gebhart/patrepeval huggingface dataset:
Population-genetic nature of copy number variations in the human genome (2009)

Copy number variations (CNVs) are universal genetic variations, and their association with disease has been increasingly recognized. We designed high-density microarrays for CNVs, and detected 3000-4000 CNVs (4-6% of the genomic sequence) per population that included CNVs previously missed because of smaller sizes and residing in segmental duplications. The patterns of CNVs across individuals were surprisingly simple at the kilo-base scale, suggesting the applicability of a simple genetic analysis for these genetic loci. We utilized the probabilistic theory to determine integer copy numbers of CNVs and employed a recently developed phasing tool to estimate the population frequencies of integer copy number alleles and CNV-SNP haplotypes. The results showed a tendency toward a lower frequency of CNV alleles and that most of our CNVs were explained only by zero-, one- and two-copy alleles. Using the estimated population frequencies, we found several CNV regions with exceptionally high population differentiation. Investigation of CNV-SNP linkage disequilibrium (LD) for 500-900 bi- and multi-allelic CNVs per population revealed that previous conflicting reports on bi-allelic LD were unexpectedly consistent and explained by an LD increase correlated with deletion-allele frequencies. Typically, the bi-allelic LD was lower than SNP-SNP LD, whereas the multi-allelic LD was somewhat stronger than the bi-allelic LD. After further investigation of tag SNPs for CNVs, we conclude that the customary tagging strategy for disease association studies can be applicable for common deletion CNVs, but direct interrogation is needed for other types of CNVs.
Long‐acting β2‐adrenergic formoterol and salmeterol induce the apoptosis of B‐chronic lymphocytic Leukaemia cells (2003)

B-cell chronic lymphocytic leukaemia (B-CLL) is a neoplastic disorder characterized by defective apoptosis, cell accumulation in G0/G1, and high expression of BCL2 oncogene. Intracellular cyclic adenosine monophosphate (cAMP) accumulation increases the chemosensitivity of B-CLL cells in vitro and in vivo. In the present study, we investigated the effects of beta2-adrenergic compounds, well known cAMP-inducing drugs, on the in vitro survival of leukaemia cells. In contrast to the short-acting beta2-mimetic (beta2Mim) salbutamol, a consistent pro-apoptotic effect was observed with the long-acting beta2Mim salmeterol and formoterol. Normal B cells isolated from control donors were totally resistant to the above molecules. These compounds also increased chlorambucil- and fludarabine-induced death of B-CLL cells. Blockade of beta-adrenergic receptor signalling or cAMP did not alter B-CLL apoptosis with beta2 Mimagents. Leukaemia cell apoptosis by beta2Mim correlated with an increase in calcium influx, decreased bcl-2 protein and mRNA levels, increase in BAX gene expression and a marked rise in BCL2/BAX mRNA ratios. Interleukin-4, a cytokine that increases bcl-2 expression in B-CLL cells, rescued leukaemia cell from apoptosis with beta2Mim. These data show that long-acting beta2-adrenergic agents promote apoptotic leukaemia cell death through an adrenoreceptor- and cAMP-independent, Ca2+-dependent mechanism.
Accumulation of Extracellular Hyaluronan by Hyaluronan Synthase 3 Promotes Tumor Growth and Modulates the Pancreatic Cancer Microenvironment (2014)

Extensive accumulation of the glycosaminoglycan hyaluronan is found in pancreatic cancer. The role of hyaluronan synthases 2 and 3 (HAS2, 3) was investigated in pancreatic cancer growth and the tumor microenvironment. Overexpression of HAS3 increased hyaluronan synthesis in BxPC-3 pancreatic cancer cells. In vivo, overexpression of HAS3 led to faster growing xenograft tumors with abundant extracellular hyaluronan accumulation. Treatment with pegylated human recombinant hyaluronidase (PEGPH20) removed extracellular hyaluronan and dramatically decreased the growth rate of BxPC-3 HAS3 tumors compared to parental tumors. PEGPH20 had a weaker effect on HAS2-overexpressing tumors which grew more slowly and contained both extracellular and intracellular hyaluronan. Accumulation of hyaluronan was associated with loss of plasma membrane E-cadherin and accumulation of cytoplasmic β-catenin, suggesting disruption of adherens junctions. PEGPH20 decreased the amount of nuclear hypoxia-related proteins and induced translocation of E-cadherin and β-catenin to the plasma membrane. Translocation of E-cadherin was also seen in tumors from a transgenic mouse model of pancreatic cancer and in a human non-small cell lung cancer sample from a patient treated with PEGPH20. In conclusion, hyaluronan accumulation by HAS3 favors pancreatic cancer growth, at least in part by decreasing epithelial cell adhesion, and PEGPH20 inhibits these changes and suppresses tumor growth.
Detecting Cancer Cells in the Peripheral Blood of Patients with Early Breast Cancer by Flow Cytometry (2000)

