gebhart/patrepeval huggingface dataset:
Elevated Serum Insulin-Like Growth Factor-Binding Protein 2 (IGFBP-2) and Decreased IGFBP-3 in Epithelial Ovarian Cancer: Correlation with Cancer Antigen 125 and Tumor-Associated Trypsin Inhibitor (1997)

Insulin-like growth factors (IGFs) and IGF-binding proteins (IGFBPs) recently have been shown to play a physiological role in the female genital system, including the ovarian follicular system. However, little is known about the role of the IGF system in malignant ovarian disease. To assess possible mutual correlations between alterations in circulating IGFBP profiles and tumuor markers in patients with epithelial ovarian cancer, we performed an RIA for IGFBP-2 and IGFBP-3 and a Western ligand blotting (WLB) in serum samples from 20 patients with epithelial ovarian cancer, 10 patients with benign ovarian tumors, and 8 healthy age-matched controls. The epithelial ovarian cancer group had a mean IGFBP-2 level that was 253% (RIA) and 105% (WLB) above that of controls. IGFBP-2 even correlated positively with the highly sensitive serum tumor marker, cancer antigen 125 (CA 125) (r = 0.71, P &lt;0.001) but not with the less sensitive tumor-associated trypsin inhibitor. In contrast, serum IGFBP-3 (by RIA and WLB) was decreased in patients with ovarian cancer, and IGFBP-3 proteolytic activity was detectable in some of the patients. Neither IGFBP-3 nor IGFBP-3 proteolytic activity correlated with CA 125; but the former correlated inversely, and the latter positively, with tumor-associated trypsin inhibitor. In conclusion, IGFBP-2 levels are high in serum of epithelial ovarian cancer patients, and the increment in serum IGFBP-2 correlates positively with CA 125. Alterations in serum IGFBP-2 levels may therefore, serve as a potential additional marker for ovarian cancer.
Transfer of Streptococcus faecalis and Streptococcus faecium to the Genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov. (1984)

The results of deoxyribonucleic acid-deoxyribonucleic acid and deoxyribonucleic acid-ribosomal ribonucleic acid hybridization studies demonstrated that Streptococcus faecalis and Streptococcus faecium are distantly related to the non-enterococcal streptococci (Streptococcus bovis and Streptococcus equinus) of serological group D and to other streptococci. On the basis of our results and those of previous studies, we propose that S . faecalis and S . faecium be transferred to the genus Enterococcus (ex Thiercelin and Jouhaud) nom. rev. as Enterococcus faecalis (Andrewes and Horder) comb. nov. and Enterococcus faecium (Orla-Jensen) comb. nov., respectively. A description of the genus Enterococcus nom. rev. and emended descriptions of E. faecalis and E. faecium are given.
Large reduction of leakage current by graded-layer La doping in (Ba0.5, Sr0.5)TiO3 thin films (2001)

A large reduction in the leakage current behavior in (Ba, Sr)TiO3 (BST) thin films was observed by graded-layer donor doping. The graded doping was achieved by introducing La-doped BST layers in the grown BST films. The films showed a large decrease (about six orders of magnitude) in the leakage current in comparison to undoped films at an electric field of 100 kV/cm. The large decrease in leakage current was attributed to the formation of highly resistive layers, originating from compensating defect chemistry involved for La-doped films grown in oxidizing environment. Temperature-dependent leakage-current behavior was studied to investigate the conduction mechanism and explanations of the results were sought from Poole–Frenkel conduction mechanism.
BDNF and the diseased nervous system: a delicate balance between adaptive and pathological processes of gene regulation (2008)

