gebhart/patrepeval huggingface dataset:
Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin (2012)

Protein interactions with peptides generally have low thermodynamic and mechanical stability. Streptococcus pyogenes fibronectin-binding protein FbaB contains a domain with a spontaneous isopeptide bond between Lys and Asp. By splitting this domain and rational engineering of the fragments, we obtained a peptide (SpyTag) which formed an amide bond to its protein partner (SpyCatcher) in minutes. Reaction occurred in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer. SpyTag could be fused at either terminus or internally and reacted specifically at the mammalian cell surface. Peptide binding was not reversed by boiling or competing peptide. Single-molecule dynamic force spectroscopy showed that SpyTag did not separate from SpyCatcher until the force exceeded 1 nN, where covalent bonds snap. The robust reaction conditions and irreversible linkage of SpyTag shed light on spontaneous isopeptide bond formation and should provide a targetable lock in cells and a stable module for new protein architectures.
ISOLATION AND PROPERTIES OF AN EXOCELLULAR NUCLEASE OF SERRATIA MARCESCENS (1963)

Eaves, George N. (Wayne State University College of Medicine, Detroit, Mich.) and Charles D. Jeffries. Isolation and properties of an exocellular nuclease of Serratia marcescens. J. Bacteriol. 85:273-278. 1963.-The exocellular nuclease of Serratia marcescens, isolated by anion-exchange chromatography on diethylaminoethyl-Sephadex, depolymerized deoxyribonucleic acid, ribonucleic acid, and the polynucleotide which is refractory to pancreatic ribonuclease activity. The enzyme was tentatively classified as a nonspecific phosphodiesterase. Magnesium was essential for activity, which was optimal at pH 8.8. The purified enzyme was completely inactivated by heating at 50 C for 15 min.
Quantification of the chemokines CCL17 and CCL22 in human colorectal adenocarcinomas (2008)

Chemokines are believed to play a crucial role in local immunoresponse by regulating leukocyte movement in various tissues, including the intestinal mucosa. It has been suggested that they are key players in cancer biology, and several studies have identified leukocyte infiltration as a hallmark of most cancers. The chemokines CCL17 and CCL22 attract CCR4-bearing cells, which are especially polarised to Th2-type cells and regulatory T cells (Treg). Recent studies have revealed the participation of the CCL17 and CCL22 proteins in diseases such as atopic dermatitis and lymphoma. The purpose of this study was to assess the role of CCL17 and CCL22 protein expression in colorectal cancer (CRC) and to ascertain whether an association exists between promoter -431C>T CCL17 and -961G>A CCL22 gene polymorphisms in CRC versus non-CRC subjects. Using the ELISA assay, we noted a significantly higher expression of CCL22 in tumour tissue with a 2.3-fold up-regulation (tumour vs. paired normal tissue, n=78) but no significant difference in CCL17 protein expression. Immunohistochemistry revealed protein expression of CCL22 and CCL17 in the epithelial compartment of cancer tissue, in epithelial cells at the resection border that reflects normal tissue, and in some stromal cells such as lymphocytes, macrophages, and fibroblasts. Using a TaqMan system we screened for -431C>T CCL17 and -961G>A CCL22 gene variants in 245 CRC patients and 256 controls, but could not find any significant difference in genotype distribution or in allelic frequencies between the two groups. The genotype and allelic distributions of CRC patients were not related to tissue levels of CCL17 and CCL22 protein, and none of the variables were associated with plasma levels or clinical characteristics. To ascertain whether the tissue expression of CCL17 and CCL22 exerts an influence on the pathogenesis of CRC, a forthcoming study on the 5-year survival rate of CRC patients will be conducted.
Toward Robustness against Label Noise in Training Deep Discriminative Neural Networks (2017)

Collecting large training datasets, annotated with high-quality labels, is costly and time-consuming. This paper proposes a novel framework for training deep convolutional neural networks from noisy labeled datasets that can be obtained cheaply. The problem is formulated using an undirected graphical model that represents the relationship between noisy and clean labels, trained in a semi-supervised setting. In our formulation, the inference over latent clean labels is tractable and is regularized during training using auxiliary sources of information. The proposed model is applied to the image labeling problem and is shown to be effective in labeling unseen images as well as reducing label noise in training on CIFAR-10 and MS COCO datasets.
A symmetrical bipolar structure (1980)

This paper presents symmetrical bipolar-transistor structures suitable for bilateral operation. Such structures were fabricated using a technique of simultaneous-growth of epitaxial and polycrystalline Si on a stack structure. Vertical symmetrical transistors have been built and showed an emitter-base diode breakdown voltage of 7V, a current gain of 17.
The Herbicide Saflufenacil (Kixor™) is a New Inhibitor of Protoporphyrinogen IX Oxidase Activity (2010)

