking-free in the nearly incompressible limit, and ease polytopal partitions in practical computation. Error estimates in $H^1$, $L^2$ and some negative norms are established for the corresponding numerical displacement. Numerical results are reported for several two-dimensional and three-dimensional test problems, including the classical benchmark Cook’s membrane problem in two dimensions as well as some three-dimensional problems involving shear-loaded phenomena. The numerical results show clearly the simplicity, stability, accuracy and efficiency of the new method.
Elastolytic activity is associated with inflammation in bladder cancer
Authors: Gruba Natalia , Stachurski Lech , Lesner Adam 
Published: June 2021

AbstractCancer development and progression is often associated with inflammation. Late diagnosis of inflammation that directly leads to the development of neoplasm—cancer is associated with a reduction in the chance of successful treatment or is associated with therapeutic difficulties. A panel of chromogenic substrates was used for the qualitative determination of the specific activity of enzymes in urine of patients with confirmed inflammatory reaction and/or epithelial neoplasms in particular tumours at various stages of development. Urine of people with excluded inflammation was used as a control group. Proteolytic activity was determined in urine samples collected from patients with epithelial neoplasms and/or inflammation. What is more, we determine human neutrophil elastase activity-related inflammation based on the examination of urine samples. We suspect that the proteolytical activity of urine samples is due to neutrophil response to inflammation, which is directly related to cancer. This is the first study to determine elastolytic activity in bladder cancer urine samples. It supports wider use of urine for inflammation screening.
Clinicopathological and Molecular Characteristics of Early-Onset Stage III Colon Adenocarcinoma: An Analysis of the ACCENT Database
Authors: Jin Zhaohui , Dixon Jesse G , Fiskum Jack M , Parekh Hiral D , Sinicrope Frank A , Yothers Greg , Allegra Carmen J , Wolmark Norman , Haller Daniel , Schmoll Hans-Joachim , de Gramont Aimery , Kerr Rachel , Taieb Julien , Van Cutsem Eric , Tweleves Christopher , O’Connell Michael , Saltz Leonard B , Sadahiro Sotaro , Blanke Charles D , Tomita Naohiro , Seitz Jean-Francois , Erlichman Charles , Yoshino Takayuki , Yamanaka Takeharu , Marsoni Silvia , Andre Thierry , Mahipal Amit , Goldberg Richard M , George Thomas J , Shi Qian 
Published: June 2021

Abstract

Background
Colon cancer (CC) incidence in young adults (age 20-49 years), termed early-onset CC (EO-CC), is increasing.

Methods
Individual patient data on 35 713 subjects with stage III colon cancer from 25 randomized studies in the Adjuvant Colon Cancer ENdpoint database were pooled. The distributions of demographics, clinicopathological features, biomarker status, and outcome data were summarized by age group. Overall survival, disease-free survival, time to recurrence, and survival after recurrence were assessed by Kaplan-Meier curves and Cox models stratified by treatment arms within studies, adjusting for sex, race, body mass index, performance status, disease stage, grade, risk group, number of lymph nodes examined, disease sidedness, and molecular markers. All statistical tests were 2-sided.

Results
Using a 5% difference between age groups as the clinically meaningful cutoff, patients with stage III EO-CC had similar sex, race, performance status, risk group, tumor sidedness, and T stage compared with patients with late-onset CC (age 50 years and older). EO-CC patients were less likely to be overweight (30.2% vs 36.2%) and more commonly had 12 or more lymph nodes resected (69.5% vs 58.7%). EO-CC tumors were more frequently mismatch repair deficient (16.4% vs 11.5%) and less likely to have BRAFV600E (5.6% vs 14.0%), suggesting a higher rate of Lynch syndrome in EO-CC. Patients with EO-CC had statistically significantly better overall survival (hazard ratio [HR] = 0.81, 95% confidence interval [CI] = 0.74 to 0.89; P &lt; .001), disease-free survival (HR = 0.91, 95% CI = 0.84 to 0.98; P = .01), and survival after recurrence (HR = 0.88, 95% CI = 0.80 to 0.97; P = .008) in the analysis without molecular markers; however, age at onset of CC lost its prognostic value when outcome was adjusted for molecular markers.

