gebhart/patrepeval huggingface dataset:
How Important is Global Structure for Characters? (2012)

This paper studies the importance of the features that represent the global structure of character strokes to character recognition. Most existing character recognition methods based on character stroke features utilize a set or a sequence of local features such as xy-coordinates and local direction of strokes. This is natural from the viewpoint that each stroke is a trajectory and thus can be represented as a sequence of local features. This viewpoint, however, has a clear limitation in that local features cannot deal with global structure directly. For example, the sequence of local features cannot deal with the fact that the two end points of character "0" should be close to each other. In this paper we propose a simple and novel global feature that describes the global structure of the character shape of each class. We prove the importance of the global feature through a feature selection experiment. Specifically, we show that the global features are more often selected than local features to enhance classification accuracy under the AdaBoost-based machine learning framework. Recognition experiments using online numeral data show also that the use of global features improves recognition accuracy.
The PEP4 Gene Encodes an Aspartyl Protease Implicated in the Posttranslational Regulation of Saccharomyces cerevisiae Vacuolar Hydrolases (1986)

pep4 mutants of Saccharomyces cerevisiae accumulate inactive precursors of vacuolar hydrolases. The PEP4 gene was isolated from a genomic DNA library by complementation of the pep4-3 mutation. Deletion analysis localized the complementing activity to a 1.5-kilobase pair EcoRI-XhoI restriction enzyme fragment. This fragment was used to identify an 1,800-nucleotide mRNA capable of directing the synthesis of a 44,000-dalton polypeptide. Southern blot analysis of yeast genomic DNA showed that the PEP4 gene is unique; however, several related sequences exist in yeasts. Tetrad analysis and mitotic recombination experiments localized the PEP4 gene proximal to GAL4 on chromosome XVI. Analysis of the DNA sequence indicated that PEP4 encodes a polypeptide with extensive homology to the aspartyl protease family. A comparison of the PEP4 predicted amino acid sequence with the yeast protease A protein sequence revealed that the two genes are, in fact, identical (see also Ammerer et al., Mol. Cell. Biol. 6:2490-2499, 1986). Based on our observations, we propose a model whereby inactive precursor molecules produced from the PEP4 gene self-activate within the yeast vacuole and subsequently activate other vacuolar hydrolases.
General strategy for the generation of human antibody variable domains with increased aggregation resistance (2012)

The availability of stable human antibody reagents would be of considerable advantage for research, diagnostic, and therapeutic applications. Unfortunately, antibody variable heavy and light domains (V(H) and V(L)) that mediate the interaction with antigen have the propensity to aggregate. Increasing their aggregation resistance in a general manner has proven to be a difficult and persistent problem, due to the high level of sequence diversity observed in human variable domains and the requirement to maintain antigen binding. Here we outline such an approach. By using phage display we identified specific positions that clustered in the antigen binding site (28, 30-33, 35 in V(H) and 24, 49-53, 56 in V(L)). Introduction of aspartate or glutamate at these positions endowed superior biophysical properties (non-aggregating, well-expressed, and heat-refoldable) onto domains derived from common human germline families (V(H)3 and V(κ)1). The effects of the mutations were highly positional and independent of sequence diversity at other positions. Moreover, crystal structures of mutant V(H) and V(L) domains revealed a surprising degree of structural conservation, indicating compatibility with V(H)/V(L) pairing and antigen binding. This allowed the retrofitting of existing binders, as highlighted by the development of robust high affinity antibody fragments derived from the breast cancer therapeutic Herceptin. Our results provide a general strategy for the generation of human antibody variable domains with increased aggregation resistance.
Molecular characterization of the genes encoding pyruvate formate-lyase and its activating enzyme of Clostridium pasteurianum (1996)

Formate is the major source of C1 units in many species of the genus Clostridium. In this study we have cloned and characterized the genes encoding pyruvate formate-lyase and its activating enzyme of Clostridium pasteurianum. The genetic and transcriptional organizations of the genes and the high level of homology exhibited by the respective gene products to their Escherichia coli counterparts indicate strong evolutionary conservation of these enzymes.
Engineering Hyperthermophilic Archaeon Pyrococcus furiosus to Overproduce Its Cytoplasmic [NiFe]-Hydrogenase (2011)

