gebhart/patrepeval huggingface dataset:
Comparison of Different Biomaterials for Glaucoma Drainage Devices (1999)

Bleb inflammation may be related to the biomaterial being used as the endplate. Endplates should be handled carefully during surgery to avoid creating rough spots.
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples (2011)

Abstract Background Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. Methods We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. Results Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%. We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG -negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines. Conclusions Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as MSMB-NCOA4 , may play functional roles in cancer.
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs (2008)

Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by a complex of TRBP and Dicer. dgcr8Delta/Delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1Delta/Delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs. To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild-type, dgcr8Delta/Delta, and dicer1Delta/Delta mESCs. Several of the resulting DGCR8-independent, Dicer-dependent RNAs were noncanonical miRNAs. These derived from mirtrons and a newly identified subclass of miRNA precursors, which appears to be the endogenous counterpart of shRNAs. Our analyses also revealed endogenous siRNAs resulting from Dicer cleavage of long hairpins, the vast majority of which originated from one genomic locus with tandem, inverted short interspersed nuclear elements (SINEs). Our results extend the known diversity of mammalian small RNA-generating pathways and show that mammalian siRNAs exist in cell types other than oocytes.
Polymer Functionalization for Air-Stable n-Type Carbon Nanotube Field-Effect Transistors (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPolymer Functionalization for Air-Stable n-Type Carbon Nanotube Field-Effect TransistorsMoonsub Shim, Ali Javey, Nadine Wong Shi Kam, and Hongjie DaiView Author Information Department of Chemistry, Stanford University Stanford, California 94305 Cite this: J. Am. Chem. Soc. 2001, 123, 46, 11512–11513Publication Date (Web):October 30, 2001Publication History Received29 August 2001Published online30 October 2001Published inissue 1 November 2001https://pubs.acs.org/doi/10.1021/ja0169670https://doi.org/10.1021/ja0169670rapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views5881Altmetric-Citations527LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Carbon nanotubes,Doping,Electrical conductivity,Functionalization,Polyethylenimine Get e-Alerts
A pseudobiospecific hollow fiber cartridge for in vitro adsorption of autoantibodies from pathological serum (2000)

The affinity filtration technique using histidine as a pseudobiospecific ligand immobilized on poly(ethylene vinyl alcohol) hollow fiber membranes (His-PEVA) was used to remove autoantibodies from serum of patients with autoimmune disease. The effects of buffering solution conditions on the efficiency of autoantibodies removal was studied. The removal of anti-dsDNA, anti-SS-A/Ro, anti-Sm, anti-Sm/RNP and anti-cardiolipin autoantibodies present in the serum was investigated, comparing the efficiency between Hepes and Tris-HCl buffers. The results showed the potential of the membrane to remove all the autoantibodies studied. Anti SS-A/Ro was removed more efficiently in Tris-HCl buffer system rather than with the Hepes buffer.
Targeting the PD-1 pathway in patients with relapsed classic Hodgkin lymphoma following allogeneic stem cell transplant is safe and effective (2016)

Patients with classic Hodgkin lymphoma (cHL) that has relapsed after autologous or allogeneic transplant have limited treatment options and a poor prognosis. Immunotherapy with agents that target the PROGRAMMED DEATH 1 (PD-1) receptor have demonstrated clinical activity with durable responses in early-phase clinical trials in this patient population; however, patients with a history of allogeneic stem cell transplantation (SCT) were intentionally excluded from participation in those studies due to concerns for reactivation of graft-versus-host disease (GVHD). We describe the clinical course of two patients with advanced cHL and prior treatment with allogeneic stem cell transplantation (SCT) that were treated with the PD-1 inhibitor pembrolizumab. Both patients had no active graft-versus-host disease (GVHD) at the time initiation of therapy and were maintained on low-dose prednisone. Treatment with pembrolizumab was well tolerated and not associated with reactivation of GVHD. Both patients responded (1 partial, 1 complete) and remain on therapy as of November 30, 2015. This report indicates that immunotherapy targeting the PD-1 pathway can be safely administered to patients with cHL and a history of allogeneic SCT and produce tumor responses. Further studies in this patient population are needed.
Pricing WiFi at Starbucks (2003)