It is clear that brain-derived neurotrophic factor (BDNF) plays a crucial role in organizing the response of the genome to dynamic changes in the extracellular environment that enable brain plasticity. BDNF has emerged as one of the most important signaling molecules for the developing nervous system as well as the impaired nervous system, and multiple diseases, such as Alzheimer's, Parkinson's, Huntington's, epilepsy, Rett's syndrome, and psychiatric depression, are linked by their association with potential dysregulation of BDNF-driven signal transduction programs. These programs are responsible for controlling the amount of activated transcription factors, such as cAMP response element binding protein, that coordinate the expression of multiple brain proteins, like ion channels and early growth response factors, whose job is to maintain the balance of excitation and inhibition in the nervous system. In this review, we will explore the evidence for BDNF's role in gene regulation side by side with its potential role in the etiology of neurological diseases. It is hoped that by bringing the datasets together in these diverse fields we can help develop the foundation for future studies aimed at understanding basic principles of gene regulation in the nervous system and how they can be harnessed to develop new therapeutic opportunities.
Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element (2017)

Chromatin structure is tightly intertwined with transcription regulation. Here we compared the chromosomal architectures of fetal and adult human erythroblasts and found that, globally, chromatin structures and compartments A/B are highly similar at both developmental stages. At a finer scale, we detected distinct folding patterns at the developmentally controlled β-globin locus. Specifically, new fetal stage-specific contacts were uncovered between a region separating the fetal (γ) and adult (δ and β) globin genes (encompassing the <i>HBBP1</i> and <i>BGLT3</i> noncoding genes) and two distal chromosomal sites (HS5 and 3'HS1) that flank the locus. In contrast, in adult cells, the <i>HBBP1</i>-<i>BGLT3</i> region contacts the embryonic ε-globin gene, physically separating the fetal globin genes from the enhancer (locus control region [LCR]). Deletion of the <i>HBBP1</i> region in adult cells alters contact landscapes in ways more closely resembling those of fetal cells, including increased LCR-γ-globin contacts. These changes are accompanied by strong increases in γ-globin transcription. Notably, the effects of <i>HBBP1</i> removal on chromatin architecture and gene expression closely mimic those of deleting the fetal globin repressor BCL11A, implicating BCL11A in the function of the <i>HBBP1</i> region. Our results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new <i>cis</i> control elements.
An adaptive crawler for locating hidden-Web entry points (2007)

In this paper we describe new adaptive crawling strategies to efficiently locate the entry points to hidden-Web sources. The fact that hidden-Web sources are very sparsely distributedmakes the problem of locating them especially challenging. We deal with this problem by using the contents ofpages to focus the crawl on a topic; by prioritizing promisinglinks within the topic; and by also following links that may not lead to immediate benefit. We propose a new frameworkwhereby crawlers automatically learn patterns of promisinglinks and adapt their focus as the crawl progresses, thus greatly reducing the amount of required manual setup andtuning. Our experiments over real Web pages in a representativeset of domains indicate that online learning leadsto significant gains in harvest rates' the adaptive crawlers retrieve up to three times as many forms as crawlers thatuse a fixed focus strategy.
Human papillomavirus testing in primary screening for the detection of high-grade cervical lesions: a study of 7932 women (2001)

High-risk human papillomaviruses (HR-HPV) are the necessary cause of cervical carcinomas. To determine whether HPR-HPV DNA detection in primary routine screening could represent a sensitive and reliable technique for the detection of high-grade squamous intraepithelial lesions (HGSIL), laboratory analysis using 2 cytologic techniques (conventional and liquid-based), HPV testing with Hybrid Capture II assay (HC-II), followed by colposcopic examination of women with abnormal cervical finding and/or persistent HR-HPV infection, was conducted in 7932 women who had routine cervical examination. The sensitivity of HPV testing for detecting a histologically proven HGSIL was 100%, higher than that of conventional (68.1%) and liquid-based (87.8%) cytology. The low specificities of 85.6% and 87.3% of HPV testing slightly increased to 88.4% and 90.1% if HPV testing was reserved for woman >30 years old. The quantitative approach provided by the HC-II assay for the assessment of the viral load was not reliable for predicting HGSIL in normal smears. HR-HPV testing could be proposed in primary screening in association with cytology. With conventional cytology it significantly improves the detection of HGSIL. With the use of the same cervical scrape for HPV testing and liquid-based cytology, HR-HPV testing would allow to select positive samples treated in a second time for cytology which gives a good specificity.
Effect of thimerosal in leukemia, in leukemic cell lines, and on normal hematopoiesis. (1990)

