tbuckley/cabot-search huggingface dataset:
Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling
Authors: Jennifer T. Lau, Fiona J. Whelan, Isiri Herath, Christine H. Lee, Stephen M. Collins, Premysl Bercik, Michael G. Surette
Journal: Genome Medicine (2016)

The human gut microbiota has been implicated in most aspects of health and disease; however, most of the bacteria in this community are considered unculturable, so studies have relied on molecular-based methods. These methods generally do not permit the isolation of organisms, which is required to fully explore the functional roles of bacteria for definitive association with host phenotypes. Using a combination of culture and 16S rRNA gene sequencing, referred to as culture-enriched molecular profiling, we show that the majority of the bacteria identified by 16S sequencing of the human gut microbiota can be cultured.Five fresh, anaerobic fecal samples were cultured using 33 media and incubation of plates anaerobically and aerobically resulted in 66 culture conditions for culture-enriched molecular profiling. The cultivable portion of the fecal microbiota was determined by comparing the operational taxonomic units (OTUs) recovered by 16S sequencing of the culture plates to OTUs from culture-independent sequencing of the fecal sample. Targeted isolation of Lachnospiraceae strains using conditions defined by culture-enriched molecular profiling was carried out on two fresh stool samples.We show that culture-enriched molecular profiling, utilizing 66 culture conditions combined with 16S rRNA gene sequencing, allowed for the culturing of an average of 95 % of the OTUs present at greater than 0.1 % abundance in fecal samples. Uncultured OTUs were low abundance in stool. Importantly, comparing culture-enrichment to culture-independent sequencing revealed that the majority of OTUs were detected only by culture, highlighting the advantage of culture for studying the diversity of the gut microbiota. Applying culture-enriched molecular profiling to target Lachnospiraceae strains resulted in the recovery of 79 isolates, 12 of which are on the Human Microbiome Project's "Most Wanted" list.We show that, through culture-enriched molecular profiling, the majority of the bacteria in the human gut microbiota can be cultured and this method revealed greater bacterial diversity compared to culture-independent sequencing. Additionally, this method could be applied for the targeted recovery of a specific bacterial group. This approach allows for the isolation of bacteria of interest from the gut microbiota, providing new opportunities to explore mechanisms of microbiota-host interactions and the diversity of the human microbiota.
Cell adhesion molecules in benign and malignant melanocytic tumors.
Authors: P. E. Stoemmer, P. Torres-Galea, C. Neusiedl
Journal: Journal of Clinical Oncology (2010)

e19024 Background: Cell adhesion molecules are of eminent significance for the intercellular connections, the resulting architecture and the biological behaviour with great local differences of their expression. Methods: We analysed ten appropriate FFPE- blocks of each junctional, compound and dermal nevi, blue nevi and different melanomas (SSM, LM and NMM) for their expression of E-, N- and P- Cadherin, catenins alpha and beta. Results: E- and N-Cadherin: Junctional (JN) and dermal nevus (DN) cells: E-Cadherin: high expression esp. in cell membranes of junctional tumourcell complexes. N-Cadherin: negative in lentigo and JN cells. Slight expression in the cellmembranes of the melanocytes type B of DN. Blue nevi and cellular blue nevi have N-Cadherin as principal CAM; often coexpression with E-Cadherin. LM and SSM: intraepidermal parts: good expression of E-Cadherin in cellmembranes and cytoplasm. In deeper parts, loss of this CAM. Nodular malignant melanoma (NMM): more intracytoplasmic than membranous E-Cadherin in spindle cells and disseminated epitheloid tumourcells High expression of N-Cadherin in invasion front melanocytes. P-Cadherin: in cell membranes of JN; DN negative. Discontinous membranous P-Cadherin in NMM. Alpha- and beta- Catenin: JN, CN, DN:membranous and intranuclear expression of beta catenin; variable reaction in JN; CN and DN high expression SSM and NMM: high expression of catenins in cellmembranes and cytoplasm in invasion front- tumourcomplexes. Conclusions: Melanocytes type A express E-Cadherin, beta-Catenin and CD44v as principal adhesioncomplex molecules; no N-cadherin and P-Cadherin. Regressing to type B-melanocytes: loss of E-cadherin without expriming N-cadherin. Malignant melanomas: shift from E-cadherin to N- and P-Catherin: coexpression of E-Cadherin and N-Cadherin in the in situ component. Massively invasive cells: subtotal shift to N- Catherin and P-Catherin. The change of celladhesion molecules may enable these tumourcells for better invasive growth and metatasis. No significant financial relationships to disclose.
Maintenance with Histamine and IL-2 Induces a Marked Expansion of Activated CD56bright NK Cells in Acute Myeloid Leukemia
Authors: Angelica Cuapio, Mirte Post, Sabine Cerny-Reiterer, Markus Osl, Volker Huppert, Karoline V Gleixner, Susanne Herndlhofer, Wolfgang R Sperr, Peter Valent, Erhard Hofer
Journal: Blood (2014)
Heart failure associated with high plasma 10-hydroxynortriptyline levels
Authors: R C Young, G S Alexopoulos, C A Shamoian, A K Dhar, H Kutt
Journal: American Journal of Psychiatry (1984)