We consider the problem of designing mechanisms for online problems in which agents arrive over time and truthfully announce their arrival. These problems are becoming extremely common in a wide variety of problems involving wireless networking and webserving. We show how the standard results of mechanism design can be modified to apply to this setting, provide conditions under which efficient and incentive compatible mechanisms exist and analyze several important online models including wireless networks and web serving.
The Next Generation of Platinum Drugs: Targeted Pt(II) Agents, Nanoparticle Delivery, and Pt(IV) Prodrugs (2016)

The platinum drugs, cisplatin, carboplatin, and oxaliplatin, prevail in the treatment of cancer, but new platinum agents have been very slow to enter the clinic. Recently, however, there has been a surge of activity, based on a great deal of mechanistic information, aimed at developing nonclassical platinum complexes that operate via mechanisms of action distinct from those of the approved drugs. The use of nanodelivery devices has also grown, and many different strategies have been explored to incorporate platinum warheads into nanomedicine constructs. In this Review, we discuss these efforts to create the next generation of platinum anticancer drugs. The introduction provides the reader with a brief overview of the use, development, and mechanism of action of the approved platinum drugs to provide the context in which more recent research has flourished. We then describe approaches that explore nonclassical platinum(II) complexes with trans geometry or with a monofunctional coordination mode, polynuclear platinum(II) compounds, platinum(IV) prodrugs, dual-threat agents, and photoactivatable platinum(IV) complexes. Nanoparticles designed to deliver platinum(IV) complexes will also be discussed, including carbon nanotubes, carbon nanoparticles, gold nanoparticles, quantum dots, upconversion nanoparticles, and polymeric micelles. Additional nanoformulations, including supramolecular self-assembled structures, proteins, peptides, metal-organic frameworks, and coordination polymers, will then be described. Finally, the significant clinical progress made by nanoparticle formulations of platinum(II) agents will be reviewed. We anticipate that such a synthesis of disparate research efforts will not only help to generate new drug development ideas and strategies, but also will reflect our optimism that the next generation of approved platinum cancer drugs is about to arrive.
pH Effects on the Kinetics of the Cystine-Cyanide Reaction (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTpH Effects on the Kinetics of the Cystine-Cyanide ReactionOscar. Gawron, Sardar. Mahboob, and Joseph. FernandoCite this: J. Am. Chem. Soc. 1964, 86, 11, 2283–2286Publication Date (Print):June 1, 1964Publication History Published online1 May 2002Published inissue 1 June 1964https://pubs.acs.org/doi/10.1021/ja01065a036https://doi.org/10.1021/ja01065a036research-articleACS PublicationsRequest reuse permissionsArticle Views116Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Immunoregulatory role of B7-H1 in chronicity of inflammatory responses. (2006)

Pathogenesis of most chronic human diseases, including chronic infections, autoimmune diseases and cancers, often involves a persistent, unresolved inflammatory response. The molecular mechanisms that determine the conversion of an acute inflammatory response into a chronic process had puzzled researchers for many years. Recent studies reveal that B7-H1 (CD274, PD-L1), a newly identified co-stimulatory molecule, possesses dual functions of co-stimulation of naive T cells and inhibition of activated effector T cells. The aberrant cellular expression and deregulated function of B7-H1 have been reported during chronic viral and intracellular bacterial infection, as well as in many autoimmune diseases and cancers. Importantly, the deregulation of B7-H1's dual functions appears to be associated with a prolonged and incomplete immune response by luring naive T cells for activation and dampening activated effector T cells. Moreover, development of strategies targeting B7-H1 signals provides a new and promising approach to manipulate the devastating diseases associated with chronic inflammation. Thus, B7-H1 may play a critical immunoregulatory role in the chronicity of inflammatory responses.
Use of Recombinant Human Bone Morphogenetic Protein-2 to Enhance Tendon Healing in a Bone Tunnel (1999)

This study examines the hypothesis that recombinant human bone morphogenetic protein-2 can enhance bone ingrowth into a tendon graft placed into a bone tunnel. We transplanted the long digital extensor tendon into a drill hole in the proximal tibia in 65 adult mongrel dogs. We applied two different doses of the bone morphogenetic protein to the tendon-bone interface in one limb using an absorbable type I collagen sponge carrier and only the collagen sponge to the contralateral (control) limb. The healed tendon-bone attachment was evaluated at serial times between 3 days and 8 weeks using radiography, histologic examination, and biomechanical testing. At all time points, histologic and radiographic examination demonstrated more extensive bone formation around the tendon with closer apposition of new bone to the tendon in the protein-treated limb than in the paired control limb. Biomechanical testing demonstrated higher tendon pull-out strength in the protein-treated side at all time points, with a statistically significant difference between the low-dose-treated side and the control side at 2 weeks. The histologic and biomechanical data suggested superior healing at the lower protein dose. This study demonstrated that bone morphogenetic protein can accelerate the healing process when a tendon graft is transplanted into a bone tunnel.
Chemical‐Modification Studies on Rat Olfactory Mucosa using a Thiol‐Specific Reagent and Enzymatic Iodination (1983)

1. A rat olfactory preparation, suitable for biochemical studies in vitro on olfactory mechanisms, is described. 2. The effects of the impermeant chemical modification reagents mersalyl (a thiol reagent) and enzymatic iodination, on the amplitude of the electroolfactogram (EOG) responses elicited from rat olfactory mucosa by pulses of odorant vapours was studied using 12 odorants differing widely in odour quality and molecular structure: amyl acetate, carvone, decanal, butylamine, cineole, citronellol, cresol, diacetyl, dimethylethyl-pyrazine, naphthalene, octanethiol and valeric acid. 3. Both reagents irreversibly reduced the EOG amplitude to all odorants to an extent dependent on the reagent concentration. Two subpopulations of animal preparations could be distinguished on the basis of the extent to which they survived the iodination whereas mersalyl appeared to sample a single population of preparations. 4. Small but statistically significant differences were observed between the responses of each odorant with each reagent but no simple correlation between either the molecular structure or odour quality of the odorants and the reagent effect is apparent for the case of mersalyl. With iodination the responses from the three flexible-aliphatic-chain odorants were reduced to a greater extent than the other odorants, all of which had a dissimilar molecular structure. 5. The ability of three odorants, amyl acetate, carvone and decanal, to protect the receptors for the odorants against chemical modification was investigated. The protecting odorants were applied directly to the mucosa as a dilute solution in Ringer's medium. No specific odorant protection effects were observed. 6. The results are discussed in relation to a model of the olfactory mechanism involving relatively non-specific receptor proteins. Each receptor type is envisaged as interacting weakly with a number of odorants and each odorant interacts with a number of receptors.
The murine urokinase-type plasminogen activator gene (1987)

The murine urokinase-type plasminogen activator (uPA) gene has been isolated from a BALB/c liver DNA cosmid library and its nucleotide sequence established. The gene is organized into 11 exons comprising 34.7% of the 6710 base pair (bp) region spanning the interval between the presumed transcription initiation and polyadenylation sites. The transcription initiation site is flanked by common RNA polymerase II promoter elements, including a TATA box and a potential transcription factor Sp1 binding site. A large polypurine tract of the structure (AG)22(AGGG)16(AG)28 is located 79 bp upstream of the 5'-terminus. It was highly sensitive to the single-strand-specific nuclease S1, suggesting a non-B-DNA conformation of unknown significance. Consistent with the well-documented influence of adenosine cyclic 3',5'-phosphate (cAMP) on uPA gene expression, there is a dodecanucleotide homologous to proposed regulatory sequences identified in other cAMP-modulated genes. Comparison of the murine uPA gene to the previously described porcine and human uPA genes revealed an unusually high degree of evolutionary (interspecies) sequence conservation that was not limited to exons but included introns and flanking sequences as well.
Cytosolic PLA2 is required for CTL-mediated immunopathology of celiac disease via NKG2D and IL-15 (2009)

IL-15 and NKG2D promote autoimmunity and celiac disease by arming cytotoxic T lymphocytes (CTLs) to cause tissue destruction. However, the downstream signaling events underlying these functional properties remain unclear. Here, we identify cytosolic phospholipase A(2) (cPLA(2)) as a central molecule in NKG2D-mediated cytolysis in CTLs. Furthermore, we report that NKG2D induces, upon recognition of MIC(+) target cells, the release of arachidonic acid (AA) by CTLs to promote tissue inflammation in association with target killing. Interestingly, IL-15, which licenses NKG2D-mediated lymphokine killer activity in CTLs, cooperates with NKG2D to induce cPLA(2) activation and AA release. Finally, cPLA(2) activation in intraepithelial CTLs of celiac patients provides an in vivo pathophysiological dimension to cPLA(2) activation in CTLs. These results reveal an unrecognized link between NKG2D and tissue inflammation, which may underlie the emerging role of NKG2D in various immunopathological conditions and define new therapeutic targets.
The distinctive roles of five different ARC genes in the chloroplast division process in Arabidopsis (1999)

ARC (accumulation and replication of chloroplasts) genes control different aspects of the chloroplast division process in higher plants. In order to establish the hierarchy of the ARC genes in the chloroplast division process and to provide evidence for their specific roles, double mutants were constructed between arc11, arc6, arc5, arc3 and arc1 in all combinations and phenotypically analysed. arc11 is a new nuclear recessive mutant with 29 chloroplasts compared with 120 in wild type. All the phenotypes of the double mutants are unambiguous. ARC1 down-regulates proplastid division but is on a separate pathway from ARC3, ARC5, ARC6 and ARC11. ARC6 initiates both proplastid and chloroplast division. ARC3 controls the rate of chloroplast expansion and ARC11 the central positioning of the final division plane in chloroplast division. ARC5 facilitates separation of the two daughter chloroplasts. ARC5 maps to chromosome 3 and ARC11 and ARC6 map approximately 60 cM apart on chromosome 5.
Organ-specific autoimmune diseases induced in mice by elimination of T cell subset. I. Evidence for the active participation of T cells in natural self-tolerance; deficit of a T cell subset as a possible cause of autoimmune disease. (1985)

Organ-specific autoimmune diseases such as oophoritis, gastritis, thyroiditis, and orchitis were induced in female or male nude (nu/nu) mice by the transfer of nu/+spleen cells from which particular Lyt T cell subset(s) had been removed: nu/+spleen cells treated with anti-Lyt-1 plus complement (C) caused disease in recipient nude mice; anti-Lyt-2 plus C-treated spleen cells, in contrast, did not. The cells responsible for disease induction are believed to be Thy-1+, Lyt-1-, 2,3- (Thy-1, Lyt-1, 2,3), since spleen cells treated with mixed antisera, including anti-Lyt-1 and anti-Lyt-2, plus C, could induce the disease with almost the same incidence as anti-Lyt-1 plus C-treated cells (oophoritis 50%, gastritis 25%, thyroiditis 10-20%, and orchitis 40%). Cells treated with mixed antisera of anti-Thy-1, anti-Lyt-1, and anti-Lyt-2, plus C, could not induce autoimmune disease. Each induced autoimmune disease could be adoptively transferred to other nude mice via spleen cells, with resulting histological lesion of corresponding organs and development of specific circulating autoantibodies. Since anti-Thy-1 plus C treatment of donor spleen cells abrogated the capacity to transfer the disease, we conclude that T cells are required as effector cells, and that these may develop from Lyt-1-, 2,3- cells. Lyt-1+, 2,3- cells were demonstrated to have suppressive activity upon the development of the diseases; induction of autoimmunity was completely inhibited by the cotransfer of Lyt-1+, 2,3- cells with Lyt-1-, 2,3- cells. When anti-Lyt-2 plus C-treated cells (i.e., Lyt-1+, 2,3- and Lyt-1-, 2,3- cells) were mixed with anti-Lyt-1 and anti-Lyt-2 plus C-treated cells (i.e., Lyt-1-, 2,3- cells) in various ratios, then transferred to nude mice, the development of each autoimmune disease was clearly inhibited, even by small doses of Lyt-1+, 2,3- cells. The autoimmune disease we were able to induce was quite similar to human organ-specific autoimmune disease in terms of the spectrum of organs involved, histopathological features, and the development of autoantibodies to corresponding organ components (oocytes, parietal cells, thyroid colloid, including thyroglobulin, and sperm).(ABSTRACT TRUNCATED AT 400 WORDS)
A semi-automatic enzymic method for estimating urinary oxalate. (1980)

Abstract A two-enzyme method is presented for estimating urinary oxalate by continuous-flow analysis. Oxalate is decarboxylated, yielding formate, which is subsequently oxidized in the presence of NAD+, yielding NADH. The NADH, measured colorimetrically, is proportional to the amount of oxalate originally present in the sample. Urine is pretreated by precipitation of the oxalate and extraction of the precipitate in citrate buffer. A correction factor for the extraction efficiency is given by the recovery of [U-14C]oxalic acid added to aliquots of the 24-h urine specimen. The normal range obtained by this method was 0.20 to 0.52 mmol/24h (18 to 47 mg/24h) with a mean value of 0.37 mmol/24 h (33 mg/24h). The between-assay CV was 7.6% (n = 12), within-assay CV 3.2% (N = 25). Unlabeled oxalate (0.5 and 1.0 mol/L) added to 28 urine samples gave a mean analytical recovery of 95% (SD 10%).