39 Works

Data from: Human endometrial transcriptome and progesterone receptor cistrome reveal important pathways and epithelial regulators

Ru-Pin Alicia Chi, Tianyuan Wang, Nyssa Adams, San-Pin Wu, Steven Young, Thomas Spencer & Francesco DeMayo
Context. Poor uterine receptivity is one major factor leading to pregnancy loss and infertility. Understanding the molecular events governing successful implantation is hence critical in combating infertility. Objective. To define PGR-regulated molecular mechanisms and epithelial roles in receptivity. Design. RNA-seq and PGR-ChIP-seq were conducted in parallel to identify PGR-regulated pathways during the WOI in endometrium of fertile women. Setting. Endometrial biopsies from the proliferative and mid-secretory phases were analyzed. Patients or Other Participants. Participants were...

Isoform specific activities of androgen receptor and its splice variants in prostate cancer cells

Harika Nagandla, Matthew Robertson, Vasanta Putluri, Nagireddy Putluri, Cristian Coarfa & Nancy Weigel
Androgen receptor (AR) signaling continues to drive castration resistant prostate cancer (CRPC) in spite of androgen deprivation therapy (ADT). Constitutively active shorter variants of AR, lacking the ligand binding domain, are frequently expressed in CRPC and have emerged as a potential mechanism for prostate cancer to escape ADT. ARv7 and ARv567es are two of the most commonly detected variants of AR in clinical samples of advanced, metastatic prostate cancer. It is not clear if variants...

Data for: Meningioangiomatosis- Multimodal analysis and insights from a systematic review

Alexandre Roux, Marc Zanello, Rossella Letizia Mancusi, Megan Still, Fábio Nascimento, Arnault Tauziède-Espariat, Gilles Huberfeld, Gilles Zah-Bi, Edouard Dezamis, Jean-François Meder, Marie Bourgeois, Eduardo Parraga, Fabrice Chrétien, Pascale Varlet, Catherine Oppenheim, Emmanuèle Lechapt-Zalcman & Johan Pallud
Background:Meningioangiomatosis is a poorly studied, rare, benign, and epileptogenic brain lesion. Objective: To demonstrate that surgical resection and a short time interval to surgery improves epileptic seizure control, we performed a systematic review and meta-analysis of meningioangiomatosis cases. Methods: Using PRISMA-IPD guidelines, the authors performed a systematic review and meta-analysis of histopathologically proven meningioangiomatosis cases.Literature search in the French and English languages (PubMed, Embase, the Cochrane Library and the Science Citation Index) including all studies...

Data from: Diflunisal inhibits prestin by chloride-dependent mechanism

Guillaume Duret, Fred A. Pereira & Robert M. Raphael
The motor protein prestin is a member of the SLC26 family of anion antiporters and is essential to the electromotility of cochlear outer hair cells and for hearing. The only direct inhibitor of electromotility and the associated charge transfer is salicylate, possibly through direct interaction with an anion-binding site on prestin. In a screen to identify other inhibitors of prestin activity, we explored the effect of the non-steroid anti-inflammatory drug diflunisal, which is a derivative...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: Novel conserved genotypes correspond to antibiotic resistance phenotypes of E. coli clinical isolates

Michael A. Evangelista, Michelle C. Swick, Truston J. Bodine, Jeremy R. Easton-Marks, Patrick Barth, Minita J. Shah, Christina A. Bormann Chung, Sarah Stanley, Stephen F. McLaughlin, Clarence C. Lee, Vrunda Sheth, Quynh Doan, Richard J. Hamill, David Steffen, Lauren B. Becnel, Richard Sucgang & Lynn Zechiedrich
Current efforts to understand antibiotic resistance on the whole genome scale tend to focus on known genes even as high throughput sequencing strategies uncover novel mechanisms. To identify genomic variations associated with antibiotic resistance, we employed a modified genome-wide association study; we sequenced genomic DNA from pools of E. coli clinical isolates with similar antibiotic resistance phenotypes using SOLiD technology to uncover SNPs unanimously conserved in each pool. The multidrug-resistant pools were genotypically similar to...

