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Long-term monitoring of cycles in Clethrionomys rutilus in the Yukon boreal forest

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Integrative Zoology 2024年第1期19卷 27-36页

作者： Charles J.KREbS Alice J.KENNEY b.scott GILbERT Rudy bOONSTRA Department of Zoology University of British ColumbiaVancouverBritish ColumbiaCanada Renewable Resources Management Program Yukon UniversityWhitehorseYukonCanada Department of biological Sciences University of Toronto ScarboroughTorontoOntarioCanada

baseline studies of small rodent populations in undisturbed ecosystems are *** report here 50 years of mon-itoring and experimentation in Yukon of a dominant rodent species in the North American boreal forest,the red-backed vole Clethrionomys *** voles breed in summer,weigh 20–25 g,and reach a maximum density of 20 to 25 per *** populations have shown consistent 3–4-year cycles for the last 50 years with the only change being that peak densities averaged 8/ha until 2000 and 18/ha since that *** the last 25 years,we have measured food resources,predator numbers,and winter weather,and for 1-year social interactions,to estimate their contribution to changes in the rate of summer increase and the rate of overwinter *** these potential limiting factors could contribute to changes in density,and we measured their relative contributions statistically with multiple *** rate of winter decline in density was related to both food supply and winter *** rate of summer increase was related to summer berry crops and white spruce cone *** measure of predator numbers was related to winter or summer changes in vole *** was a large signal of climate change effects in these *** is no density dependence in summer population growth and only a weak one in winter population *** of our results provide a clear understanding of what generates 3–4-year cycles in these voles,and the major missing piece may be an understanding of social interactions at high density.

关键词： boreal forest climate change density dependence population cycles predation winter severity

APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control

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GENOMICS PROTEOMICS & bIOINFORMATICS 2024年第2期22卷 qzae042页

作者： Chen, Yiling Elaine Ge, Xinzhou Woyshner, Kyla McDermott, Meilu Manousopoulou, Antigoni Ficarro, scott b. Marto, Jarrod A. Li, Kexin Wang, Leo David Li, Jingyi Jessica Univ Calif Los Angeles Dept Stat & Data Sci Los Angeles CA 90095 USA Univ Calif Los Angeles Bioinformat Interdept Program Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Computat Med Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Biostat Los Angeles CA 90095 USA City Hope Natl Med Ctr Beckman Res Inst Dept Immuno Oncol Duarte CA 91010 USA Univ Southern Calif Dept Quantitat & Computat Biol Los Angeles CA 90007 USA City Hope Natl Med Ctr Dept Pediat Duarte CA 91010 USA brigham & Womens Hosp Dept Canc Biol Boston MA 02215 USA brigham & Womens Hosp Dana Farber Canc Inst Blais Prote Ctr Dept Pathol Boston MA 02215 USA Harvard Med Sch Boston MA 02215 USA

Advances in mass spectrometry (MS) have enabled high-throughput analysis of proteomes in biological systems. The state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide-spectrum matches (PSMs), which convert mass spectra to peptide sequences. Different database search algorithms use distinct search strategies and thus may identify unique PSMs. However, no existing approaches can aggregate all user-specified database search algorithms with a guaranteed increase in the number of identified peptides and a control on the false discovery rate (FDR). To fill in this gap, we proposed a statistical framework, Aggregation of Peptide Identification Results (APIR), that is universally compatible with all database search algorithms. Notably, under an FDR threshold, APIR is guaranteed to identify at least as many, if not more, peptides as individual database search algorithms do. Evaluation of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the FDR. Real data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search algorithms. The APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis, e.g., differential gene expression analysis on RNA sequencing data. The APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide-spectrum match Peptide identification Aggregation of lists FDR control PROTEIN IDENTIFICATION bRCA2 MUTATIONS CELL-CYCLE TANDEM TARGET CANCER PREVALENCE EXPRESSION GENE APOPTOSIS

2024 Wheelchair Compendium of Physical Activities:An update of activity codes and energy expenditure values

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Journal of Sport and Health Science 2024年第1期13卷 18-23页

作者： scott A.Conger Stephen D.Herrmann Erik A.Willis Tom E.Nightingale Joseph R.Sherman barbara E.Ainsworth Department of Kinesiology Boise State UniversityBoiseID 83725USA Kansas Center for Metabolism and Obesity Research The University of Kansas Medical CenterKansas CityKS 66160USA Center for Health Promotion and Disease Prevention University of North Carolina at Chapel HillChapel HillNC 27599USA School of Sport Exercise and Rehabilitation SciencesUniversity of BirminghamBirmingham AL B152TTUK Centre for Trauma Sciences Research University of BirminghamEdgbastonBirmingham AL B152TTUK College of Health Solutions Arizona State UniversityPhoenixAZ 85003USA School of Exercise and Health Shanghai University of SportShanghai 200438China

