985 Works

Data from: Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management

Veronica F. Frans, Amélie A. Augé, Jim Fyfe, Yuqian Zhang, Nathan McNally, Hendrik A. Edelhoff, Niko Balkenhol & Jan O. Engler
1. Species’ ranges are changing at accelerating rates. Species distribution models (SDMs) are powerful tools that help rangers and decision-makers prepare for reintroductions, range shifts, reductions, and/or expansions by predicting habitat suitability across landscapes. Yet, range-expanding or -shifting species in particular face other challenges that traditional SDM procedures cannot quantify, due to large differences between a species’ currently-occupied range and potential future range. The realism of SDMs is thus lost and not as useful for...

Data from: Spatial variation in bioclimatic relationships for a snow-adapted species along a discontinuous southern range boundary

Sean Sultaire
Documenting variation in the relationship between climate variables and species occurence at range boundaries can help reveal how species will respond to global climate change. We collected snowshoe hare (Lepus americanus) presence-absence data from snow-track surveys conducted in the U.S. states of Michigan and Wisconsin in winters from 2012-2014 at their southern range boundary in the region. A series of 125m transects were walked at each site within a week of fresh snowfall, and the...

Data from: Multi-generation genomic prediction of maize yield using parametric and non-parametric sparse selection indices

Marco Lopez-Cruz, Yoseph Beyene, Manje Gowda, Jose Crossa, Paulino Perez-Rodriguez & Gustavo De Los Campos
Genomic prediction models are often calibrated using multi-generation data. Over time, as data accumulates, training data sets become increasingly heterogeneous. Differences in allele frequency and linkage disequilibrium patterns between the training and prediction genotypes may limit prediction accuracy. This leads to the question of whether all available data or a subset of it should be used to calibrate genomic prediction models. Previous research on training set optimization has focused on identifying a subset of the...

Antwren times to approach Dusky-throated Antshrike based on antshrike behavior

Sean Williams
We investigated whether context-specific behavior is responsible for the cohesion of mixed-species flocks of antshrikes and antwrens in Amazonian Peru. Antshrikes perform a behavior given while spatially repositioning, to which antwrens respond by approaching. Cohesion of interspecific associations requires communication, although the mechanisms often are unexplored. In monospecific groups, cohesion among individuals is maintained with actions or vocalizations given in a certain context. Dusky-throated Antshrikes (Thamnomanes ardesiacus) vocalize while in flight and the number of...

Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation

Acer Van Wallendael
Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic datasets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid...

Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry

Michael Hardigan, Mitchell Feldmann, Randi Famula, Michaela Vachev, Mary Madera, Philipp Zerbe, Kristin Mars, Paul Peluso, David Rank, Shujun Ou, Christopher Saski, Charlotte Acharya, Glenn Cole, Alan Yocca, Patrick Edger & Steven Knapp
The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its progenitors are outbred octoploids in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the...

Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development

Y Hoang, Joshua Franklin, Yann Dufour & Lee Kroos
Starving Myxococcus xanthus bacteria use short-range C-signaling to coordinate their movements and construct multicellular mounds, which mature into fruiting bodies as rods differentiate into spherical spores. Differentiation requires efficient C-signaling to drive the expression of developmental genes, but how the arrangement of cells within nascent fruiting bodies (NFBs) affects C-signaling is not fully understood. Here, we used confocal microscopy and cell segmentation to visualize and quantify the arrangement, morphology, and gene expression of cells near...

Using a WeChat mini-program-based lactation consultant intervention to increase the consumption of mother’s own milk by preterm infants in the neonatal intensive care unit: a study protocol for a cluster randomized controlled trial

Jie Huo, Xinping Wu, Chuanli Gu, Zhangbin Yu, Jun Zhang, Xiaohui Chen, Jingai Zhu, Feng Liu, Beibei Liu, Qianqian Li & Shuping Han
Abstract Background The benefits of mother’s own milk (MOM) for preterm infants have been widely recognized. Many studies have shown that the rate of breastfeeding of premature infants remains very low. Although many studies use measures to promote breastfeeding, few high-quality cluster randomized controlled studies have evaluated the effectiveness of these measures. WeChat is an instant messaging software for smart terminals, and WeChat mini-programs have been widely used to promote health and self-management in China....

Larval yellow perch locations during locomotion assays after exposure to MeHg and PCB126

Janice Albers, Rebekah Klingler, Michael Carvan & Cheryl Murphy
Fish swimming behavior is a commonly measured response in aquatic ecotoxicology because behavior is considered a whole organism-level effect that integrates many sensory systems. Recent advancements in animal behavior models, such as hidden Markov chain models (HMM), suggest an improved analytical approach for toxicology. Using both new and traditional approaches, we examined the sublethal effects of PCB126 and methylmercury on yellow perch (YP) larvae (Perca flavescens) using three doses. Both approaches indicate larvae increase activity...