Conclusion
Tumor biology was found to be a more important prognostic factor than age of onset among stage III colon cancer patients in the Adjuvant Colon Cancer ENdpoint database.
Cell-free genomics reveal intrinsic, cooperative and competitive determinants of chromatin interactions
Authors: Eggers Nikolas , Becker Peter B 
Published: June 2021

Abstract
Metazoan transcription factors distinguish their response elements from a large excess of similar sequences. We explored underlying principles of DNA shape read-out and factor cooperativity in chromatin using a unique experimental system. We reconstituted chromatin on Drosophila genomes in extracts of preblastoderm embryos, mimicking the naïve state of the zygotic genome prior to developmental transcription activation. We then compared the intrinsic binding specificities of three recombinant transcription factors, alone and in combination, with GA-rich recognition sequences genome-wide. For MSL2, all functional elements reside on the X chromosome, allowing to distinguish physiological elements from non-functional ‘decoy’ sites. The physiological binding profile of MSL2 is approximated through interaction with other factors: cooperativity with CLAMP and competition with GAF, which sculpts the profile by occluding non-functional sites. An extended DNA shape signature is differentially read out in chromatin. Our results reveal novel aspects of target selection in a complex chromatin environment.
Seawater exposure causes hydraulic damage in dying Sitka-spruce trees
Authors: Zhang Hongxia , Li Xinrong , Wang Wenzhi , Pivovaroff Alexandria L. , Li Weibin , Zhang Peipei , Ward Nicholas D. , Myers-Pigg Allison , Adams Henry D. , Leff Riley , Wang Anzhi , Yuan Fenghui , Wu Jiabing , Yabusaki Steve , Waichler Scott , Bailey Vanessa L. , Guan Dexin , McDowell Nate G. 
Published: June 2021

Abstract
Sea-level rise is one of the most critical challenges facing coastal ecosystems under climate change. Observations of elevated tree mortality in global coastal forests are increasing, but important knowledge gaps persist concerning the mechanism of salinity stress-induced nonhalophytic tree mortality. We monitored progressive mortality and associated gas exchange and hydraulic shifts in Sitka-spruce (Picea sitchensis) trees located within a salinity gradient under an ecosystem-scale change of seawater exposure in Washington State, USA. Percentage of live foliated crown (PLFC) decreased and tree mortality increased with increasing soil salinity during the study period. A strong reduction in gas exchange and xylem hydraulic conductivity (Ks) occurred during tree death, with an increase in the percentage loss of conductivity (PLC) and turgor loss point (πtlp). Hydraulic and osmotic shifts reflected that hydraulic function declined from seawater exposure, and dying trees were unable to support osmotic adjustment. Constrained gas exchange was strongly related to hydraulic damage at both stem and leaf levels. Significant correlations between foliar sodium (Na+) concentration and gas exchange and key hydraulic parameters (Ks, PLC, and πtlp) suggest that cellular injury related to the toxic effects of ion accumulation impacted the physiology of these dying trees. This study provides evidence of toxic effects on the cellular function that manifests in all aspects of plant functioning, leading to unfavourable osmotic and hydraulic conditions.
Signaling and transport processes related to the carnivorous lifestyle of plants living on nutrient-poor soil
Authors: Böhm Jennifer , Scherzer Sönke 
Published: June 2021

AbstractIn Eukaryotes, long-distance and rapid signal transmission is required in order to be able to react fast and flexibly to external stimuli. This long-distance signal transmission cannot take place by diffusion of signal molecules from the site of perception to the target tissue, as their speed is insufficient. Therefore, for adequate stimulus transmission, plants as well as animals make use of electrical signal transmission, as this can quickly cover long distances. This update summarises the most important advances in plant electrical signal transduction with a focus on the carnivorous Venus flytrap. It highlights the different types of electrical signals, examines their underlying ion fluxes and summarises the carnivorous processes downstream of the electrical signals.
Using a daily diary approach to examine the early effects of COVID-19 on daily physical activity bouts and contexts among residents of Colorado and California
Authors: Courtney Jimikaye , Nuss Kayla , Wang Shirlene , Do Bridgette , Dunton Genevieve 
Published: June 2021

