gebhart/patrepeval huggingface dataset:
HYR, an extracellular module involved in cellular adhesion and related to the immunoglobulin‐like fold (2000)

Domains belonging to the immunoglobulin-like fold are responsible for a wide variety of molecular recognition processes. Here we describe a new family of domains, the HYR family, which is predicted to belong to this fold, and which appears to be involved in cellular adhesion. HYR domains were identified in several eukaryotic proteins, often associated with Complement Control Protein (CCP) modules or arranged in multiple copies. Our analysis provides a sequence and structural basis for understanding the role of these domains in interaction mechanisms and leads to further characterization of heretofore undescribed repeated domains with similar folds found in several bacterial proteins involved in enzymatic activities (some chitinases) or in cell surface adhesion (streptococcal C-alpha antigen).
Nature of Tumor Control by Permanently and Transiently Modified GD2 Chimeric Antigen Receptor T Cells in Xenograft Models of Neuroblastoma (2014)

Chimeric antigen receptor (CAR) therapy has begun to demonstrate success as a novel treatment modality for hematologic malignancies. The success observed thus far has been with T cells permanently engineered to express chimeric receptors. T cells engineered using RNA electroporation represent an alternative with the potential for similar efficacy and greater safety when initially targeting novel antigens. Neuroblastoma is a common pediatric solid tumor with the potential to be targeted using immunotherapy. We performed xenograft studies in NSG mice in which we assessed the efficacy of both permanently modified and transiently modified CAR T cells directed against the neuroblastoma antigen GD2 in both local and disseminated disease models. Disease response was monitored by tumor volume measurement and histologic examination, as well as in vivo bioluminescence. RNA-modified GD2 CAR T cells mediated rapid tumor destruction when delivered locally. A single infusion of lentivirally modified GD2 CAR T cells resulted in long-term control of disseminated disease. Multiple infusions of RNA GD2 CAR T cells slowed the progression of disseminated disease and improved survival, but did not result in long-term disease control. Histologic examination revealed that the transiently modified cells were unable to significantly penetrate the tumor environment when delivered systemically, despite multiple infusions of CAR T cells. Thus, we demonstrate that RNA-modified GD2 CAR T cells can mediate effective antitumor responses in vivo, and permanently modified cells are able to control disseminated neuroblastoma in xenograft mice. Lack of long-term disease control by RNA-engineered cells resulted from an inability to penetrate the tumor microenvironment.
The Power of Speech (2003)

In the multimedia world of future communications, speech will play an increasingly important role. From speaker verification to automatic speech recognition and the understanding of key phrases by computers, the spoken word will replace keyboards and pointing devices like the mouse. In his Perspective, [Rabiner][1] discusses recent advances and remaining challenges in the processing of speech by communication devices. The key challenge is to make the user interface for 21st-century services and devices as easy to learn and use as a telephone is today for voice conversations.

 [1]: http://www.sciencemag.org/cgi/content/full/301/5639/1494
Shear Stress Increases ICAM-1 and Decreases VCAM-1 and E-selectin Expressions Induced by Tumor Necrosis Factor-α in Endothelial Cells (2003)

Our findings suggest that shear stress plays differential roles in modulating the TNF-alpha-induced expressions of ICAM-1 versus VCAM-1 and E-selectin genes in ECs.
Site-specific recombination between cloned attP and attB sites from the Haemophilus influenzae bacteriophage HP1 propagated in recombination-deficient Escherichia coli (1989)

Plasmids were constructed which contain both attP and attB DNA segments derived from the insertion sites of the lysogenic bacteriophage HP1 and its host, Haemophilus influenzae. Similar plasmids containing the two junction segments (attL and attR regions) between the phage genome and the lysogenic host chromosome were also prepared. The formation of recombinant dimer plasmids was observed when attP-attB plasmids were propagated in Escherichia coli HB101 (recA), while plasmids containing the junction segments did not form recombinant dimers. Deletion of the phage DNA segment adjacent to the attP site from the attP-attB constructions eliminated detectable recombination, suggesting that this sequence contains the gene encoding the HP1 integrase. No plasmid recombination was observed in strains of E. coli defective in integration host factor. This suggests that integration host factor is important in the expression or activity of the system which produces the site-specific recombination of sequences derived from HP1 and H. influenzae. Further, it suggests that a protein functionally analogous to E. coli integration host factor may be present in H. influenzae.
The Case of the Perfect Pangram (1985)

Inspector Ashley Halsey slammed down his copy of the newspaper as he heard a loud knock at the door of his tiny office. "Confound it," he muttered angrily. "Can't a man take a few minutes to finish solving a crossword puzzle!" Reluctantly, he swiveled his huge body in his chair to reach the doorknob.
Infusion of recombinant human acid sphingomyelinase into Niemann‐Pick disease mice leads to visceral, but not neurological, correction of the pathophysiology (2000)

An inherited deficiency of acid sphingomyelinase (ASM) activity results in the Type A and B forms of Niemann-Pick disease (NPD). Using the ASM-deficient mouse model (ASMKO) of NPD, we evaluated the efficacy of enzyme replacement therapy (ERT) for the treatment of this disorder. Recombinant human ASM (rhASM) was purified from the media of overexpressing Chinese Hamster ovary cells and i.v. injected into 16 five-month-old ASMKO mice at doses of 0.3, 1, 3, or 10 mg/kg every other day for 14 days (7 injections). On day 16, the animals were killed and the tissues were analyzed for their sphingomyelin (SPM) content. Notably, the SPM levels were markedly reduced in the hearts, livers, and spleens of these animals, and to a lesser degree in the lungs. Little or no substrate depletion was found in the kidneys or brains. Based on these results, three additional 5-month-old ASMKO animals were injected every other day with 5 mg/kg for 8 days (4 injections) and killed on day 10 for histological analysis. Consistent with the biochemical results, marked histological improvements were observed in the livers, spleens, and lungs, indicating a reversal of the disease pathology. A group of 10 ASMKO mice were then i.v. injected once a week with 1 mg/kg rhASM for 15 wk, starting at 3 wk of age. Although anti-rhASM antibodies were produced in these mice, the antibodies were not neutralizing and no adverse effects were observed from this treatment. Weight gain and rota-rod performance were slightly improved in the treated animals as compared with ASMKO control animals, but significant neurological deficits were still observed and their life span was not extended by ERT. In contrast with these CNS results, striking histological and biochemical improvements were found in the reticuloendothelial system organs (livers, spleens, and lungs). These studies indicate that ERT should be an effective therapeutic approach for Type B NPD, but is unlikely to prevent the severe neurodegeneration associated with Type A NPD.
Transient Paralysis Shortly after Anterior Cervical Corpectomy and Fusion (2013)

The precise cause for transient paralysis after these anterior cervical surgeries is not yet clear. Spinal cord ischemia-reperfusion injury is generally regarded as the most likely cause. Therefore, a combination of cervical spinal cord edema and limited anterior decompression space may have been the main contributing factors to the paralysis reported here. Early diagnosis and early intervention to relieve the paralysis can restore spinal cord function and result in a satisfactory prognosis.
A Simple and Useful Method for Simultaneous Screening of Elevated Levels of Expression of a Variety of Oncogenes in Malignant Cells (1988)

Abnormal expression of various oncogenes has been implicated in the development of many malignant tumors. Although RNA blotting methods have been used to measure abnormal expression, they involve the time-consuming process of individually labeling the oncogene probes. To simplify this process we have attempted to develop a new method, termed simultaneous screening, which is based on the synthesis of radiolabeled cDNA corresponding to the mRNA population of malignant cells and on hybridization with various oncogene probes, immobilized on a membrane filter. This method circumvents the time-consuming process of the prevailing RNA blotting methods and is also sensitive enough to detect accurately a five- to ten-fold level of expression of rare mRNA (approximately 10 copies per cell). Overexpression of ten oncogenes was detected in a variety of malignant cells and mitogen-stimulated cells with this method. These results suggest that our simultaneous screening method can be used to examine the overexpression of oncogenes.
The Molecular Biology Database Collection: an online compilation of relevant database resources (2000)

The Molecular Biology Database Collection represents an effort geared at making molecular biology database resources more accessible to biologists. This online resource, available at http://www.oup.co.uk/nar/Volume_28/Issue_01/html /gkd115_gml.html, is intended to serve as a searchable, up-to-date, centralized jumping-off point to individual Web sites. An emphasis has also been placed on including databases where new value is added to the underlying data by virtue of curation, new data connections, or other innovative approaches.
Osteogenesis in in vivo diffusion chamber cultures of human marrow cells. (1988)

The osteogenic diffusion chamber culture of rodent marrow cells is a well established system. In the present study, marrow cells from children and adult human donors were incubated in diffusion chambers implanted intraperitoneally in athymic mice. After 4 or 8 weeks, the chamber content was examined by light and electron microscopy. Child-cell cultures showed osteogenic tissue consisting of a mineralizing fibrous component and cartilage. Ultrastructurally, the fibrous tissue was similar to osteoid and exhibited osteoblast-like cells and mineralizing nodules. Mineral aggregates were also found in the cartilage. These features in child-cell chambers were similar to those found in control chambers of rabbit marrow cells. Adult-cell chambers showed only unmineralized fibrous tissue. These results render previous findings in animal-cell diffusion chamber systems relevant to the understanding of bone formation in man. It is suggested that the difference between child- and adult-cell chambers reflects an age-related decline in the number of marrow osteoprogenitor cells or their potential to undergo terminal osteogenic differentiation.
Safety Surveillance for Ustekinumab and Other Psoriasis Treatments From the Psoriasis Longitudinal Assessment and Registry (PSOLAR). (2015)

Analysis of 2014 PSOLAR data identified no increased risk of malignancy, MACE, serious infection, or mortality with ustekinumab.
Cloning and Nucleotide Sequences of NADH-Putidaredoxin Reductase Gene (camA) and Putidaredoxin Gene (camB) Involved in Cytochrome P-450cam Hydroxylase of Pseudomonas putida1 (1989)

Pseudomonas putida PpGl, which carries the CAM plasmid encoding enzymes involved in the degradation pathway of D-camphor, can utilize D-camphor as a sole carbon source. Cytochrome P-450cam and related enzymes participate in the early oxidation steps of D-camphor degradation metabolism. We cloned from a HindIII DNA library of PpGl a 2.9 kbp CAM segment which carries the major part of camA gene encoding NADH-putidaredoxin reductase and the entire camB gene encoding putidaredoxin. The 2.9 kbp CAM segment was adjacent to the 4.27 kbp HindIII CAM segment which has been previously cloned (Koga et al. (1986) J. Bacteriol. 166, 1089-1095). Thus, the total 7.17 kbp HindIII CAM directed all the genes responsible for early steps of D-camphor degradation, i.e. 5-exo-hydroxycamphor dehydrogenase (camD gene), cytochrome P-450cam (camC), NADH-putidaredoxin reductase (camA), and putidaredoxin (camB). These cam genes form an operon, camDCAB, and are under negative control by the gene camR located immediately upstream from the camD gene. The total number of amino acids deduced from the nucleotide sequence is 422 for putidaredoxin reductase, and 106 for putidaredoxin.
A Biochemical Approach to Periodontal Regeneration (1987)

Recent investigations on regeneration of the periodontium have attempted to define factors involved in the formation of a new connective tissue attachment. One essential biological event involved in tissue regeneration is directed cell migration (chemotaxis). Extracellular matrix proteins have been shown to influence chemotaxis, cell proliferation and differentiation. Recently, the extracellular matrix proteins, fibronectin (FN) and laminin (LM), and the polypeptide, endothelial cell growth factor (ECGF), have been shown to stimulate a variety of biological processes. Current assay systems which attempt to define cell migration are the Boyden chamber assay and a random cell migration assay. Neither assay system adequately defines in vivo cell migration. Here we present a new in vitro assay system that tests the capacity of several biological response modifiers applied on dentin to stimulate a chemotactic and proliferative response from various cell types. The assay system consists of two types of assays. Assay I measures the chemotactic activity of test substances bound to dentin. In this assay cells must actively move through a filter (Nuclepore) towards a factor bound to dentin. Assay II examines the ability of dentin-bound biological response modifiers to stimulate directed movement and proliferation of cells on dentin surfaces. We report that periodontal ligament (PDL) cells migrate towards FN and ECGF; that PDL cell migration is enhanced when dentin is preconditioned with tetracycline HCl; that PDL cells have an increased proliferative response when dentin is conditioned with both FN and ECGF; that gingival epithelial cells have increased migratory and proliferative responses when LM is used to condition dentin; and that there is a reciprocal utilization of biological response modifiers by gingival epithelial cells and PDL cells.
NEW MECHANISMS OF DRUG RESISTANCE IN PARASITIC PROTOZOA (1995)

The main line of defense now available against parasitic protozoa--which are responsible for major diseases of humans and domestic animals--is chemotherapy. This defense is being eroded by drug resistance and, with few new drugs in the pipeline, prevention and circumvention of resistance are medical and veterinary priorities. Although studies of resistance mechanisms in parasites have lagged behind similar studies in bacteria and cancer cells, the tools to tackle this problem are rapidly improving. Transformation with exogenous DNA is now possible with all major parasitic protozoa of humans. Hence, putative resistance genes can be tested in sensitive protozoa, allowing an unambiguous reconstruction of resistance mechanisms. Gene cloning, the polymerase chain reaction, and monoclonal antibodies against resistance-related proteins have made it possible to analyze potential resistance mechanisms in the few parasites that can be obtained from infected people. Hence, the prospect of applying new knowledge about resistance mechanisms to parasites in patients is good, even though today virtually all knowledge pertains to parasites selected for resistance in the laboratory. Resistance mechanisms highlighted in this review include: 1. Decrease of drug uptake because of the loss of a transporter required for uptake. This decrease contributes to resistance to arsenicals and diamidines in African trypanosomes. 2. The export of drugs from the parasite by P-glycoproteins and other traffic ATPases. This export could potentially be an important mechanism of resistance, as these proteins are richly represented in the few protozoa analyzed. There are indications that such transmembrane transporters can be involved in resistance to emetine in Entamoeba spp., to mefloquine in Plasmodium spp., and to antimonials in Leishmania spp. 3. The possible involvement of the P-glycoprotein encoded by the Plasmodium falciparum pfmdr1 gene in chloroquine resistance. We present the available data that lead to the conclusion that overproduction of the wild-type version of this protein results in chloroquine hypersensitivity rather than resistance. 4. The involvement of the PgpA P-glycoprotein of Leishmania spp. in low-level resistance to arsenite and antimonials. We raise the possibility that this protein transports glutathione conjugates of arsenite and antimonials rather than the compounds themselves. 5. Loss of drug activation as the main mechanism of metronidazole resistance in Trichomonas and Giardia spp. Recent evidence indicates that a decrease of the proximal cellular electron donor for metronidazole activation, ferredoxin, is the main cause of resistance in Trichomonas. 6. Resistance arising through alteration of drug targets. The amino acid substitutions in the dihydrofolate reductase-thymidylate synthase of Plasmodium spp. are good examples of this mechanism.(ABSTRACT TRUNCATED AT 400 WORDS)
Inhibition of Scytalone Dehydratase in Melanin Biosynthesis by Carpropamid, a Novel Rice Blast Controlling Agent (1998)

イネいもち病に対して優れた防除効果を持つカルプロパミドは in vivo でメラニン合成系のシタロン脱水過程を阻害する. この阻害がシタロン脱水酵素を直接阻害することによるか否かについて調べた結果, カルプロパミドはイネいもち病菌の粗酵素抽出液中のシタロン脱水酵素活性を強く抑制した. さらに, 大腸菌で大量発現したイネいもち病菌のシタロン脱水酵素を用いてカルプロパミドによるシタロン脱水酵素の阻害をみたところ, 非常に特異的に (Ki=0.14nM) 基質と競合的に阻害するととが示唆された.
Vc: A C++ library for explicit vectorization (2011)

SUMMARY It is an established trend that CPU development takes advantage of Moore's Law to improve in parallelism much more than in scalar execution speed. This results in higher hardware thread counts (MIMD) and improved vector units (SIMD), of which the MIMD developments have received the focus of library research and development in recent years. To make use of the latest hardware improvements, SIMD must receive a stronger focus of API research and development because the computational power can no longer be neglected and often auto‐vectorizing compilers cannot generate the necessary SIMD code, as will be shown in this paper. Nowadays, the SIMD capabilities are sufficiently significant to warrant vectorization of algorithms requiring more conditional execution than was originally expected for Streaming SIMD Extension to handle. The Vc library ( http://compeng.uni‐frankfurt.de/?vc ) was designed to support developers in the creation of portable vectorized code. Its capabilities and performance have been thoroughly tested. Vc provides portability of the source code, allowing full utilization of the hardware's SIMD capabilities, without introducing any overhead. Copyright © 2011 John Wiley &amp; Sons, Ltd.
Male Infertility Caused by Epididymal Dysfunction in Transgenic Mice Expressing a Dominant Negative Mutation of Retinoic Acid Receptor α1 (1997)

Retinoids are thought to be required for the normal development and maturation of a number of tissues, including most epithelia. The action of retinoids appears to be mediated through the binding to retinoic acid receptors (RARs) in the nucleus. The activity of retinoic acid can be inhibited in cells carrying dominant negative mutations of RAR alpha. We created transgenic mice expressing a dominant negative mutant of RAR alpha driven by the murine mammary tumor virus promoter. Expression of the transgene was evident in the epididymis and vas deferens in transgenic males. These males were either infertile or had reduced fertility, and the epithelium lining the ducts of the epididymis and vas deferens had undergone squamous metaplasia. Sperm developed normally in the testis but degenerated in the epididymis and vas deferens because inspissated ductal fluid blocked the normal passage of the sperm.
A New Iterative Approach to the Corrective Security-Constrained Optimal Power Flow Problem (2008)

This paper deals with techniques to solve the corrective security-constrained optimal power flow (CSCOPF) problem. To this end, we propose a new iterative approach that comprises four modules: a CSCOPF which considers only a subset of potentially binding contingencies among the postulated contingencies, a (steady-state) security analysis (SSSA), a contingency filtering (CF) technique, and an OPF variant to check post-contingency state feasibility when taking into account post-contingency corrective actions. We compare performances of our approach and its possible variants with classical CSCOPF approaches such as the direct approach and Benders decomposition (BD), on three systems of 60, 118, and 1203 buses.
THE ELECTRON-TRANSPORT PROTEINS OF HYDROXYLATING BACTERIAL DIOXYGENASES (1992)

The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the substrate by nonheme iron-containing dioxygenases. These enzymes consist of two or three soluble proteins that interact to form an electron-transport chain that transfers electrons from reduced nucleotides (NADH) via flavin and [2Fe-2S] redox centers to a terminal dioxygenase. The dioxygenases may be classified in terms of the number of constituent components and the nature of the redox centers. Class I consists of two-component enzymes in which the first protein is a reductase containing both a flavin and a [2Fe-2S] redox center and the second component is the oxygenase; Class II consists of three-component enzymes in which the flavin and [2Fe-2S] redox centers of the reductase are on a separate flavoprotein and ferredoxin, respectively; and Class III consists of three-component enzymes in which the reductase contains both a flavin and [2Fe-2S] redox center but also requires a second [2Fe-2S] center on a ferredoxin for electron transfer to the terminal oxygenase. Further subdivision is based on the the type of flavin (FMN or FAD) in the reductase, the coordination of the [2Fe-2S] center in the ferredoxin, and the number of terminal oxygenase subunits. From the deduced amino acid sequence of several dioxygenases the ligands involved in the coordination of the nucleotides, iron-sulfur centers, and mononuclear nonheme iron active site are proposed. On the basis of their spectroscopic properties and unusually high redox potentials, the [2Fe-2S] clusters of the ferredoxins and terminal oxygenases have been assigned to the class of Rieske-type iron-sulfur proteins. The iron atoms in the Rieske iron-sulfur cluster are coordinated to the protein by two histidine nitrogens and two cysteine sulfurs.