Objective To measure the cancer cell numbers in the peripheral blood(PBCC) of patients with early breast cancer.Methods Peripheral blood was examined by flow cytometry for the presence of circulating epithelial cells defined as CD45 - and cytokeratin+.Multi parameter flow cytometric (FCM) analysis was used for the detection of cancer cells in human peripheral blood.Results A significant correlation was found between PBCC preoperation and the size of tumor,the status of axilla lymph node,vascular invasion and pathology stage( P 0.01).However,the same correlation was only observed between PBCC and the status of axilla lymph node,stage and vascular invasion after operation( P 0.05).Conclusion The result showed that detection of tumor cells in the peripheral blood by multi parameter FCM is a high sensitive,quantitative method.It may be a new method to guide the treatment of breast cancer and estimate the prognosis.
Role of cellular membranes in hyperthermia: Some observations and theories reviewed (1993)

We have re-examined critically the evidence for and against the involvement of membranes in determining the response of cells to acute and chronic heat stress. Although frequently dismissed by many in the past, we believe that the bulk of evidence presented supports the view that physical and compositional alterations of membrane lipid components, both during and subsequent to heat exposure may, at least in part, account for cell adaptation, malfunction and lethality. Our primary goal in this review is to generate renewed interest in testing the validity of this hypothesis.
Feasibility of Combined Unipolar and Bipolar Voltage Maps to Improve Sensitivity of Endomyocardial Biopsy (2015)

These findings suggest that use of a combined bipolar/unipolar map may be able to improve the diagnostic yield of endomyocardial ventricular biopsy.
Spin-valve films using synthetic ferrimagnets for pinned layer (1999)

The magnetic behavior of spin-valve films using Co(t/sub 1/)/Ru(0.8 nm)/Co(t/sub 2/) synthetic ferrimagnets for the pinned layer were investigated, in which the Co(t/sub 2/) layer is exchange-biased by a CrMnPt antiferromagnetic layer. As compared with experimental results, the magnetic behavior of Co/Ru/Co/CrMnPt films could be qualitatively explained on the basis of a coherent rotation model and was roughly classified into two cases according to the thickness of t/sub 1/ and t/sub 2/. For t/sub 1/=t/sub 2/ the magnetization of the two Co layers changed the direction only in gentle rotation mode, which resulted in very large pinning fields. For t/sub 1//spl ne/t/sub 2/ the direction of the magnetization of the two Co layers rapidly reversed, maintaining an antiparallel magnetic configuration, at a relatively small applied field. The field where the rapid magnetization reversal was caused agreed with the exchange-bias field in the spin-valve film with a single Co pinned layer whose thickness was t/sub 1/-t/sub 2/.
New Animal Models of Human Neurological Diseases. Bio Valley Monographs. Volume 2. 2008. Edited by P. Poindron, P. Piguet. Published by Karger. 100 pages. Price C$109. (2009)

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[Clinical analysis of non-clear cell renal cell carcinoma]. (2015)

Clinicopathological features and prognosis of metastatic renal cell carcinoma (mRCC) vary by histopathological type. In this study, we analyzed these relationships with regard to non-clear cell RCC (nccRCC). We also analyzed the therapeutic trends for patients with mRCC. We initially identified 367 patients who were diagnosed with RCC and treated in our hospital between 2001 and 2013 ; 55 patients of whom were diagnosed with nccRCC. We reviewed their backgrounds, histopathological types and outcomes. Median age at diagnosis for patients with nccRCC was significantly younger (58.5 years) than for those with clear-cell RCC (66.3 years ; P=0.008) ; however, these histological types did not significantly differ by sex, affected side or rate of mRCC. Of the 55 nccRCC cases, 19 were mRCC, including 5 of the 8 cases of papillary type-2 RCC, and all patients who had either collecting duct carcinoma, sarcomatoid RCC or Xp11 translocation RCC. The most common metastatic site was lymph nodes. Although patients with papillary type-1 and Xp11 translocation RCC had relatively good prognoses, those with papillary type-2, collecting duct carcinoma and sarcomatoid RCC had poor prognoses. Among the 9 patients with nccRCC who received molecular targeted therapy, median survival was 13.3 months. Although existing therapeutic agents may be effective for some patients with nccRCC, identification of new target molecules and innovative drug development are needed in the future.
Fast High‐Dimensional Filtering Using the Permutohedral Lattice (2010)

