304 Works

Data from: Phylogenetic inference of reciprocal effects between geographic range evolution and diversification

Emma E. Goldberg, Lesley T. Lancaster & Richard H. Ree
Geographic characters---traits relating to the spatial distribution of a species---may both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of traits and the growth of phylogenetic trees. Here we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model...

Data from: Field evaluation of the safety, acceptability, and feasibility of early infant male circumcision using the AccuCirc device

Robert C. Bailey, Irene Nyaboke, Mary Ellen Mackesy-Amiti, Erick Okello, Valentine Pengo, Betha Ochomo, Mary Emmaculate Ouma, Simon Were, Stella Ojuok, Evelyne Adoyo, Mildred Adhiambo, Marisa R. Young, Rebeca M. Plank & Fredrick O. Otieno
Background: As countries scale up adult voluntary medical male circumcision (VMMC) for HIV prevention, they are looking ahead to long term sustainable strategies, including introduction of early infant male circumcision (EIMC). Although a number of devices for EIMC are prequalified by the World Health Organization, evaluation of additional devices can provide policy-makers and clinicians the information required to make informed decisions. We undertook a field evaluation of the safety and acceptability of the AccuCirc device...

Data from: Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species)

Dawson M. White, Melissa B. Islam & Roberta J. Mason-Gamer
This investigation establishes the first sequence-based phylogenetic hypothesis of species relationships in the Coca family (Erythroxylaceae). We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O. E. Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. We show that Neotropical Erythroxylum are monophyletic within the Paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack...

Data from: Symposium article: Which line to follow? the utility of different line-fitting methods to capture the mechanism of morphological scaling

Alexander W Shingleton
Bivariate morphological scaling relationships describe how the sizes of two traits co-vary among adults in a population. In as much as body shape is reflected by the relative size of various traits within the body, morphological scaling relationships capture how body shape varies with size, and therefore have been used widely as descriptors of morphological variation within and among species. Despite their extensive use, there is continuing discussion over which line-fitting method should be used...

Data from: Interaction among ploidy, breeding system, and lineage diversification

Rosana Zenil-Ferguson, J. Gordon Burleigh, William A. Freyman, Boris Igic, Itay Mayrose & Emma E. Goldberg
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) are both thought to be drivers of...

The Effect of Repeat Exposure to Simulation Based Items

Xiaodan Tang & Matthew Schultz

Yards, block groups, and vegetation cover measures

Dexter Locke, Alessandro Ossola, Emily Minor & Brenda Lin
Residential yards are a significant component of urban socio-ecological systems; residential land covers 11% of the United States and is often the dominant land use within urban areas. Residential yards also play an important role in the sustainability of urban socio-ecological systems, affecting biogeochemical cycles, water, and the climate via individual- and household-level behaviors. Vegetation, such as trees and grasses, are unevenly distributed across front and back yards, and we sought to understand how similar...

Alteration of the N6-methyladenosine epitranscriptomic profile in synthetic phthalate-treated human induced pluripotent stem cell-derived endothelial cells. Supplemental Materials

Sang-Ging Ong, Won Hee Lee, Sang-Bing Ong, Ya Li, Hoai Huong Thi Le, Youjeong Kwon, Sarath Babu Nukala, Gege Yan, Jordan Jousma & Zhenbo Han
Supplementary figures 1-3 MEHP supplementary data Supplementary materials

Supplementary Figure 2: MFAP5 is strongly expressed in human keloid.

Chen Han, Trevor Leonardo, Bruna Romana de Souza, Junhe Shi, Shalyn Keiser, Heidi Yuan, Mohamad Altakriti, Matthew Ranzer, Sammy Ferri-Borgogno, Samuel C. Mok, Timothy Koh, Lin Chen & Luisa DiPietro
A representative image of immunofluorescence detection of MFAP5 (red) in human keloid scars. Nuclei in blue (DAPI).

