gebhart/patrepeval huggingface dataset:
Executive Summary of IPITA-TTS Opinion Leaders Report on the Future of β-Cell Replacement (2016)

The International Pancreas and Islet Transplant Association (IPITA), in conjunction with the Transplantation Society (TTS), convened a workshop to consider the future of pancreas and islet transplantation in the context of potential competing technologies that are under development, including the artificial pancreas, transplantation tolerance, xenotransplantation, encapsulation, stem cell derived beta cells, beta cell proliferation, and endogenous regeneration. Separate workgroups for each topic and then the collective group reviewed the state of the art, hurdles to application, and proposed research agenda for each therapy that would allow widespread application. Herein we present the executive summary of this workshop that focuses on obstacles to application and the research agenda to overcome them; the full length article with detailed background for each topic is published as an online supplement to Transplantation.
Acquired immunodeficiency syndrome-associated lymphomas: Clinical, pathologic, immunologic, and viral characteristics of 111 cases (1991)

The incidence of lymphomas in individuals infected with the human immunodeficiency virus has increased progressively since the beginning of the acquired immunodeficiency syndrome (AIDS) epidemic. The present series includes 111 patients, all diagnosed and studied at one hospital in New York City. There were 108 men and three women; the average age was 39 years and male homosexuality was the predominant risk factor. The materials examined originated from 138 surgical specimens and 24 autopsies. There were 11 cases of Hodgkin's lymphoma and 100 cases of non-Hodgkin's lymphomas (NHL), a proportion strongly skewed in favor of the latter. Hodgkin's lymphoma in AIDS patients was characterized by advanced clinical stage, high histologic grade, and frequent bone marrow involvement. Non-Hodgkin's lymphoma in AIDS patients, in contrast to the general population, originated predominantly in extranodal locations (61 cases) versus locations in which the lymph nodes were the site of the primary tumors (39 cases). In the digestive tract, the unusual oral and anal primary locations were often noted and were possibly related to specific risk factors. There were 15 cases of NHL of the central nervous system, an incidence 14 times greater than that recorded in the general population. The majority of NHLs were of high histologic grade, Burkitt's and large cell immunoblastic, representing most of the cerebral and gastrointestinal tumors. All NHLs were of B-cell immunophenotype. Lymphadenopathies with the histologic features of human immunodeficiency virus infection, particularly of the late stage (type C), often preceded NHL. Probing for Epstein-Barr virus genome was more frequently positive in Hodgkin's lymphoma than in NHL. Immunologic evaluations showed severely depressed T cell counts and CD4 to CD8 cell ratios as well as markedly increased levels of antilymphocyte antibodies. Reflecting the background of profound immune deficiency, the AIDS-associated lymphomas were characterized by high aggressiveness, early tendency to generalization, frequent post-treatment relapse, and short periods of survival.
A single chain 19-kDa fragment from bovine thrombospondin binds to type V collagen and heparin (1993)

Location of the type V collagen-binding domain within bovine thrombospondin (TSP) was investigated by using fragments of reduced and alkylated TSP. A fragment of relative molecular mass (19 kDa) was isolated, which inhibited binding of 125I-TSP to type V collagen in a solid-phase binding assay. A direct binding assay using the 125I-labeled fragment confirmed that the fragment actually bound to collagen. The fragment retained specificity for the native structure of type V collagen like the intact TSP molecule. Its binding to the collagen, however, was not inhibited by Ca2+ in contrast to intact TSP. Amino acid sequence analysis of the 19-kDa fragment suggested that this fragment corresponded to Val333-Lys412, a part of the stalklike region in the human TSP primary structure. It was found that the fragment also bound well to heparin in a specific and saturable manner and, furthermore, binding to type V collagen was inhibited by soluble heparin. Removal of the N-linked sugar chain from this fragment resulted in a 14-kDa fragment. The deglycosylated fragment retained the ability to bind to type V collagen as well as heparin. These results suggest that a type V collagen-binding site is present in the 80-residue portion of bovine TSP (Val333-Lys412) and is likely to be identical or lie very close to a heparin-binding site, which exists in the type I repeat structure.
Epitaxial growth of aligned polydiacetylene films on anisotropic orienting polymers (1990)

We report an epitaxial method for orienting thin films of polydiacetylenes on ordinary alignment polymers that have been stretched by rubbing. By selectively removing the alignment polymer using standard photolithographic techniques, we show that it is possible to obtain well-oriented polydiacetylene films in desired regions. Typical values for the birefringence are 0.14±0.01 for epitaxially grown films, enough to allow the formation of gratings and channel waveguides on patterned surfaces.
1728: A Novel Resectoscope for Transurethral Resection of Bladder Tumors and the Prostate (2007)

You have accessJournal of UrologyModerated Poster 54, Wednesday, May 23, 2007 10:00 am - 12:00 pm1 Apr 20071728: A Novel Resectoscope for Transurethral Resection of Bladder Tumors and the Prostate Allan J. Pantuck, Jack Baniel, Ziya Kirkali, Nazy Zomorodian, Ofer Yossepowitch, and Arie S. Belldegrun Allan J. PantuckAllan J. Pantuck More articles by this author , Jack BanielJack Baniel More articles by this author , Ziya KirkaliZiya Kirkali More articles by this author , Nazy ZomorodianNazy Zomorodian More articles by this author , Ofer YossepowitchOfer Yossepowitch More articles by this author , and Arie S. BelldegrunArie S. Belldegrun More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)31916-5AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1728: A Novel Resectoscope for Transurethral Resection of Bladder Tumors and the Prostate." The Journal of Urology, 177(4S), p. 575 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 575 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Allan J. Pantuck More articles by this author Jack Baniel More articles by this author Ziya Kirkali More articles by this author Nazy Zomorodian More articles by this author Ofer Yossepowitch More articles by this author Arie S. Belldegrun More articles by this author Expand All Advertisement PDF DownloadLoading ...
Bio‐Click Chemistry: Enzymatic Functionalization of PEGylated Capsules for Targeting Applications (2012)

All sorted: The enzyme Sortase A was used to catalyze functionalization of PEGylated capsules with an activation-specific anti-platelet single-chain antibody (scFv). This enzymatic method allows fast, covalent, and site-directed functionalization of delivery vehicles under mild conditions. Activation-specific anti-platelet scFv-coated PEGylated capsules exhibited a high level of selective binding to thrombi, thus suggesting their potential for thrombosis therapy.
Cloning and Expression of a Novel pH-sensitive Two Pore Domain K+ Channel from Human Kidney (1998)

A complementary DNA encoding a novel K+ channel, called TASK-2, was isolated from human kidney and its gene was mapped to chromosome 6p21. TASK-2 has a low sequence similarity to other two pore domain K+ channels, such as TWIK-1, TREK-1, TASK-1, and TRAAK (18-22% of amino acid identity), but a similar topology consisting of four potential membrane-spanning domains. In transfected cells, TASK-2 produces noninactivating, outwardly rectifying K+ currents with activation potential thresholds that closely follow the K+ equilibrium potential. As for the related TASK-1 and TRAAK channels, the outward rectification is lost at high external K+ concentration. The conductance of TASK-2 was estimated to be 14.5 picosiemens in physiological conditions and 59.9 picosiemens in symmetrical conditions with 155 mM K+. TASK-2 currents are blocked by quinine (IC50 = 22 microM) and quinidine (65% of inhibition at 100 microM) but not by the other classical K+ channel blockers tetraethylammonium, 4-aminopyridine, and Cs+. They are only slightly sensitive to Ba2+, with less than 17% of inhibition at 1 mM. As TASK-1, TASK-2 is highly sensitive to external pH in the physiological range. 10% of the maximum current was recorded at pH 6. 5 and 90% at pH 8.8. Unlike all other cloned channels with two pore-forming domains, TASK-2 is essentially absent in the brain. In human and mouse, TASK-2 is mainly expressed in the kidney, where in situ hybridization shows that it is localized in cortical distal tubules and collecting ducts. This localization, as well as its functional properties, suggest that TASK-2 could play an important role in renal K+ transport.
Monocytes in children with leukemias and lymphomas -- down-regulation of HLA and costimulatory molecules. (2004)

