gebhart/patrepeval huggingface dataset:
Overview (2015)

Recounts South Asia’s struggles with urbanization, as population growth has occurred fastest on peripheries outside official administrative boundaries. Congestion places strains on land, housing, infrastructure, basic services, and the environment. Most urban local governments in South Asia suffer from unclear institutional roles and limited functional and revenue assignments. By fostering messy and hidden urbanization, growth forces also constrain the potential of agglomeration economies to achieve prosperity. Although progress since 2000 has been impressive, the majority of South Asia’s cities remain characterized by high levels of poverty, bad housing conditions, and generally poor livability. Improvements in urban governance and finance, in empowerment, and in accountability systems, hold the keys to meeting these challenges. Three interrelated areas for policy action may address congestion and facilitate the further leveraging of urbanization for prosperity and livability: connectivity and planning for market flows, land management and affordable housing to replace slums, and resilience to disaster and the effects of climate change by identifying potential hazards and developing catastrophe insurance products.
Glide:  A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy (2004)

Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 A in nearly half of the cases and are greater than 2 A in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.
Antifungal Susceptibility ofCandidaBiofilms: Unique Efficacy of Amphotericin B Lipid Formulations and Echinocandins (2002)

Biofilms, likely the predominant mode of device-related microbial infection, exhibit resistance to antimicrobial agents. Evidence suggests that Candida biofilms have dramatically reduced susceptibility to antifungal drugs. We examined antifungal susceptibilities of Candida albicans and Candida parapsilosis biofilms grown on a bioprosthetic model. In addition to conventional agents, we determined if new antifungal agents (triazoles, amphotericin B lipid formulations, and echinocandins) have activities against Candida biofilms. We also explored effects of preincubation of C. albicans cells with subinhibitory concentrations (sub-MICs) of drugs to see if they could modify subsequent biofilm formation. Finally, we used confocal scanning laser microscopy (CSLM) to image planktonic- and biofilm-exposed blastospores to examine drug effects on cell structure. Candida biofilms were formed on silicone elastomer and quantified by tetrazolium and dry weight (DW) assays. Susceptibility testing of fluconazole, nystatin, chlorhexidine, terbenafine, amphotericin B (AMB), and the triazoles voriconazole (VRC) and ravuconazole revealed resistance in all Candida isolates examined when grown as biofilms, compared to planktonic forms. In contrast, lipid formulations of AMB (liposomal AMB and AMB lipid complex [ABLC]) and echinocandins (caspofungin [Casp] and micafungin) showed activity against Candida biofilms. Preincubation of C. albicans cells with sub-MIC levels of antifungals decreased the ability of cells to subsequently form biofilm (measured by DW; P < 0.0005). CSLM analysis of planktonic and biofilm-associated blastospores showed treatment with VRC, Casp, and ABLC resulted in morphological alterations, which differed with each agent. In conclusion, our data show that Candida biofilms show unique susceptibilities to echinocandins and AMB lipid formulations.
Analysis of cellular responses to free radicals: focus on exercise and skeletal muscle (1999)

Muscular exercise results in an increased production of radicals and other forms of reactive oxygen species (ROS). Recent evidence suggests that radicals and other ROS are an underlying aetiology in exercise-induced disturbances in muscle redox status. These exercise-induced redox disturbances in skeletal muscle are postulated to contribute to both muscle fatigue and/or exercise-induced muscle injury. To defend against ROS, muscle cells contain complex cellular defence mechanisms to reduce the risk of oxidative injury. Two major classes (enzymic and non-enzymic) of endogenous protective mechanisms work together to reduce the harmful effects of oxidants in the cell. Primary antioxidant enzymes include superoxide dismutase (EC 1.15.1.1; SOD), GSH peroxidase (EC 1.11.1.9; GPX), and catalase (EC 1.11.1.6); these enzymes are responsible for removing superoxide radicals, H2O2 and organic hydroperoxides, and H2O2 respectively. Important non-enzymic antioxidants include vitamins E and C, beta-carotene, GSH and ubiquinones. Vitamin E, beta-carotene and ubiquinone are located in lipid regions of the cell, whereas GSH and vitamin C are in aqueous compartments of the cell. Regular endurance training promotes an increase in both total SOD and GPX activity in actively-recruited skeletal muscles. High-intensity exercise training has been shown to be generally superior to low-intensity exercise in the upregulation of muscle SOD and GPX activities. Also, training-induced upregulation of antioxidant enzymes is limited to highly-oxidative skeletal muscles. The effects of endurance training on non-enzymic antioxidants remain a relatively uninvestigated area.
Homologous Transplantation of Neural Stem Cells to the Injured Spinal Cord of Mice (2005)

