bluuebunny/crossref_metadata_2025_split huggingface dataset:
Total protein concentration as a predictor of neoplastic peritoneal and pleural effusions of dogs
Authors: Parsley Ashley L. , Schnelle Amy N. , Gruber Erika J. , Sander William E. , Barger Anne M. 
Published: May 2022

AbstractBackgroundThe diagnosis of neoplastic cavitary effusions requires the identification of neoplastic cells in effusions, yet the cytologic appearance of neoplastic effusions can be highly variable due to the varied mechanisms of formation. Additional parameters might aid in the interpretation of equivocal cytologic results.ObjectivesOur goal was to evaluate whether total protein concentrations can be used to support the diagnosis of neoplasia in the peritoneal and pleural effusions of dogs with lower cellularities (≤5000 nucleated cells/μL).MethodsPleural and peritoneal fluid analyses from dogs presented to the University of Illinois Veterinary Teaching Hospital between 2014 and 2019 were evaluated retrospectively. Effusions were categorized as neoplastic or non‐neoplastic based on histology or cytology. Non‐neoplastic effusions were subcategorized according to mechanism: decreased oncotic pressure, increased hydrostatic pressure, increased vascular permeability, leakage of urine, and leakage of lymph. The TP and blood albumin to fluid TP ratio (Albblood:TPfluid) were compared among groups.ResultsTwenty‐seven neoplastic and 65 non‐neoplastic cases were evaluated. TP was higher in the neoplastic group (P = .001) than in the non‐neoplastic group. Neoplastic effusions had a lower Albblood:TPfluid than non‐neoplastic (P = .001), and effusions with Albblood:TPfluid of ≤0.6 were 5.6 times more likely to be neoplastic (95% CI 1.69–17.36; P = .003).ConclusionsFluid TP concentrations were significantly greater in neoplastic than non‐neoplastic effusions; however, given the considerable overlap between groups, the diagnostic utility of this difference is low. A neoplastic etiology might be more likely in cases with an Albblood:TPfluid ≤0.6.
Modeling and Experimental Evaluation of the Effects of Reflective Film and Vacuum on the Performance of Concentric Double Tube Direct Flow Solar Collector
Authors: Ismail Kamal A. R. , Teles Mavd P. R. , Lino Fatima A. M. 
Published: May 2022

Abstract
The present study is focused on investigating experimentally and numerically the four versions of a concentric double tube solar collector with and without vacuum, and with and without a reflective solar film. The conservation equations were used to formulate the thermal model and treated numerically to develop a home-made numerical code in matlab. An experimental setup is constructed to test the four versions of the collector under outdoor conditions and hence validate both the thermal model and the numerical procedure. The tests were performed during the summer and autumn seasons. The numerical outcomes agreed well with the experiments showing a maximum error of about 2.1%. The results indicated that the vacuum effect is significant and enhanced the efficiency by about 13.6% in the presence of the reflective film. An average increase of 6.6% was found in the case of the collector without reflective film but with the vacuum. The reflective solar film increased the efficiency by about 4.3% for all cases with or without vacuum.
Ultrasonic Rayleigh Wave Interrogation of Directed Energy Deposition Ti–6Al–4V Having a Rough Surface
Authors: Bakre Chaitanya , Nassar Abdalla R. , Reutzel Edward W. , Lissenden Cliff J. 
Published: May 2022

Abstract
In-situ monitoring techniques for additive manufacturing are in high demand to help produce reliable parts. The structural integrity of these parts depends on both the presence of flaws and their microstructure. Ultrasonic Rayleigh waves have the potential to identify flaws and assess the local microstructure during directed energy deposition (DED) additive manufacturing processes, but the scattering associated with the surface roughness degrades the ultrasonic signal and must be understood to extract useful information. Herein, the microstructures and surface profiles of DED and wrought Ti–6Al–4V are compared to provide context for measured Rayleigh wave speeds and second harmonic generation. The Rayleigh wave speed and second harmonic generation for DED and wrought Ti–6Al–4V materials having comparable surface roughness are significantly different. The wave speed measured in DED material is 3% slower than in wrought material, and the relative nonlinearity parameter, commonly used to characterize second harmonic generation, is 3.5–6.0 times higher for polished surfaces. Wave speed and second harmonic generation measurements are also made along the hatch and across the hatch for both as-built and glazed DED surfaces. Based on our results, we conclude that in-situ Rayleigh wave linear and nonlinear measurements are possible; although we acknowledge that in-situ angle-beam transducer generation would be challenging, and thus we will investigate pulsed laser generation in future work.
Thermal Performance of Double-Sided, Partial Height Strip Fin Arrays in a High Aspect Ratio, Rectangular Channel
Authors: Tracy Nathaniel J. , Wright Lesley M. , Han Je-Chin 
Published: May 2022