Purpose:This paper presents an update of the 2011 Wheelchair Compendium of Physical Activities designed for wheelchair users and is referred to as the 2024 Wheelchair *** Wheelchair Compendium aims to curate existing knowledge of the energy expenditure for wheelchair physical activities(PAs).Methods:A systematic review of the published energy expenditure of PA for wheelchair users was completed between 2011 and May *** added these data to the 2011 Wheelchair Compendium data that was compiled previously in a systematic review through ***:A total of 47 studies were included,and 124 different wheelchair PA reported energy expenditure values ranging from 0.8 metabolic equivalents for wheelchair users(filing papers,light effort)to 11.8 metabolic equivalents for wheelchair users(Nordic sit skiing).Conclusion:In introducing the updated 2024 Wheelchair Compendium,we hope to bridge the resource gap and challenge the prevailing narratives that inadvertently exclude wheelchair users from physical fitness and health PAs.

关键词： Disability Exercise MET Mobility

EZH2 inhibitors promote β-like cell regeneration in young and adult type 1 diabetes donors

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Signal Transduction and Targeted Therapy 2024年第2期9卷 679-692页

作者： Keith Al-Hasani Safiya Naina Marikar Harikrishnan Kaipananickal scott Maxwell Jun Okabe Ishant Khurana Thomas Karagiannis Julia J.Liang Lina Mariana Thomas Loudovaris Thomas Kay Assam El-Osta Epigenetics in Human Health and Disease Program Baker Heart and Diabetes Institute75 Commercial RoadMelbourne 3004 VICAustralia Department of Diabetes Central Clinical SchoolMonash UniversityMelbourne 3004 VICAustralia Epigenetics in Human Health and Disease Laboratory Central Clinical SchoolMonash UniversityMelbourne 3004 VICAustralia School of Science STEM CollegeRMIT UniversityMelbourne 3001 VICAustralia Immunology and Diabetes Unit St Vincent’s Institute of Medical ResearchFitzroy 3065 VICAustralia Department of Medicine and Therapeutics The Chinese University of Hong KongSha TinHong Kong SAR Hong Kong Institute of Diabetes and Obesity Prince of Wales HospitalThe Chinese University of Hong Kong3/F Lui Che Woo Clinical Sciences Building30-32-Ngan Shing StreetSha TinHong Kong SAR Li Ka Shing Institute of Health Sciences The Chinese University of Hong KongSha TinHong Kong SAR biomedical Laboratory Science Department of TechnologyFaculty of HealthUniversity College CopenhagenCopenhagenDenmark

β-cells are a type of endocrine cell found in pancreatic islets that synthesize,store and release *** type 1 diabetes(T1D),T-cells of the immune system selectively destroy the insulin-producingβ-*** of these cells leads to a lifelong dependence on exogenous insulin administration for ***,there is an urgent need to identify novel therapies that stimulateβ-cell growth and induceβ-cell *** and others have shown that pancreatic ductal progenitor cells are a promising source for regeneratingβ-cells for T1D owing to their inherent differentiation *** transcriptional suppression is refractory to exocrine reaction and tightly controls the regenerative potential by the EZH2 *** the present study,we show that transient stimulation of exocrine cells,derived from juvenile and adult T1D donors to the FDAapproved EZH2 inhibitors GSK126 and Tazemetostat(Taz)influence a phenotypic shift towards aβ-like cell *** transition from repressed to permissive chromatin states are dependent on bivalent H3K27me3 and H3K4me3 chromatin *** EZH2 is fundamental toβ-cell regenerative *** pancreatic ductal cells exhibit insulin production and secretion in response to a physiological glucose challenge ex *** pre-clinical studies underscore the potential of small molecule inhibitors as novel modulators of ductal progenitor differentiation and a promising new approach for the restoration ofβ-like cell function.