In the traumatically injured mice SC, NSC grafting improves motor recovery. Although differentiation of engrafted NSCs is restricted exclusively toward the astrocytic phenotype, the NSC-derived astrocytes show features that are typical of the early phase after SC injury when the glial scar is still permissive to regenerating axons. The immature phenotype of the NSC-derived astrocytes suggests that these cells might support neurite outgrowth by the host neurons. Thus, modifying the glial scar with NSCs might enhance axonal regeneration in the injured area. The use of genetically engineered NSCs that express trophic factors appears to be an attractive tool in SC transplantation research.
Early and Sustained Dual Oral Antiplatelet Therapy Following Percutaneous Coronary Intervention (2002)

Following PCI, long-term (1-year) clopidogrel therapy significantly reduced the risk of adverse ischemic events. A loading dose of clopidogrel given at least 3 hours before the procedure did not reduce events at 28 days, but subgroup analyses suggest that longer intervals between the loading dose and PCI may reduce events.
Sex-Sorted Sperm and Fertility: An Alternative View (2006)

Although contemporary methods of physically separating X from Y chromosome-bearing spermatozoa are now very efficient, overall fertility rates following the use of sex-sorted sperm are not as impressive, in spite of many attempts to improve them. At the same time, there are suggestions from evolutionary biology, and from sex allocation theory in particular, that there may need to be a modification to the chance theory of sex determination in mammals. This is because it now appears that the mammalian female could have some influence on the sex of her offspring, and furthermore, that this influence could be preconceptual. If so, this could go some way towards accounting for the putative inefficiencies in fertilization following insemination with sex-sorted sperm.
Identification of a conserved lipopolysaccharide-plus-interleukin-4-responsive element located at the promoter of germ line epsilon transcripts. (1991)

Treatment of splenic B lymphocytes and certain B-lineage cell lines with the mitogen lipopolysaccharide (LPS) and the lymphokine interleukin-4 (IL-4) induces expression of germ line immunoglobulin C epsilon transcripts and class switching to the C epsilon gene. We show that LPS-plus-IL-4 induction of germ line epsilon transcripts (termed I epsilon transcripts) occurs at the transcriptional level in an Abelson murine leukemia virus-transformed pre-B-cell line. A 1.1-kb region of DNA surrounding the I epsilon promoter endows inducible transcription to a heterologous reporter gene stably transfected into these cells; such inducible expression depends on combined treatment with LPS and IL-4. Analyses of constructs transiently introduced into a B-cell lymphoma line demonstrated that LPS-plus-IL-4-inducible expression can be conferred by a 179-bp segment of DNA spanning the I epsilon transcriptional initiation site. Mutational analyses demonstrated that this expression depended on DNA sequences within a conserved region directly upstream from the I epsilon transcriptional initiation region. One nuclear protein that is constitutively expressed in normal B cells binds to the downstream end of the conserved sequence; its binding specificity correlates with the functional effect of several mutations. Two additional proteins, which are induced by IL-4 treatment of splenic B cells, bind to the transcription initiation sites of I epsilon. These proteins are indistinguishable in binding assays from proteins previously shown to bind an enhancer region of the class II major histocompatibility complex gene A alpha.
Advances in Corticosteroid Therapy for Ocular Inflammation: Loteprednol Etabonate (2012)