AbstractCOVID-19 restrictions may prevent adults from achieving sufficient physical activity (PA) and may affect PA context. This study examined the early effects of COVID-19 on daily PA bouts and contexts during April–June 2020 using a daily diary approach. Adults (N = 390) completed daily diary surveys for 28 days assessing number of PA bouts and social (e.g., alone), locational (i.e., home, neighborhood, recreational space), and technology (e.g., using streaming videos) contexts of PA. Mixed-effects models examined the effects of days since the pandemic started (on 3/13/2020), state residence, and demographics on number of daily PA bouts. Models examined demographic and temporal effects on PA context. Participants were 18–77 years, 15% Hispanic/Latino, and 80% female. PA bouts per day decreased significantly over time among Californians versus Coloradans (bsimple = −0.01, p &lt; .001) and Hispanics/Latinos (vs. non-Hispanic Latinos) did fewer PA bouts per day (b = −0.17, p = .04). Most PA bouts occurred while alone (56.7%), at home (43.4%), or in any neighborhood (40.5%). Older (60+ years) versus younger (&lt;40 years) adults were less likely to do PA with others (odds ratio [OR] = 0.40, 95% confidence interval [CI]: 0.18–0.90). PA bouts in recreational spaces were more common on weekends versus weekdays (OR = 1.59, 95% CI: 1.32–1.92) and were less common among California versus Colorado residents (OR = 0.23, 95% CI: 0.12–0.42). PA bouts decreased from April to June 2020, and these changes disparately affected subgroups. Resources are needed to counteract the negative effects of COVID-19 restrictions intended to slow disease spread on PA.
Clustering of multiple health-risk factors among vocational education students: a latent class analysis
Authors: Atorkey Prince , Paul Christine , Wiggers John , Bonevski Billie , Nolan Erin , Oldmeadow Christopher , Mitchell Aimee , Byrnes Emma , Tzelepis Flora 
Published: June 2021

Abstract
Physical and mental health risks often commence during young adulthood. Vocational education institutions are an ideal setting for understanding how health-risks cluster together in students to develop holistic multiple health-risk interventions. This is the first study to examine clustering of tobacco smoking, fruit intake, vegetable intake, alcohol consumption, physical inactivity, overweight/obesity, depression, and anxiety in vocational education students and the socio-demographic characteristics associated with cluster membership. A cross-sectional survey with vocational education students (n = 1134, mean age = 24.3 years) in New South Wales, Australia. Latent class analysis identified clusters and latent class regression examined characteristics associated with clusters. Four clusters were identified. All clusters had moderate inadequate fruit intake and moderate overweight/obesity. Cluster 1 (13% of sample) had “high anxiety, high inadequate vegetable intake, low tobacco, and low alcohol use.” Cluster 2 (16% of sample) had “high tobacco smoking, high alcohol use, high anxiety, high depression, and high inadequate vegetable intake.” Cluster 3 (52% of sample) had “high risky alcohol use, high inadequate vegetable intake, low depression, low anxiety, low tobacco smoking, and low physical inactivity.” Cluster 4 (19% of sample) was a “lower risk cluster with high inadequate vegetable intake.” Compared to cluster 4, 16–25-year-olds and those experiencing financial stress were more likely to belong to clusters 1, 2, and 3. Interventions for vocational education students should address fruit and vegetable intake and overweight/obesity and recognize that tobacco use and risky alcohol use sometimes occurs in the context of mental health issues.
Bacterial Disease Complex Including Bleached Spot, Soft Rot, and Blight on Onion Seedlings Caused by Complex Infections
Authors: Choi Okhee , Kang Byeongsam , Lee Yeyeong , Kim Seunghoe , Kwon Jin-Hyeuk , Lee Jong-Tae , Kim Jinwoo 
Published: June 2021