Data from: Predictors of alcohol responsiveness in dystonia

Johanna Junker, Valerie Brandt, Brian D. Berman, Marie Vidailhet, Emmanuel Roze, Anne Weissbach, Cynthia Comella, Irene A. Malaty, Joseph Jankovic, Mark S. LeDoux, Alfredo Berardelli, Richard Barbano, Stephen G. Reich, Joel S. Perlmutter, Hyder A. Jinnah & Norbert Brüggemann
Objective: To determine predictors of alcohol responsiveness in a large cohort of dystonia patients. Methods: 2159 participants with dystonia were prospectively enrolled in the cross-sectional Dystonia Coalition multicenter study. Patients with secondary, combined or confirmed genetic dystonia (total n=164) or unknown alcohol responsiveness (n= 737) were excluded. Patients answered a standardized questionnaire and were clinically examined using a standardized video protocol and the Burke-Fahn-Marsden Dystonia Rating Scale. Alcohol responsiveness was determined by patients’ self-report. Results:...

Data from: The majority of the pre-antiretroviral population who were lost to follow-up stopped their care in Freetown, Sierra Leone: a 12-month prospective cohort study starting with HIV diagnosis

J. Daniel Kelly, Gabriel Warren Schlough, Sulaiman Conteh, M. Bailor Barrie, Brima Kargbo & Thomas P. Giordano
Background: The heterogeneity of the pre-antiretroviral (pre-ART) population calls for more granular depictions of the cascade of HIV care. Methods: We studied a prospective cohort of persons newly diagnosed with HIV infection from a single center in Freetown, Sierra Leone, over a 12-month period and then traced those persons who were lost to follow-up (LTFU) during pre-ART care (before ART initiation). ART eligibility was based on a CD4 cell count result of < 350 mm/cells...

Hemotological and morphometric measurements from geladas

Kenneth L. Chiou, Mareike C. Janiak, India A. Schneider-Crease, Sharmi Sen, Ferehiwot Ayele, Idrissa S. Chuma, Sascha Knauf, Alemayehu Lemma, Anthony V. Signore, Anthony M. D’Ippolito, Belayneh Abebe, Abebaw Azanaw Haile, Fanuel Kebede, Peter J. Fashing, Nga Nguyen, Colleen McCann, Marlys L. Houck, Jeffrey D. Wall, Andrew S. Burrell, Christina M. Bergey, Jeffrey Rogers, Jane E. Phillips-Conroy, Clifford J. Jolly, Amanda D. Melin, Jay F. Storz … & Noah Snyder-Mackler
Primates have adapted to numerous environments and lifestyles but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of haematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers...

Two-photon calcium recordings of cones

Takeshi Yoshimatsu, Philipp Bartel, Cornelius Schröder, Filip Janiak, Francois St-Pierre, Philipp Berens & Tom Baden
For colour vision, retinal circuits separate information about intensity and wavelength. This requires circuit-level comparison of at least two spectrally distinct photoreceptors. However, many vertebrates use all four ‘ancestral’ photoreceptors (‘red’, ‘green’, ‘blue’, ‘UV’), and in those cases the nature and implementation of this computation remains poorly understood. Here, we establish the complete circuit architecture of outer retinal circuits underlying colour processing in the tetrachromatic larval zebrafish, which involves all four ancestral cone types and...

Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild

Emily Humble, Pavel Dobrynin, Helen Senn, Justin Chuven, Alan F. Scott, David W. Mohr, Olga Dudchenko, Arina D. Omer, Zane Colaric, Erez Lieberman Aiden, Shaikha Salem Al Dhaheri, David Wildt, Shireen Oliaji, Gaik Tamazian, Budhan Pukazhenthi, Rob Ogden & Klaus‐Peter Koepfli
Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar‐horned oryx (Oryx dammah) is a North African antelope that has...

A relationship between Autism-Spectrum Quotient and face viewing behavior in 98 participants

Kira Wegner-Clemens, Johannes Rennig & Michael S Beauchamp
Faces are one of the most important stimuli that we encounter, but humans vary dramatically in their behavior when viewing a face: some individuals preferentially fixate the eyes, others fixate the mouth, and still others show an intermediate pattern. The determinants of these large individual differences are unknown. However, individuals with Autism Spectrum Disorder (ASD) spend less time fixating the eyes of a viewed face than controls, suggesting the hypothesis that autistic traits in healthy...

Risk factors for cardiovascular disease (CVD) in adults with type 1 diabetes: findings from prospective real-life T1D exchange registry

Nicole Foster, Viral N Shah, Ryan Bailey, Mengdi Wu, Rodica Pop-Busui, Michelle Katz, Jill Crandall, Fida Bacha, Kristen Nadeau, Ingrid Libman, Paul Hiers, Kara Mizokami-Stout, Linda A DiMeglio, Jennifer Sherr, Richard Pratley, Shivani Agarwal, Janet Snell-Bergeon, Eda Cengiz, Sarit Polsky & Sanjeev N Mehta
Context Cardiovascular disease (CVD) is a major cause of mortality in adults with type 1 diabetes. Objective We prospectively evaluated CVD risk factors in a large, contemporary cohort of adults with type 1 diabetes living in the United States. Design Observational study of CVD and CVD risk factors over a median of 5.3 years. Setting The T1D Exchange clinic network. Patients Adults (age ≥18 years) with type 1 diabetes and without known CVD diagnosed before...

Unfolding the Genome

Gupi Ranganathan & Erez Lieberman Aiden
From 2009-2011, we worked together at the Broad Institute of MIT and Harvard (Broad Institute, n.d.), building on a study (Lieberman-Aiden & Van Berkum et al., 2009) that made it possible to explore how the human genome, the DNA contained in every cell of the body, folds in 3D. At the outset of our collaboration, our approaches seemed so different as to be, perhaps, incommensurable. The scientists used tools like mathematics, computer science, and molecular...

Data from: Clinical factors associated with long-term complete remission versus poor response to chemotherapy in HIV-infected children and adolescents with Kaposi sarcoma receiving bleomycin and vincristine: a retrospective observational study

Nader Kim El-Mallawany, William Kamiyango, Jeremy S. Slone, Jimmy Villiera, Carrie L. Kovarik, Carrie M. Cox, Dirk P. Dittmer, Saeed Ahmed, Gordon E. Schutze, Michael E. Scheurer, Peter N. Kazembe & Parth S. Mehta
Kaposi sarcoma (KS) is the most common HIV-associated malignancy in children and adolescents in Africa. Pediatric KS is distinct from adult disease. We evaluated the clinical characteristics associated with long-term outcomes. We performed a retrospective observational analysis of 70 HIV-infected children and adolescents with KS less than 18 years of age diagnosed between 8/2010 and 6/2013 in Lilongwe, Malawi. Local first-line treatment included bleomycin and vincristine plus nevirapine-based highly active anti-retroviral therapy (HAART). Median age...

Data from: Perturbing the cellular cevels of steroid receptor coactivator-2 impairs murine endometrial function

Maria M. Szwarc, Ramakrishna Kommagani, Jae-Wook Jeong, San-Pin Wu, Sophia Y. Tsai, Ming-Jer Tsai, Bert W. O'Malley, Francesco J. DeMayo & John P. Lydon
As pleiotropic coregulators, members of the p160/steroid receptor coactivator (SRC) family control a broad spectrum of transcriptional responses that underpin a diverse array of physiological and pathophysiological processes. Because of their potent coregulator properties, strict controls on SRC expression levels are required to maintain normal tissue functionality. Accordingly, an unwarranted increase in the cellular levels of SRC members has been causally linked to the initiation and/or progression of a number of clinical disorders. Although knockout...

Data from: Fruit flies diversify their offspring in response to parasite infection

Nadia D. Singh, Dallas R. Criscoe, Shelly Skolfield, Kathryn P. Kohl, Erin S. Keebaugh & Todd A. Schlenke
The evolution of sexual reproduction is often explained by Red Queen dynamics: Organisms must continually evolve to maintain fitness relative to interacting organisms, such as parasites. Recombination accompanies sexual reproduction and helps diversify an organism’s offspring, so that parasites cannot exploit static host genotypes. Here we show that Drosophila melanogaster plastically increases the production of recombinant offspring after infection. The response is consistent across genetic backgrounds, developmental stages, and parasite types but is not induced...

Data from: Sociosexual and communication deficits after traumatic injury to the developing murine brain

Bridgette D. Semple, Linda J. Noble-Haeusslein, Yong Jun Kwon, Pingdewinde N. Sam, A. Matt Gibson, Sarah Grissom, Sienna Brown, Zahra Adahman, Christopher A. Hollingsworth, Alexander Kwakye, Kayleen Gimlin, Elizabeth A. Wilde, Gerri Hanten, Harvey S. Levin, A. Katrin Schenk & Elisabeth A. Wilde
Despite the life-long implications of social and communication dysfunction after pediatric traumatic brain injury, there is a poor understanding of these deficits in terms of their developmental trajectory and underlying mechanisms. In a well-characterized murine model of pediatric brain injury, we recently demonstrated that pronounced deficits in social interactions emerge across maturation to adulthood after injury at postnatal day (p) 21, approximating a toddler-aged child. Extending these findings, we here hypothesized that these social deficits...

Supplementary material from: A 59-year-old woman with multiple myeloma and lower extremity weakness and numbness

Fábio A. Nascimento
Supplementary Table 1. Upper motor neuron (UMN) vs. lower motor neuron (LMN) syndromes.

A 12-month-old with hypotonia and developmental delays

Elizabeth Ames, Kerri Neville, Nancy Mcnamara, Catherine Keegan & Sarah Elsea
This data shows the references cited in the case report for the diagnosis of a 12-month-old girl who was referred to the pediatric neuromuscular clinic for evaluation of hypotonia and weakness and ultimately found to have 2 variants of uncertain significance in the NFU1 gene (NM _001002755.2 c.398T>C; p.Leu133Pro and NM _001002755.2 c.299C>G; p.Ala100Gly). Biochemical testing including CSF metabolomics confirmed her diagnosis of NFU1-related multiple mitochondrial dysfunctions syndrome (type 1).

Neonatal exposure to BPA, BDE-99, and PCB produces persistent changes in hepatic transcriptome associated with gut dysbiosis in adult mouse livers

Joe Lim, Moumita Dutta, Joseph Dempsey, Hans-Joachim Lehmler, James MacDonald, Theo Bammler, Cheryl Walker, Terrance Kavanagh, Haiwei Gu, Sridhar Mani & Julia Cui
Background. Recent evidence suggests that multigenic and complex environmentally modulated diseases result from early life exposure to toxicants at least partly via gut microbial influences. Environmental toxicants, polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs) are breast milk-enriched persistent organic pollutants (POPs) and thus remain a continuing threat to human health despite being banned from production. Recent findings focused on the liver developmental reprogramming capabilities from neonatal BPA exposure; however, little is known on how...

Data from: Faster processing of moving compared to flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion

Manivannan Subramaniyan, Alexander S. Ecker, Saumil S. Patel, R. James Cotton, Matthias Bethge, Xaq Pitkow, Philipp Berens & Andreas S. Tolias
When the brain has determined the position of a moving object, due to anatomical and processing delays, the object will have already moved to a new location. Given the statistical regularities present in natural motion, the brain may have acquired compensatory mechanisms to minimize the mismatch between the perceived and the real position of moving objects. A well-known visual illusion — the flash lag effect — points towards such a possibility. Although many psychophysical models...

Data from: Genetic signatures of microbial altruism and cheating in social amoebas in the wild

Suegene Noh, Katherine S. Geist, Xiangjun Tian, Joan E. Strassmann & David C. Queller
Many microbes engage in social interactions. Some of these have come to play an important role in the study of cooperation and conflict, largely because, unlike most animals, they can be genetically manipulated and experimentally evolved. However, whereas animal social behavior can be observed and assessed in natural environments, microbes usually cannot, so we know little about microbial social adaptations in nature. This has led to some difficult-to-resolve controversies about social adaptation even for well-studied...

Supplementary data for: Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Dan Vanderpool, Bin Quang Minh, Robert Lanfear, Daniel Hughes, Shwetha Murali, R. Alan Harris, Muthuswamy Raveendran, Donna M. Muzny, Richard A. Gibbs, Kim C. Worley, Jeffrey Rogers, Matthew W. Hahn, Mark S. Hibbins & Robert J. Williamson
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time....

Data from: Pediatric intensive care unit admissions for COVID-19: insights using state-level data

Enrique G. Villarreal, Rohit S. Loomba, Saul Flores, Juan S. Farias & Ron A. Bronicki
Introduction Intensive care has played a pivotal role during the COVID-19 pandemic as many patients developed severe pulmonary complications. The availability of information in pediatric intensive care (PICUs) remains limited. The purpose of this study is to characterize COVID-19 positive admissions (CPAs) in the United States and to determine factors that may impact those admissions. Materials and Methods This is a retrospective cohort study using data from the COVID-19 dashboard virtual pediatric system) containing information...

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  • Baylor College of Medicine
  • University of Pennsylvania
  • Rice University
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  • Indiana University
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  • Washington University in St. Louis
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  • University of Florida
  • University of Missouri