Topical corticosteroids are effective in reducing anterior segment inflammation but are associated with adverse drug reactions (ADRs) including elevation of intraocular pressure (IOP) and cataract formation. Retrometabolic drug design has advanced the development of new corticosteroids with improved therapeutic indices. Engineered from prednisolone, loteprednol etabonate (LE) has a 17α-chloromethyl ester, in lieu of a ketone group, and a 17β-etabonate group. LE is highly lipophilic and binds with high affinity to the glucocorticoid receptor; any unbound LE is metabolized to inactive metabolites. LE has been studied in several anterior segment inflammatory conditions (giant papillary conjunctivitis, allergic conjunctivitis, anterior uveitis, and keratoconjunctivitis sicca), and in postoperative ocular inflammation and pain. Combined with tobramycin, it is effective in blepharokeratoconjunctivitis. Elevations in IOP are infrequent with LE, and the absence of a C-20 ketone precludes formation of Schiff base intermediates with lens proteins, a common first step implicated in cataract formation with ketone steroids.
Comparison of azathioprine, methotrexate, and the combination of the two in the treatment of rheumatoid arthritis (1995)

This study establishes that the combination of MTX and AZA in the dosages utilized is not associated with more toxicity than treatment with single agents; however, enhanced efficacy is also not seen. There is a trend toward decreased radiologic progression in patients treated with MTX.
Ultrashort Light Pulse Code-Division Multiple Access Communication Systems (1990)

We analyze a new technique for encoding and decoding of coherent ultrashort light pulses. In particular, we discuss the temporal and statistical behavior of pseudonoise bursts generated by spectral phase coding of ultrashort optical pulses. Our analysis is motivated by recent experiments that demonstrate high resolution spectral phase coding of picosecond and femtosecond pulses and suggest the possibil- ity of ultrahigh speed code-division multiple access (CDMA) commu- nications using this technique. We trace the evolution of coherent ul- trashort pulses into low intensity pseudonoise bursts as a function of the degree of phase coding. For random coding we find that the en- coded pulse obeys Gaussian statistics and that the intensity probability distribution function is a negative exponential. These results are uti- lized to analyze the performance of a proposed CDMA optical com- munications system based upon encoding and decoding of ultrashort light pulses. We derive the bit error rate (BER) as a function of data rate, number of users, and receiver threshold; and we discuss the per- formance characteristics for a variety of system parameters. We find that performance improves dramatically with increasing code length. Lltrashort light pulse CDMA could provide tens to hundreds of users with asynchronously multiplexed, random access to a common optical channel.
Dynamic O-GlcNAcylation of the Small Heat Shock Protein αB-Crystallin (1996)

alphaB-Crystallin, originally described as a structural lens protein, is now known to be a member of the small heat shock protein family and is expressed in a number of nonlens tissues. This highly conserved 20 kDa protein aggregates with homologous proteins, including alphaA-crystallin and the small heat shock protein HSP28, to form large heteromeric complexes. Recently, Roquemore et al. (1992) have established that both phosphorylated and unphosphorylated forms of lens alphaB-crystallin are modified with O-linked N-acetylglucosamine, a dynamic posttranslational modification abundant on nuclear and cytoplasmic proteins. In this paper, we have identified the major site of O-GlcNAcylation on lens alphaB as Thr 170. We have further shown that this modification is not restricted to lens alphaB-crystallin but occurs on alphaB isolated from rat heart tissue and human astroglioma cells. Two-dimensional electrophoresis of rat heart alphaB-crystallin revealed two O-GlcNAcylated forms with mobilities corresponding to the unphosphorylated form (alphaB2) and an unidentified, slightly more acidic form. Phosphorylated alphaB-crystallin (alphaB1) was not detected in the rat heart preparation. The major O-GlcNAcylation site on alphaB-crystallins from rat heart also appears to be at Thr 170. Metabolic pulse-chase labeling studies of U373-MG astroglioma cells indicated that turnover of the carbohydrate on alphaB-crystallin is not static but proceeds many-fold more rapidly than turnover of the protein backbone itself, consistent with a regulatory role for O-GlcNAc on this small heat shock protein.
Improved purification of hematopoietic stem cells based on their elevated aldehyde dehydrogenase activity (2007)