关键词： EZH2 struction inhibitors

Manipulation of photosensory and circadian signaling restricts phenotypic plasticity in response to changing environmental conditions in Arabidopsis

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Molecular Plant 2024年第9期17卷 1458-1471页

作者： Martin William battle scott Fraser Ewing Cathryn Dickson Joseph Obaje Kristen N.Edgeworth Rebecca bindbeutel Rea LAntoniou-Kourounioti Dmitri A.Nusinow Matthew Alan Jones Plant Science Group School of Molecular BiosciencesUniversity of GlasgowGlasgow G128QQUK Danforth Plant Science Center St.LouisMO 63132USA Department of biological and biomedical Sciences Washington University in St.LouisSt.LouisMO 63130USA Present address:School of biological and Environmental Sciences Liverpool John Moores UniversityLiverpool L22QPUK

Plants exploit phenotypic plasticity to adapt their growth and development to prevailing environmental *** of light and temperature signals is aided by the circadian system,which provides a temporal *** plasticity provides a selective and competitive advantage in nature but is obstructive during large-scale,intensive agricultural practices since economically important traits(including vegetative growth and flowering time)can vary widely depending on local environmental *** prevents accurate prediction of harvesting times and produces a variable *** this study,we sought to restrict phenotypic plasticity and circadian regulation by manipulating signaling systems that govern plants'responses to environmental *** modeling of plant growth and develop-ment predicted reduced plant responses to changing environments when circadian and light signaling pathways were *** tested this prediction by utilizing a constitutively active allele of the plant photoreceptor phytochrome b,along with disruption of the circadian systemvia mutation of *** found that these manipulations produced plants that are less responsive to light and temper-ature cues and thus fail to anticipate *** engineered plants have uniform vegetative growth and flowering time,demonstrating how phenotypic plasticity can be limited while maintaining plant *** has significant implications for future agriculture in both open fields and controlled environments.

关键词： circadian developmental plasticity phenotypic plasticity external coincidence light temperature

Participatory Disaster Recovery Simulation Modeling for Community Resilience Planning

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International Journal of Disaster Risk Science 2018年第4期9卷 519-529页

作者： scott b.Miles Department of Human Centered Design and Engineering University of Washington

A major challenge in enhancing the resilience of communities stems from current approaches used to identify needs and strategies that build the capacity of jurisdictions to mitigate loss and improve recovery. A new generation of resilience-based planning processes has emerged in the last several years that integrate goals of community well-being and identity into recovery-based performance measurement frameworks. Specific tools and refined guidance are needed to facilitate evidence-based development of recovery estimates. This article presents the participatory modeling process, a planning system designed to develop recovery-based resilience measurement frameworks for community resilience planning initiatives. Stakeholder engagement is infused throughout the participatory modeling process by integrating disaster recovery simulation modeling into community resilience planning. Within the process, participants get a unique opportunity to work together to deliberate on community concerns through facilitated participatory modeling. The participatory modeling platform combines the DESaster recovery simulation model and visual analytics *** is an open source Python Library for creating discrete event simulations of disaster recovery. The simulation model was developed using a human-centered design approach whose goal is to be open, modular, and extensible. The process presented in this article is the first participatory modeling approach for analyzing recovery to aid creation of community resilience measurement frameworks.

关键词： Community resilience planning Disasters Disaster recovery Participatory modeling Recovery-based performance targets Simulation modeling

Fire occurrence in relation to bamboo dominance in the Qinling Mountains of China: Evidence from phytolith and charcoal records in Holocene sediments

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Science China Earth Sciences 2015年第7期58卷 1182-1190页

作者： Courtney Marie RAYLE scott b.FRANKLIN LU ZhiJun School of biological Sciences University of Northern Colorado Key Laboratory of Aquatic botany and Watershed Ecology the Chinese Academy of Sciences

he internal genetic clock of semelparous mast-flowering bamboo species creates gregarious regions of flowering and death, thus leading to fuel-load accumulation that potentially promotes fire（Fire-Cycle Hypothesis）. Higher abundance of bamboo could be expected to provide greater fuel loads after flowering. Here, we investigated the possible link between bamboo dominance and fire occurrence. As the main food source for the giant panda in the Qinling Mountains of China, bashania fargesii（Farges Canebrake） and Fargesia qinlingensis（Arrow bamboo） dominate lower（1000–1900 m） and higher elevations（1800–2700 m）, respectively. Four soil profiles（elevation ranging from 1240 to 2170 m） in areas of known recent bamboo flowering events（~1980） and adjacent non-flowering sites were assessed for phytoliths and charcoal. Characteristic phytoliths were chosen to describe bamboo dynamics, and charcoal particles were extracted from the soil to reconstruct fire history. Carbon 14 dating of soil charcoal samples was conducted using an accelerator mass spectrometry technique. In addition, we chose two depths（28–52 and 90–100 cm） in one bashania profile（b. fargesii forest） and one Fargesia profile（F. qinlingensis forest） for phytolith dating. Our findings indicate that bamboo has been a dominant component of these ecosystems almost for the entire profile; some 6400 yrs for bashania and ca. 10000 yrs for the Fargesia. It is also clear from the charcoal and phytolith data that bamboo abundance and recent mast flowering were significantly related to fire occurrence for lower elevation bashania while the higher elevation Fargesia was not. One of the four profiles had chronological charcoal records throughout and the oldest charcoal aged was ~1410 yr bP, suggesting an anthropogenic origin. The mixing of phytolith and charcoal made it unrealistic to describe temporal dynamics of bamboo and fire events, and thus our interpretation is cognizant of the dating discrepancies and conservative（less-sp