B7 family member H4 induces epithelial-mesenchymal transition and promotes the proliferation, migration and invasion of colorectal cancer cells

Yuzhen Yin, Lili Shi, Jing Yang, Hui Wang, Hang Yang & Qiang Wang
Colorectal cancer (CRC) is a common malignancy of the gastrointestinal tract, which has the second highest incidence among gastrointestinal tumors. At present, due to the limitations of current CRC treatment strategies, there is an urgent need for developing more effective therapies. B7 family member H4 (B7-H4) is associated with the progression of a wide spectrum of cancers, but its functional role in CRC is unknown. The purpose of this study is to clarify the role...

Additional file 2 of Using a WeChat mini-program-based lactation consultant intervention to increase the consumption of mother’s own milk by preterm infants in the neonatal intensive care unit: a study protocol for a cluster randomized controlled trial

Jie Huo, Xinping Wu, Chuanli Gu, Zhangbin Yu, Jun Zhang, Xiaohui Chen, Jingai Zhu, Feng Liu, Beibei Liu, Qianqian Li & Shuping Han
Additional file 2.

Ubiquitin-specific peptidase 2 inhibits epithelial-mesenchymal transition in clear cell renal cell carcinoma metastasis by downregulating the NF-κB pathway

Jiachen Duan, Mengyuan Jin, Dongjing Yang, Jihua Shi, Jie Gao, Danfeng Guo, Hongwei Tang, Shuijun Zhang & Baoping Qiao
Clear cell renal cell carcinoma, the most common type of renal cancer, is associated with poor survival. Ubiquitin-specific peptidase 2 regulates the molecular mechanisms of cancer cells. However, its mechanism in clear cell renal cell carcinoma remains unclear. Quantitative real-time polymerase chain reaction, enzyme-linked immunosorbent assay, and immunohistochemistry were performed to assess ubiquitin-specific peptidase 2 expression in human clear cell renal cell carcinoma samples. Ubiquitin-specific peptidase 2 was weakly expressed in clear cell renal cell...

Complex landscapes stabilize farm bird communities and their expected ecosystem services

Olivia Smith, Christina M. Kennedy, Alejandra Echeverri, Daniel Karp, Christopher Latimer, Joseph Taylor, Erin Wilson-Rankin, Jeb Owen & William Snyder
1. Birds play many roles within agroecosystems including as consumers of crops and pests, carriers of pathogens, and beloved icons. Birds are also rapidly declining across North America, in part due to agricultural intensification. Thus, it is imperative to identify how to manage agroecosystems to best support birds for multi-functional outcomes (e.g., crop production and conservation). Both the average amounts of services/disservices provided and their temporal stability are important for effective farm planning. 2. Here,...

Cryptic species in a colorful genus: integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species

Yang Liu, Chentao Wei, George Sangster, Urban Olsson, Pamela Rasmussen, Lars Svensson, Cheng-Te Yao, Geoff Carey, Paul Leader, Ruiying Zhang, Guoling Chen, Gang Song, Fumin Lei, David Wilcove & Per Alström
Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study,we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic...

Incorporating Complex Sampling Weights in Multilevel Analyses of Educational Data

Ting Shen & Spyros Konstantopoulos
Large-scale assessment survey (LSAS) data are collected via complex sampling designs with special features (e.g., clustering and unequal probability of selection). Multilevel models have been utilized to account for clustering effects whereas the probability weighting approach (PWA) has been used to deal with design informativeness derived from the unequal probability selection. However, the difficulty of applying PWA in multilevel models (MLM) has been generally underestimated and practical guidance is scarce. This study utilizes an empirical...

dLOC as Practice: Decolonial Approaches to Listening and Remembering

Ricia Anne Chansky & Christina Boyles

X-ray imaging of 30 year old wine grape wood reveals cumulative impacts of rootstocks on scion secondary growth and harvest index

Michelle Y. Quigley, Joey Mullins & Daniel H. Chitwood
Annual rings from vines in a 30 year old, California rootstock trial were measured to determine the effects of 15 different rootstocks on Chardonnay and Cabernet Sauvignon scions. Viticultural traits measuring vegetative growth, yield, berry quality, and nutrient uptake were measured at the beginning and end of the lifetime of the vineyard. X-ray Computed Tomography (CT) was used to measure ring widths in 103 vines. Ring width was modeled as a function of ring number...

Extreme natural size variation in both sexes of a sexually cannibalistic mantidfly

Laurel Lietzenmayer, Lauren Goldstein, Josephine Pasche & Lisa Taylor
In sexually cannibalistic animals, the relative sizes of potential mates often predict the outcome of aggressive encounters. Mantidflies are spider egg predators as larvae and generalist predators as adults. Unlike most cannibalistic species, individual mantidflies can be substantially larger than other individuals, regardless of sex. Using preserved collections of Dicromantispa sayi, we focused on three body size metrics that we found to be positively correlated and accurately measured across researchers. We found extreme size variation...