Elevated ALDH activity is a broadly inclusive property of primitive human cord blood cells that, in combination with other markers, allows easy isolation of the stem cell fraction at unprecedented purities.
Syk Mutation in Jurkat E6-derived Clones Results in Lack of p72syk Expression (1995)

The human leukemic Jurkat cell line is commonly used as a model cellular system to study T lymphocyte signal transduction. Various clonal derivatives of Jurkat T cells exist which display different characteristics with regard to responses to external stimuli. Among these, the E6-1 clone of Jurkat T cells has been used as a parental line from which numerous important somatic mutant clones have been generated. During the course of experiments examining signals initiated by the T cell antigen receptor in an E6-1-derived Jurkat cell clone J.CaM1, we observed that the 72-kilodalton Syk protein tyrosine kinase previously found in other Jurkat cells was not detected. Upon further analysis it was determined that Syk transcripts from the J.CaM1 cells as well as the parental E6-1 cells contain a single guanine nucleotide insertion at position 92. This nucleotide insertion results in a shift in the Syk open reading frame leading to alternate codon usage as well as the generation of a termination codon at position 109. Thus, Syk transcripts in E6-1 cells and E6-1-derived clones are predicted to be capable of encoding only the first 33 amino acids of the 630-amino acid wild type Syk. These findings are incompatible with a recently proposed model of T cell antigen receptor signal transduction based, in part, on experiments conducted using E6-1-derived cells, suggesting that Syk might play a role upstream of Lck and Zap70.
Unbounded Transactional Memory (2005)

Hardware transactional memory should support unbounded transactions: transactions of arbitrary size and duration. We describe a hardware implementation of unbounded transactional memory, called UTM, which exploits the common case for performance without sacrificing correctness on transactions whose footprint can be nearly as large as virtual memory. We performed a cycle-accurate simulation of a simplified architecture, called LTM. LTM is based on UTM but is easier to implement, because it does not change the memory subsystem outside of the processor. LTM allows nearly unbounded transactions, whose footprint is limited only by physical memory size and whose duration by the length of a timeslice. We assess UTM and LTM through microbenchmarking and by automatically converting the SPECjvm98 Java benchmarks and the Linux 2.4.19 kernel to use transactions instead of locks. We use both cycle-accurate simulation and instrumentation to understand benchmark behavior. Our studies show that the common case is small transactions that commit, even when contention is high, but that some applications contain very large transactions. For example, although 99.9% of transactions in the Linux study touch 54 cache lines or fewer, some transactions touch over 8000 cache lines. Our studies also indicate that hardware support is required, because some applications spend over half their time in critical regions. Finally, they suggest that hardware support for transactions can make Java programs run faster than when run using locks and can increase the concurrency of the Linux kernel by as much as a factor of 4 with no additional programming work.
Bulk superconductivity at 91 K in single-phase oxygen-deficient perovskiteBa2YCu3O9−δ (1987)

We have prepared and identified as a single phase the high-temperature superconducting compound in the chemical system Y-Ba-Cu-O, an orthorhombic, distorted oxygen-deficient perovskite of stoichiometry ${\mathrm{Ba}}_{2}$${\mathrm{YCu}}_{3}$${\mathrm{O}}_{9\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\delta}}}$ (\ensuremath{\delta}\ensuremath{\simeq}2.1). Samples exhibit zero resistance at 91 K, with a transition width of 1.5 K. The Meissner effect attains a value of 76% of the independently measured diamagnetic susceptibility. We estimate parameters that characterize this superconductor, e.g., \ensuremath{\gamma}\ensuremath{\simeq}3--5 mJ (mole Cu${)}^{\mathrm{\ensuremath{-}}1}$ ${\mathrm{K}}^{\mathrm{\ensuremath{-}}2}$. The critical current density at 77 K and H=0 exceeds 1100 A/${\mathrm{cm}}^{2}$.
Thymopentin loaded Microsphere Preparation by w/o/w Emulsion Technique: In Vitro/ex Vivo Evaluation (1997)