Anti-thymocyte globulin (ATG), a horse antiserum to human thymus tissue, has been shown to induce granulocytic differentiation of the HL-60 human leukemia cell line. In this paper we describe the effect of ATG on leukemic blasts and its effect on other human leukemia cell lines in vitro. The in vitro differentiation effect of ATG was observed in blasts from two patients with leukemia and the human leukemia cell line K562. The differentiation effect of ATG was attributable to its preservative, thimerosal, separable from ATG by high pressure liquid chromatography or dialysis. Subsequent studies with thimerosal alone showed it to induce differentiation in leukemic blasts from three patients and the human leukemia cell lines U937, K562, and KG-1. The differentiation effect of thimerosal is blocked by a sulfhydryl-protective agent, dithiothreitol, suggesting that the mechanism of differentiation may be mediated via a sulfhydryl group-dependent process.
Large-scale cover song recognition using hashed chroma landmarks (2011)

Cover song recognition, also called version identification, can only be solved by exposing the underlying tonal content of music. Apart from obvious applications in copyright enforcement, techniques for cover identification can also be used to find patterns and structure in music datasets too large for any musicologist to even listen to. Much progress has been made on cover song recognition, but work to date has been reported on datasets of at most a few thousand songs, using algorithms that simply do not scale beyond the capacity of a small portable music player. In this paper, we consider the problem of finding covers in a database of a million songs, and we only consider algorithms that can deal with such data. Using a fingerprinting-inspired model, we present the first results of cover song recognition on the Million Song Dataset. This task has been renewed by the availability of so many tracks, and this work is intended to be the first step towards a practical solution.
<title>Key elements of high-speed WDM terrestrial free-space optical communications systems</title> (2000)

This paper presents key operational elements which impact upon performance characteristics for terrestrial free-space laser communications systems within the 1550 nm window. These elements include; optical transmit and receive functionality of the telescope terminals, electro-optic components as well as atmospheric conditions affecting link performance.
Synthesis of an oxorhenium(V) corrolate from porphyrin with detrifluoromethylation and ring contraction (1998)

Metallation of highly electron deficient 5,10,15,20-tetrakis(trifluoromethyl)porphyrin 1 with [Re2(CO)10] in refluxing PhCN resulted in a novel synthesis of oxorhenium(V) 5,10,15-tris(trifluoromethyl)corrolate 2 characterized by single crystal X-ray crystallography.
Holographically formed polymer dispersed liquid crystal films for transmission mode spectrometer applications (2007)

We show proof of concept of a transmission-mode wavelength filtering device consisting of layered holographically formed polymer dispersed liquid crystal (H-PDLC) cells. H-PDLC cells were fabricated from a thiolene based polymer composite to have transmission notches in the near-IR wavelength range. Wavelength filtering was achieved by stacking four H-PDLC cells with transmission notches spaced at 10 nm intervals. Results show a broad transmission notch spanning the spectral width of the constituent cells. With bias applied to an individual cell within the stack, the transmission notch of the cell inverts and the overall transmission envelope changes shape. Using a transmitted energy sensing device and a lineshape mapping algorithm, spectral content can be determined to a resolution of 0.1 nm for narrow banded signals. Applications for this switchable wavelength filtering device include serial detection of spectral content for telecom data signals or chemical and biological sample identification through absorption or emission spectroscopy.
Inhibition of prostate cancer proliferation by interference with SONIC HEDGEHOG-GLI1 signaling (2004)