The aim of the study was to evaluate the function of monocytes in children with leukemias and lymphomas based on the expression of critical costimulatory, activatory and adhesion molecules (CD80, CD86, HLA-DR and CD54 = ICAM-1), estimated with tricolor flow cytometry. In comparison to the control group we found a lower percentage of monocytes with costimulatory molecules (CD80 before and CD86 after lipopolysaccharide stimulation) at the time of diagnosis and of monocytes with HLA-DR molecules after remission induction. We also noted a lower percentage of monocytes with HLA-DR expression in the group with severe or therapy resistant infections. The results of our investigation suggest some defect in costimulation and antigen presentation in lymphoproliferative diseases in children.
Targeted Therapies for Non–Small Cell Lung Cancer: An Evolving Landscape (2010)

Over the past decade, a multitude of targeted agents have been explored in the treatment of advanced non-small cell lung cancer (NSCLC). Thus far, two broad classes of agents have been implemented in clinical practice: (a) vascular endothelial growth factor (VEGF)-directed therapies and (b) antagonists of the epidermal growth factor receptor (EGFR). In the former category, the agent bevacizumab (a monoclonal antibody) has shown landmark improvements in survival when added to cytotoxic therapy. Small molecule tyrosine kinase inhibitors (TKI) targeting the VEGF receptor (i.e., sunitinib, sorafenib, and vandetanib) show activity in phase II clinical studies. With respect to EGFR-directed therapies, the TKIs gefitinib and erlotinib have shown significant benefit, and have uncovered valuable information about the biology of lung cancer. Outside of therapies directed specifically at VEGF- and EGFR-mediated signaling, trials evaluating insulin-like growth factor-1 receptor (IGF-IR)-targeting agents, cyclooxygenase-2 (COX-2) inhibitors, c-met inhibitors, irreversible pan-HER inhibitors, mammalian target of rapamycin (mTOR) inhibitors, and histone deacetylase (HDAC) inhibitors are ongoing. Inhibitors of ALK show great promise in patients with the relevant gene translocation. Herein, the clinical development of novel therapies for NSCLC is described, including some discussion of relevant biomarkers and determination of synergy with both cytotoxic therapy and other targeted agents.
Autophagy-lysosome pathway associated neuropathology and axonal degeneration in the brains of alpha-galactosidase A-deficient mice (2014)

Together these findings indicate widespread neuropathology and focused axonal neurodegeneration in alpha-galactosidase A-deficient mouse brain in association with disruption of the autophagy-lysosome pathway, and provide the basis for future mechanistic assessment of the contribution of the autophagy-lysosome pathway to this histologic phenotype.
Estimation of standard Gibbs energy changes of biotransformations (1991)

Contributions and corrections for the estimation of standard Gibbs energies are given. The group contribution method, applicable to both cyclic and acyclic compounds, permits the approximate estimation of the standard Gibbs energy of a biotransformation, given the stoichiometry and structures of the metabolites involved. Estimated standard Gibbs energies of formation for a number of acyclic biochemical compounds are provided.
Titanium-Catalyzed Enantioselective Additions of Alkyl Groups to Aldehydes:  Mechanistic Studies and New Concepts in Asymmetric Catalysis (2003)

The catalytic asymmetric addition of alkyl groups to aldehydes is an important reaction in the enantioselective synthesis of secondary alcohols. This reaction can be catalyzed by zinc- or titanium-based catalysts. While the mechanism of the zinc/amino alcohol catalysts has received significant attention, the titanium-based catalysts have been less studied. This Account summarizes our mechanistic studies with bis(sulfonamide) and BINOL-derived titanium catalysts. It also describes our use of this reaction in the development of new approaches to asymmetric catalysis, including applications of diastereomeric catalysts and optimization of asymmetric catalysts with achiral and meso ligands.
Protecting superconducting qubits from radiation (2011)

We characterize a superconducting qubit before and after embedding it along with its package in an absorptive medium. We observe a drastic improvement in the effective qubit temperature and over a tenfold improvement in the relaxation time up to 5.7 μs. Our results suggest the presence of external radiation inside the cryogenic apparatus can be a limiting factor for both qubit initialization and coherence. Calculations support the hypothesis that the relaxation is not limited by direct coupling of thermal photons to the qubit prior to embedding, but by dissipation arising from quasiparticle generation.
Polyadenylylated RNA complementary to a mouse retrovirus-like multigene family is rapidly and specifically induced by epidermal growth factor stimulation of quiescent cells. (1982)