The authors describe a patient who developed congestive heart failure and had a high plasma concentration of 10-hydroxynortriptyline. They discuss the need for further research to define the contribution of antidepressants' active metabolites to toxic and therapeutic effects.
Physician caseloads at public mental hospitals
Authors: A L Pelonero, R L Elliott, J W Barber, A Best
Journal: American Journal of Psychiatry (1996)

The purpose of the study was to gather baseline data on physician caseloads, particularly psychiatric caseloads, at public mental hospitals.A 26-item survey was sent to medical directors of public mental hospitals in the United States and its territories. Questions focused on hospital demographics, programs, and medical staffing. Survey data were analyzed and descriptive statistics were determined.Of 295 surveys mailed, 195 (66%) usable surveys were returned. The hospitals had a mean bed capacity of 347 (SD=301, range=10-1,926), a mean current patient population of 321 (SD=277, range=7-1,815), and 950 mean annual admissions (SD=891, range=3-5,100). Acute care was the most common treatment program (81%), followed by long-term care (71%). A wide range of psychiatric caseloads by type of program existed, with approximately equal mean and median amounts.The caseloads reported were, overall, reasonable and expected by the type of treatment program. The range of caseloads, however, included extremely high outliers that raise concerns about the quality of care delivered.
Associations of Perfluoroalkyl Substances (PFAS) with Lower Birth Weight: An Evaluation of Potential Confounding by Glomerular Filtration Rate Using a Physiologically Based Pharmacokinetic Model (PBPK)
Authors: Marc-André Verner, Anne E. Loccisano, Nils-Halvdan Morken, Miyoung Yoon, Huali Wu, Robin McDougall, Mildred Maisonet, Michele Marcus, Reiko Kishi, Chihiro Miyashita, Mei-Huei Chen, Wu-Shiun Hsieh, Melvin E. Andersen, Harvey J. Clewell, Matthew P. Longnecker
Journal: Environmental Health Perspectives (2015)

BackgroundPrenatal exposure to perfluoroalkyl substances (PFAS) has been associated with lower birth weight in epidemiologic studies. This association could be attributable to glomerular filtration rate (GFR), which is related to PFAS concentration and birth weight.ObjectivesWe used a physiologically based pharmacokinetic (PBPK) model of pregnancy to assess how much of the PFAS–birth weight association observed in epidemiologic studies might be attributable to GFR.MethodsWe modified a PBPK model to reflect the association of GFR with birth weight (estimated from three studies of GFR and birth weight) and used it to simulate PFAS concentrations in maternal and cord plasma. The model was run 250,000 times, with variation in parameters, to simulate a population. Simulated data were analyzed to evaluate the association between PFAS levels and birth weight due to GFR. We compared simulated estimates with those from a meta-analysis of epidemiologic data.ResultsThe reduction in birth weight for each 1-ng/mL increase in simulated cord plasma for perfluorooctane sulfonate (PFOS) was 2.72 g (95% CI: –3.40, –2.04), and for perfluorooctanoic acid (PFOA) was 7.13 g (95% CI: –8.46, –5.80); results based on maternal plasma at term were similar. Results were sensitive to variations in PFAS level distributions and the strength of the GFR–birth weight association. In comparison, our meta-analysis of epidemiologic studies suggested that each 1-ng/mL increase in prenatal PFOS and PFOA levels was associated with 5.00 g (95% CI: –21.66, –7.78) and 14.72 g (95% CI: –8.92, –1.09) reductions in birth weight, respectively.ConclusionResults of our simulations suggest that a substantial proportion of the association between prenatal PFAS and birth weight may be attributable to confounding by GFR and that confounding by GFR may be more important in studies with sample collection later in pregnancy.CitationVerner MA, Loccisano AE, Morken NH, Yoon M, Wu H, McDougall R, Maisonet M, Marcus M, Kishi R, Miyashita C, Chen MH, Hsieh WS, Andersen ME, Clewell HJ III, Longnecker MP. 2015. Associations of perfluoroalkyl substances (PFAS) with lower birth weight: an evaluation of potential confounding by glomerular filtration rate using a physiologically based pharmacokinetic model (PBPK). Environ Health Perspect 123:1317–1324; http://dx.doi.org/10.1289/ehp.1408837
HIV-1 and HCV Infections among Antibody-Negative Blood Donors
Authors: Alfred M Prince
Journal: New England Journal of Medicine (2004)

