gebhart/patrepeval huggingface dataset:
AlgR, a response regulator controlling mucoidy in Pseudomonas aeruginosa, binds to the FUS sites of the algD promoter located unusually far upstream from the mRNA start site (1991)

Strong transcriptional activation of algD, a key event in the overproduction of alginate and establishment of mucoidy in Pseudomonas aeruginosa, depends on the functional algR gene. The predicted gene product of algR shows homologies to response regulators from bacterial signal transduction systems. The algR gene was overexpressed in Escherichia coli, its product (AlgR) was purified by utilizing its apparent affinity for heparin, and its sequence was verified by partial amino acid sequence analysis. AlgR was found to interact directly with the algD promoter. Deletion mapping analysis, in conjunction with mobility shift DNA-binding assays, indicated the presence of three regions within the algD promoter capable of specifically binding AlgR. A relatively weak interaction was observed with the algD promoter fragment containing the region immediately upstream of the algD mRNA start site (-144 to +11). However, when fragments spanning regions located very far upstream from the algD mRNA initiation site (-533 and -332) were used, strong specific binding was observed. These regions were separated by a DNA segment not binding AlgR and spanning positions -332 to -144. DNase I footprinting analysis further established the presence of discrete AlgR binding sites overlapping with FUS, the far-upstream sites required for full induction of algD transcription and its environmental modulation. There were two distinct binding sites: RB1, spanning nucleotides -479 to -457, and RB2, spanning nucleotides -400 to -380. Both of these sequences shared a highly conserved core region, ACCGTTCGTC. These results established a direct interaction of AlgR with the algD promoter and revealed an arrangement of binding sites highly unusual for response regulators of the AlgR type.
Physico-chemical properties and specific activity of a purified allergen (codfish). (1975)

The major allergen (Allergen M) from codfish is an acidic protein, mol. wt. 15000 with 114 amino acid residues and only one sugar (glucose) residue. It is highly active in skin testing on codfish-allergic individuals, in passive transfer (PK) testing and in the radioallergosorbent test (RAST). The activity resists denaturation and incomplete tryptic hydrolysis. Two fragments (TM 1, mol. wt. 8500, and TM 2, mol. wt. 6500) are obtained from allergen M. The fragments are equally active and allergenically identical in biological tests, but somewhat less active than Allergen M itself. Smaller peptides obtained from TM 2 are inactive. The amino acid sequence of TM 2 is given as the first reported example of a full structural analysis of an active allergen. The information obtained in studies of this model allergen is compared with information published from other studies of allergens. Similarities and differences are pointed out.
A POSITIVE CONTACT BALL AND RING IMPLANT FOR USE AFTER ENUCLEATION (1947)

THIS IS a preliminary report on a new type of implant based on one year's use. This implant has a positive mechanical contact between the implant and the prosthesis, which provides a wide range and spontaneity of movement. The implant, in addition, eliminates sagging of the lower lid and minimizes sinking in of the upper lid. Previously described implants, with the exception of the combined implant and prosthesis recently described by Ruedemann,<sup>1</sup>have been totally enclosed within Tenon's capsule and the conjunctiva or, in the case of evisceration, within the sclera and conjunctiva. In these circumstances, the available conjunctiva left to permit the prosthesis to rotate in the fornices has been diminished from that in the natural eye by the area occupied by the cornea. In the implant to be described, the anterior face is exposed, and thus the fornices have not been diminished. The exposed face, with an
Rational Use of New and Existing Disease-Modifying Agents in Rheumatoid Arthritis (2001)