Complementary DNA probes prepared from total polysomal poly(A)+RNA populations were used to identify clones of mouse DNA containing sequences whose expression is specifically enhanced after epidermal growth factor (EGF) stimulation of quiescent mouse embryo cells in culture. Three such clones were isolated and used to study changes in the levels of clone-specific poly(A)+RNA in the polysomes of cells after mitogenic stimulation by EGF. RNA complementary to sequences present in these clones increased approximately equal to 10-fold as a fraction of the total poly(A)+RNA by 6 hr after stimulation. All three clones were found by hybridization criteria to contain sequences related to the class of mouse retrovirus or transposon-like elements termed VL30. These VL30-related sequences were further found to be complementary to EGF-inducible poly(A)+RNAs and enhanced expression was detectable as early as 1 hr after EGF stimulation. In contrast, nine additional clones, including an AKR-type murine leukemia provirus DNA clone, contained no detectable VL30 sequence elements and were complementary to poly(A)+RNA species whose relative concentration was essentially constant in quiescent and EGF-stimulated cells. Therefore, VL30 sequence elements appear distinct in that they encompass members whose expression is specifically regulated in response to a defined peptide growth factor.
Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy (2017)

The underlying molecular mechanisms of autoimmune diseases are poorly understood. To unravel the autoimmune processes across diseases, comprehensive and unbiased analyses of proteins targets recognized by the adaptive immune system are needed. Here we present an approach starting from high-density peptide arrays to characterize autoantibody repertoires and to identify new autoantigens. A set of ten plasma and serum samples from subjects with multiple sclerosis, narcolepsy, and without any disease diagnosis were profiled on a peptide array representing the whole proteome, hosting 2.2 million 12-mer peptides with a six amino acid lateral shift. On the basis of the IgG reactivities found on these whole-proteome peptide microarrays, a set of 23 samples was then studied on a targeted array with 174 000 12-mer peptides of single amino acid lateral shift. Finally, verification of IgG reactivities was conducted with a larger sample set (n = 448) using the bead-based peptide microarrays. The presented workflow employed three different peptide microarray formats to discover and resolve the epitopes of human autoantibodies and revealed two potentially new autoantigens: MAP3K7 in multiple sclerosis and NRXN1 in narcolepsy. The presented strategy provides insights into antibody repertoire reactivity at a peptide level and may accelerate the discovery and validation of autoantigens in human diseases.
Spontaneous Formation of Macroscopic Chiral Domains in a Fluid Smectic Phase of Achiral Molecules (1997)

A smectic liquid-crystal phase made from achiral molecules with bent cores was found to have fluid layers that exhibit two spontaneous symmetry-breaking instabilities: polar molecular orientational ordering about the layer normal and molecular tilt. These instabilities combine to form a chiral layer structure with a handedness that depends on the sign of the tilt. The bulk states are either antiferroelectric-racemic, with the layer polar direction and handedness alternating in sign from layer to layer, or antiferroelectric-chiral, which is of uniform layer handedness. Both states exhibit an electric field-induced transition from antiferroelectric to ferroelectric.
Social and cultural issues in urban communities (2004)

Abstract To better understand the world of adult learners, we must remove ourselves from our ivory towers, classrooms, and offices and engage in the practice of adult education programs in urban settings.
The Choroid Plexus–Arachnoid Membrane–Cerebrospinal Fluid System (2003)

The choroid plexus traditionally has been considered the major, but not sole, component of the blood-CSF barrier (BCFB). Most analyses of the BCFB have been directed to the choroid plexuses, rather than to the arachnoid, because of the predominant function of the former in CSF secretion and homeostasis, The physiological literature on the choroid plexus (CP) is much more extensive than on the arachnoid membrane; consequently this review emphasizes methodologies employed to evaluate choroidal function.
Dietary modulation of the human gut microflora using prebiotics (1998)

