293 Works

In Their Own Words

Patricia Nola Eugene Roberson, Gina Cortez, Laura H. Trull & Katherine Allison Lenger
Introduction: The opioid epidemic is ravaging people, families, and communities in Appalachia. However, limited research has examined how “everyday” people (e.g., not chronic pain patients, not medical professionals) living in these communities how opioids have impacted their lives. Objective: Identify the perception of the opioid epidemic on individuals, families, and communities from people living in region most impacted regions. Methods: Patients were recruited at Remote Area Medical clinics throughout Central and Southern Appalachia to complete...

Protected area, easement, and rental contract data reveal five communities of land protection in the United States

Heather Bird Jackson, Kailin Kroetz, James Sanchirico, Alexandra Thompson & Paul Armsworth
Land protection efforts represent large societal investments and are critical to biodiversity conservation. Land protection involves a complex mosaic of areas managed by multiple organizations, using a variety of mechanisms to achieve different levels of protection. We develop an approach to synthesize, describe, and map this land protection diversity over large spatial scales. We use cluster analysis to find distinct “communities” of land protection based on the organizations involved, the strictness of land protection, and...

Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Gustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...

The Critical Need for Peer Clinical Supervision Among School Counselors

Pamelia E. Brott, Lorraine DeKruyf, Jung Hyun, Christopher LaFever, Sarah Patterson-Mills, Mariama Sandifer & Victoria Stone

Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex

Robert De Moya
This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) Species Complex". Valenzuela flavidus is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, Valenzuela aurantiacus was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain...

Altitude-mediated soil properties, not geography or climatic distance, explain the distribution of a tropical endemic herb

Jacob Moutouama & Orou Gaoue
Understanding the ecological processes that govern species’ range margins is a fundamental question in ecology with practical implications in conservation biology. The centre-periphery hypothesis (CPH) predicts that organisms have higher abundance at the centre of their geographic range. However, most tests of the CPH often used raster data, assuming that climatic conditions are consistent across one square km. This assumption is not always justified, particularly for species that live in mountainous regions where climatic conditions...

Chloroplast genome of the invasive Pyrus calleryana

Marcin Nowicki, Matthew Huff, Margaret Staton & Robert Trigiano
The complete chloroplast genome of Pyrus calleryana (BioSample SAMC013142) was developed by de novo assembly from whole-genome sequencing data. Reference-guided (P. phaeocarpa) read mapping and assembly were followed by annotation and phylogenetic comparisons. The Pyrus calleryana chloroplast genome of 159,965 bp in length (36,56% of GC content) represents a classical quadripartite architecture, with two inverted repeats regions (IRs; each 26,392 bp in length) separating the large single-copy region (LSC; 87,942 bp) and the small single-copy...

Methodological advances for hypothesis‐driven ethnobiology

Orou G. Gaoue, Jacob Moutouama, Michael Coe, Matthew Bond, Elizabeth Green, Nadejda Sero, Bezeng Simmy & Kowiyou Yessoufou
Ethnobiology as a discipline has evolved recently to increasingly embrace theory-inspired and hypothesis driven approaches to study why and how local people choose plants and animals they interact with and use for their livelihood. However, testing complex hypotheses or a network of ethnobiological hypotheses is challenging, particularly for datasets with non-independent observations due to species phylogenetic relatedness or socio-relational links between participants. Further, to fully account for the dynamics of local ecological knowledge, it is...

MALDI-MS raw files of primary human lung cancer samples, lung cancer patient derived xenografts and lung cancer mouse models

Caterina Bartolacci, Cristina Andreani, A. Colleen Crouch & Pier Paolo Scaglioni
Human primary lung cancer samples, patient derived lung cancer xenografts and lung tumors from the TetO-KRASG12D mouse model were analyzed using MALDI-MS. We determined the spatial distribution and relative abundance of lipids of interest.

DateLife: leveraging databases and analytical tools to reveal the dated Tree of Life

Luna Luisa Sanchez Reyes, Emily Jane McTavish & Brian O'Meara
Achieving a high-quality reconstruction of a phylogenetic tree with branch lengths proportional to absolute time (chronogram) is a difficult and time-consuming task. But the increased availability of fossil and molecular data, and time-efficient analytical techniques has resulted in many recent publications of large chronograms for a large number and wide diversity of organisms. Knowledge of the evolutionary time frame of organisms is key for research in the natural sciences. It also represent valuable information for...