to the editor: As reported by Stramer et al. (Aug. 19 issue), 1 testing for human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) by nucleic acid amplification with the use of minipools has markedly reduced the transmission of HIV-1 and HCV through blood products. Testing of individual units is now being considered, but such a procedure would still not completely abolish transmission. 2
PBPK modeling and simulation in drug research and development
Authors: Xiaomei Zhuang, Chuang Lu
Journal: Acta Pharmaceutica Sinica B (2016)

Physiologically based pharmacokinetic (PBPK) modeling and simulation can be used to predict the pharmacokinetic behavior of drugs in humans using preclinical data. It can also explore the effects of various physiologic parameters such as age, ethnicity, or disease status on human pharmacokinetics, as well as guide dose and dose regiment selection and aid drug–drug interaction risk assessment. PBPK modeling has developed rapidly in the last decade within both the field of academia and the pharmaceutical industry, and has become an integral tool in drug discovery and development. In this mini-review, the concept and methodology of PBPK modeling are briefly introduced. Several case studies were discussed on how PBPK modeling and simulation can be utilized through various stages of drug discovery and development. These case studies are from our own work and the literature for better understanding of the absorption, distribution, metabolism and excretion (ADME) of a drug candidate, and the applications to increase efficiency, reduce the need for animal studies, and perhaps to replace clinical trials. The regulatory acceptance and industrial practices around PBPK modeling and simulation is also discussed.
Proton Pump Inhibitors and Dementia Incidence
Authors: Jineane V. Venci, Katherine W. Eisenberg
Journal: JAMA Neurology (2016)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Neurology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Neurology journal
Additional Mutations in SRSF2, ASXL1 and/or RUNX1 Identify a High Risk Group of Patients with KIT D816V+ Advanced Systemic Mastocytosis
Authors: Mohamad Jawhar, Juliana Schwaab, Susanne Schnittger, Manja Meggendorfer, Karl Sotlar, Hans-Peter Horny, Georgia Metzgeroth, Sebastian Kluger, Nicole Naumann, Claudia Haferlach, Torsten Haferlach, Peter Valent, Wolf-Karsten Hofmann, Alice Charlotte Fabarius, Nicholas C.P. Cross, Andreas Reiter
Journal: Blood (2015)
Thyrotoxicosis during Pregnancy
Authors: F Pekonen, B A Lamberg
Journal: New England Journal of Medicine (1965)

The diagnosis of thyrotoxicosis during pregnancy is difficult on clinical grounds only. The determination of free thyroid hormones or free thyroid hormone indices is important and is possibly supplemented by the TRH stimulation test. Thyrotoxicosis during pregnancy should always be treated actively. The authors recommend subtotal thyroidectomy if there are indications for surgical therapy (nodular goitre or large diffuse goitre). Otherwise treatment with thyrostatic agents is used. After operation during pregnancy, substitution with thyroid hormones should be given throughout the pregnancy in order to avoid deterious effects of possible maternal hypothyroidism. Antithyroid treatment should be continued till after delivery. Beta-receptor blockers are used only as adjuncts but are not recommended as the sole therapy.
The Hybrid Molecule, Edo-S101, Impairs Double Strand Breaks Repair in Multiple Myeloma and Synergizes with Bortezomib and Dexamethasone
Authors: Ana Alicia López-Iglesias, Ana Belen Herrero, Laura San-Segundo, Susana Hernández-García, Lorena González-Méndez, Montserrat Martín-Sánchez, Esperanza M Algarín, Teresa Paino, Mercedes Garayoa, Thomas Mehrling, Norma C Gutierrez, Jesús F. San-Miguel, Maria-Victoria Mateos, Enrique M. Ocio
Journal: Blood (2015)
Cigar and Pipe Smoking in Relation to Lung Cancer and Excess Mortality&lt;xref ref-type="fn" rid="FN1"&gt;1&lt;/xref&gt;
Authors: O R Gsell, R Abelin
Journal: JNCI Journal of the National Cancer Institute (1972)