In 2018, a bacterial disease complex composed of bleached spots and soft rot–blight on onion seedlings was observed in nursery beds in Changnyeong, a major onion-producing county in South Korea. Four bacteria isolated from the diseased lesions were identified: Pseudomonas viridiflava, Acidovorax avenae subsp. avenae, Pantoea ananatis, and Xanthomonas axonopodis, respectively. We referred to the four strains as a “bacterial disease complex” because they were isolated from the same sample with multiple symptoms. We examined the synergistic activity among the four strains to understand their relationships and roles. We monitored in vivo bacterial population density and disease progression after artificially inoculating the bacteria on onion seedlings at a temperature of 22 or 28°C. The disease pattern progressed sooner at 28 than at 22°C (by an average of 4 to 6 days). The rate of disease progression induced by inoculation of P. ananatis alone was consistent with that induced by coinoculation of P. ananatis with the other strains, regardless of the temperature (22 or 28°C). The in vivo growth of P. ananatis on onion seedlings was not different after inoculation alone versus together with the other strains. The rate of disease progression induced by P. viridiflava was similar when inoculated alone and when inoculated with other tree strains at 28°C, but disease progression induced by inoculation alone was slower at 22°C. The in vivo growth of P. viridiflava or X. axonopodis on onion seedlings decreased rapidly or gradually, respectively, when inoculated with the other strains. Coinfection with the other three strains had repression effects on the growth of P. viridiflava, a slight effect on X. axonopodis, and no effect on P. or A. avenae subsp. avenae in vivo. These results indicate that the strains coexist or interact antagonistically, rather than synergistically, depending on the conditions. These results were consistent with the results of the in vitro growth inhibition assay, in which P. viridiflava growth was inhibited by X. axonopodis or P. ananatis. These results also confirmed that X. axonopodis is present on bleached spots and P. viridiflava on soft rot–blight lesions, and that P. viridiflava and P. ananatis cause soft rot–blight but do not coexist. A. avenae subsp. avenae is a minor causative pathogen of bleached spots on onion seedlings, but it is not significantly affected by temperature and has no antagonistic or synergistic interactions with X. axonopodis.
Chemo‐Transcriptomic Methods to Measure RNA Structure Inside Living Cells
Authors: Spitale Robert 
Published: June 2021

The advent of deep sequencing technology has unexpectedly advanced our structural understanding of molecules composed of nucleic acids. A significant amount of progress has been made recently extrapolating the chemical methods to probe RNA structure into sequencing methods. Herein we review some of the canonical methods to analyze RNA structure, and then we outline how these have been used to probe the structure of many RNAs in parallel. The key is the transformation of structural biology problems into sequencing problems, whereby sequencing power can be interpreted to understand nucleic acid proximity, nucleic acid conformation, or nucleic acid‐protein interactions. Utilizing such technologies in this way has the promise to provide novel structural insights into the mechanisms that control normal cellular physiology and provide insight into how structure could be perturbed in disease.Support or Funding InformationNational Institutes of Health (1DP2GM119164; R01MH109588; R21MH113062; UM1HG009443)Pew Biomedical Scholars ProgramUniversity of California, IrvineThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Clinical Relevance of VM‐M3 in Modeling Cancer Cachexia
Authors: Koutnik Andrew P. , Poff Angela M. , DeBlasi Janine , Ward Nate M. , D'Agostino Dominic P. 
Published: June 2021