Supplementary Figure 1: MFAP5 is significantly upregulated during the later phases of wound healing in a 1-mm wound.

Chen Han, Trevor Leonardo, Bruna Romana-Souza, Junhe Shi, Shalyn Keiser, Heidi Yuan, Mohamad Altakriti, Matthew Ranzer, Sammy Ferri-Borgogno, Samuel C. Mok, Timothy Koh, Lin Chen & Luisa DiPietro
Microarray analysis of full thickness 1-mm dorsal mouse wounds over the time course of healing. Bars indicate mean ± SD. N=3 at each time point. 0 days post-wounding is normal skin. * = p < 0.05, ** = p < 0.001, *** = p < 0.001. One-way ANOVA followed by two-stage linear step-up procedure of Benjamini, Krieger and Yekutieli post-hoc testing (vs 0).

Otros conflictos internos en escena: San Bartolo y el teatro testimonial del abuso sexual en el Perú

Margarita Saona
La publicación de Mitad monjes/Mitad soldados causó un escándalo en la sociedad limeña a cuyas élites pertenecían tanto los perpetradores como sus víc-timas. Pero el foco de este ensayo es la capacidad del teatro para poner literal-mente en escena el tipo de trauma que supone un estigma para sus víctimas. El tipo de obra testimonial / documental / coral que representa San Bartolo no ofrece la resolución catártica de la tragedia clásica ni el distanciamiento...

Deep learning based short-range forecasting of Indian summer monsoon rainfall using earth observation and ground station datasets

Bipin Kumar, Namit Abhishek, Rajib Chattopadhyay, Sandeep George, Bhupendra Bahadur Singh, Arya Samanta, B.S.V. Patnaik, Sukhpal Singh Gill, Ravi S. Nanjundiah & Manmeet Singh
We develop a deep learning model (DL) for Indian Summer Monsoon (ISM) short-range precipitation forecasting using a ConvLSTM network. The model is built using daily precipitation records from both ground-based observations and remote sensing. Precipitation datasets from the Tropical Rainfall Measuring Mission and the India Meteorological Department are used for training, testing, forecasting, and comparison. For lead days 1 and 2, the correlation coefficient (CC), which was determined using predicted data from the previous five...

Carrying L’Intrus: The transport-station of an organ transplant

Margarita Saona
The experience of heart transplantation shocks not only the body, but also the sense of self. As a heart transplant survivor, I find that the Ettingerian concepts of the transport-station of trauma, of wit(h)nessing, metramorphosis, and carriance provide an understanding of how—as humans—we are able to transcend the traditional notions of self through borderlinking. Jean-Luc Nancy’s L’Intrus explored the limits of the self as he wrote about his heart transplant, when he was confronted with...

Connecting the dots on vertical transmission of SARS-CoV-2 using protein-protein interaction network analysis – Potential roles of placental ACE2 and ENDOU

Hongwu Jing, William Ackerman, Guomao Zhao, Yara El Helou, Catalin Buhimschi & Irina Buhimschi
We conducted a protein-protein interaction (PPI) network study searching for proteins relevant to pregnancy-associated COVID-19 in pregnancy complicated with severe preeclampsia (sPE) and intra-amniotic infection and/or inflammation (Triple-I). PPI networks from sPE and Triple-I were intersected with the PPI network from coronavirus infection. Common proteins included the SARS-CoV-2 entry receptor ACE2 and ENDOU, a placental endoribonuclease homologous to Nsp15, a protein produced by the virus to escape host immunity. Remarkably, placental ENDOU mRNA expression far...