Journal Article Cigar and Pipe Smoking in Relation to Lung Cancer and Excess Mortality Get access O. R. Gsell, O. R. Gsell Planungsstelle der Hochschule für klinische Medizin, St. Gallen, Switzerland, and Institut für Sozial- und Präventivmedizin, Universität Bern, Bern, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar T. Abelin T. Abelin Planungsstelle der Hochschule für klinische Medizin, St. Gallen, Switzerland, and Institut für Sozial- und Präventivmedizin, Universität Bern, Bern, Switzerland Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 48, Issue 6, June 1972, Pages 1795–1803, https://doi.org/10.1093/jnci/48.6.1795 Published: 01 June 1972
Outbreak of<i>Escherichia coli</i>O157:H7 Infections Associated with Dairy Education Event Attendance — Whatcom County, Washington, 2015
Authors: Kathryn Curran, Katherine E. Heiman, Tushar Singh, Zachary Doobovsky, Joni Hensley, Beth Melius, Laura Burnworth, Ian Williams, Megin Nichols
Journal: MMWR Morbidity and Mortality Weekly Report (2015)

On April 27, 2015, the Whatcom County Health Department (WCHD) in Bellingham, Washington, was notified by a local laboratory regarding three children with presumptive Escherichia coli O157 infection. WCHD interviewed the parents, who indicated that all three children had attended a dairy education event held in a barn April 20–24, 2015, during a school field trip. WCHD, the Washington State Department of Health, and CDC investigated to determine the magnitude of the outbreak, identify risk factors and potential environmental sources of infection, and develop recommendations. A total of 60 cases (25 confirmed and 35 probable) were identified, and 11 patients were hospitalized.
Expression of the CAMPATH-1 Antigen (CD52) on CD34+/CD38- Progenitor Cells in Patients with 5q- MDS and in a Subset of AML
Authors: Katharina Blatt, Harald Herrmann, Sabine Cerny-Reiterer, Susanne Herndlhofer, Wolfgang R. Sperr, Peter Valent
Journal: Blood (2011)
Legislating social control of the mentally ill in California
Authors: H R Lamb, A P Sorkin, J Zusman
Journal: American Journal of Psychiatry (1981)

The Lanterman-Petris-Short Act in California has been acclaimed for protecting the civil rights of the mentally ill and curbing unnecessary involuntary psychiatric hospitalization. Its passage, however, has not prevented an increase in the rate of involuntary admissions to state hospitals and a marked decrease in the rate of voluntary admissions. This has greatly changed the functions and problems of state hospitals. In local as well as state hospitals large numbers of people continue to become involuntary psychiatric patients. In many cases this results from gaps between the law and its implementation. It appears that professionals, the courts, families, and society generally feel a continuing need for social control of the mentally ill.
Protein Kinase C Epsilon Inhibition Restores In-Vitro Megakaryocyte Differentiation Of Primary Myelofibrosis Hematopoietic Progenitors
Authors: Elena Masselli, Prisco Mirandola, Giuliana Gobbi, Cecilia Carubbi, Sabrina Bonomini, Monica Crugnola, Filomena Russo, Luisa Craviotto, Benedetta Cambò, Caterina Plenteda, Elena Rossetti, Cecilia Caramatti, Franco Aversa, Marco Vitale
Journal: Blood (2013)
Cell-Specific Promoters Enable Lipid-Based Nanoparticles to Deliver Genes to Specific Cells of the Retina <i>In Vivo</i>
Authors: Yuhong Wang, Ammaji Rajala, Binrui Cao, Michelle Ranjo-Bishop, Martin-Paul Agbaga, Chuanbin Mao, Raju V S Rajala
Journal: Theranostics (2016)

Non-viral vectors, such as lipid-based nanoparticles (liposome-protamine-DNA complex [LPD]), could be used to deliver a functional gene to the retina to correct visual function and treat blindness. However, one of the limitations of LPD is the lack of cell specificity, as the retina is composed of seven types of cells. If the same gene is expressed in multiple cell types or is absent from one desired cell type, LPD-mediated gene delivery to every cell may have off-target effects. To circumvent this problem, we have tested LPD-mediated gene delivery using various generalized, modified, and retinal cell-specific promoters. We achieved retinal pigment epithelium cell specificity with vitelliform macular dystrophy (VMD2), rod cell specificity with mouse rhodopsin, cone cell specificity with red/green opsin, and ganglion cell specificity with thymocyte antigen promoters. Here we show for the first time that cell-specific promoters enable lipid-based nanoparticles to deliver genes to specific cells of the retina in vivo. This work will inspire investigators in the field of lipid nanotechnology to couple cell-specific promoters to drive expression in a cell- and tissue-specific manner.
Results of Treatment with Tyrosine Kinase Inhibitors(TKIs) in Combination with Intensive Chemotherapy in Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia(Ph+ALL)
Authors: Taiichi Kyo, Takeshi Okatani, Kouhei Kyo, Ryouta Imanaka, Mitsuhiro Itagaki, Yuuta Katayama, Koji Iwato, Hideki Asaoku
Journal: Blood (2011)
A Bicuspid Aortic Valve Imaging Classification for the TAVR Era
Authors: Hasan Jilaihawi, Mao Chen, John Webb, Dominique Himbert, Carlos E. Ruiz, Josep Rodés-Cabau, Gregor Pache, Antonio Colombo, Georg Nickenig, Michael Lee, Corrado Tamburino, Horst Sievert, Yigal Abramowitz, Giuseppe Tarantini, Faisal Alqoofi, Tarun Chakravarty, Mohammad Kashif, Nobuyuki Takahashi, Yoshio Kazuno, Yoshio Maeno, Hiroyuki Kawamori, Alaide Chieffo, Philipp Blanke, Danny Dvir, Henrique Barbosa Ribeiro, Yuan Feng, Zhen-Gang Zhao, Jan-Malte Sinning, Chad Kliger, Gennaro Giustino, Basia Pajerski, Sebastiano Imme, Eberhard Grube, Jonathon Leipsic, Alec Vahanian, Iassen Michev, Vladimir Jelnin, Azeem Latib, Wen Cheng, Raj Makkar
Journal: JACC. Cardiovascular imaging (2016)
Effect of a new type androgen receptor antagonist, TAS3681, on ligand-independent AR activation through its AR downregulation activity.
Authors: Daisuke Kajiwara, Kazuhisa Minamiguchi, Masanao Seki, Hiroya Mizutani, Hiroki Aoyagi, Shigeo Okajima, Eiji Sasaki, Teruhiro Utsugi, Yoshikazu Iwasawa
Journal: Journal of Clinical Oncology (2016)

199 Background: Two new therapies, enzalutamide and abiraterone, directed at the androgen receptor (AR) signaling axis, represent important advances in the management of castration-resistant prostate cancer (CRPC). However, eventually almost all of patients acquire resistance to these drugs by a variety of mechanisms. Ligand independent AR activation such as induction of AR splice variants and AR overexpression are major issues of current CRPC progression. In the present study, we report the biological characterization of TAS3681, which is a new AR antagonist with AR downregulation activity, and propose this concept as a potential new approach for the treatment of CRPC. Methods: For assay of AR transactivation, prostate cancer (PCa) cells were transiently transfected with androgen-responsive reporter gene construct. The transfected cells were treated with growth factor and cytokine in steroid-depleted media, and luciferase activity was measured. To evaluate the effect of TAS3681 on AR and c-Myc protein expression, PCa cells were treated with TAS3681 in steroid-depleted media. AR and c-Myc protein levels were determined by western blot. Real-time PCR was used to analyze the mRNA levels of c-Myc and c-Myc target gene. Chromatin immunoprecipitation was performed to determine the enrichment of AR at the element. Results: TAS3681 dose-dependently reduced AR protein levels in PCa cells. In contrast to enzalutamide, TAS3681 suppressed androgen-independent AR transactivation by growth factor and cytokine. In PCa cells which express full-length AR and splice variant AR-v7, TAS3681 suppressed AR-v7 target gene expression through downregulation of AR-v7. Moreover, TAS3681 reduced expression of c-Myc, critical driver of androgen-independent mechanisms of PCa progression, via AR downregulation activity. In addition, real-time PCR assay showed the transcriptional suppression of c-Myc and its target gene by TAS3681. Conclusions: TAS3681 exhibits suppressive effects on ligand-independent AR activation via AR decreasing activity. These finding suggest that TAS3681 could be a candidate of breakthrough therapy for resistance to current AR pathway target drugs.