Novel, Selective Calix[6]Arene - Polyethylene Glycol (C6A-PEG) Stationary Phase for Capillary Gas Chromatography (GC)

Qiuchen Huang, Zhiqiang Cai, Wei Li, Ruonan Chen, Wei Zhang, Keyun Jin, Yi Zhao, Yiwen Li & Tao Sun
A novel calix[6] arene polymer stationary phase (C6A-PEG) is reported that combines the π-electron-rich cavity of calix[6] arene (C6A) with polyethylene glycol (PEG) units for gas chromatography (GC). Thermogravimetric analysis revealed a 5% weight loss of C6A-PEG at 318 °C, and its static-coated capillary column showed high efficiency of 2924 plates/m (k = 3.48) determined by 1-octanol at 120 °C. As a result, the moderate polar C6A-PEG column showed clearly advantageous performance for the Grob...

Fecal microbiota transplantation combined with ruxolitinib as a salvage treatment for intestinal steroid-refractory acute GVHD

Yin Liu, Ye Zhao, Jiaqian Qi, Xiao Ma, Xiaofei Qi, Depei Wu & Yang Xu
Abstract Acute graft-versus-host disease (aGVHD), especially intestinal aGVHD, is one of the most severe complications after allogeneic hematopoietic stem cell transplantation (HSCT). Fecal microbiota transplantation (FMT) has been applied to the treatment of intestinal steroid-refractory aGVHD (SR-aGVHD). Ruxolitinib is the first drug recommended for SR-aGVHD. Here, we reported the outcome data from 21 patients who had received the combined treatment of FMT with ruxolitinib as a salvage treatment in intestinal SR-aGVHD after HSCT. The overall...

Additional file 1 of Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis

Zhangyang Xu, Bo Peng, Reta Birhanu Kitata, Carrie D. Nicora, Karl K. Weitz, Yunqiao Pu, Tujin Shi, John R. Cort, Arthur J. Ragauskas & Bin Yang
Additional file 1: Figure S1. The overall workflow for identifying bacterial lignin degradation pathways. Figure S2. GC–MS analysis of lignin breakdown products. Figure S3. Lignin breakdown products identified by GC–MS. Figure S4. The variation of peaks area of all lignin breakdown products. Figure S5. Main detected lignin linkages. Table S1. Occurrence of putative degradation products of lignin in different treatment conditions. Table S2. Grouped lignin breakdown products among all treatments. Table S3. Main lignin 2D...

Additional file 2 of Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis

Zhangyang Xu, Bo Peng, Reta Birhanu Kitata, Carrie D. Nicora, Karl K. Weitz, Yunqiao Pu, Tujin Shi, John R. Cort, Arthur J. Ragauskas & Bin Yang
Additional file 2: Table S4. Proteomic analysis of the intracellular and secretome in P. putida KT2440.

Additional file 3 of Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis

Zhangyang Xu, Bo Peng, Reta Birhanu Kitata, Carrie D. Nicora, Karl K. Weitz, Yunqiao Pu, Tujin Shi, John R. Cort, Arthur J. Ragauskas & Bin Yang
Additional file 3. A list of abbreviations is included.

Phototherapy with theranostic Co3O4 nanoplates eliminates metastatic solid tumors by activating systemic tumor immunity and memory

Shuxiang Xu, Qingjiao Li, Miaomiao Yuan, zhou shuyi, Rongjun Zhang, Qianbing Zhang, Xuemei Fu & Yang Xu
Solid tumors develop complex and heterogenous immune suppressive environment, and thus are frequently resistant to existing immunotherapies. To effectively treat malignant solid tumors especially the metastatic ones, it is critical to develop strategies to activate tumor immunity by reversing the tumor-induced immune suppression. Here, we describe a near-infrared (NIR) responsive porous Co3O4 nanoplates (pCo3O4 NPs) that can deliver a single laser triggered photothermal/photodynamic combination therapy. This phototherapy can eliminate the treated primary tumors and suppress...

Phototherapy with theranostic Co3O4 nanoplates eliminates metastatic solid tumors by activating systemic tumor immunity and memory

Shuxiang Xu, Qingjiao Li, Miaomiao Yuan, zhou shuyi, Rongjun Zhang, Qianbing Zhang, Xuemei Fu & Yang Xu
Solid tumors develop complex and heterogenous immune suppressive environment, and thus are frequently resistant to existing immunotherapies. To effectively treat malignant solid tumors especially the metastatic ones, it is critical to develop strategies to activate tumor immunity by reversing the tumor-induced immune suppression. Here, we describe a near-infrared (NIR) responsive porous Co3O4 nanoplates (pCo3O4 NPs) that can deliver a single laser triggered photothermal/photodynamic combination therapy. This phototherapy can eliminate the treated primary tumors and suppress...