Dysregulation of Lipid Metabolism in Mkp-1 Deficient Mice during Gram-Negative Sepsis

Jinhui Li, Xiantao Wang, William Ackerman, Abel J Batty, Sean G Kirk, William M White, Xianxi Wang, Dimitrios Anastasakis, Lobelia Samavati, Irina Buhimschi, Leif D Nelin, Markus Hafner & Yusen Liu
Mitogen-activated protein kinase phosphatase (Mkp)-1 exerts its anti-inflammatory activities during Gram-negative sepsis by deactivating p38 and c-Jun N-terminal kinase (JNK). We have previously shown that Mkp-1+/+ mice, but not Mkp-1-/- mice, exhibit hypertriglyceridemia during severe sepsis. However, the regulation of hepatic lipid stores and the underlying mechanism of lipid dysregulation during sepsis remains an enigma. To understand the molecular mechanism underlying the sepsis-associated metabolic changes and the role of Mkp-1 in the process, we infected...

The hexokinase “HKDC1” interaction with the mitochondria is essential for liver cancer progression

Md Wasim Khan, Alexander R Terry, Medha Priyadarshini, Vladimir Ilievski, Zeenat Farooq, Grace Guzman, Jose Cordoba-Chacon, Issam Ben-Sahra, Barton Wicksteed & Brian Layden
Liver cancer (LC) is the fourth leading cause of death from cancer malignancies. Recently, a putative fifth hexokinase, hexokinase domain containing 1 (HKDC1), was shown to have significant overexpression in LC compared to healthy liver tissue. Using a combination of in vitro and in vivo tools, we examined the role of HKDC1 in LC development and progression. Importantly, HKDC1 ablation stops LC development and progression via its action at the mitochondria by promoting metabolic reprogramming...

The hexokinase “HKDC1” interaction with the mitochondria is essential for liver cancer progression

Md Wasim Khan, Alexander R Terry, Medha Priyadarshini, Vladimir Ilievski, Zeenat Farooq, Grace Guzman, Jose Cordoba-Chacon, Issam Ben-Sahra, Barton Wicksteed & Brian Layden
Liver cancer (LC) is the fourth leading cause of death from cancer malignancies. Recently, a putative fifth hexokinase, hexokinase domain containing 1 (HKDC1), was shown to have significant overexpression in LC compared to healthy liver tissue. Using a combination of in vitro and in vivo tools, we examined the role of HKDC1 in LC development and progression. Importantly, HKDC1 ablation stops LC development and progression via its action at the mitochondria by promoting metabolic reprogramming...

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery

Kara M Rood, Irina Buhimschi, Joseph A Jurcisek, Taryn L Summerfield, Guomao Zhao, William Ackerman, Weiwei Wang, R Wolfgang Rumpf, Stephen F Thung, Lauren O Bakaletz & Catalin Buhimschi
The obesity pandemic in the obstetrical population plus increased frequency of Cesarean delivery (CD) has increased vulnerability to surgical site infection (SSI). Here we characterized the microbiome at the site of skin incision before and after CD. Skin and relevant surgical sites were sampled before and after surgical antisepsis from obese (n = 31) and non-obese (n = 27) pregnant women. We quantified bacterial biomass by qPCR, microbial community composition by 16sRNA sequencing, assigned operational...

Distinct cellular pools of perilipin 5 point to roles in lipid trafficking

Sadie R Bartholomew, Erica Hlavin Bell, Taryn Summerfield, Leslie C Newman, Erin L Miller, Brian Patterson, Zach P Niday, William Ackerman & John T Tansey
The PAT family of lipid storage droplet proteins comprised five members, each of which has become an established regulator of cellular neutral lipid metabolism. Perilipin 5 (also known as lsdp-5, MLDP, PAT-1, and OXPAT), the most recently discovered member of the family, has been shown to localize to two distinct intracellular pools: the lipid storage droplet (LD), and a poorly characterized cytosolic fraction. We have characterized the denser of these intracellular pools and find that...