The human colonic flora has both beneficial and pathogenic potentials with respect to host health. There is now much interest in manipulation of the microbiota composition in order to improve the potentially beneficial aspects. The prebiotic approach dictates that non-viable food components are specifically fermented in the colon by indigenous bacteria thought to be of positive value, e.g. bifidobacteria, lactobacilli. Any food ingredient that enters the large intestine is a candidate prebiotic. However, to be effective, selectivity of the fermentation is essential. Most current attention and success has been derived using non-digestible oligosaccharides. Types primarily being looked at include those which contain fructose, xylose, soya, galactose, glucose and mannose. In particular, fructose-containing oligosaccharides, which occur naturally in a variety of plants such as onion, asparagus, chicory, banana and artichoke, fulfil the prebiotic criteria. Various data have shown that fructo-oligosaccharides (FOS) are specifically fermented by bifidobacteria. During controlled feeding studies, ingestion of these prebiotics causes bifidobacteria to become numerically dominant in faeces. Recent studies have indicated that a FOS dose of 4 g/d is prebiotic. To exploit this concept more fully, there is a need for assessments of (a) improved determination of the gut microbiota composition and activity; (b) the use of molecular methodologies to assess accurately prebiotic identities and develop efficient bacterial probing strategies; (c) the prebiotic potential of raw and processed foods; and (d) the health consequences of dietary modulation.
A performance comparison of object and relational databases using the Sun Benchmark (1988)

A general concern about object-oriented systems has been whether or not they are able to meet the performance demands required to be useful for the development of significant production software systems. Attempts to evaluate this assertion have been hampered by a lack of meaningful performance benchmarks that compare database operations across different kinds of databases.
Diastereoselektive Alkylierung von 3‐Aminobutansäure in der 2‐Stellung (1988)

Diastereoselective Alkylation 3‐Aminobutanoic Acid in the 2‐Position The enantiomerically pure 3‐aminobutanoic acids ( R )‐ and ( S )‐ 6 are readily available by preparative HPLC separation of the two diastereoisomers 5 obtained from addition of ( S )‐phenethylamine to methyl crotonate and subsequent hydrogenolysis ( Scheme 2 ). ( S )‐Methyl 3‐(benzoylamino) butanoate (( S )‐ 3 ) is also available by enzymatic kinetic resolution with pig‐liver esterase. The N ‐benzyl‐ and N ‐ benzyloxycarbonyl derivatives rac 3 , 8 , and 9 of 3‐aminobutanoates are doubly deprotonated with LDA and alkylated or aminated in high selectivity (17 examples, relative topicity like ; see Tables 1 and 2 ). The configuration of three of the products is assigned ( Schemes 4 – 6 ), and in four cases, the free α‐substituted β‐amino acid is prepared by acidic hydrolysis (see Table 3 ). It is shown that the doubly lithiated β‐amino‐acid derivative is solubilized, and its reactivity may be strongly influenced by the presence of 3 equiv. of LiCl.
Global gene expression analysis of gastric cancer by oligonucleotide microarrays. (2002)

To gain molecular understanding of carcinogenesis, progression, and diversity of gastric cancer, 22 primary human advanced gastric cancer tissues and 8 noncancerous gastric tissues were analyzed by high-density oligonucleotide microarray in this study. Based on expression analysis of approximately 6800 genes, a two-way clustering algorithm successfully distinguished cancer tissues from noncancerous tissues. Subsequently, genes that were differentially expressed in cancer and noncancerous tissues were identified; 162 and 129 genes were highly expressed (P < 0.05) >2.5-fold in cancer tissues and noncancerous tissues, respectively. In cancer tissues, genes related to cell cycle, growth factor, cell motility, cell adhesion, and matrix remodeling were highly expressed. In noncancerous tissues, genes related to gastrointestinal-specific function and immune response were highly expressed. Furthermore, we identified several genes associated with lymph node metastasis including Oct-2 or histological types including Liver-Intestine Cadherin. These results provide not only a new molecular basis for understanding biological properties of gastric cancer, but also useful resources for future development of therapeutic targets and diagnostic markers for gastric cancer.
Interphase cytogenetic analysis of myxoid soft tissue tumors by fluorescence in situ hybridization and DNA flow cytometry using paraffin-embedded tissue (1997)

FISH analysis performed on paraffin embedded materials can be used to differentiate myxoid liposarcomas from other myxoid soft tissue tumors.