tbuckley/cabot-search huggingface dataset:
Metassembler: merging and optimizing de novo genome assemblies
Authors: Alejandro Hernandez Wences, Michael C. Schatz
Journal: Genome biology (2015)

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for meta-assembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition. The software is open-source at http://metassembler.sourceforge.net .
Elevated Inosine Monophosphate Levels in Resting Muscle of Patients with Stable Chronic Obstructive Pulmonary Disease
Authors: ELLEN M. POUW, ANNEMIE M. W. J. SCHOLS, GER J. van der VUSSE, EMIEL F. M. WOUTERS
Journal: American Journal of Respiratory and Critical Care Medicine (1998)

In order to investigate disturbances in energy metabolism in resting muscle of patients with stable chronic obstructive pulmonary disease (COPD), concentrations of adenine nucleotides and related compounds were examined comparing 34 COPD patients with eight age-matched healthy control subjects. Biopsies were taken from the anterior tibialis muscle. Special attention was paid to the muscle content of inosine monophosphate (IMP), a deamination product of adenosine monophosphate (AMP), because IMP formation is thought to reflect an imbalance between resynthesis and utilization of adenosine triphosphate (ATP). The absolute concentrations of high-energy phosphate compounds did not differ between patients and control subjects, but the ATP/ADP and the phosphocreatine/creatine ratio were significantly lower in the patients. IMP (detection level = 0.06 mmol/kg dry weight) was detected in 25 of 34 patients versus one of eight control subjects (p = 0.001). Mean (SD) IMP level in these patients was 0.18 (0.14) versus 0.06 mmol/kg dry weight in the one control subject. Based on the presence of detectable levels of muscle IMP, the patient group was divided into two subgroups. In IMP-positive patients, ATP/ADP and phosphocreatine/creatine ratios were significantly lower than in IMP-negative patients. IMP-positive patients were furthermore characterized by a significantly lower Dl CO. The results of this study indicate an imbalance between the utilization and resynthesis of ATP in resting muscle of patients with stable COPD.
Early Progressive Renal Decline Precedes the Onset of Microalbuminuria and Its Progression to Macroalbuminuria
Authors: Andrzej S. Krolewski, Monika A. Niewczas, Jan Skupien, Tomhito Gohda, Adam Smiles, Jon H. Eckfeldt, Alessandro Doria, James H. Warram
Journal: Diabetes Care (2013)

OBJECTIVE Progressive decrease in the glomerular filtration rate (GFR), or renal decline, in type 1 diabetes (T1D) is observed in patients with macroalbuminuria. However, it is unknown whether this decline begins during microalbuminuria (MA) or normoalbuminuria (NA). RESEARCH DESIGN AND METHODS The study group (second Joslin Kidney Study) comprises patients with T1D and NA (n = 286) or MA (n = 248) who were followed for 4-10 years (median 8 years). Serial measurements (median 6, range 3-16) of serum creatinine and cystatin C were used jointly to estimate GFR (eGFRcr-cys) and assess its trajectories during follow-up. RESULTS Renal decline (progressive eGFRcr-cys loss of at least 3.3% per year) occurred in 10% of the NA and 35% of the MA (P < 0.001). In both groups, the strongest determinants of renal decline were baseline serum concentrations of uric acid (P < 0.001) and tumor necrosis factor receptor 1 or 2 (TNFR-1 or -2, P < 0.001). Other significant risk factors included baseline HbA1c, age/diabetes duration, and systolic blood pressure. Relative impacts of these determinants were similar in NA and MA. Renal decline was not associated with sex or baseline serum concentration of TNF-α, IL-6, IL-8, IP-10, MCP-1, VCAM, ICAM, Fas, or FasL. CONCLUSIONS Renal decline in T1D begins during NA and it is determined by multiple factors, similar to MA. Thus, this early decline is the primary disease process leading to impaired renal function in T1D. Changes in albumin excretion rate, such as the onset of MA or its progression to macroalbuminuria, are either caused by or develop in parallel to the early renal decline.
Guidelines of care for acne vulgaris
Authors: Lynn A. Drake, Roger I. Ceilley, Raymond L. Cornelison, William L. Dobes, William Dorner, Charles W. Lewis, Stuart J. Salasche, Maria L. Chanco Turner, Peter E. Pochi, Ralph J. Coskey, Edward A. Krull, Orlando G. Rodman, Maria L. Chanco Turner, Stephen B. Webster, Peter E. Pochi, Ralph J. Coskey, Lynn A. Drake, G. Thomas Jansen, Roger I. Ceilley, Orlando G. Rodman, Maria L. Chanco Turner, Stephen B. Webster
Journal: Journal of the American Academy of Dermatology (1990)
Structure, expression, and T cell costimulatory activity of the murine homologue of the human B lymphocyte activation antigen B7.
Authors: G J Freeman, G S Gray, C D Gimmi, D B Lombard, L J Zhou, M White, J D Fingeroth, J G Gribben, L M Nadler
Journal: The Journal of Experimental Medicine (1991)