Evidence for participation of neutrophil gelatinase‐associated lipocalin/matrix metalloproteinase‐9 (NGAL•MMP‐9) complex in the inflammatory response to infection in pregnancies complicated by preterm birth

Kara M Rood, Irina Buhimschi, Katherine Rodewald Millen, Mert O Bahtiyar, Stephen Thung, Taryn Summerfield, Guomao Zhao, William Ackerman, Cynthia Shellhaas, Philip Samuels & Catalin Buhimschi
PROBLEM: Neutrophil gelatinase-associated lipocalin (NGAL) is expressed in neutrophils and involved in innate immunity by sequestering iron. NGAL's ability to complex with matrix metalloproteinase-9 (MMP-9) and extend its gelatinolytic activity led us to investigate its role in pregnancies complicated by preterm birth (PTB) and intra-amniotic infection/inflammation (IAI). METHOD OF STUDY: We assayed the amniotic fluid (AF) levels of NGAL and MMP-9 in 308 women that had a clinically indicated amniocentesis and a normal pregnancy outcome...

Integrated microRNA and mRNA network analysis of the human myometrial transcriptome in the transition from quiescence to labor,

William Ackerman, Irina Buhimschi, Douglas Brubaker, Sean Maxwell, Kara M Rood, Mark R Chance, Hongwu Jing, Sam Mesiano & Catalin Buhimschi
We conducted integrated transcriptomics network analyses of miRNA and mRNA interactions in human myometrium to identify novel molecular candidates potentially involved in human parturition. Myometrial biopsies were collected from women undergoing primary Cesarean deliveries in well-characterized clinical scenarios: (1) spontaneous term labor (TL, n = 5); (2) term nonlabor (TNL, n = 5); (3) spontaneous preterm birth (PTB) with histologic chorioamnionitis (PTB-HCA, n = 5); and (4) indicated PTB nonlabor (PTB-NL, n = 5). RNAs...

Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology

Grace C Bingham, Fred Lee, Alexandra Naba & Thomas H Barker
Complex intercellular interactions as well as biomolecular and biomechanical cues from the extracellular matrix (ECM) profoundly affect cellular functions. Traditional transcriptomic and proteomic approaches have provided insight into disease progression by identifying discrete cellular subpopulations or microenvironmental signatures characteristic of normal or pathological tissues, however these techniques do not examine how a given cellular state relates to its interactions with neighboring cells or its surrounding ECM with multiparametric characterization (i.e. ECM alignment, mechanical forces, crosslinking,...

Supplementary Table 1: Primer sequences for real time PCR

Chen Han, Trevor Leonardo, Bruna Romana de Souza, Junhe Shi, Shalyn Keiser, Heidi Yuan, Mohamad Altakriti, Matthew Ranzer, Sammy Ferri-Borgogno, Samuel C. Mok, Timothy Koh, Lin Chen & Luisa DiPietro
Table of primers used.

In-silico definition of the Drosophila melanogaster matrisome

Martin N Davis, Sally Horne-Badovinac & Alexandra Naba
The extracellular matrix (ECM) is an assembly of hundreds of proteins that structurally supports the cells it surrounds and biochemically regulates their functions. Drosophila melanogaster has emerged as a powerful model organism to study fundamental mechanisms underlying ECM protein secretion, ECM assembly, and ECM roles in pathophysiological processes. However, as of today, we do not possess a well-defined list of the components forming the ECM of this organism. We previously reported the development of computational...

Agonist-Dependent Downregulation of Progesterone Receptors in Human Cervical Stromal Fibroblasts

William Ackerman, Taryn L Summerfield, Sam Mesiano, Frederick Schatz, Charles J Lockwood & Douglas A Kniss
Progesterone (P(4)) maintains uterine quiescence during the majority of pregnancy, whereas diminished progesterone receptor (PR) expression and/or activity (ie, functional P(4) withdrawal) promotes parturition. To investigate the regulation of PR expression in cervical stroma, fibroblasts from premenopausal hysterectomy specimens were prepared. Greater than 99% of the cultures were vimentin positive (mesenchymal cell marker) with only occasional cytokeratin-8 positivity (epithelial cell marker) and no evidence of CD31-positive (endothelial cell marker) cells. Cells were immunolabeled with antibodies...

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