Radical Humility Forum

Gretel Van Weiren, Todd Shaw, Beronda Montgomery, Nimot Ogunfemi, Morgan Shipley, Paulina Camacho Valencia, Rebekah Modrak, Jamie Vander Broek, Ruth Nicole Brown & Christian B. Miller

Feminization of channel catfish with 17β-oestradiol involves methylation and expression of a specific set of genes independent of the sex determination region

Wenwen Wang, Suxu Tan, Yujia Yang, Tao Zhou, De Xing, Baofeng Su, Jinhai Wang, Shangjia Li, Mei Shang, Dongya Gao, Rex Dunham & Zhanjiang Liu
Exogenous oestrogen 17β-oestradiol (E2) has been shown to effectively induce feminization in teleosts. However, the molecular mechanisms underlying the process remain unclear. Here, we determined global DNA methylation and gene expression profiles of channel catfish (Ictalurus punctatus) during early sex differentiation after E2 treatment. Overall, the levels of global DNA methylation after E2 treatment were not significantly different from those of controls. However, a specific set of genes were differentially methylated, which included many sex...

Data for: The visual ecology of selective predation: Are unhealthy hosts less stealthy hosts?

Nina Wale
Predators can strongly influence disease transmission and evolution, particularly when they prey selectively on infected hosts. Although selective predation has been observed in numerous systems, why predators select infected prey remains poorly understood. Here, we use a mathematical model of predator vision to test a longstanding hypothesis about the mechanistic basis of selective predation in a Daphnia-microparasite system, which serves as a model for the ecology and evolution of infectious diseases. Bluegill sunfish feed selectively...

Does the presence of the biological control agent, Hypena opulenta (Lepidoptera: Erebidae) on Swallow-Worts deter Monarch oviposition?

Marianna Szucs, Brianna Alred, Ruth Hufbauer, Nathan Haan & Douglas A Landis
Abstract Invasive black and pale swallow-worts (Vincetoxicum nigrum (L.) Moench, and Vincetoxicum rossicum Kelopow), which are related to milkweeds, can act as ecological traps for monarch butterflies (Danaus plexippus L. (Lepidoptera: Nymphalidae)) as they lay eggs on them that fail to develop. A recently approved biological control agent against swallow-worts, Hypena opulenta Christoph, occupies the same feeding guild on swallow-worts as monarch larvae and could be perceived as a competitor to monarchs. We tested how...

Feasibility of hybrid in-stream generator–photovoltaic systems for Amazonian off-grid communities

Erik Brown, Igor Cavallini Johansen, Ana Paula Bortoleto, Yadu Pokhrel, Suyog Chaudhari, Anthony Cak, Samer Sulaeman, Laura Castro-Diaz, Maria Claudia Lopez, Adam Mayer, Judith Walgren, Norbert Müller & Emilio Moran
While there have been efforts to supply off-grid energy in the Amazon, these attempts have focused on low upfront costs and deployment rates. These “get-energy-quick” methods have almost solely adopted diesel generators, ignoring the environmental and social risks associated with the known noise and pollution of combustion engines. Alternatively, it is recommended, herein, to supply off-grid needs with renewable, distributed microgrids comprised of photovoltaics (PV) and in-stream generators (ISG). Utilization of a hybrid combination of...

The role of immunotherapy plus chemotherapy versus chemotherapy alone as first-line treatment for advanced non-small cell lung cancer: an updated systematic review and meta-analysis of randomized controlled trials

Basel Abdelazeem, Kirellos Said Abbas, Fatma Labieb, Abdul Karim Arida, Nahla Ahmed El-Shahat, Joseph Shehata, Emad Kandah, Bilal Malik, Maxwell Akanbi, Abdul Rafae, Ahsan Wahab & Hamid Ehsan
Recently published randomized controlled trials (RCTs) showed improved overall survival (OS) and progression-free survival (PFS) with the combination of immunotherapy and chemotherapy as compared to chemotherapy alone in advanced non-small cell lung cancer (NSCLC). We aimed to provide a systematic review and meta-analysis of RCTs regarding the efficacy and safety of immunotherapy and chemotherapy combinations for advanced NSCLC. On December 23rd, 2021, we searched databases for RCTs that reported PFS and OS as primary outcomes....

Weightlifting injuries in master athletes

Marianne Huebner
Data collection: A total of 976 Masters weightlifters from Australia, Canada, Europe, and the USA, ages 35 to 88 (51.1% female), completed an online survey in June 2021 that included questions on weightlifting injuries, chronic diseases, sport history, and training practices. Definition of injuries: Injuries were defined in relation to participation to weightlifting, namely whether training restriction occurred due to acute injuries sustained during weightlifting. The correspoding srurvey question was “Have you ever had training...

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