Following occupancy of the T cell receptor by antigen, T cell proliferation and lymphokine production are determined by a second costimulatory signal delivered by a ligand expressed on antigen presenting cells. The human B cell activation antigen B7, which is expressed on antigen presenting cells including activated B cells and gamma interferon treated monocytes, has been shown to deliver such a costimulatory signal upon attachment to its ligand on T cells, CD28. We have cloned and sequenced the murine homologue of the human B7 gene. The predicted murine protein has 44% amino acid identity with human B7. The greatest similarity is in the Ig-V and Ig-C like domains. Murine B7 mRNA was detected in murine hematopoietic cells of B cell but not T cell origin. Cells transfected with murine B7 provided a costimulatory signal to human CD28+ T lymphocytes. These results demonstrate the costimulatory activity of murine B7 and provide evidence that the ligand attachment site is conserved between the two species.
Folate and Asthma
Authors: Joshua Blatter, Yueh-Ying Han, Erick Forno, John Brehm, Lisa Bodnar, Juan C. Celedón
Journal: American Journal of Respiratory and Critical Care Medicine (2013)

Section:ChooseTop of pageAbstract <<Folate Metabolism and Phy...Assessment of Folate Stat...Animal Models of Folate S...Epidemiologic Studies of ...Gene-By-Folate Interactio...Conclusions and Future Di...ReferencesCITING ARTICLES
Distribution of galanin immunoreactivity in the respiratory tract of pig, guinea pig, rat, and dog.
Authors: A Cheung, J M Polak, F E Bauer, A Cadieux, N D Christofides, D R Springall, S R Bloom
Journal: Thorax (1985)

Galanin, a newly discovered peptide isolated from porcine intestine, is known to cause contraction in rat smooth muscle preparations and to induce hyperglycaemia in dogs. By the use of radioimmunoassay and immunohistochemical techniques the concentration and distribution of galanin immunoreactivity were determined in several areas of the respiratory tract of five dogs, five guinea pigs, five rats, and two pigs. Antibodies were raised in rabbits to whole unconjugated natural porcine galanin. The highest galanin concentrations were found in the bronchus and the trachea of the dog, guinea pig, rat (2 pmol/g in each case), and pig (less than 1 pmol/g). The lowest galanin concentrations were found in the lung parenchyma. Gel chromatographic analysis in the pig showed one molecular form of galanin coeluting with the porcine galanin standard. By means of the indirect immunofluorescence technique on sections of tissues fixed in benzoquinone solution, galanin was found to be confined to nerve fibres in different regions of the respiratory tract. In the nasal mucosa of the pig nerve fibres containing galanin were distributed around seromucous glands and blood vessels and beneath the epithelium. In the trachea, bronchus, and major intrapulmonary airways of the pig, dog, and guinea pig galanin immunoreactive fibres were detected predominantly in smooth muscle, as well as around seromucous glands and in the adventitia of blood vessels. Rarely, galanin immunoreactive nerve fibres were found in the lung parenchyma. A few galanin immunoreactive ganglion cells also containing vasoactive intestinal polypeptide were found in the adventitia of the tracheobronchial wall of the pig and dog. The distribution of galanin suggests that it may have some influence on airway, vascular, and secretory functions in the mammalian respiratory tract.
Curcumin Sensitizes Human Colorectal Cancer Xenografts in Nude Mice to γ-Radiation by Targeting Nuclear Factor-κB–Regulated Gene Products
Authors: Ajaikumar B. Kunnumakkara, Parmeswaran Diagaradjane, Sushovan Guha, Amit Deorukhkar, Shujun Shentu, Bharat B. Aggarwal, Sunil Krishnan
Journal: Clinical Cancer Research (2008)

How colorectal cancer develops resistance to gamma-radiation is not fully understood, but the transcription factor nuclear factor-kappaB (NF-kappaB) and NF-kappaB-regulated gene products have been proposed as mediators. Because curcumin, a component of turmeric (Curcuma longa), has been shown to suppress NF-kappaB activation, whether it can sensitize the colorectal cancer to gamma-radiation was investigated in colorectal cancer xenografts in nude mice.We established HCT 116 xenograft in nude mice, randomized into four groups, and treated with vehicle (corn oil), curcumin, gamma-radiation, and curcumin in combination with gamma-radiation. NF-kappaB modulation was ascertained using electrophoretic mobility shift assay and immunohistochemistry. Markers of proliferation, angiogenesis, and invasion were monitored by immunohistochemistry and Western blot analysis.Curcumin significantly enhanced the efficacy of fractionated radiation therapy by prolonging the time to tumor regrowth (P=0.02) and by reducing the Ki-67 proliferation index (P<0. 001). Moreover, curcumin suppressed NF-kappaB activity and the expression of NF-kappaB-regulated gene products (cyclin D1, c-myc, Bcl-2, Bcl-xL, cellular inhibitor of apoptosis protein-1, cyclooxygenase-2, matrix metalloproteinase-9, and vascular endothelial growth factor), many of which were induced by radiation therapy and mediate radioresistance. The combination of curcumin and radiation therapy also suppressed angiogenesis, as indicated by a decrease in vascular endothelial growth factor and microvessel density (P=0.002 versus radiation alone).Collectively, our results suggest that curcumin potentiates the antitumor effects of radiation therapy in colorectal cancer by suppressing NF-kappaB and NF-kappaB-regulated gene products, leading to inhibition of proliferation and angiogenesis.
Practice parameter for the diagnosis and management of primary immunodeficiency
Authors: Francisco A. Bonilla, David A. Khan, Zuhair K. Ballas, Javier Chinen, Michael M. Frank, Joyce T. Hsu, Michael Keller, Lisa J. Kobrynski, Hirsh D. Komarow, Bruce Mazer, Robert P. Nelson, Jordan S. Orange, John M. Routes, William T. Shearer, Ricardo U. Sorensen, James W. Verbsky, David I. Bernstein, Joann Blessing-Moore, David Lang, Richard A. Nicklas, John Oppenheimer, Jay M. Portnoy, Christopher R. Randolph, Diane Schuller, Sheldon L. Spector, Stephen Tilles, Dana Wallace, Francisco A. Bonilla, David A. Khan, David I. Bernstein, Joann Blessing-Moore, David Khan, David Lang, Richard A. Nicklas, John Oppenheimer, Jay M. Portnoy, Christopher R. Randolph, Diane Schuller, Sheldon L. Spector, Stephen Tilles, Dana Wallace, Francisco A. Bonilla, Zuhair K. Ballas, Javier Chinen, Michael M. Frank, Joyce T. Hsu, Michael Keller, Lisa J. Kobrynski, Hirsh D. Komarow, Bruce Mazer, Robert P. Nelson, Jordan S. Orange, John M. Routes, William T. Shearer, Ricardo U. Sorensen, James W. Verbsky
Journal: Journal of Allergy and Clinical Immunology (2015)
Phase II study of irinotecan (CPT-11) in children with high-risk malignant brain tumors: The Duke experience
Authors: Christopher D. Turner, Sridharan Gururangan, James Eastwood, Krystal Bottom, Melody Watral, Rodney Beason, Roger E. McLendon, Allan H. Friedman, Sandra Tourt-Uhlig, Langdon L. Miller, Henry S. Friedman
Journal: Neuro-Oncology (2002)

A phase II study of irinotecan (CPT-11) was conducted at Duke University Medical Center, Durham, NC, to evaluate the activity of this agent in children with high-risk malignant brain tumors. A total of 22 children were enrolled in this study, including 13 with histologically verified recurrent malignant brain tumors (glioblastoma multiforme [GBM] 4, anaplastic astrocytoma 1, ependymoma 5, and medulloblastoma/primitive neuroectodermal tumor 3), 5 with recurrent diffuse pontine glioma, and 4 with newly diagnosed GBM. All patients with recurrent tumor had prior chemotherapy and/or irradiation. Each course of CPT-11 consisted of 125 mg/m2 per week given i.v. for 4 weeks followed by a 2-week rest period. Patients with recurrent tumors received therapy until disease progression or unacceptable toxicity. Patients with newly diagnosed tumors initially received 3 cycles of treatment to assess tumor response and then were allowed radiotherapy at physician's choice; patients who demonstrated a response to CPT-11 prior to radiotherapy were allowed to continue the drug after radiation until disease progression or unacceptable toxicity. A 25% to 50% dose reduction was made for grade III-IV toxicity. Responses were assessed after every course by gadolinium-enhanced MRI of the brain and spine. Twenty-two patients received a median of 2 courses of CPT-11 (range, 1-16). Responses were seen in 4 of 9 patients with GBM or anaplastic astrocytoma (44%; 95% confidence interval, 11%-82%) (complete response in 2 patients with recurrent GBM lasting 9 months and 48+ months; partial response in one patient with a newly diagnosed midbrain GBM lasting 18 months prior to radiotherapy; and partial response lasting 11 months in 1 patient with recurrent anaplastic astrocytoma), 1 of 5 patients with recurrent ependymoma (partial response initially followed by stable disease lasting 11 months), and none of 5 patients with recurrent diffuse pontine glioma. Two of 3 patients with medulloblastoma/primitive neuroectodermal tumor had stable disease for 9 and 13 months. Toxicity was mainly myelosuppression, with 12 of 22 patients (50%) suffering grade II-IV neutropenia. Seven patients required dose reduction secondary to neutropenia. CPT-11, given in this schedule, appears to be active in children with malignant glioma, medulloblastoma, and ependymoma with acceptable toxicity. Ongoing studies will demonstrate if activity of CPT-11 can be enhanced when combined with alkylating agents, including carmustine and temozolomide.
Cd8 T Cell Detection of Bacterial Infection
Authors: Gregoire Lauvau, Eric G. Pamer
Journal: The Journal of Experimental Medicine (2001)

Bacteria remain a major cause of human disease and a formidable foe of the mammalian immune system. Bacter-ial entry into normally sterile compartments has long been recognized as a potential calamity for the mammalian host, in the most extreme circumstances resulting in circulatory collapse and multiorgan failure. In contrast to viruses, most bacteria are self-sufficient, producing their own lipid membranes, cell walls, nucleic acids, and proteins. Although many synthetic pathways used by bacteria and mammals are similar, others are subtly different and some are completely distinct. The mammalian immune system has evolved an array of mechanisms to recognize and respond to these distinct bacterial products upon infection. While it has been appreciated for over a century that the mammalian immune system uses receptors to specifically recognize bacterial products and initiate inflammatory defenses upon infection, the last decade has witnessed the molecular characterization of a number of remarkable pathways of immune defense against bacteria.
Improvement in the Frequency of Allergic Rhinitis Symptoms After Four Weeks of Treatment with Intranasal Ciclesonide 200 Mcg Qd
Authors: Francisco Javier Saynes-Marin, Carmen Cano-Salas, Araceli Arellano-Plancarte, Jazmin Chiu-Ugalde, José Antonio Vargas-Romero, Juan Carlos López-Alvarenga
Journal: Journal of Allergy and Clinical Immunology (2013)
Physiology of the Neurotrophins
Authors: Gary R. Lewin, Yves-Alain Barde
Journal: Annual Review of Neuroscience (1996)

The neurotrophins are a small group of dimeric proteins that profoundly affect the development of the nervous system of vertebrates. Recent studies have established clear correlations between the survival requirements for different neurotrophins of functionally distinct subsets of sensory neurons. The biological role of the neurotrophins is not limited to the prevention of programmed cell death of specific groups of neurons during development. Neurotrophin-3 in particular seems to act on neurons well before the period of target innervation and of normally occuning cell death. In animals lacking functional neurotrophin or receptor genes, neuronal numbers do not seem to be massively reduced in the CNS, unlike in the PNS. Finally, rapid actions of neurotrophins on synaptic efficacy, as well as the regulation of their mRNAs by electrical activity, suggest that neurotrophins might play important roles in regulating neuronal connectivity in the developing and in the adult central nervous system.
Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: a retrospective study of two independent tumour tissue collections
Authors: Sergio Marchini, Duccio Cavalieri, Robert Fruscio, Enrica Calura, Daniela Garavaglia, Ilaria Fuso Nerini, Costantino Mangioni, Giorgio Cattoretti, Luca Clivio, Luca Beltrame, Dionyssios Katsaros, Luca Scarampi, Guido Menato, Patrizia Perego, Giovanna Chiorino, Alessandro Buda, Chiara Romualdi, Maurizio D'Incalci
Journal: The Lancet Oncology (2011)
Phase I and Pharmacologic Studies of Topotecan in Patients With Impaired Hepatic Function
Authors: S. O'Reilly, E. Rowinsky, W. Slichenmyer, R. C. Donehower, A. Forastiere, D. Ettinger, T. L. Chen, S. Sartorius, K. Bowling, J. Smith, A. Brubaker, B. Lubejko, V. Ignacio, L. B. Grochow
Journal: JNCI Journal of the National Cancer Institute (1996)

Background:Topotecan, a topoisomerase I inhibitor that has demonstrated anticancer activity toward leukemias and solid tumors in clinical trials, is eliminated via hepatic and renal routes. However, dosing guidelines for the administration of topotecan to patients with impaired hepatic function have not yet been established.
HOXC9 Links Cell-Cycle Exit and Neuronal Differentiation and Is a Prognostic Marker in Neuroblastoma
Authors: Ling Mao, Jane Ding, Yunhong Zha, Liqun Yang, Brian A. McCarthy, William King, Hongjuan Cui, Han-Fei Ding
Journal: Cancer Research (2011)

Abstract Differentiation status in neuroblastoma strongly affects clinical outcomes and inducing differentiation is a treatment strategy in this disease. However, the molecular mechanisms that control neuroblastoma differentiation are not well understood. Here, we show that high-level HOXC9 expression is associated with neuroblastoma differentiation and is prognostic for better survival in neuroblastoma patients. HOXC9 induces growth arrest and neuronal differentiation in neuroblastoma cells by directly targeting both cell-cycle–promoting and neuronal differentiation genes. HOXC9 expression is upregulated by retinoic acid (RA), and knockdown of HOXC9 expression confers resistance to RA-induced growth arrest and differentiation. Moreover, HOXC9 expression is epigenetically silenced in RA-resistant neuroblastoma cells, and forced HOXC9 expression is sufficient to inhibit their proliferation and tumorigenecity. These findings identified HOXC9 as a key regulator of neuroblastoma differentiation and suggested a therapeutic strategy for RA-resistant neuroblastomas through epigenetic activation of HOXC9 expression. Cancer Res; 71(12); 4314–24. ©2011 AACR.
The Seattle-King County healthy homes project: implementation of a comprehensive approach to improving indoor environmental quality for low-income children with asthma.
Authors: James K Krieger, Tim K Takaro, Carol Allen, Lin Song, Marcia Weaver, Sanders Chai, Phillip Dickey
Journal: Environmental Health Perspectives (2002)

Pediatric asthma is a growing public health issue, disproportionately affecting low-income people and people of color. Exposure to indoor asthma triggers plays an important role in the development and exacerbation of asthma. We describe the implementation of the Seattle-King County Healthy Homes Project, a randomized, controlled trial of an outreach/education intervention to improve asthma-related health status by reducing exposure to allergens and irritants in the home. We randomly assigned 274 low-income children with asthma ages 4-12 to either a high- or a low-intensity group. In the high-intensity group, community health workers called Community Home Environmental Specialists (CHES) conducted initial home environmental assessments, provided individualized action plans, and made additional visits over a 12-month period to provide education and social support, encouragement of participant actions, provision of materials to reduce exposures (including bedding encasements), assistance with roach and rodent eradication, and advocacy for improved housing conditions. Members of the low-intensity group received the initial assessment, home action plan, limited education during the assessment visit, and bedding encasements. We describe the recruitment and training of CHES and challenges they faced and explain the assessment and exposure reduction protocols addressing dust mites, mold, tobacco smoke, pets, cockroaches, rodents, dust, moisture, and toxic or hazardous chemicals. We also discuss the gap between the practices recommended in the literature and what is feasible in the home. We accomplished home interventions and participants found the project very useful. The project was limited in resolving structural housing quality issues that contributed to exposure to indoor triggers.
Clinical outcome after laparoscopic pure management of borderline ovarian tumors: results of a series of 34 patients
Authors: S. Camatte, P. Morice, D. Atallah, A. Thoury, P. Pautier, C. Lhommé, P. Duvillard, D. Castaigne
Journal: Annals of Oncology (2004)

The aim of this study was to assess clinical outcome after laparoscopic treatment of borderline ovarian tumor (BOT).Thirty-four patients treated initially and/or for recurrent disease using a laparoscopic approach for BOT from 1984 to January 2002.Thirty-four patients underwent laparoscopic pure treatment (without conversion by laparotomy and/or reassessment surgery by laparotomy) for BOT. Conservative treatment was performed in 31 (91%) patients. Median follow-up time was 45 months (range 6-228). Six (17%) patients recurred (in the remaining ovary following conservative surgery in five patients and in the peritoneum in one patient). Two port-site metastases were observed. None of the patients had recurrent disease in the form of ovarian carcinoma. Nine spontaneous pregnancies were observed in six patients from a group of 15 patients desiring pregnancy. All patients are alive today and disease-free.These results seem to demonstrate that laparoscopic treatment can be safely performed in young patients with early stage BOT. Such a procedure is then feasible, but should be evaluated in patients with BOT and peritoneal implants.