Poly-D,L-lactide (PDLLA) and polylactide-co-glycolide (PLGA) microspheres containing thymopentin have been prepared by a water-in-oil-in-water-emulsion/solvent evaporation technique. The goal is to stabilize the active compound thymopentin, and to prolong its therapeutic activity, by embedding the drug in a polymeric matrix. The microspheres obtained have been characterized for their morphology and drug content. In-vitro dissolution tests have been performed on the microspheres. Results show that the type of polymer employed (PDLLA or PLGA) does not seem to affect microsphere morphology, while in-vitro dissolution profiles are greatly influenced by the composition of polymer matrix. Ex-vivo evaluation of PLGA microspheres performed on mouse thymocites shows that biological activity of Thymopentin is maintained after loading into PLGA microspheres.
Role of Monocytes in the Up‐Regulation of the Early Activation Marker CD69 on B and T Murine Lymphocytes Induced by Microbial Mitogens (1996)

CD69 is an early marker of lymphoid cell activation. The authors report on an up-regulation of CD69 in splenic B and T cells of C57Bl/6 mice after administration of lipopolysaccharide (LPS) or microbial immunosuppressive/mitogenic (ISM) proteins produced by C. albicans (p43) and African Swine Fever Virus (p36). This up-regulation of CD69 was observed 6 and 24 h after mitogenic treatments. The same pattern of increased CD69 expression was observed in the lymph nodes of mice treated with p43 or LPS, whereas p36 treatment failed to induce increased CD69 expression in this organ. Intracellular calcium mobilization was induced in splenic B and T lymphocytes after incubation of total spleen cells with LPS, p43 or p36. This increase was higher in B than in T cells. Increased calcium mobilization was also seen in lymph node B cells after incubation with p43 or p36 and in lymph node T cells after p43 stimulation. Up-regulation of CD69 expression on B and T cells was also observed after in vitro stimulation of spleen cells with the three mitogens used. Similar results were obtained with culture supernatants of macrophage/monocyte (M phi) cells activated with LPS (LPS/M phi CS). Stimulation of M phi cells with LPS or with the ISM proteins is demonstrated by the increased production of nitrites by these cells. The increased in vitro expression of CD69 was, however, not abolished by monoclonal antibodies to M phi cytokines such as IL-6, IL-10 or TNF alpha. No increased expression of CD69 was found in vitro on purified B or T cells, even when mixed upon stimulation with p43, p36, LPS or with LPS/M phi CS. However, an increase in the expression of CD69 was observed on B cells co-cultured with M phi cells after treatment with LPS or p36. All three mitogens failed to induce increased CD69 expression on cultured T cells mixed with M phi cells.
Stable linker peptides for a cellulose-binding domain–lipase fusion protein expressed in Pichia pastoris (2001)

Fusion proteins composed of a cellulose-binding domain from Neocallimastix patriciarum cellulase A and Candida antarctica lipase B were constructed using different linker peptides. The aim was to create proteolytically stable linkers that were able to join the functional modules without disrupting their function. Six fusion variants containing linkers of 4-44 residues were expressed in Pichia pastoris and analysed. Three variants were found to be stable throughout 7-day cultivations. The cellulose-binding capacities of fusion proteins containing short linkers were slightly lower compared with those containing long linkers. The lipase-specific activities of all variants, in solution or immobilized on to cellulose, were equal to that of the wild-type lipase.
Function Generation With Finitely Separated Precision Points Using Geometric Constraint Programming (2006)

This paper extends geometric constraint programming (GCP) to function generation problems involving large numbers of finitely separated precision points and complex mechanisms. In parametric design software, GCP uses the sketching mode to graphically impose geometric constraints in kinematic diagrams and the numerical solvers to solve the relevant nonlinear equations without the user explicitly formulating them. For function generation, the same approach can be applied to any mechanism, requiring no unique algorithms. Implementation is straightforward, so the designer can quickly generate solutions for a large number of precision points and/or with complex mechanisms to accurately match the function. Examples of function generation with a four-bar linkage, a Stephenson III six-bar linkage, and a seven-bar linkage with a mobility of two are presented.