Abstract Many useful algorithms for processing images and geometry fall under the general framework of high‐dimensional Gaussian filtering. This family of algorithms includes bilateral filtering and non‐local means. We propose a new way to perform such filters using the permutohedral lattice, which tessellates high‐dimensional space with uniform simplices. Our algorithm is the first implementation of a high‐dimensional Gaussian filter that is both linear in input size and polynomial in dimensionality. Furthermore it is parameter‐free, apart from the filter size, and achieves a consistently high accuracy relative to ground truth (&gt; 45 dB). We use this to demonstrate a number of interactive‐rate applications of filters in as high as eight dimensions.
Thromboelastometric and platelet responses to silk biomaterials (2014)

Silkworm's silk is natural biopolymer with unique properties including mechanical robustness, all aqueous base processing and ease in fabrication into different multifunctional templates. Additionally, the nonmulberry silks have cell adhesion promoting tri-peptide (RGD) sequences, which make it an immensely potential platform for regenerative medicine. The compatibility of nonmulberry silk with human blood is still elusive; thereby, restricts its further application as implants. The present study, therefore, evaluate the haematocompatibility of silk biomaterials in terms of platelet interaction after exposure to nonmulberry silk of Antheraea mylitta using thromboelastometry (ROTEM). The mulberry silk of Bombyx mori and clinically used Uni-Graft W biomaterial serve as references. Shortened clotting time, clot formation times as well as enhanced clot strength indicate the platelet mediated activation of blood coagulation cascade by tested biomaterials; which is comparable to controls.
The Human Immunodeficiency Virus and the Adrenal Medulla (1986)

Letters and Corrections1 August 1986The Human Immunodeficiency Virus and the Adrenal MedullaCAROL D. WEISS, M.D.CAROL D. WEISS, M.D.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-105-2-300_1 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptTo the editor: Several reports over the past few years have called attention to the striking incidence of adrenal gland disease in patients with the acquired immunodeficiency syndrome (AIDS) (1-4). Adrenal inflammation, often with severe hemorrhagic necrosis, has been commonly observed at autopsy, frequently in association with coexistent cytomegalovirus infection of the gland. Similarly, adrenal insufficiency has been reported in patients with AIDS (5).In reviewing the autopsy reports of 32 patients with AIDS who died at St. Vincent's Hospital in the years 1981 to 1985, I found 15 cases with reported adrenal disease. All but 1 were associated with...References1. KLEINMANNFRIEDLANSURKS RDGM. Adrenocortical function in the acquired immunodeficiency syndrome [Letter]. Ann Intern Med. 1983;99:566. LinkGoogle Scholar2. MACHERREICHERTSTRAUSS ACS. Death in the AIDS patient: role of cytomegalovirus. N Engl J Med. 1983;309:1454. CrossrefMedlineGoogle Scholar3. TAPPERHEIDRUNLERNERAL' KHAFAJISEITZMAN MZCKP. Adrenal necrosis in the acquired immunodeficiency syndrome. Ann Intern Med. 1984;100:239-41. LinkGoogle Scholar4. GREENECOLEGREENE LWJ. Adrenal insufficiency as a complication of the acquired immunodeficiency syndrome. Ann Intern Med. 1984;101:497-8. LinkGoogle Scholar5. GUENTHNERRABINOWEVAN NIELNAFTILANDLUTHY ESAAR. Primary Addison's disease in a patient with the acquired immunodeficiency syndrome. Ann Intern Med. 1984;100:847-8. LinkGoogle Scholar This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAuthors: CAROL D. WEISS, M.D.Affiliations: St. Vincent's Hospital and Medical Center New York, NY 10011 PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics Cited byThe HPA Axis and HIV InfectionInsuffisance surrénale périphérique au cours du sidaEndocrine Implications of Human Immunodeficiency Virus InfectionThe adrenal gland in AIDSHyponatremia in hospitalized patients with the acquired immunodeficiency syndrome (AIDS) and the AIDS-Related complexEndocrine Manifestations of Human Immunodeficiency Virus (HIV) InfectionMycobacterium avium-intracellulare and adrenal insufficiency in AIDSPathology of the pituitary gland in patients with the acquired immune deficiency syndrome (AIDS) 1 August 1986Volume 105, Issue 2Page: 300-300KeywordsAIDSAdrenal glandsAutopsyCytomegalovirus infectionHIVInflammationNecrosis ePublished: 1 December 2008 Issue Published: 1 August 1986 PDF downloadLoading ...
Mass-producible microtags for security applications: calculated fabrication tolerances by rigorous coupled-wave analysis (1998)

We develop a method for encoding phase and amplitude in microscopic computer-generated holograms (microtags) for security applications. An 8{times}8 cell phase-only and an 8{times}8 cell phase-and-amplitude microtag design are fabricated in photoresist using an extreme ultraviolet (13.4-nm) lithography (EUVL) tool. Each microtag measures 80{times}160{mu}m and contains features 0.2 {mu}m wide. Fraunhofer-zone diffraction patterns can be obtained from fabricated microtags without any intervening optics and compare very favorably with predicted diffraction patterns [Descour {ital et al.} (1996)]. We present the results of a rigorous coupled-wave analysis (RCWA) of microtags. Microtags are modeled as consisting of subwavelength gratings of a trapezoidal profile. Transverse-electric (TE) and TM readout polarizations are modeled. The analysis concerns the determination of optimal microtag-grating design parameter values and tolerances on those parameters. The parameters are grating wall-slope angle, grating duty cycle, grating depth, and metal coating thickness. Optimal microtag-grating parameter values result in maximum diffraction efficiency, which is calculated at 16{percent} for microtag gratings in air and 12{percent} for microtag gratings underneath a protective dielectric coating, within fabrication constraints. TM-polarized readout illumination is diffracted with higher efficiency than TE-polarized illumination by microtag gratings. {copyright} {ital 1998 Society of Photo-Optical Instrumentation Engineers.}{ital Key words:} computer-generated holograms; security and anticounterfeitingmore » devices; grating fabrication tolerances; rigorous coupled-wave analysis. {copyright} {ital 1998} {ital Society of Photo-Optical Instrumentation Engineers}« less
Real-Time Intraoperative Ureteral Guidance Using Invisible Near-Infrared Fluorescence (2007)

A convenient intravenous injection of CW800-CA or direct injection of indocyanine green permits high sensitivity visualization of the ureters under steady state and abnormal conditions using invisible light.
Primary structure and functional expression of human Glycyl-tRNA synthetase, an autoantigen in myositis. (1994)

Two identical cDNAs encoding human glycyl-tRNA synthetase were isolated from K562 and HEL cell lambda gt11 libraries by screening with "anti-EJ" autoantibodies from a patient with dermatomyositis, previously shown to specifically inhibit this enzyme. The sequenced cDNA had 2,385 base pairs, with a predicted protein of 685 amino acids and M(r) 77,500. The antigen reactive with anti-EJ was immunoaffinity-purified from HeLa cells, and two proteolytic peptides matched areas of the predicted amino acid sequence. The sequence was 61.6% identical with that of silk moth glycyl-tRNA synthetase. Several very highly conserved regions were identified, including the single class II synthetase motif region and an N-terminal region similar to one found in at least three other synthetases. Near identity in other regions suggested that they also had important functions. Expression of the cDNA in Escherichia coli yielded a protein of expected size that reacted with the autoantibodies and was active as glycyl-tRNA synthetase.
VEGF‐C induced lymphangiogenesis is associated with lymph node metastasis in orthotopic MCF‐7 tumors (2002)

The spread of cancer cells to regional lymph nodes through the lymphatic system is the first step in the dissemination of breast cancer. In several human cancers including those of the breast and prostate, the expression of vascular endothelial growth factor C (VEGF-C) is associated with lymph node metastasis. Our study was undertaken to evaluate the effect of VEGF-C on metastasis of poorly invasive, estrogen dependent human MCF-7 breast cancer cells. MCF-7 breast cancer cells transfected with VEGF-C (MCF-7-VEGF-C) were grown as tumors in the mammary fat pads of nude mice implanted with subcutaneous estrogen pellets. Tumor lymphangiogenesis and lymph node metastasis were studied immunohistochemically using antibodies against lymphatic vessel hyaluronan receptor -1 (LYVE-1), VEGF receptor-3 (VEGFR-3), PECAM-1, pan-cytokeratin and estrogen dependent pS2 protein. Overexpression of VEGF-C in transfected MCF-7 cells stimulated in vivo tumor growth in xenotransplanted mice without affecting estrogen responsiveness. The resulting tumors metastasized to the regional lymph nodes in 75% (in 6 mice out of 8, Experiment I) and in 62% (in 5 mice out of 8, Experiment II) of mice bearing orthotopic tumors formed by MCF-7-VEGF-C cells whereas no metastases were observed in mice bearing tumors of control vector-transfected MCF-7 cells (MCF-7-Mock). The density of intratumoral and peritumoral lymphatic vessels was increased in tumors derived from MCF-7-VEGF-C cells but not MCF-7-Mock cells. Taken together, our results show that VEGF-C overexpression stimulates tumor lymphangiogenesis and induces normally poorly metastatic estrogen-dependent MCF-7 tumors to disseminate to local lymph nodes. These data suggest that VEGF-C has an important role in lymph node metastasis of breast cancer even at its hormone-dependent early stage.
Recombinant Paramyxovirus Type 1-Avian Influenza-H7 Virus as a Vaccine for Protection of Chickens Against Influenza and Newcastle Disease (2003)

Current vaccines to prevent avian influenza rely upon labor-intensive parenteral injection. A more advantageous vaccine would be capable of administration by mass immunization methods such as spray or water vaccination. A recombinant vaccine (rNDV-AIV-H7) was constructed by using a lentogenic paramyxovirus type 1 vector (Newcastle disease virus [NDV] B1 strain) with insertion of the hemagglutinin (HA) gene from avian influenza virus (AIV) A/chicken/NY/13142-5/94 (H7N2). The recombinant virus had stable insertion and expression of the H7 AIV HA gene as evident by detection of HA expression via immunofluorescence in infected Vero cells. The rNDV-AIV-H7 replicated in 9-10 day embryonating chicken eggs and exhibited hemagglutinating activity from both NDV and AI proteins that was inhibited by antisera against both NDV and AIV H7. Groups of 2-week-old white Leghorn chickens were vaccinated with transfectant NDV vector (tNDV), rNDV-AIV-H7, or sterile allantoic fluid and were challenged 2 weeks later with viscerotropic velogenic NDV (vvNDV) or highly pathogenic (HP) AIV. The sham-vaccinated birds were not protected from vvNDV or HP AIV challenge. The transfectant NDV vaccine provided 70% protection for NDV challenge but did not protect against AIV challenge. The rNDV-AIV-H7 vaccine provided partial protection (40%) from vvNDV and HP AIV challenge. The serologic response was examined in chickens that received one or two immunizations of the rNDV-AIV-H7 vaccine. Based on hemagglutination inhibition and enzyme-linked immunosorbent assay (ELISA) tests, chickens that received a vaccine boost seroconverted to AIV H7, but the serologic response was weak in birds that received only one vaccination. This demonstrates the potential for NDV for use as a vaccine vector in expressing AIV proteins.
Infant mortality statistics from the 2007 period linked birth/infant death data set. (2011)

The U.S. infant mortality rate was 6.75 infant deaths per 1,000 live births in 2007, not significantly different than the rate of 6.68 in 2006. Infant mortality rates ranged from 4.57 per 1,000 live births for mothers of Central and South American origin to 13.31 for non-Hispanic black mothers. Infant mortality rates were higher for those infants who were born in multiple deliveries; for those whose mothers were born in the 50 states or the District of Columbia; and for mothers who were unmarried. Infant mortality was also higher for male infants and infants born preterm or at low birthweight. The neonatal mortality rate was essentially unchanged from 2006 (4.46) to 2007 (4.42). The postneonatal mortality rate increased 5 percent from 2.22 in 2006 to 2.33 in 2007, similar to the rate in 2005 (2.32). Infants born at the lowest gestational ages and birthweights have a large impact on overall U.S. infant mortality. For example, more than one-half of all infant deaths in the United States in 2007 (54 percent) occurred to the 2 percent of infants born very preterm (less than 32 weeks of gestation). Still, infant mortality rates for late preterm infants (34-36 weeks of gestation) were 3.6 times, and those for early term (37-38 weeks) infants were 1.5 times, those for infants born at 39-41 weeks of gestation, the gestational age with the lowest infant mortality rate. The three leading causes of infant death--congenital malformations, low birthweight, and sudden infant death syndrome--accounted for 45 percent of all infant deaths. The percentage of infant deaths that were "preterm-related" was 36.0 percent in 2007. The preterm-related infant mortality rate for non-Hispanic black mothers was 3.4 times higher, and the rate for Puerto Rican mothers was 71 percent higher than for non-Hispanic white mothers.