Prostate cancer is the most common solid tumor in men, and it shares with all cancers the hallmark of elevated, nonhomeostatic cell proliferation. Here we have tested the hypothesis that the SONIC HEDGEHOG (SHH)-GLI signaling pathway is implicated in prostate cancer. We report expression of SHH-GLI pathway components in adult human prostate cancer, often with enhanced levels in tumors versus normal prostatic epithelia. Blocking the pathway with cyclopamine or anti-SHH antibodies inhibits the proliferation of GLI1+/PSA+ primary prostate tumor cultures. Inversely, SHH can potentiate tumor cell proliferation, suggesting that autocrine signaling may often sustain tumor growth. In addition, pathway blockade in three metastatic prostate cancer cell lines with cyclopamine or through GLI1 RNA interference leads to inhibition of cell proliferation, suggesting cell-autonomous pathway activation at different levels and showing an essential role for GLI1 in human cells. Our data demonstrate the dependence of prostate cancer on SHH-GLI function and suggest a novel therapeutic approach.
Holographic data storage technology (2000)

We present an overview of our research effort on volume holographic digital data storage. Innovations, developments, and new insights gained in the design and operation of working storage platforms, novel optical components and techniques, data coding and signal processing algorithms, systems tradeoffs, materials testing and tradeoffs, and photon-gated storage materials are summarized.
Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes (2001)

Allosteric ribozymes are engineered RNAs that operate as molecular switches whose rates of catalytic activity are modulated by the binding of specific effector molecules. New RNA molecular switches can be created by using "allosteric selection," a molecular engineering process that combines modular rational design and in vitro evolution strategies. In this report, we describe the characterization of 3',5'-cyclic nucleotide monophosphate (cNMP)-dependent hammerhead ribozymes that were created using allosteric selection (Koizumi et al., Nat Struct Biol, 1999, 6:1062-1071). Artificial phylogeny data generated by random mutagenesis and reselection of existing cGMP-, cCMP-, and cAMP-dependent ribozymes indicate that each is comprised of distinct effector-binding and catalytic domains. In addition, patterns of nucleotide covariation and direct mutational analysis both support distinct secondary-structure organizations for the effector-binding domains. Guided by these structural models, we were able to disintegrate each allosteric ribozyme into separate ligand-binding and catalytic modules. Examinations of the independent effector-binding domains reveal that each retains its corresponding cNMP-binding function. These results validate the use of allosteric selection and modular engineering as a means of simultaneously generating new nucleic acid structures that selectively bind ligands. Furthermore, we demonstrate that the binding affinity of an allosteric ribozyme can be improved through random mutagenesis and allosteric selection under conditions that favor tighter binding. This "affinity maturation" effect is expected to be a valuable attribute of allosteric selection as future endeavors seek to apply engineered allosteric ribozymes as biosensor components and as controllable genetic switches.
TreeAlign (1994)

Several approaches to the multiple alignment problem are conceivable, but virtually all are based on the Parsimony Principle: Choose the history of a set of sequences that minimizes the overall amount of change (insertion-deletions and substitutions/mutations). This formulation was first presented by Sankoff () together with a dynamic programming algorithm solving the problem. However, this was so slow that all programs in use have opted for heuristic, but much faster algorithms, and so has TreeAlign. Given the large growth in the data involving sets of homologous sequences, a good solution to this problem has high priority.
Right Ventricular Fibrosis and Conduction Delay in a Patient With Clinical Signs of Brugada Syndrome (2005)

In this patient with BS, conduction slowing based on interstitial fibrosis, but not transmural repolarization differences, caused the ECG signs and was the origin of ventricular fibrillation.
Human Bone Marrow-Derived Mesenchymal (Stromal) Progenitor Cells (MPCs) Cannot Be Recovered from Peripheral Blood Progenitor Cell Collections (1997)