Saflufenacil (Kixor™) is a new herbicide of the pyrimidinedione chemical class for preplant burndown and selective preemergence dicot weed control in multiple crops, including corn. In this study, the mode of action of saflufenacil was investigated. For initial characterization, a series of biotests was used in a physionomics approach for comprehensive physiological profiling of saflufenacil effects. With the use of treated duckweed plants, metabolite profiling was performed based on quantification of metabolite changes, relative to untreated controls. Physiological and metabolite profiling suggested a mode of action similar to inhibitors of protoporphyrinogen IX oxidase (PPO) in tetrapyrrole biosynthetic pathway. Saflufenacil inhibited PPO enzyme activity in vitro with 50% inhibition of 0.4 nM for the enzymes isolated from black nightshade, velvetleaf, and corn. PPO inhibition by saflufenacil caused accumulations of protoporphyrin IX (Proto) and hydrogen peroxide (H 2 O 2 ) in leaf tissue of black nightshade and velvetleaf. In corn, only slight increases in Proto and H 2 O 2 were found, which reflects in planta tolerance of this crop. The results show that saflufenacil is a new PPO-inhibiting, peroxidizing herbicide.
Wheeze monitoring in children for assessment of nocturnal asthma and response to therapy (2003)

The utilisation of nocturnal wheeze monitoring and quantification for assessment of asthma activity was studied in symptomatic school-aged children before and during treatment. Twelve children 6-14 yrs of age with mild or moderate untreated asthma were studied at home three times: before, 48 h and 6 weeks into treatment with 5 mg montelukast daily. Lung sounds were recorded overnight by an automatic wheeze detection device (PulmoTrack). Per cent wheezing within each respiratory cycle was calculated every 30 s throughout the night and a Nocturnal Wheeze Index (NWI) was calculated for the total night. The results were compared with spirometric indices (forced expiratory volume in one second (FEV1), forced vital capacity), bronchial reactivity (provocative concentration causing a 20% fall in FEV1 by adenosine 5'-monophosphate (PC20)) and daily symptom scores, performed in parallel at each stage of the study. The pretreatment NWI was 814+/-898 (mean+/-SD), which declined to 318+/-199 2 days after onset, and to 137+/-101 after 6 weeks of treatment. The NWI in seven healthy children was 47+/-43. The FEV1, PC20 and symptom scores improved in parallel. Wheeze monitoring provides quantitative and noninvasive information about the extent of nocturnal wheezing in children, correlates well with conventional indices of asthma activity and can assist in assessing efficacy of treatment.
Chimpanzee genomic diversity reveals ancient admixture with bonobos (2016)

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.
Local-constrained quadtree plus binary tree block partition structure for enhanced video coding (2016)

In the latest Joint Video Exploration Team (JVET) development, a quadtree plus binary tree (QTBT) block partition structure is proposed for enhanced video coding. Compared to the quadtree block partition in HEVC, QTBT can achieve much better compression performance at the expense of largely increased encoding computational complexity. In this paper, a fast QTBT block partition algorithm based on the local constraint is proposed. Given the decoded information of the previous frame, the partition parameters can be dynamically derived for each coding tree unit (CTU) without any overhead. Furthermore, a constrained binary tree partition algorithm is proposed to reduce the redundancy between the quadtree partition and the binary tree partition. Experimental results have shown that the proposed scheme can speed up QTBT block partition structure by 30% on average without obvious performance decrease, which enables its practical implementations in real application scenarios.
The Chemokine Receptor CCR7 Activates in Dendritic Cells Two Signaling Modules That Independently Regulate Chemotaxis and Migratory Speed (2005)

CCR7 is necessary to direct dendritic cells (DCs) to secondary lymphoid nodes and to elicit an adaptative immune response. Despite its importance, little is known about the molecular mechanisms used by CCR7 to direct DCs to lymph nodes. In addition to chemotaxis, CCR7 regulates the migratory speed of DCs. We investigated the intracellular pathways that regulate CCR7-dependent chemotaxis and migratory speed. We found that CCR7 induced a G(i)-dependent activation of MAPK members ERK1/2, JNK, and p38, with ERK1/2 and p38 controlling JNK. MAPK members regulated chemotaxis, but not the migratory speed, of DCs. CCR7 induced activation of PI3K/Akt; however, these enzymes did not regulate either chemotaxis or the speed of DCs. CCR7 also induced activation of the GTPase Rho, the tyrosine kinase Pyk2, and inactivation of cofilin. Pyk2 activation was independent of G(i) and Src and was dependent on Rho. Interference with Rho or Pyk2 inhibited cofilin inactivation and the migratory speed of DCs, but did not affect chemotaxis. Interference with Rho/Pyk2/cofilin inhibited DC migratory speed even in the absence of chemokines, suggesting that this module controls the speed of DCs and that CCR7, by activating its components, induces an increase in migratory speed. Therefore, CCR7 activates two independent signaling modules, one involving G(i) and a hierarchy of MAPK family members and another involving Rho/Pyk2/cofilin, which control, respectively, chemotaxis and the migratory speed of DCs. The use of independent signaling modules to control chemotaxis and speed can contribute to regulate the chemotactic effects of CCR7.
Assembling Old Tricks for New Tasks: A Neural Model of Instructional Learning and Control (2013)