The cytoplasmic hydrogenase (SHI) of the hyperthermophilic archaeon Pyrococcus furiosus is an NADP(H)-dependent heterotetrameric enzyme that contains a nickel-iron catalytic site, flavin, and six iron-sulfur clusters. It has potential utility in a range of bioenergy systems in vitro, but a major obstacle in its use is generating sufficient amounts. We have engineered P. furiosus to overproduce SHI utilizing a recently developed genetic system. In the overexpression (OE-SHI) strain, transcription of the four-gene SHI operon was under the control of a strong constitutive promoter, and a Strep-tag II was added to the N terminus of one subunit. OE-SHI and wild-type P. furiosus strains had similar rates of growth and H(2) production on maltose. Strain OE-SHI had a 20-fold higher transcription of the polycistronic hydrogenase mRNA encoding SHI, and the specific activity of the cytoplasmic hydrogenase was ∼10-fold higher when compared with the wild-type strain, although the expression levels of genes encoding processing and maturation of SHI were the same in both strains. Overexpressed SHI was purified by a single affinity chromatography step using the Strep-tag II, and it and the native form had comparable activities and physical properties. Based on protein yield per gram of cells (wet weight), the OE-SHI strain yields a 100-fold higher amount of hydrogenase when compared with the highest homologous [NiFe]-hydrogenase system previously reported (from Synechocystis). This new P. furiosus system will allow further engineering of SHI and provide hydrogenase for efficient in vitro biohydrogen production.
A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families (2015)

<i>Candida albicans</i> is a pathogenic yeast that causes mucosal and systematic infections with high mortality. The absence of facile molecular genetics has been a major impediment to analysis of pathogenesis. The lack of meiosis coupled with the absence of plasmids makes genetic engineering cumbersome, especially for essential functions and gene families. We describe a <i>C. albicans</i> CRISPR system that overcomes many of the obstacles to genetic engineering in this organism. The high frequency with which CRISPR-induced mutations can be directed to target genes enables easy isolation of homozygous gene knockouts, even without selection. Moreover, the system permits the creation of strains with mutations in multiple genes, gene families, and genes that encode essential functions. This CRISPR system is also effective in a fresh clinical isolate of undetermined ploidy. Our method transforms the ability to manipulate the genome of <i>Candida</i> and provides a new window into the biology of this pathogen.
Discovery and analysis of inflammatory disease-related genes using cDNA microarrays (1997)

cDNA microarray technology is used to profile complex diseases and discover novel disease-related genes. In inflammatory disease such as rheumatoid arthritis, expression patterns of diverse cell types contribute to the pathology. We have monitored gene expression in this disease state with a microarray of selected human genes of probable significance in inflammation as well as with genes expressed in peripheral human blood cells. Messenger RNA from cultured macrophages, chondrocyte cell lines, primary chondrocytes, and synoviocytes provided expression profiles for the selected cytokines, chemokines, DNA binding proteins, and matrix-degrading metalloproteinases. Comparisons between tissue samples of rheumatoid arthritis and inflammatory bowel disease verified the involvement of many genes and revealed novel participation of the cytokine interleukin 3, chemokine Gro alpha and the metalloproteinase matrix metallo-elastase in both diseases. From the peripheral blood library, tissue inhibitor of metalloproteinase 1, ferritin light chain, and manganese superoxide dismutase genes were identified as expressed differentially in rheumatoid arthritis compared with inflammatory bowel disease. These results successfully demonstrate the use of the cDNA microarray system as a general approach for dissecting human diseases.
Political parties and political Engineering in the Asia-Pacific region (2003)

Democracies need both strength and flexibility--enough structure to transform a kaleidoscope of public opinion into coherent debate and effective policy, but enough openness to protect individual rights. Finding this balance is a particular challenge in ethnically diverse emerging democracies. Political parties usually serve a country best when they are limited in number, strong, and broad-based. Their evolution was once left mainly to chance; today, governments often seek to influence the process. Among those attempting reforms are Papua New Guinea, home to hundreds of languages; Indonesia, with its separatist movements; the Philippines, experimenting with ways to balance party interests with other social concerns; and Thailand, whose once fragmented political scene seems headed toward domination by one party. Their strategies for encouraging stable party systems range from minimum-vote thresholds to efforts to stiffen internal party discipline. Much can be learned from these Asia Pacific efforts at political engineering--including the need for a cautious approach that minimizes unforeseen consequences and costs.
Aptamer Antagonists of Myelin-Derived Inhibitors Promote Axon Growth (2010)

Myelin of the adult central nervous system (CNS) is one of the major sources of inhibitors of axon regeneration following injury. The three known myelin-derived inhibitors (Nogo, MAG, and OMgp) bind with high affinity to the Nogo-66 receptor (NgR) on axons and limit neurite outgrowth. Here we show that RNA aptamers can be generated that bind with high affinity to NgR, compete with myelin-derived inhibitors for binding to NgR, and promote axon elongation of neurons in vitro even in the presence of these inhibitors. Aptamers may have key advantages over protein antagonists, including low immunogenicity and the possibility of ready modification during chemical synthesis for stability, signaling, or immobilization. This first demonstration that aptamers can directly influence neuronal function suggests that aptamers may prove useful for not only healing spinal cord and other neuronal damage, but may be more generally useful as neuromodulators.
Critical numbers of neural crest cells are required in the pathways from the neural tube to the foregut to ensure complete enteric nervous system formation (2008)

The enteric nervous system (ENS) is mainly derived from vagal neural crest cells (NCC) that arise at the level of somites 1-7. To understand how the size and composition of the NCC progenitor pool affects ENS development, we reduced the number of NCC by ablating the neural tube adjacent to somites 3-6 to produce aganglionic gut. We then back-transplanted various somite lengths of quail neural tube into the ablated region to determine the 'tipping point', whereby sufficient progenitors were available for complete ENS formation. The addition of one somite length of either vagal, sacral or trunk neural tube into embryos that had the neural tube ablated adjacent to somites 3-6, resulted in ENS formation along the entire gut. Although these additional cells contributed to the progenitor pool, the quail NCC from different axial levels retained their intrinsic identities with respect to their ability to form the ENS; vagal NCC formed most of the ENS, sacral NCC contributed a limited number of ENS cells, and trunk NCC did not contribute to the ENS. As one somite length of vagal NCC was found to comprise almost the entire ENS, we ablated all of the vagal neural crest and back-transplanted one somite length of vagal neural tube from the level of somite 1 or somite 3 into the vagal region at the position of somite 3. NCC from somite 3 formed the ENS along the entire gut, whereas NCC from somite 1 did not. Intrinsic differences, such as an increased capacity for proliferation, as demonstrated in vitro and in vivo, appear to underlie the ability of somite 3 NCC to form the entire ENS.
Peripheral and tumor immune correlates in patients with advanced melanoma treated with nivolumab (anti-PD-1, BMS-936558, ONO-4538) monotherapy or in combination with ipilimumab (2014)

Peripheral and tumor immune correlates in patients with advanced melanoma treated with nivolumab (anti-PD-1, BMS-936558, ONO-4538) monotherapy or in combination with ipilimumab Michael A Postow, Diana M Cardona, Janis M Taube, Robert A Anders, Clive R Taylor, Jedd D Wolchok, Margaret K Callahan, Michael A Curran, Alexander M Lesokhin, Joseph F Grosso, Christine E Horak, John Cogswell, Jason S Simon, Ashok K Gupta, Mario Sznol
Repositioning salicylanilide anthelmintic drugs to treat adenovirus infections (2019)

The repositioning of drugs already approved by regulatory agencies for other indications is an emerging alternative for the development of new antimicrobial therapies. The repositioning process involves lower risks and costs than the de novo development of novel antimicrobial drugs. Currently, infections by adenovirus show a steady increment with a high clinical impact in immunosuppressed and immunocompetent patients. The lack of a safe and efficacious drug to treat these infections supports the search for new antiviral drugs. Here we evaluated the anti-adenovirus activity of niclosanide, oxyclozanide, and rafoxanide, three salicylanilide anthelmintic drugs. Also, we carried out the cytotoxicity evaluation and partial characterization of the mechanism of action of these drugs. The salicylanilide anthelmintic drugs showed significant anti-adenovirus activity at low micromolar concentrations with little cytotoxicity. Moreover, our mechanistic assays suggest differences in the way the drugs exert anti-adenovirus activity. Niclosamide and rafoxanide target transport of the HAdV particle from the endosome to the nuclear envelope, whilst oxyclozanide specifically targets adenovirus immediately early gene E1A transcription. Data suggests that the studied salicylanilide anthelmintic drugs could be suitable for further clinical evaluation for the development of new antiviral drugs to treat infections by adenovirus in immunosuppressed patients and in immunocompetent individuals with community-acquired pneumonia.
Kinematics and the Implementation of an Elephant's Trunk Manipulator and Other Continuum Style Robots (2003)

Traditionally, robot manipulators have been a simple arrangement of a small number of serially connected links and actuated joints. Though these manipulators prove to be very effective for many tasks, they are not without their limitations, due mainly to their lack of maneuverability or total degrees of freedom. Continuum style (i.e., continuous "back-bone") robots, on the other hand, exhibit a wide range of maneuverability, and can have a large number of degrees of freedom. The motion of continuum style robots is generated through the bending of the robot over a given section; unlike traditional robots where the motion occurs in discrete locations, i.e., joints. The motion of continuum manipulators is often compared to that of biological manipulators such as trunks and tentacles. These continuum style robots can achieve motions that could only be obtainable by a conventionally designed robot with many more degrees of freedom. In this paper we present a detailed formulation and explanation of a novel kinematic model for continuum style robots. The design, construction, and implementation of our continuum style robot called the elephant trunk manipulator is presented. Experimental results are then provided to verify the legitimacy of our model when applied to our physical manipulator. We also provide a set of obstacle avoidance experiments that help to exhibit the practical implementation of both our manipulator and our kinematic model.
Model-Based Self-Managing Systems Engineering (2006)

For many years, the vision of smart computing where systems can function and/or manage themselves independently from human intervention has provided numerous theoretical challenges to research communities ranging from intelligent systems and cybernetics to AI communities. These research trends have now been further fuelled by the IBM autonomic computing initiative, where biologically inspired concepts inform the development of systems that can adapt autonomously to their users’ requirements and environments. This paper considers the extent to which well-established general systems concepts might be valuable in the design of autonomic systems. The main two approaches considered are Checkland’s Soft Systems Methodology (SSM) and Beer’s Viable Systems Model (VSM). The paper summarizes the relevant aspects of each approach and demonstrates their potential through the provision of an illustrative case study. Moreover, the paper illustrates how SSM and VSM approaches facilitate autonomic systems engineering by the capture of functional and non-functional application requirements such as lifetime self-management policies and operational tolerances.
Chimeric antigen receptor T cells persist and induce sustained remissions in relapsed refractory chronic lymphocytic leukemia (2015)

Patients with multiply relapsed or refractory chronic lymphocytic leukemia (CLL) have a poor prognosis. Chimeric antigen receptor (CAR)-modified T cells targeting CD19 have the potential to improve on the low complete response rates with conventional therapies by inducing sustained remissions in patients with refractory B cell malignancies. We previously reported preliminary results on three patients with refractory CLL. We report the mature results from our initial trial using CAR-modified T cells to treat 14 patients with relapsed and refractory CLL. Autologous T cells transduced with a CD19-directed CAR (CTL019) lentiviral vector were infused into patients with relapsed/refractory CLL at doses of 0.14 × 10(8) to 11 × 10(8) CTL019 cells (median, 1.6 × 10(8) cells). Patients were monitored for toxicity, response, expansion, and persistence of circulating CTL019 T cells. The overall response rate in these heavily pretreated CLL patients was 8 of 14 (57%), with 4 complete remissions (CR) and 4 partial remissions (PR). The in vivo expansion of the CAR T cells correlated with clinical responses, and the CAR T cells persisted and remained functional beyond 4 years in the first two patients achieving CR. No patient in CR has relapsed. All responding patients developed B cell aplasia and experienced cytokine release syndrome, coincident with T cell proliferation. Minimal residual disease was not detectable in patients who achieved CR, suggesting that disease eradication may be possible in some patients with advanced CLL.
Double-Blind, Randomised, Placebo-Controlled Study of Two Concentrations of Azelastine Eye Drops in Seasonal Allergic Conjunctivitis or Rhinoconjunctivitis (1997)

This double-blind, randomised, placebo-controlled study was carried out to assess the efficacy and safety of 0.025% and 0.05% azelastine eye drops twice daily administered for 14 days to patients with seasonal allergic conjunctivitis or rhinoconjunctivitis. A total of 278 patients were recruited and 226 patients were evaluable for per protocol analysis. The target parameter was the response rate. Four eye symptoms, including the main symptom (itching) were recorded by patients in diaries and eight symptoms were assessed by physicians before and after seven and 14 days of treatment. Severity of symptoms was measured on a four-point scale. The response rates for itching (improvement of at least one score point within the first three days) according to patient assessment were 43% for placebo, 52% for 0.025% and 56% for 0.05% azelastine (NS). However, a more objective assessment of the three main eye symptoms by physicians showed a concentration-dependent improvement in response rate compared with placebo (a decrease of > or = 3 points from a baseline total score of > or = 6), which reached statistical significance for 0.05% azelastine on Day 7 (p < 0.002). In the evaluable patient population, the scores of the three main eye symptoms as well as of all eight recorded eye symptoms, as assessed by the physician, were significantly (p < 0.05) lower in the 0.05% azelastine eye drops group in comparison with the placebo group at Day 7. Inefficacy was the cause of withdrawal in five and three patients on 0.025% and 0.05% azelastine, respectively, and in six patients on placebo. Adverse drug effects, mainly a mild, transient irritation and a bitter or unpleasant taste, were reported by 14% (0.025%), 20% (0.05%) and 15% (placebo) of the patients. No serious side-effects occurred. Azelastine eye drops are effective and well tolerated at a concentration of 0.05% for the treatment of seasonal allergic conjunctivitis.
It's Elementary, Dear Watson: Applying Logic Programming To Convergent System Management Processes (1999)

In an ideal world, the system administrator would simply specify a complete model of system requirements and the system would automatically fulfill them. If requirements changed, or if the system deviated from requirements, the system would change itself to converge with requirements. Current specialized tools for convergent system administration already provide some ability to do this, but are limited by specification languages that cannot adequately represent all possible sets of requirements. We take the opposite approach of starting with a general-purpose logic programming language intended for specifying requirements and analyzing system state, and adapting that language for system administration. Using Prolog with appropriate extensions, one can specify complex system requirements and convergent processes involving multiple information domains, including information about files, filesystems, users, and processes, as well as information from databases. By hiding unimportant details, Prolog allows a simple relationship between requirements and the scripts that implement them. We illustrate these observations by use of a simple proof-of-concept prototype.
Characteristics of the local interstellar hydrogen determined from PROGNOZ 5 and 6 interplanetary Lyman-alpha line profile measurements with a hydrogen absorption cell (1985)

International audience
Gapped sequence alignment using artificial neural networks: application to the MHC class I system (2015)

The NetMHC-4.0 method for the prediction of peptide-MHC class I binding affinity using gapped sequence alignment is publicly available at: http://www.cbs.dtu.dk/services/NetMHC-4.0.