Additional file 1 of Linking Immuno-Epidemiology Principles to Violence

Anna Sisk, Patricia Bamwine, Judy Day & Nina Fefferman
Additional file 1.

Linking Immuno-Epidemiology Principles to Violence

Anna Sisk, Patricia Bamwine, Judy Day & Nina Fefferman
Abstract Background Societies have always struggled with violence, but recently there has been a push to understand violence as a public health issue. This idea has unified professionals in medicine, epidemiological, and psychology with a goal to end violence and heal those exposed to it. Recently, analogies have been made between community-level infectious disease epidemiology and how violence spreads within a community. Experts in public health and medicine suggest an epidemiological framework could be used...

Linking Immuno-Epidemiology Principles to Violence

Anna Sisk, Patricia Bamwine, Judy Day & Nina Fefferman
Abstract Background Societies have always struggled with violence, but recently there has been a push to understand violence as a public health issue. This idea has unified professionals in medicine, epidemiological, and psychology with a goal to end violence and heal those exposed to it. Recently, analogies have been made between community-level infectious disease epidemiology and how violence spreads within a community. Experts in public health and medicine suggest an epidemiological framework could be used...

Integrated analysis of the genomic and transcriptional profile of gliomas with isocitrate dehydrogenase-1 and tumor protein 53 mutations

Han-Qing Liu, Wei-Xin Li, Ya-Wen An, Tao Wu, Guang-Yu Jiang, Yu Dong, Wei-Xin Chen, Jian-Chun Wang, Cheng Wang & Shuo Song
Background: The gene mutation of isocitrate dehydrogenase-1 (IDH1) is commonly found in LGG and some GBM patients and usually carries tumor protein 53 (TP53) mutations. However, the underlying mechanisms on both mutations of glioma patients in IDH1 and TP53 are still unclear. Aim: To find the potential target markers in GBM and LGG patients with IDH1 and TP53 mutation.Method: A total of 1122 glioma patients from The Cancer Genome Atlas were enrolled and divided as...

Integrated analysis of the genomic and transcriptional profile of gliomas with isocitrate dehydrogenase-1 and tumor protein 53 mutations

Han-Qing Liu, Wei-Xin Li, Ya-Wen An, Tao Wu, Guang-Yu Jiang, Yu Dong, Wei-Xin Chen, Jian-Chun Wang, Cheng Wang & Shuo Song
Background: The gene mutation of isocitrate dehydrogenase-1 (IDH1) is commonly found in LGG and some GBM patients and usually carries tumor protein 53 (TP53) mutations. However, the underlying mechanisms on both mutations of glioma patients in IDH1 and TP53 are still unclear. Aim: To find the potential target markers in GBM and LGG patients with IDH1 and TP53 mutation.Method: A total of 1122 glioma patients from The Cancer Genome Atlas were enrolled and divided as...

Additional file 1 of The public health exposome and pregnancy-related mortality in the United States: a high-dimensional computational analysis

E. W. Harville, S.K. Grady, MA Langston, P. J. Juarez, D. Vilda & M. E. Wallace
Additional file 1.

Prevalence and influence of hypouricemia on cardiovascular diseases in patients with rheumatoid arthritis

Yao-Wei Zou, Qian-Hua Li, Ying-Ying Zhu, Jie Pan, Jing-Wei Gao, Jian-Zi Lin, Tao Wu, Qian Zhang, Hu-Wei Zheng, Ying-Qian Mo, Jian-Da Ma & Lie Dai
Abstract Background Serum uric acid (SUA) acts as an antioxidant and abnormally low SUA may raise the risk of developing atherosclerotic disorders. There is a U-shaped association between SUA with cardiovascular diseases (CVDs) in general population. However, the prevalence of hypouricemia and its influence on CVDs in rheumatoid arthritis (RA) remains unclear. Methods This cross-sectional study collected clinical data from a Chinese RA cohort. Hypouricemia was defined as SUA ≤ 3.0 mg/dL, and hyperuricemia was...

Additional file 1 of Prevalence and influence of hypouricemia on cardiovascular diseases in patients with rheumatoid arthritis

Yao-Wei Zou, Qian-Hua Li, Ying-Ying Zhu, Jie Pan, Jing-Wei Gao, Jian-Zi Lin, Tao Wu, Qian Zhang, Hu-Wei Zheng, Ying-Qian Mo, Jian-Da Ma & Lie Dai
Additional file 1: Table S1. Comparisons of clinical characteristics between RA patients with and without CVD. Table S2. Logistic regression analysis of the associations between SUA levels and CVD in RA patients.

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