We can learn from the wisdom of others to maximize success. However, it is unclear how humans take advice to flexibly adapt behavior. On the basis of data from neuroanatomy, neurophysiology, and neuroimaging, a biologically plausible model is developed to illustrate the neural mechanisms of learning from instructions. The model consists of two complementary learning pathways. The slow-learning parietal pathway carries out simple or habitual stimulus-response (S-R) mappings, whereas the fast-learning hippocampal pathway implements novel S-R rules. Specifically, the hippocampus can rapidly encode arbitrary S-R associations, and stimulus-cued responses are later recalled into the basal ganglia-gated pFC to bias response selection in the premotor and motor cortices. The interactions between the two model learning pathways explain how instructions can override habits and how automaticity can be achieved through motor consolidation.
Reduced total energy expenditure and physical activity in cachectic patients with pancreatic cancer can be modulated by an energy and protein dense oral supplement enriched with n-3 fatty acids (2004)

The aim of the study was to assess the total energy expenditure (TEE), resting energy expenditure (REE) and physical activity level (PAL) in home-living cachectic patients with advanced pancreatic cancer. The influence of an energy and protein dense oral supplement either enriched with or without the n-3 fatty acid eicosapentaenoic acid (EPA) and administered over an 8-week period was also determined. In total, 24 patients were studied at baseline. The total energy expenditure was measured using doubly labelled water and REE determined by indirect calorimetry. Patients were studied at baseline and then randomised to either oral nutritional supplement. Measurements were repeated at 8 weeks. At baseline, REE was increased compared with predicted values for healthy individuals (1387(42) vs 1268(32) kcal day(-1), P=0.001), but TEE (1732(82) vs 1903(48) kcal day(-1), P=0.023) and PAL (1.24(0.04) vs 1.50) were reduced. After 8 weeks, the REE, TEE and PAL of patients who received the control supplement did not change significantly. In contrast, although REE did not change, TEE and PAL increased significantly in those who received the n-3 (EPA) enriched supplement. In summary, patients with advanced pancreatic cancer were hypermetabolic. However, TEE was reduced and this was secondary to a reduction in physical activity. The control energy and protein dense oral supplement did not influence the physical activity component of TEE. In contrast, administration of the supplement enriched with EPA was associated with an increase in physical activity, which may reflect improved quality of life.
Edgel index for large-scale sketch-based image search (2011)

Retrieving images to match with a hand-drawn sketch query is a highly desired feature, especially with the popularity of devices with touch screens. Although query-by-sketch has been extensively studied since 1990s, it is still very challenging to build a real-time sketch-based image search engine on a large-scale database due to the lack of effective and efficient matching/indexing solutions. The explosive growth of web images and the phenomenal success of search techniques have encouraged us to revisit this problem and target at solving the problem of web-scale sketch-based image retrieval. In this work, a novel index structure and the corresponding raw contour-based matching algorithm are proposed to calculate the similarity between a sketch query and natural images, and make sketch-based image retrieval scalable to millions of images. The proposed solution simultaneously considers storage cost, retrieval accuracy, and efficiency, based on which we have developed a real-time sketch-based image search engine by indexing more than 2 million images. Extensive experiments on various retrieval tasks (basic shape search, specific image search, and similar image search) show better accuracy and efficiency than state-of-the-art methods.
Human interferon-inducible protein 10: expression and purification of recombinant protein demonstrate inhibition of early human hematopoietic progenitors. (1993)