Because of radiographic evidence of progressive bone loss and the inability to eliminate synovial proliferation with methotrexate, it became apparent that therapy for rheumatoid arthritis needed further advancement. Methotrexate is not a remission-inducing drug and may have dose-limiting toxicity. In the past 2 years, three new disease-modifying antirheumatic drugs (DMARDs) have been approved: leflunomide, etanercept, and infliximab. Each of these agents has demonstrated efficacy compared with placebo in randomized, controlled studies. Because methotrexate had a dominant therapeutic role, the new drugs were also studied in combination with it. Other established DMARDs, such as sulfasalazine and hydroxychloroquine, have also demonstrated efficacy when used together with methotrexate. The results of these combination studies clearly demonstrate that clinical responses can be meaningfully improved when new and existing DMARDs are added to methotrexate. Although toxicity remains a serious concern when powerful immune modulators and antimetabolites are used in combination, relatively few serious adverse events have been reported during 2-year treatment periods. It has also become apparent that combinations of new DMARDs and methotrexate virtually halt radiographic progression over 2 years. The new agents are expensive, but annual costs must be weighed against the personal and societal expense of joint arthroplasty, hospitalizations, disability, and diminished quality of life that accompanies poorly controlled rheumatoid arthritis. The ultimate value of combination DMARD therapy with methotrexate will be determined by long-term data on safety, efficacy, and effects on radiographic deterioration of bone. Additional long-term observational data on the incidence of joint arthroplasty and disability will help to place the issue of societal costs in a better perspective. This will allow the value of aggressive treatment to be established with certainty.
A randomized phase II study to evaluate tacrolimus in combination with sirolimus or methotrexate after allogeneic hematopoietic cell transplantation (2012)

These data demonstrate that sirolimus/tacrolimus prevents grade II-IV acute graft-versus-host disease and moderate-severe chronic graft-versus-host disease more effectively than does methotrexate/tacrolimus, and supports regulatory T-cell reconstitution following allogeneic hematopoietic cell transplantation.
New Insights into Biliverdin Reductase Functions: Linking Heme Metabolism to Cell Signaling (2005)

Biliverdin reductase (BVR) functions in cell signaling through three distinct tracks: a dual-specificity kinase that functions in the insulin receptor/MAPK pathways (25, 29, 51); a bzip-type transcription factor for ATF-2/CREB and HO-1 regulation (1, 25); and a reductase that catalyzes the conversion of biliverdin to bilirubin (27). These, together with the protein's primary and secondary features, intimately link BVR to the entire spectrum of cell-signaling cascades.
8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors (2016)

We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site; incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 54j and 54k which demonstrate equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and, for 54k, inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay.
Hyperactive Antifreeze Protein from Fish Contains Multiple Ice-Binding Sites (2008)

Antifreeze proteins (AFPs) are produced to prevent freezing in many fish species that are exposed to icy seawater. There are a number of nonhomologous types of AFPs, diverse in both sequence and structure, which share the function of binding to ice and inhibiting its growth. We recently discovered a hyperactive AFP in the winter flounder and related species that is many-fold more active than other fish AFPs. Like the 3-4-kDa type I AFPs, it is alanine-rich and highly helical, but this 17-kDa protein is considerably larger and forms a dimer. We have sequenced the cDNA encoding this new AFP to gain insight into its structure and evolutionary relationship to the type I AFP family. The gene is clearly homologous to the righteye flounder type I AFP genes. Thus we have designated this protein "hyperactive type I AFP" (hyp-type I). The sequence of hyp-type I AFP supports a structural model in which two extended 195-amino acid alpha-helices form an amphipathic homodimer with a series of linked Ala- and Thr-rich patches on the surface of the dimer, each of which resembles ice-binding sites of type I AFPs. The superior activity of hyp-type I AFP may derive from the large combined surface area of the ice-binding sites, recognition of multiple planes of ice, and protection of the basal plane from ice growth.
Identification and characterization of a novel RPGR isoform in human retina (2007)