Cancer cachexia has been redefined since the early 20th century. The current consensus is that cancer cachexia involves loss of skeletal muscle and body fat, accompanied by inflammation, anorexia, metabolic dysfunction, anemia, and hypoalbuminemia. Cachexia has been further defined through progressive staging of the disease from pre‐cachexia, cachexia, and refractory cachexia based on both weight and biochemical changes, and metastasis has been associated with higher incidence of cachexia. To date, no model system encapsulates all aspects of the cachexia condition. The VM‐M3 model of systemic metastasis presents progressive loss of skeletal muscle and adipose tissue. It also exhibits elevated levels of proinflammatory cytokines by 2 weeks, and elevated spleen weight, white blood cells counts, and pro‐inflammatory cytokines at end‐of‐life, indicating a progressive and prolonged inflammatory state as is seen in cachexic patients. The VM‐M3 model develops a primary tumor at the site of implantation followed by systemic metastasis to all major organ systems, replicating the metastatic process seem in metastatic disease. Additionally, aerobic fermentation is present in VM‐M3 cells matching the metabolic phenotype often seen in tumors prone to metastasis. VM‐M3 mice develop anemia, hypoalbuminemia, and reduced total protein, all characteristics commonly reported in cachexic patients. VM‐M3 mice also have elevated lactate levels indicating potential metabolic dysfunction which is reported in cachexia patients. Additionally, the VM‐M3 model provides a repeatable and logistically feasible model for assessing cachexia therapeutics against a phenotype that replicates many hallmark characteristics of cancer cachexia. This recent evidence indicates that the VM‐M3 model of systemic metastasis may present an ideal system for evaluating the multifactorial cachexia syndrome and testing emerging therapeutic interventions.Support or Funding InformationDonner Foundation; Disruptive Nutrition; USF FoundationThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Microbiota‐Derived Indole Metabolites Provide a Novel Pathway for Regulation of Intestinal Homeostasis
Authors: Alexeev Erica E. , Kao Daniel J. , Mills Kirsta B. , Lemke Timothy R. , Lanis Jordi M. , Lee J. Scott , Dowdell Alexander S. , Colgan Sean P. 
Published: June 2021

Inflammatory bowel disease (IBD) is a multifactorial chronic condition that results in numerous perturbations in the gastrointestinal mucosa. IBD is characterized by the continual breakdown of the intestinal epithelial barrier leading to an inappropriate immune response towards intestinal microbiota. This exposure promotes inflammation and continued mucosal injury, though the pathogenesis of the disease remains unknown. There is currently significant interest in understanding the role of gut microbiota in IBD. Loss of commensal bacteria and their metabolites may play a role in homeostasis of the intestinal epithelia. Microbes benefit the host through the local synthesis of numerous metabolites. One such metabolite is indole. Indoles are gut microbiota‐derived tryptophan metabolites that are abundant in the healthy mammalian gut and positively influence intestinal health. Using an unbiased metabolomics profiling approach, we identified a selective reduction in microbiota‐derived indole metabolites in active murine colitis. We have developed HPLC‐based technologies to validate these results and quantify indole and indole‐derived metabolites within murine and human colitis samples. We show that exposure of intestinal epithelial cells to indole metabolites induces genes important in formation and maintenance of intestinal barrier. For instance, IL‐10 is an anti‐inflammatory cytokine that inhibits production of numerous pro‐inflammatory mediators in various cell types. This cytokine functions through binding to the IL‐10 receptor alpha subunit (IL‐10R1) and colitis is strongly associated with the induction of the epithelial IL‐10R. Our results have revealed a prominent induction of IL‐10R1 mRNA and protein expression following treatment of intestinal epithelial cells with indole metabolites. Ongoing work has shown a potential role for selective indole metabolites, particularly indole‐3‐propionic acid (IPA), to alleviate disease severity and decrease inflammatory mediators in models of murine colitis. Together, these data suggest that microbial‐derived indoles play a central role in mucosal homeostasis. Based on these findings and ongoing studies, we show that microbial‐derived indole metabolites inhibit inflammation‐induced damage and promote mucosal homeostasis. These studies elucidate a novel role for microbial metabolites in innate immune responses during intestinal inflammation using in vitro and in vivo models. This work will provide new insight to improved therapeutic approaches for treating IBD.Support or Funding InformationThis work was supported by NIH grants DK1047893, DK50189, DK095491, DK103639, DK103712 and VA Merit BX002182.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.