The purpose of this study was to compare the ability to collect human bone marrow-derived mesenchymal (stromal) progenitor cells (MPC) from bone marrow versus peripheral blood hematopoietic progenitor cell (PBPC) collections using in vitro and in vivo assays. Ten milliliter samples of PBPC collections mobilized from 11 patients undergoing autotransplants using chemotherapy followed by G-CSF 5-10 micrograms/kg were evaluated using in vitro and in vivo assays for hematopoietic progenitors and MPCs. Additionally, 10 ml samples of unstimulated bone marrow aspirates as well as PBPC collected after mobilization using G-CSF 10 micrograms/kg obtained from 3 normal, histocompatible allogeneic donors were analyzed for hematopoietic progenitors and MPCs. The MPCs were isolated and culture-expanded as adherent cells in vitro and subsequently tested for the capacity to differentiate into mesenchymal phenotypes in vivo using calcium hydroxyapatite porous ceramic cubes implanted s.c. in athymic mice. Demineralized sections of these cubes were analyzed histologically for the appearance of bone and cartilage. Seven autotransplant subjects with cancer received G-CSF after chemotherapy administration, whereas 4 cancer patients and all 3 normal donors received G-CSF alone as the mobilizing regimen. For the autologous PBPC collections and the normal marrow aspirations, median hematopoietic progenitor content was in the normal range for our institution. MPCs were detected in in vitro cultures and as bone-positive ceramic cubes in samples of all 3 allogeneic donor bone marrows but in none of the 14 autologous and 6 allogeneic PBPC collections. In conclusion, MPCs could not be recovered in PBPC collections obtained from either normal donors or patients who underwent PBPC collections after mobilization therapy but could be obtained routinely from bone marrow samples. Although the role of transplanted MPCs is an area of clinical investigation, this study points out a fundamental differences in the population of cells transplanted after collection from bone marrow versus peripheral blood.
Therapy for Fibrotic Diseases: Nearing the Starting Line (2013)

Fibrosis, or the accumulation of extracellular matrix molecules that make up scar tissue, is a common feature of chronic tissue injury. Pulmonary fibrosis, renal fibrosis, and hepatic cirrhosis are among the more common fibrotic diseases, which in aggregate represent a huge unmet clinical need. New appreciation of the common features of fibrosis that are conserved among tissues has led to a clearer understanding of how epithelial injury provokes dysregulation of cell differentiation, signaling, and protein secretion. At the same time, discovery of tissue-specific features of fibrogenesis, combined with insights about genetic regulation of fibrosis, has laid the groundwork for biomarker discovery and validation, and the rational identification of mechanism-based antifibrotic drugs. Together, these advances herald an era of sustained focus on translating the biology of fibrosis into meaningful improvements in quality and length of life in patients with chronic fibrosing diseases.
Investigations on Steroids. XI. Synthesis of Steroidal Oxazole, Imidazole, and Triazole (1968)

Steroidal oxazoles, imidazoles, and triazoles were synthesized for biological studies. 2α-Acetoxy-or 2α-bromo-3-ketones of androstane and cholestane series were converted into 2'-methylsteroidal [3, 2-d] oxazoles (III) by reaction with ammonium acetate. Reductive acetylation of 2-hydroxyimino-3-oxo steroids (V) gave 2α-acetamido-3-ketones (VI) which were cyclized by the use of sulfuric acid to 2'-methyl-steroidal [2, 3-d] oxazoles (XI). 2'-methyl-steroidal [2, 3-d] imidazoles (XII) were prepared from VI by reaction with ammonium acetate. 2α-Amino-3-ketone hydrochlorides, obtained by catalytic hydrogenation of V, were converted by reaction with thiocyanate into steroidal [2, 3-d] imidazoline-2'-thiones which were desulfurized to afford imidazoles (XIV). Androst-4-eno[2, 3-d]-triazoles (XX) were prepared from the 2-acetoxymethylene-3-ketone via the 2-hydroxyimino-3-one hydrazone by application of the established procedures. The ORD (and CD) data of VI and the corresponding 3β-alcohol (VIIId) are presented.
Phase Partition—A Method for Purification and Analysis of Cell Organelles and Membrane Vesicles (1982)

This chapter contains sections titled: Introduction Phase Systems Factors Determining Partition of Membrane Particles Cross Partition Counter-Current Distrubution Applications Experimental Procedures General Discussion