Abstract
Friction loss and heat transfer enhancement measurements were obtained for double-sided, partial height, strip fin arrays in a high aspect ratio (AR = 8), rectangular channel. Fins were arranged in a staggered array configuration with channel height to fin thickness ratio H/W = 9.6, spanwise spacing distance to fin thickness ratio S/W = 8.0, and streamwise spacing distance to fin length ratio X/L = 1.0. Within the channel, shortened strip fins of equal length are positioned directly opposite to each other on two heat transfer surfaces with three gap size to channel height ratios considered G/H = 0.2, 0.3, and 0.4, respectively. The thermal performance of each fin configuration is determined from the measured pressure drop across the array and regionally averaged heat transfer coefficients at flow Reynolds numbers ranging Re = 20,000–80,000. Partial height strip fin results are compared to the baseline cases of full height strip fins and the smooth channel. Correlations of friction loss, heat transfer enhancement, and thermal performance are provided as functions of flow Reynolds numbers for all cases. Full height strip fins provide the greatest heat transfer enhancement of all cases but introducing a gap size can significantly reduce friction losses. The thermal performance is greatest when using full height strip fins for Reynolds numbers ranging Re = 20,000–30,000 and using partial height strip fins with the gap size of G/H = 0.3 for Re = 40,000–80,000.
NovelPOLEmutations identified in patients with IMAGE-I syndrome cause aberrant subcellular localisation and protein degradation in the nucleus
Authors: Nakano Tomohiro , Sasahara Yoji , Kikuchi Atsuo , Moriya Kunihiko , Niizuma Hidetaka , Niihori Tetsuya , Shirota Matsuyuki , Funayama Ryo , Nakayama Keiko , Aoki Yoko , Kure Shigeo 
Published: May 2022

BackgroundDNA replisome is a molecular complex that plays indispensable roles in normal DNA replication. IMAGE-I syndrome is a DNA replisome-associated genetic disease caused by biallelic mutations in the gene encoding DNA polymerase epsilon catalytic subunit 1 (POLE). However, the underlying molecular mechanisms remain largely unresolved.MethodsThe clinical manifestations in two patients with IMAGE-I syndrome were characterised. Whole-exome sequencing was performed and altered mRNA splicing and protein levels of POLE were determined. Subcellular localisation, cell cycle analysis and DNA replication stress were assessed using fibroblasts and peripheral blood from the patients and transfected cell lines to determine the functional significance ofPOLEmutations.ResultsBoth patients presented with growth retardation, adrenal insufficiency, immunodeficiency and complicated diffuse large B-cell lymphoma. We identified three novelPOLEmutations: namely, a deep intronic mutation, c.1226+234G>A, common in both patients, and missense (c.2593T>G) and in-frame deletion (c.711_713del) mutations in each patient. The unique deep intronic mutation produced aberrantly spliced mRNAs. All mutants showed significantly reduced, but not null, protein levels. Notably, the mutants showed severely diminished nuclear localisation, which was rescued by proteasome inhibitor treatment. Functional analysis revealed impairment of cell cycle progression and increase in the expression of phospho-H2A histone family member X in both patients.ConclusionThese findings provide new insights regarding the mechanism via whichPOLEmutants are highly susceptible to proteasome-dependent degradation in the nucleus, resulting in impaired DNA replication and cell cycle progression, a characteristic of DNA replisome-associated diseases.
A need for multi-sector and multi-pronged solutions to address the many barriers inhibiting change from unhealthy food environments in publicly funded recreation facilities: a mixed-method study
Authors: Warken Melanie , Sanden Tracy , Shanks Naomi , Engler-Stringer Rachel , Vatanparast Hassan 
Published: May 2022

Public recreation facilities are preferred gathering places for families to participate in physical, social, intellectual, and creative pursuits, and the importance of food environments in these facilities is gaining recognition. Evidence from other Canadian jurisdictions describes such food environments as unsupportive of health, which contradicts national recreation priorities to have healthy choices as the easy choices. This study aimed to characterize food environments in a convenient sample of Saskatchewan public recreation facilities. A convergent/parallel mixed methods study design used quantitative methods to determine the healthfulness of concession stands and vending machines and qualitative methods to examine barriers and facilitators to healthy eating in facilities. The results found that 5% of concession main dishes were defined as healthy and packaged foods/beverages in concession stands and vending machines were defined as Offer Most Often 6% and 8% of the time, respectively, according to Saskatchewan Nutrition Standards. Reported barriers to healthy eating were more than twice as prevalent as facilitators. To align with population health recommendations in Saskatchewan, food environments in public recreation facilities require immediate attention. The results and recommendations can be used to build collective action to address the problem and as a benchmark to measure change. Novelty: Only 5% of concession main dishes were defined as healthy. Only 6% of packaged foods and beverages in concessions, and 8% in vending, were defined as Offer Most Often. Reported barriers to healthy eating were more than twice as prevalent as facilitators, resulting in a current state that is difficult to change.
Mutation Testing in Evolving Systems: Studying the Relevance of Mutants to Code Evolution
Authors: Ojdanic Milos , Soremekun Ezekiel , Degiovanni Renzo , Papadakis Mike , Le Traon Yves 
Published: May 2022

Context:When software evolves, opportunities for introducing faults appear. Therefore, it is important to test the evolved program behaviors during each evolution cycle. However, while software evolves, its complexity is also evolving, introducing challenges to the testing process. To deal with this issue, testing techniques should be adapted to target the effect of the program changes instead of the entire program functionality. To this end,commit-aware mutation testing, a powerful testing technique, has been proposed. Unfortunately, commit-aware mutation testing is challenging due to the complex program semantics involved. Hence, it is pertinent to understand the characteristics, predictability, and potential of the technique.Objective:We conduct an exploratory study to investigate the properties ofcommit-relevant mutants, i.e., the test elements of commit-aware mutation testing, by proposing a general definition and an experimental approach to identify them. We thus aim at investigating the prevalence, location, and comparative advantages of commit-aware mutation testing over time (i.e., the program evolution). We also investigate the predictive power of several commit-related features in identifying and selecting commit-relevant mutants to understand the essential properties for its best-effort application case.Method:Our commit-relevant definition relies on the notion of observational slicing, approximated by higher-order mutation. Specifically, our approach utilizes the impact of mutants, effects of one mutant on another in capturing and analyzing the implicit interactions between the changed and unchanged code parts. The study analyses millions of mutants (over 10 million), 288 commits, five (5) different open-source software projects involving over 68,213 CPU days of computation and sets a ground truth where we perform our analysis.Results:Our analysis shows that commit-relevant mutants arelocated mainly outside of program commit change(81%), suggesting a limitation in previous work. We also note that effective selection of commit-relevant mutants has the potential of reducing the number of mutants by up to 93%. In addition, we demonstrate that commit relevant mutation testing is significantly more effective and efficient than state-of-the-art baselines, i.e., random mutant selection and analysis of only mutants within the program change. In our analysis of the predictive power of mutants and commit-related features (e.g., number of mutants within a change, mutant type, and commit size) in predicting commit-relevant mutants, we found that mostproxy features do not reliably predict commit-relevant mutants.Conclusion:This empirical study highlights the properties of commit-relevant mutants and demonstrates the importance of identifying and selecting commit-relevant mutants when testing evolving software systems.
Variable Mutation Expression in Human Cancers: A “Hide-and-Seek” Mechanism Linked to Differential MHC-I Presentation Dynamics
Authors: Boichard Amélie , Kurzrock Razelle 
Published: May 2022

Abstract
Not all genomic mutations are expressed at the transcript/protein level, which may explain variation in cancer development, prognosis, and treatment response/resistance. In this study, our aim was to describe the prevalence of somatic mutation loss of expression (‘variant silencing’) in a large collection of human samples, and the potential impact of such variant silencing on tumor immunogenicity. Whole-exome mutation description and tumor-normal paired mRNA expression data originating from 636 unique patients diagnosed with 21 distinct tumor types (all solid tumors) were retrieved from The Cancer Genome Atlas (TCGA). Antigenicity and immunogenicity of neopeptides originating from mutated proteins within a same tumor sample were predicted using the tools available from the Immune Epitope Database (IEDB). A total of 65,072 missense mutations were studied. We demonstrated that 9.06% (N = 10,604 silenced/117,505 total variants) somatic variants were silenced in human tumors. Transciptomic silencing is significantly associated with proteins presenting better peptide processing, MHC-I binding, and T-cell recognition; and is more likely observed in lymphocyte-depleted tumors. Silencing may participate in tumor resistance by clonal selection and immune evasion. In the era of precision medicine, we suggest that therapeutic choices should be informed by both the presence of a genomic mutation and its actual transcript expression.
Defects in the Proteome and Metabolome in Human Hypertrophic Cardiomyopathy
Authors: Previs Michael J. , O’Leary Thomas S. , Morley Michael P. , Palmer Bradley M. , LeWinter Martin , Yob Jaime M. , Pagani Francis D. , Petucci Christopher , Kim Min-Soo , Margulies Kenneth B. , Arany Zoltan , Kelly Daniel P. , Day Sharlene M. 
Published: May 2022

Background:
Defects in energetics are thought to be central to the pathophysiology of hypertrophic cardiomyopathy (HCM); yet, the determinants of ATP availability are not known. The purpose of this study is to ascertain the nature and extent of metabolic reprogramming in human HCM, and its potential impact on contractile function.

Methods:
We conducted proteomic and targeted, quantitative metabolomic analyses on heart tissue from patients with HCM and from nonfailing control human hearts.

Results:
In the proteomic analysis, the greatest differences observed in HCM samples compared with controls were increased abundances of extracellular matrix and intermediate filament proteins and decreased abundances of muscle creatine kinase and mitochondrial proteins involved in fatty acid oxidation. These differences in protein abundance were coupled with marked reductions in acyl carnitines, byproducts of fatty acid oxidation, in HCM samples. Conversely, the ketone body 3-hydroxybutyrate, branched chain amino acids, and their breakdown products, were all significantly increased in HCM hearts. ATP content, phosphocreatine, nicotinamide adenine dinucleotide and its phosphate derivatives, NADP and NADPH, and acetyl CoA were also severely reduced in HCM compared with control hearts. Functional assays performed on human skinned myocardial fibers demonstrated that the magnitude of observed reduction in ATP content in the HCM samples would be expected to decrease the rate of cross-bridge detachment. Moreover, left atrial size, an indicator of diastolic compliance, was inversely correlated with ATP content in hearts from patients with HCM.

Conclusions:
HCM hearts display profound deficits in nucleotide availability with markedly reduced capacity for fatty acid oxidation and increases in ketone bodies and branched chain amino acids. These results have important therapeutic implications for the future design of metabolic modulators to treat HCM.
Type 1 Angiotensin Receptors on CD11c-Expressing Cells Protect Against Hypertension by Regulating Dendritic Cell–Mediated T Cell Activation
Authors: Lu Xiaohan , Zhang Jiandong , Wen Yi , Ren Jiafa , Griffiths Robert , Rudemiller Nathan P. , Ide Shintaro , Souma Tomokazu , Crowley Steven D. 
Published: May 2022

Background:

Type 1 angiotensin (AT
1
) receptors are expressed on immune cells, and we previously found that bone marrow–derived AT
1
receptors protect against Ang (angiotensin) II-induced hypertension. CD11c is expressed on myeloid cells derived from the bone marrow, including dendritic cells (DCs) that activate T lymphocytes. Here, we examined the role of AT
1
receptors on CD11c
+
cells in hypertension pathogenesis.

Methods:

Mice lacking the dominant murine AT
1
receptor isoform, AT
1a,
on CD11c
+
cells (dendritic cell [DC] AT1aR knockout [KO]) and wild-type (WT) littermates were subjected to Ang II-induced hypertension. Blood pressures were measured by radiotelemetry.

Results:

DC AT1aR KO mice had exaggerated hypertensive responses to chronic Ang II infusion with enhanced renal accumulation of effector memory T cells and CD40
+
DCs. CCL5 (C-C motif chemokine ligand 5) recruits T cells into injured tissues, and CCR7 (C-C motif chemokine receptor 7) facilitates DC and T cell interactions in the kidney lymph node to allow T cell activation. DCs from the hypertensive DC AT1aR KO kidneys expressed higher levels of CCL5 and CCR7. mRNA expressions for CCR7 and tumor necrosis factor-α were increased in CD4
+
T cells from the renal lymph nodes of DC AT1aR KO mice. During the second week of Ang II infusion when blood pressures between groups diverged, DC AT1aR KO mice excreted less sodium than WTs. Expressions for epithelial sodium channel subunits were increased in DC AT1aR KO kidneys.

Conclusions:
Following activation of the renin angiotensin system, AT1aR stimulation on DCs suppresses renal DC maturation and T cell activation with consequent protection from sodium retention and blood pressure elevation.
Detailed Mapping and Modeling of Urban Vegetation: What Are the Benefits for Microclimatic Simulations with Town Energy Balance (TEB) at Neighborhood Scale?
Authors: Bernard Émilie , Munck Cécile de , Lemonsu Aude 
Published: May 2022

Abstract
Cities develop a specific climate related to their morphology and the materials that constitute them. The addition of vegetation in urban areas induces cooling and shading effects that can modify local climate and thermal comfort conditions. The Town Energy Balance (TEB) urban canopy model offers several configurations for a more or less fine-tuned consideration of natural covers and associated physical processes in the urban environment. This study aims to evaluate the sensitivity of TEB to the representation of vegetation and the resolution of the chosen databases in the simulation of microclimatic variables, at the scale of a heterogeneous urban neighborhood located in Toulouse, France. First, the effect of the improved description of the vegetation input to the model is highlighted by comparing the results obtained with a readily available national database and then with a very-high-resolution satellite-derived vegetation database. Second, the two vegetation parameterizations, with or without explicit tree stratum, that are available in the TEB model are evaluated and compared. Measurements carried out on specific routes and stop points in a neighborhood of Toulouse allowed microclimatic variables to be evaluated. Results show that refining the vegetation database can somehow improve the modeling of air temperature. As a result of enhancing the vegetation description in the model, that is, physical processes associated with the presence of trees in urban canyons, the air temperature, but also the wind and the thermal comfort index, are better simulated. These results are encouraging for the use of TEB as a decision support tool for urban planning purposes.
Extratropical Transition of Tropical Cyclones in a Multiresolution Ensemble of Atmosphere-Only and Fully Coupled Global Climate Models
Authors: Baker Alexander J. , Roberts Malcolm J. , Vidale Pier Luigi , Hodges Kevin I. , Seddon Jon , Vannière Benoît , Haarsma Rein J. , Schiemann Reinhard , Kapetanakis Dimitris , Tourigny Etienne , Lohmann Katja , Roberts Christopher D. , Terray Laurent 
Published: May 2022

Abstract
Tropical cyclones undergo extratropical transition (ET) in every ocean basin. Projected changes in ET frequency under climate change are uncertain and differ between basins, so multimodel studies are required to establish confidence. We used a feature-tracking algorithm to identify tropical cyclones and performed cyclone phase-space analysis to identify ET in an ensemble of atmosphere-only and fully coupled global model simulations, run at various resolutions under historical (1950–2014) and future (2015–50) forcing. Historical simulations were evaluated against five reanalyses for 1979–2018. Considering ET globally, ensemble-mean biases in track and genesis densities are reduced in the North Atlantic and western North Pacific when horizontal resolution is increased from ∼100 to ∼25 km. At high resolution, multi-reanalysis-mean climatological ET frequencies across most ocean basins as well as basins’ seasonal cycles are reproduced better than in low-resolution models. Skill in simulating historical ET interannual variability in the North Atlantic and western North Pacific is ∼0.3, which is lower than for all tropical cyclones. Models project an increase in ET frequency in the North Atlantic and a decrease in the western North Pacific. We explain these opposing responses by secular change in ET seasonality and an increase in lower-tropospheric, pre-ET warm-core strength, both of which are largely unique to the North Atlantic. Multimodel consensus about climate change responses is clearer for frequency metrics than for intensity metrics. These results help clarify the role of model resolution in simulating ET and help quantify uncertainty surrounding ET in a warming climate.