Retinitis pigmentosa (RP) constitutes a major cause of blindness and the Retinitis Pigmentosa GTPase Regulator (RPGR) gene accounts for up to 80% of all X-linked RP cases. A novel isoform of RPGR, expressed in the human retina, was identified and characterized. It truncates the Regulator of Chromosome Condensation 1 (RCC1) homologous protein domain (RCC1h) of RPGR and mediates the formation of isoform-specific complexes with the RPGR-interacting protein 1 (RPGRIP1). Immunohistochemistry localized the novel RPGR isoform predominantly to inner segments of cone photoreceptors, where it colocalizes with RPGRIP1 in the human retina. In a patient with a mild RP phenotype, we identified a nucleotide substitution in a splicing regulator, which leads to 3.5 times higher levels of the transcripts coding for the novel RPGR isoform. The nucleotide substitution affects regulated alternative splicing of the novel RPGR isoform and suggests a tight adjustment of splicing as a prerequisite for proper function of photoreceptors.
The secretory proprotein convertase neural apoptosis-regulated convertase 1 (NARC-1): Liver regeneration and neuronal differentiation (2003)

Seven secretory mammalian kexin-like subtilases have been identified that cleave a variety of precursor proteins at monobasic and dibasic residues. The recently characterized pyrolysin-like subtilase SKI-1 cleaves proproteins at nonbasic residues. In this work we describe the properties of a proteinase K-like subtilase, neural apoptosis-regulated convertase 1 (NARC-1), representing the ninth member of the secretory subtilase family. Biosynthetic and microsequencing analyses of WT and mutant enzyme revealed that human and mouse pro-NARC-1 are autocatalytically and intramolecularly processed into NARC-1 at the (Y,I)VV(V,L)(L,M) downward arrow motif, a site that is representative of its enzymic specificity. In vitro peptide processing studies andor Ala substitutions of the P1-P5 sites suggested that hydrophobicaliphatic residues are more critical at P1, P3, and P5 than at P2 or P4. NARC-1 expression is highest in neuroepithelioma SK-N-MCIXC, hepatic BRL-3A, and in colon carcinoma LoVo-C5 cell lines. In situ hybridization and Northern blot analyses of NARC-1 expression during development in the adult and after partial hepatectomy revealed that it is expressed in cells that have the capacity to proliferate and differentiate. These include hepatocytes, kidney mesenchymal cells, intestinal ileum, and colon epithelia as well as embryonic brain telencephalon neurons. Accordingly, transfection of NARC-1 in primary cultures of embryonic day 13.5 telencephalon cells led to enhanced recruitment of undifferentiated neural progenitor cells into the neuronal lineage, suggesting that NARC-1 is implicated in the differentiation of cortical neurons.
Metalloprotease inhibitors as anti-inflammatory agents: an evolving target? (2004)

The metalloproteases (MMPs) are a family of enzymes that are important for tissue remodeling. These enzymes have been implicated in a number of pathologies, including cancer, arthritis, atherosclerosis and chronic obstructive pulmonary disease. Thus, inhibitors of MMPs may have utility in the therapy of inflammatory diseases, particularly in arthritis where current therapies do not halt the progression of the disease. Many compounds have been identified as inhibitors of MMPs, and some have progressed to the clinic. However, no compound developed as an MMP inhibitor has been licensed for clinical use thus far. This review discusses this therapeutic area and compares inhibitors of MMPs with other novel therapeutic approaches in the treatment of inflammatory disease. Inhibitors of MMPs may find utility in disorders not currently targeted, but where MMPs are involved in the pathology.
Mechanism of GTP: Can all of the available data be accommodated? (1993)

Abstract Group transfer polymerization (GTP) a of acrylic monomers is a living system mediated by a trialkylsilyl capped growing chain end. The fact that it operates at temperatures as high as 100° C differentiates GTP from living anionic polymerization, which at best operates at 25° C for hindered methacrylates. To accommodate all of the mechanistic data available it appears that at least two mechanistic pathways are required: an associative process for mild nucleophilic catalysts and a dissociative process for strong nucleophilic catalysts.
Long-term remission durability and functional status of patients treated for diffuse histiocytic lymphoma with the CHOP regimen. (1984)

Thirty-eight (51%) of 75 patients treated with CHOP for diffuse histiocytic lymphoma achieved complete remission. Twenty-three of the complete responders are currently alive in complete remission 24-78 months (median, 38 months) after discontinuing therapy. Eleven patients died from recurrent lymphoma and four patients died in complete remission from other causes. Evaluation of the 23 patients alive in complete remission found them mostly well and without serious sequelae to therapy. Comparison with 20 patients who were in the same age range, were disease free after surgery, and had no other therapy for colon cancer revealed only an increased frequency of sexual dysfunction in the chemotherapy-treated lymphoma patients. Sixty-one percent of patients who achieved complete remission with the CHOP regimen are long-term disease-free survivors and are generally well except for an apparently high frequency of sexual dysfunction.
The Secure HyperText Transfer Protocol (1999)

This memo describes a syntax for securing messages sent using the Hypertext Transfer Protocol (HTTP), which forms the basis for the World Wide Web. Secure HTTP (S-HTTP) provides independently applicable security services for transaction confidentiality, authenticity/integrity and non-repudiability of origin.
Technology and applications of edible protective films (1995)

Abstract Edible films or coatings have provided an interesting and often essential complementary means for controlling the quality and stability of numerous food products. There are many potential uses of edible films (e.g. wrapping various products, individual protection of dried fruits, meat and fish, control of internal moisture transfer in pizzas, pies, etc.) which are based on the films properties (e.g. organoleptic, mechanical, gas and solute barrier). Polysaccharide (cellulose, starch, dextrin, vegetable and other gums, etc) and protein (gelatin, gluten, casein, etc) based films have suitable mechanical and organoleptic properties, while wax (beeswax, carnauba wax, etc) and lipid or lipid derivative films have enhanced water vapour barrier properties. The film‐forming technology, solvent characteristics, plasticizing agents, temperature effects, solvent evaporation rate, coating operation and usage conditions of the film (relative humidity, temperature) can also substantially modify the ultimate properties of the film.
Clinical variables which serve as predictors of cancer-specific survival among patients treated with radical cystectomy for transitional cell carcinoma of the bladder and prostate (1994)

Although clinical T classification and tumor grade remain the best predictors of survival in patients with transitional cell carcinoma of the bladder or prostate, clinical variables such as age, preoperative creatinine and hemoglobin levels, a history of nephroureterectomy or pelvic irradiation, and irritative voiding symptoms at presentation may provide additional prognostic information independent of tumor grade and stage.
A gel delivery system for coccidiosis vaccine: uniformity of distribution of oocysts. (2000)

A patented gel delivery system being used to deliver coccidiosis vaccine to poultry hatchlings is assessed. For effective vaccination, the coccidial oocysts must be uniformly suspended before exposure to birds. The uniformity of distribution within the gel was evaluated by incorporating a culture of chicken gut flora into gel sausages, placing sections of the sausage on culture plates, determining the appearance and distribution of bacterial colonies on culture plates after incubation, and verifying by cell counts. The uniformity of distribution of similarly prepared coccidial oocysts was verified by infecting birds with 40,000 Eimeria tenella oocysts delivered via the gel. Gel-inoculated birds were compared with control birds inoculated PO with 40,000 oocysts suspended in water by using cecal lesion scores. Both the appearance and colony counts of chicken gut flora from the gel were uniform. The standard deviation in the lesion scores for the gel-inoculated group and the water-inoculated groups were 0.51 and 0.69, respectively. The results indicate that a gel delivery system can provide uniform distribution of live organisms and vaccine agents to birds.
Fast hierarchical intra angular mode selection for high efficiency video coding (2014)

In this work, we address the complexity of the most time consuming module of High Efficiency Video Coding (HEVC) Intra-encoding, i.e. the Intra prediction generation. We reduce the computational complexity by estimating the candidates list (most probable Intra prediction modes), using content- and priority-driven gradient detection and hierarchically gathering the results of previous computations. This complexity reduction scheme is adaptive and can be controlled, depending upon the requirements, e.g. frame rate and video quality. On average, our scheme is capable of delivering 44% more time savings than the state-of-the-art scheme for fast Intra mode estimation.
Real-time vector APC speech coding at 4800 bps with adaptive postfiltering (2005)

An improved Vector APC (VAPC) speech coder at 4800 bps produces speech with very good communications quality while maintaining a complexity low enough to allow a real-time implementation with at most two commercially available DSP chips. The VAPC algorithm combines APC with vector quantization and incorporates analysis-by-synthesis, perceptual noise weighting, and adaptive postfiltering. A novel adaptive postfiltering technique helps to achieve an essentially inaudible level of coding noise. Real-time software has been developed for an implementation using the AT&T DSP32 floating-point processor chip. The overall complexity of the implemented VAPC system is about 3 million multiply-adds/second of computation and 6 kwords of memory.
p21 loss compromises the relative quiescence of forebrain stem cell proliferation leading to exhaustion of their proliferation capacity (2005)

Adult stem cells in various tissues are relatively quiescent. The cell cycle inhibitor p21cip1/waf1 (p21) has been shown to be important for maintaining hematopoietic stem cell quiescence and self-renewal. We examined the role of p21 in the regulation of adult mammalian forebrain neural stem cells (NSCs). We found that p21-/- mice between post-natal age 60-240 d have more NSCs than wild-type (+/+) controls due to higher proliferation rates of p21-/- NSCs. Thereafter, NSCs in p21-/- mice decline and are reduced in number at 16 mo relative to p21+/+ mice. Similarly, both p21-/- and p21+/+ NSCs display self-renewal in vitro; however, p21-/- NSCs display limited in vitro self-renewal (surviving a few passages, then exhausting). Thus, p21 contributes to adult NSC relative quiescence, which we propose is necessary for the life-long maintenance of NSC self-renewal because NSCs may be limited to a finite number of divisions.
Complexation of thorium(IV) with desmethyldesferrithiocin (2000)

The complexation of Th(IV) with desmethyldesferrithiocin (H 2 DMDFT), a derivative of the siderophore desferrithiocin (H 2 DFT), was studied by potentiometry, spectrophotometry and NMR. Three protonation constants of the ligand were determined by potentiometric titrations and 1 H-NMR and assigned to the phenolate group, the nitrogen at the hydroxypyridine ring, and the carboxylate group. The formation constant of the 1:2 complex, Th(DMDFT) 2 , was determined by absorption spectrophotometry with oxalate as a competing ligand. A tridentate complex with Th(IV) involving the phenolate oxygen, the thiazoline nitrogen and the carboxylate group of H 2 DMDFT was proposed.
Effects of simvastain combined with omega-3 fatty acids on high sensitive C-reactive protein, lipidemia, and fibrinolysis in patients with mixed dyslipidemia. (2004)

In CHD and CHD risk equivalent patients with mixed dyslipidemia, dyslipidemia's therapeutic effect using simvastatin and omega-3 fatty acids may result from not only the combination of lipid adjustment, but also enhancement of their own nonlipid influences.
Fluorine Substituted Conjugated Polymer of Medium Band Gap Yields 7% Efficiency in Polymer−Fullerene Solar Cells (2011)

Recent research advances on conjugated polymers for photovoltaic devices have focused on creating low band gap materials, but a suitable band gap is only one of many performance criteria required for a successful conjugated polymer. This work focuses on the design of two medium band gap (~2.0 eV) copolymers for use in photovoltaic cells which are designed to possess a high hole mobility and low highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels. The resulting fluorinated polymer PBnDT-FTAZ exhibits efficiencies above 7% when blended with [6,6]-phenyl C(61)-butyric acid methyl ester in a typical bulk heterojunction, and efficiencies above 6% are still maintained at an active layer thicknesses of 1 μm. PBnDT-FTAZ outperforms poly(3-hexylthiophene), the current medium band gap polymer of choice, and thus is a viable candidate for use in highly efficient tandem cells. PBnDT-FTAZ also highlights other performance criteria which contribute to high photovoltaic efficiency, besides a low band gap.