bluuebunny/crossref_metadata_2025_split huggingface dataset:
AP‐3 complex subunit delta gene, ap3d1, regulates melanogenesis and melanophore survival via autophagy in zebrafish (Danio rerio)
Authors: Neuffer Sam J. , Beltran‐Cardona David , Jimenez‐Perez Kevin , Clancey Lauren F. , Brown Alexander , New Leslie , Cooper Cynthia D. 
Published: July 2022

AbstractZebrafish are an emerging model organism to study the syndromic albinism disorder, Hermansky–Pudlak syndrome (HPS), due to visible pigment development at 24 hours postfertilization, and conserved melanogenesis mechanisms. We describe crasher, a novel HPS type 10 (HPS10) zebrafish model, with a mutation in AP‐3 complex subunit delta gene, ap3d1. Exon 14 of ap3d1 is overexpressed in crasher mutants, while the expression of ap3d1 as a whole is reduced. ap3d1 knockout in *AB zebrafish recapitulates the mutant crasher phenotype. We show ap3d1 loss‐of‐function mutations cause significant expression changes in the melanogenesis genes, dopachrome tautomerase (dct) and tyrosinase‐related protein 1b (tyrp1b), but not tyrosinase (tyr). Last, Generally Applicable Gene‐set Enrichment (GAGE) analysis suggests autophagy pathway genes are upregulated together in crasher. Treatment with autophagy‐inhibitor, bafilomycin A1, significantly decreases melanophore number in crasher, suggesting ap3d1 promotes melanophore survival by limiting excessive autophagy. crasher is a valuable model to explore the regulation of melanogenesis gene expression and pigmentation disease.
Antimicrobial photodynamic therapy using chloro‐aluminum phthalocyanine for treating advanced stage‐III periodontitis in smoking patients
Authors: Al‐Kheraif Abdulaziz A. , Alshahrani Obaid Abdullah , Al‐Shehri Abdullah M. , Khan Aftab Ahmed 
Published: July 2022

AbstractPurposeTo evaluate the bacterial, clinical, and cytokine profile of adjunctive photodynamic therapy using chloro‐aluminum phthalocyanine (CAP/aPDT) with root surface debridement (RSD) versus RSD alone in cigarette smokers (CS) and never‐smokers (NS) during the period of 6 months.MethodsTwenty‐nine patients [CS – 14 and NS – 15] were recruited for the trial having stage‐III periodontitis. All candidates from the study groups were subjected to a split‐mouth treatment technique receiving CAP/aPDT + RSD and RSD alone. Periodontal parameters including plaque levels (PL), bleeding on probing (BP), probing depth (PD), clinical attachment loss (CAL), and marginal bone loss (MBL) were assessed. Polymerase chain reaction (qPCR) assay was used to analyze the copy numbers of Porphyromonas gingivalis (Pg) and Tannerella forsythia (Tf). Levels of tumor necrosis factor‐alpha (TNF‐α) interleukin (IL)‐6 in the crevicular fluid were evaluated by enzyme‐linked immunosorbent assay (ELISA).ResultsCAP/aPDT+RSD decreased BP in smokers after 6 months (p < .05). Probing depth and CAL reported statistically significant reductions within both CAP/aPDT+RSD and RSD groups and also within the NS and CS (p < .05). Pg and Tf stayed elevated in smokers at the 6‐month evaluation period (p < .01). Only CAP/aPDT+RSD significantly decreased Pg and Tf at 3‐ and 6‐month follow‐up in smokers (p < .05). CAP/aPDT+RSD showed decreased IL‐6 levels in the NS during the 6‐month follow‐up (p < .01). TNF‐α levels were significantly reduced in the CS group with CAP/aPDT+RSD and RSD alone until 6 months (p < .01).ConclusionCAP‐mediated aPDT along with nonsurgical periodontal therapy helped to improve the bacteriological outcomes among smokers and never‐smokers with stage‐III CP patients.
Genomic regions associate with major axes of variation driven by gas exchange and leaf construction traits in cultivated sunflower (Helianthus annuus L.)
Authors: Earley Ashley M. , Temme Andries A. , Cotter Christopher R. , Burke John M. 
Published: July 2022

SUMMARYStomata and leaf veins play an essential role in transpiration and the movement of water throughout leaves. These traits are thus thought to play a key role in the adaptation of plants to drought and a better understanding of the genetic basis of their variation and coordination could inform efforts to improve drought tolerance. Here, we explore patterns of variation and covariation in leaf anatomical traits and analyze their genetic architecture via genome‐wide association (GWA) analyses in cultivated sunflower (Helianthus annuus L.). Traits related to stomatal density and morphology as well as lower‐order veins were manually measured from digital images while the density of minor veins was estimated using a novel deep learning approach. Leaf, stomatal, and vein traits exhibited numerous significant correlations that generally followed expectations based on functional relationships. Correlated suites of traits could further be separated along three major principal component (PC) axes that were heavily influenced by variation in traits related to gas exchange, leaf hydraulics, and leaf construction. While there was limited evidence of colocalization when individual traits were subjected to GWA analyses, major multivariate PC axes that were most strongly influenced by several traits related to gas exchange or leaf construction did exhibit significant genomic associations. These results provide insight into the genetic basis of leaf trait covariation and showcase potential targets for future efforts aimed at modifying leaf anatomical traits in sunflower.
Orthology‐based analysis helps map evolutionary diversification and predict substrate class use of BAHD acyltransferases
Authors: Kruse Lars H. , Weigle Austin T. , Irfan Mohammad , Martínez‐Gómez Jesús , Chobirko Jason D. , Schaffer Jason E. , Bennett Alexandra A. , Specht Chelsea D. , Jez Joseph M. , Shukla Diwakar , Moghe Gaurav D. 
Published: July 2022

SUMMARYLarge enzyme families catalyze metabolic diversification by virtue of their ability to use diverse chemical scaffolds. How enzyme families attain such functional diversity is not clear. Furthermore, duplication and promiscuity in such enzyme families limits their functional prediction, which has produced a burgeoning set of incompletely annotated genes in plant genomes. Here, we address these challenges using BAHD acyltransferases as a model. This fast‐evolving family expanded drastically in land plants, increasing from one to five copies in algae to approximately 100 copies in diploid angiosperm genomes. Compilation of >160 published activities helped visualize the chemical space occupied by this family and define eight different classes based on structural similarities between acceptor substrates. Using orthologous groups (OGs) across 52 sequenced plant genomes, we developed a method to predict BAHD acceptor substrate class utilization as well as origins of individual BAHD OGs in plant evolution. This method was validated using six novel and 28 previously characterized enzymes and helped improve putative substrate class predictions for BAHDs in the tomato genome. Our results also revealed that while cuticular wax and lignin biosynthetic activities were more ancient, anthocyanin acylation activity was fixed in BAHDs later near the origin of angiosperms. The OG‐based analysis enabled identification of signature motifs in anthocyanin‐acylating BAHDs, whose importance was validated via molecular dynamic simulations, site‐directed mutagenesis and kinetic assays. Our results not only describe how BAHDs contributed to evolution of multiple chemical phenotypes in the plant world but also propose a biocuration‐enabled approach for improved functional annotation of plant enzyme families.
The efficacy of a novel topical spray composed of sodium benzoate, alcohol and botanical oils for the treatment of Malassezia dermatitis in dogs – a split body, randomised, blinded study
Authors: Hoes Nicole P. M. , van den Broek Jan , Vroom Margreet W. 
Published: July 2022

AbstractBackgroundTreatment of Malassezia pachydermatis dermatitis can be performed by systemic or topical route. As M. pachydermatis is located on the stratum corneum, topical therapy alone may be sufficient to resolve the infection. Owing to systemic antifungal resistance and adverse effects, topical treatment alone may improve treatment outcome.Hypothesis/ObjectivesTo evaluate the efficacy of a topical spray composed of sodium benzoate, alcohol and botanical oils, compared to a shampoo containing 2% chlorhexidine gluconate and 2% miconazole nitrate for the treatment of Malassezia pachydermaitis dermatitis in dogs.AnimalsSixteen client owned dogs diagnosed with symmetrical interdigital lesions as a result of secondary Malassezia dermatitis.MethodsThe study design was prospective, randomised and single‐blinded, using a split body protocol. Malassezia yeasts were determined by cytology at the inclusion day (day0) and after treatment (day14). All dogs were treated during 14 days with both shampoo at one paw and spray on the other paw.ResultsAt day 14 a reduction of Malassezia dermatitis was shown at both paws. No statistical difference was demonstrated between treatment with shampoo or spray.Conclusions and clinical importanceWe could not show a difference in efficacy between application of the test spray once daily and the topical use of 2%miconazole/2%chlorhexidine shampoo every other day. No adverse effects were reported.
Concurrent Validity and Reliability of Sprinting Force–Velocity Profile Assessed With GPS Devices in Elite Athletes
Authors: Clavel Pauline , Leduc Cedric , Morin Jean-Benoît , Owen Cameron , Samozino Pierre , Peeters Alexis , Buchheit Martin , Lacome Mathieu 
Published: July 2022

Purpose: The aims of this study were to (1) assess the concurrent validity of global positioning systems (GPSs) against a radar device to measure sprinting force–velocity (F–v) profiles and (2) evaluate the interunit reliability of 10-Hz GPS devices (Vector S7, Catapult Innovations). Methods: Sixteen male elite U18 rugby union players (178.3 [7.6] cm; 78.3 [13.2] kg) participated. Two 50-m sprints interspersed with at least 5 minutes of recovery were completed to obtain input (maximal sprint speed and acceleration time constant τ) and output (theoretical maximal horizontal force, sprinting speed, and horizontal power) F–v profile variables. Sprint running speed was concurrently measured with a radar and 2 GPS units placed on the upper back of each player. Concurrent validity and interunit reliability analyses were performed. Results: Moderate to nearly perfect correlations were observed between radar and GPS-derived F–v variables, with small to large typical errors. Trivial to small coefficients of variation were found regarding the GPS interunit reliability. Conclusion: The GPS devices tested in this study represent a valid and reliable alternative to a radar device when assessing sprint acceleration F–v profiles in team-sport players.
Duplex kinematics reduces both frontal advance and seismic moment deficit in the Himalaya
Authors: Hu Wan-Lin , Stevens Victoria L. 
Published: July 2022

Abstract
Duplexing plays important roles in the evolution of fold-and-thrust belts and accretionary wedges, and causes internal shortening of the system, which then impacts both rates of frontal advance and seismic-moment deficit. Nevertheless, the significance of this internal shortening has not yet been highlighted in previous studies in the Himalaya or elsewhere. We invoke geometric solutions to constrain the ratio of transferred slip (R; i.e., the ratio of updip slip to downdip slip) for the midcrustal ramp—the most active ramp within the midcrustal duplex—in the Himalayan wedge. We find that R is ~0.9, and then used this ratio to calculate the accumulating seismic moment. The reduction in seismic-moment accumulation over the past 1000 yr along the entire Himalayan arc (~2200 km) is equivalent to at least one ~Mw 8.72 earthquake, and potentially reduces the seismic moment deficit by ~23%–54%, which may reconcile the long-term unbalanced seismic moment in the Himalaya.
Unusual complication of Herpes simplex encephalitis: complete Klüver-Bucy syndrome
Authors: Hernandez-Vega Melissa , Badial-Ochoa Sandra , Rivas-Ruvalcaba Francisco Javier , Rodriguez-Leyva Ildefonso 
Published: July 2022

Klüver-Bucy syndrome is a rare neurobehavioral disorder caused by a bilateral temporal lobe lesion affecting the hippocampus and amygdala; clinically characterised by hyperorality, hypermetamorphosis, placidity, altered sexual behaviour, eating, disorders and visual impairment, agnosia and amnesia. However, the complete syndrome is rarely seen, and diagnosis does not require all the symptoms to be manifested simultaneously.We describe a patient who developed a complete Klüver-Bucy syndrome secondary to bilateral temporal involvement due to herpetic encephalitis.
Occupational differences in SARS-CoV-2 infection: analysis of the UK ONS COVID-19 infection survey
Authors: Rhodes Sarah , Wilkinson Jack , Pearce Neil , Mueller William , Cherrie Mark , Stocking Katie , Gittins Matthew , Katikireddi Srinivasa Vittal , Tongeren Martie Van 
Published: July 2022

BackgroundConcern remains about how occupational SARS-CoV-2 risk has evolved during the COVID-19 pandemic. We aimed to ascertain occupations with the greatest risk of SARS-CoV-2 infection and explore how relative differences varied over the pandemic.MethodsAnalysis of cohort data from the UK Office of National Statistics COVID-19 Infection Survey from April 2020 to November 2021. This survey is designed to be representative of the UK population and uses regular PCR testing. Cox and multilevel logistic regression were used to compare SARS-CoV-2 infection between occupational/sector groups, overall and by four time periods with interactions, adjusted for age, sex, ethnicity, deprivation, region, household size, urban/rural neighbourhood and current health conditions.ResultsBased on 3 910 311 observations (visits) from 312 304 working age adults, elevated risks of infection can be seen overall for social care (HR 1.14; 95% CI 1.04 to 1.24), education (HR 1.31; 95% CI 1.23 to 1.39), bus and coach drivers (1.43; 95% CI 1.03 to 1.97) and police and protective services (HR 1.45; 95% CI 1.29 to 1.62) when compared with non-essential workers. By time period, relative differences were more pronounced early in the pandemic. For healthcare elevated odds in the early waves switched to a reduction in the later stages. Education saw raises after the initial lockdown and this has persisted. Adjustment for covariates made very little difference to effect estimates.ConclusionsElevated risks among healthcare workers have diminished over time but education workers have had persistently higher risks. Long-term mitigation measures in certain workplaces may be warranted.
One week of overeating upregulates angiogenic and lipolytic gene expression in human subcutaneous adipose tissue from exercise trained and untrained adults
Authors: Ludzki Alison C. , Krueger Emily M. , Gillen Jenna B. , Taylor Natalie M. , Middlebrook Darby O. , Baldwin Toree C. , Karabetsos Konstantinos C. , Schleh Michael W. , Horowitz Jeffrey F. 
Published: July 2022

Effective storage of excess energy in abdominal subcutaneous adipose tissue during periods of overeating may help attenuate weight-gain-related insulin resistance. The objective of this study was to assess changes in the expression of factors regulating abdominal subcutaneous adipose tissue storage capacity in response to a brief exposure to overeating in nonobese adults. Because exercise can alter the expression of genes involved in regulating adipose tissue storage capacity, we compared the responses to overeating in regular exercisers (EX, n = 11) and nonexercisers (nonEX, n = 11). Abdominal subcutaneous adipose tissue samples and oral glucose tolerance tests were performed before and after participants ate 30% above their estimated daily energy requirements for 1 week. Both EX and nonEX gained ∼1 kg ( P < 0.01), and Matsuda insulin sensitivity index was reduced ∼15% ( P = 0.04) in both groups. Gene expression of factors involved in lipid metabolism ( HSL, ATGL, DGAT, and PPARγ) and angiogenesis ( HIF1α and KDR) were increased ( P < 0.05), with no differences observed between EX and nonEX. In contrast, protein abundance of these factors did not change. The modest overeating stimulus did not increase markers of inflammation in the systemic circulation or adipose tissue. Overall, our findings indicate that a brief and modest overeating stimulus can impair insulin sensitivity and upregulate genes involved in abdominal adipose tissue storage capacity similarly in exercisers and nonexercisers. ClinicalTrials.gov ID#: NCT02701738.
Reducing Minor Page Fault Overheads through Enhanced Page Walker
Authors: Tirumalasetty Chandrahas , Chou Chih Chieh , Reddy Narasimha , Gratz Paul , Abouelwafa Ayman 
Published: July 2022

Application virtual memory footprints are growing rapidly in all systems from servers down to smartphones. To address this growing demand, system integrators are incorporating ever larger amounts of main memory, warranting rethinking of memory management. In current systems, applications produce page fault exceptions whenever they access virtual memory regions that are not backed by a physical page. As application memory footprints grow, they induce more and more minor page faults. Handling of each minor page fault can take a few thousands of CPU cycles and blocks the application till the OS kernel finds a free physical frame. These page faults can be detrimental to the performance when their frequency of occurrence is high and spread across application runtime. Specifically, lazy allocation-induced minor page faults are increasingly impacting application performance. Our evaluation of several workloads indicates an overhead due to minor page faults as high as 29% of execution time.
In this article, we propose to mitigate this problem through a hardware, software co-design approach. Specifically, we first propose to parallelize portions of the kernel page allocation to run ahead of fault time in a separate thread. Then we propose the Minor Fault Offload Engine (MFOE), a per-core hardware accelerator for minor fault handling. MFOE is equipped with a pre-allocated page frame table that it uses to service a page fault. On a page fault, MFOE quickly picks a pre-allocated page frame from this table, makes an entry for it in the TLB, and updates the page table entry to satisfy the page fault. The pre-allocation frame tables are periodically refreshed by a background kernel thread, which also updates the data structures in the kernel to account for the handled page faults. We evaluate this system in the gem5 architectural simulator with a modified Linux kernel running on top of simulated hardware containing the MFOE accelerator. Our results show that MFOE improves the average critical path fault handling latency by 33× and tail critical path latency by 51×. Among the evaluated applications, we observed an improvement of runtime by an average of 6.6%.
Standards column: VQEG
Authors: Gutiérrez Jesús , Brunnström Kjell 
Published: July 2022

The Video Quality Experts Group (VQEG) was born from a need to bring together experts in subjective video quality assessment and objective quality measurement. The first VQEG meeting, held in Turin in 1997, was attended by a small group of experts drawn from ITU-T and ITU-R Study Groups. VQEG was first grounded in basic subjective methodology and objective tool development/verification for video quality assessment such that the industry could be moved forward with standardization and implementation. At the beginning it was focused around measuring the perceived video quality since the distribution path for video and audio were limited and known.
Over the last 20 years from the formation of VQEG the ecosystem has changed dramatically and thus so must the work. Multimedia is now pervasive on all devices and methods of distribution from broadcast to cellular data networks. This shift has the expertise within VQEG to move from the visual (no-audio) quality of video to Quality of Experience (QoE).
The march forward of technologies means that VQEG needs to react and be on the leading edge of developing, defining and deploying methods and tools that help address these new technologies and move the industry forward. This also means that we need to embrace both qualitative and quantitative ways of defining these new spaces and terms. Taking a holistic approach to QoE will enable VQEG to drive forward and faster with unprecedented collaboration and execution.
VQEG is open to all interested from industry, academia, government organizations and Standard-Developing Organizations (SDOs). There are no fees involved, no membership applications and no invitations are needed to participate in VQEG activities. Subscription to the main VQEG email list (ituvidq@its.bldrdoc.gov) constitutes membership in VQEG.
VQEG conducts work via discussions over email reflectors, regularly scheduled conference calls and, in general, two face-to-face meetings per year. There are currently more than 500 people registered across 11 email reflectors, including a main reflector for general announcements relevant to the entire group, and different project reflectors dedicated to technical discussions of specific projects. A LinkedIn group exists as well.
Presurgery Adhesion Molecules and Angiogenesis Biomarkers Are Differently Associated with Outcomes in Colon and Rectal Cancer: Results from the ColoCare Study
Authors: Ose Jennifer , Gigic Biljana , Hardikar Sheetal , Lin Tengda , Himbert Caroline , Warby Christy A. , Peoples Anita R. , Lindley Clara L. , Boehm Juergen , Schrotz-King Petra , Figueiredo Jane C. , Toriola Adetunji T. , Siegel Erin M. , Li Christopher I. , Ulrich Alexis , Schneider Martin , Shibata David , Ulrich Cornelia M. 
Published: July 2022

Abstract

Background:
Cell-to-cell adhesion and angiogenesis are hallmarks of cancer. No studies have examined associations of adhesion molecules and angiogenesis biomarkers with clinical outcomes in colorectal cancer.

Methods:
In presurgery serum from n = 426 patients with colorectal cancer (stage I–III), we investigated associations of CRP, SAA, adhesion molecules (sICAM-1, sVCAM-1), and angiogenesis markers (VEGF-A and VEGF-D) with overall survival (OS), disease-free survival (DFS), and risk of recurrence. We computed HRs and 95% confidence intervals; adjusted for age, sex, BMI, stage, site, and study site, stratified by tumor site in exploratory analyses.

Results:
N = 65 (15%) were deceased, and 39 patients (14%) had a recurrence after a median follow-up of 31 months. We observed significant associations of biomarkers with OS, DFS, and risk of recurrence on a continuous scale and comparing top to bottom tertile, with HRs ranging between 1.19 and 13.92. CRP was associated with risk of death and recurrence in patients in the top tertile compared with patients in the bottom tertile, for example, risk of recurrence HRQ3-Q1: 13.92 (1.72–112.56). Significant heterogeneity between biomarkers and clinical outcomes was observed in stratified analysis by tumor site for CRP, SAA, sICAM-1, sVCAM-1, and VEGF-D. VEGF-D was associated with a 3-fold increase in risk of death for rectal cancer (HRlog2: 3.26; 95% CI, 1.58–6.70) compared with no association for colon cancer (HRlog2: 0.78; 95% CI, 0.35–1.73; Pheterogenity = 0.01).

Conclusions:
Adhesion molecules and angiogenesis biomarkers are independent prognostic markers for colorectal cancer, with differences by tumor site.

Impact:
There is need for tailored treatment for colon and rectal cancer.