关键词： bamboo dynamics bashania Fargesia fire cycle hypothesis phytolith Qinling Mountains

Spatially biased dispersal of acorns by a scatter-hoarding corvid may accelerate passive restoration of oak habitat on California＇s largest island

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Current Zoology 2017年第4期63卷 363-367页

作者： Mario b. PESENDORFER T. scott SILLETT scott A. MORRISON School of biological Sciences University of Nebraska - Lincoln 348 Manter Hall Lincoln NE 68588-0118 USA Migratory bird Center Smithsonian Conservation Biology Institute National Zoological Park MRC 5503 Washington D.C. 20013-7012 USA Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA The Nature Conservancy 4th Floor 201 Mission Street San Francisco CA 94105 USA

Scatter hoarding by corvids （crows, jays, magpies, and nutcrackers） provides seed dispersal for many large-seeded plants, including oaks and pines. When hoarding seeds, corvids often choose nonrandom locations throughout the landscape, resulting in differential survival of seeds. In the context of habitat restoration, such disproportional storing of seeds in areas suitable for germin- ation and establishment can accelerate expansion and recovery of large-seeded tree populations and their associated ecosystems. Here, we investigate the spatial preferences of island scrub jays Aphelocoma insularis during scatter hoarding of acorns （Quercus spp.） on Santa Cruz Island. We use a large behavioral data set on the birds＇ behavior in combination with seedling surveys and spatial analysis to determine whether 1） island scrub jays disproportionally cache seeds in specific habitat types, and 2） whether the preferred habitat type is suitable for oak regeneration. Our results show that the jays nonrandomly cache acorns across the landscape; they use chaparral and coastal sage scrub disproportionally while avoiding open and grassy areas. The areas used most often for caching were also the areas with the highest oak seedling densities. We discuss the potential role of these findings for the recovery of Santa Cruz Island＇s oak habitat since the 1980s.

关键词： Aphelocoma insularis directional dispersal habitat restoration Quercus spp. scatter hoarding seed dispersal.

“建构它们的生存空间”:作为地理媒介实践的“助猫”研究

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热带地理 2024年第8期44卷 1487-1499页

作者：胡康斯科特·麦夸尔李昕恬北京外国语大学国际新闻与传播学院北京100087 墨尔本大学文化与传播学院墨尔本3010澳大利亚

流浪猫作为边缘动物活跃于人类的生存空间之中,数智技术的发展使人类围绕流浪猫所展开的混合性空间交互具有特殊的文化生产与人际互动意义。文章运用技术漫游、深度访谈等方法,结合媒介地理学中的地理媒介理论,对深度媒介化社会中的“... 详细信息

流浪猫作为边缘动物活跃于人类的生存空间之中,数智技术的发展使人类围绕流浪猫所展开的混合性空间交互具有特殊的文化生产与人际互动意义。文章运用技术漫游、深度访谈等方法,结合媒介地理学中的地理媒介理论,对深度媒介化社会中的“助猫实践”展开研究,主要考察助猫者如何建构媒介化助猫空间、以何种方式与流浪猫产生空间性交互、助猫空间中存在何种媒介化期待与解释、产生了哪些人际交往或矛盾,又会如何影响地点的形塑与认知。研究发现,人与媒介在动态交互中建构出突破虚实维度的助猫空间,人的“数字化漫游”、流浪猫的“超可见性”在其中上演;基于所建构的助猫空间,猫与猫屋的流动(转移、搬迁、拆除)伴随着人与空间的对话、协商与斗争,具有丰富的空间生产意义;助猫者凭借数字媒介在具有混合性质的助猫空间中与不同行动方相遇,同一或对立的关系在此过程中生成,编谱着地方性的记忆情结,折射出存在于社会的现实问题,乃至不同物种之间的共生问题。在此基础上,从理论层面对过往媒介地理学研究进行反思,细分出“技术型地理媒介”与“生命型地理媒介”,以拓展地理媒介的研究版图,并勾勒出人与流浪猫共生空间建构的机制。

关键词：地理媒介边缘动物流浪猫 “助猫” 生存空间生存意义

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