Human interferon-inducible protein 10 (IP-10), a member of the family of the small secreted proteins called intercrine cytokines or chemokines, is secreted by interferon gamma-stimulated T cells, monocytes, endothelial cells, and keratinocytes. We have begun to explore the biological properties of IP-10 by cloning and overexpression in baculovirus and in bacterial protein expression systems. A 9.9-kD protein was secreted by infected insect cells, which on sodium dodecyl sulfate-polyacrilamide gel electrophoresis comigrated with keratinocyte IP-10 and with f(22-98), a bacterial recombinant fragment lacking the signal sequence but containing all other residues of IP-10. All three reacted with antibodies recognizing residues 10-98 (alpha IP-10) and 77-98 of IP-10 (alpha 22), demonstrating that it is secreted by keratinocytes and insect cells after removal of the signal sequence but without proteolysis of the COOH-terminal end. Purified rIP-10 suppresses in vitro colony formation by early human bone marrow progenitor cells which need r-steel factor (rSLF) and rGM-CSF or rSLF and r-erythropoeitin (rEPO). The inhibition is dose dependent, is complete at concentrations > or = 50 ng/ml, is prevented by preincubation of rIP-10 with alpha IP-10, but not by alpha 22, and is seen with highly purified CD34+ cells, suggesting direct effect of rIP-10 on the progenitors. Combination of rIP-10 and other chemokines at inactive concentrations inhibited colony formation in a synergistic manner. rIP-10 did not affect colony formation in the absence of any growth factors or in the presence of rEPO or rGM-CSF but in absence of rSLF. The effects of IP-10 may be relevant to normal marrow function and might be harnessed to protect human hematopoietic progenitors from the cytotoxic effects of chemotherapy.
Evidence of Cytocidal Effects of Pasteurella haemolytica on Bovine Peripheral Blood Mononuclear Leukocytes (1980)

Pasteurella haemolytica had a pronounced cytocidal effect on bovine mononuclear leukocytes. Mononuclear leukocytes separated from venous blood on Ficoll-diatrizoate and incubated with either P haemolytica or Escherichia coli showed a significantly greater percentage cell death than did cells incubated with Staphylococcus epidermidis or controls. Neither heat-killed nor x-irradiated P haemolytica caused a significant percentage cell death. The cytotoxic potential of P haemolytica was dose related in that cell death among mononuclear leukocytes increased as the ratio of bacteria-to-cells increased. Enriched monocyte cultures showed a higher and less variable rate of cell death than either enriched lymphocyte or mixed leukocyte cultures.
Genetic interaction between porcine reproductive and respiratory syndrome virus (PRRSV) strains in cell culture and in animals (2002)

Objective: The need to obtain protective immunity and full reduction of disease associated with porcine reproductive and respiratory syndrome virus (PRRSV) infections has encouraged the use of multiple vaccine types to possibly obtain broader protection against genotypically variable PRRSV isolates. This strategy introduces potential risks of genetic rearrangements that might accelerate the natural rate of genetic change, facilitating the emergence of new PRRSV strains. Our goal was to determine if recombination was occurring between vaccine strains in porcine cells and in vivo. Methods: Attenuated vaccine viruses were grown together in cultured cells or administered simultaneously to pigs. Cell culture fluids and pig sera were evaluated for recombinant viruses. Results: Genetic recombination occurred between attenuated vaccine strains of PRRSV grown together in porcine alveolar macrophages and in simian MA-104 cell cultures. However, animals inoculated with both strains simultaneously did not provide evidence of viral recombination between vaccine strains in vivo. Implications: Practices which favor co-infection of cells with different virus strains might accelerate the rate of genetic change in PRRSV due to recombination. However, the probability of recombination of vaccine strains in animals appears to be low and recombinants appear to grow poorly. Mixing of vaccine strains for simultaneous administration in swine must be considered with the knowledge that recombination could occur. Vaccinating infected herds also introduces the possibility of recombination between vaccine and field strains. The likelihood of producing viable recombinant vaccine viruses is low, since they did not persist in cell culture and were not observed in vivo.
Development of a light-weight biped humanoid robot (2002)

In order to meet the demand of a research platform for intelligent robotics, a humanoid robot named Saika-3 has been developed. It is a self-sustaining biped robot with dual arms and a robotic head. It is equipped with a PC (IBM PC/AT clone), batteries, a wireless ethernet modem, a gyroscope and motor drivers inside its body. Saika-3 can be teleoperated via wireless' ethernet communication. A graphic dynamic simulator is also developed to study control strategy. The paper presents an outline of the hardware of Saika-3 and a simulation result.
Evidence for the Cardioprotective Effects of Omega-3 Fatty Acids (2002)

Omega-3 Fatty acids may be beneficial and should be considered in patients with documented coronary heart disease. They may be particularly beneficial for patients with risk factors for sudden cardiac death.
Phosphoniosilylation. An efficient and practical method for the .beta.-functionalization of enones (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhosphoniosilylation. An efficient and practical method for the .beta.-functionalization of enonesAlan P. Kozikowski and Sun Ho JungCite this: J. Org. Chem. 1986, 51, 17, 3400–3402Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://pubs.acs.org/doi/10.1021/jo00367a040https://doi.org/10.1021/jo00367a040research-articleACS PublicationsRequest reuse permissionsArticle Views1586Altmetric-Citations59LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts