gebhart/patrepeval huggingface dataset:
Rhizomucor miehei triglyceride lipase is synthesized as a precursor (1988)

A Rhizomucor miehei cDNA library constructed in Escherichia coli was screened with synthetic oligonucleotides designed from knowledge of a partial amino acid sequence of the secreted triglyceride lipase (triacylglycerol acylhydrolase EC 3.1.1.3) from this fungus. Lipase-specific recombinants were isolated and their insert sequenced. Unlike characterized bacterial and mammalian triglyceride lipases, the fungal enzyme is synthesized as a precursor, including a 70 amino acid residue propeptide between the 24 amino acid residues of the signal peptide and the 269 residues of the mature enzyme. The precursor processing mechanism, which involves cleavage between a methionine and a serine residue, is unknown. By sequence comparison with other lipases, a serine residue involved in substrate binding was identified in the fungal lipase. The sequence around this residue is well-conserved among characterized lipases. Conservation of an intron in an isolated cDNA recombinant and immunoprecipitation of in vitro synthesized R. miehei translation products indicates that the expression of the lipase gene might involve inefficient mRNA splicing.
Single-Wall Carbon Nanotubes Supported Platinum Nanoparticles with Improved Electrocatalytic Activity for Oxygen Reduction Reaction (2006)

Significant enhancement in the electrocatalytic activity of Pt particles toward oxygen reduction reaction (ORR) has been achieved by depositing them on a single wall carbon nanotubes (SWCNT) support. Compared to a commercial Pt/carbon black catalyst, Pt/SWCNT films cast on a rotating disk electrode exhibit a lower onset potential and a higher electron-transfer rate constant for oxygen reduction. Improved stability of the SWCNT support is also confirmed from the minimal change in the oxygen reduction current during repeated cycling over a period of 36 h. These studies open up ways to utilize SWCNT/Pt electrocatalyst as a cathode in the proton-exchange-membrane-based hydrogen and methanol fuel cells.
Synovium as a source of interleukin 6 in vitro. Contribution to local and systemic manifestations of arthritis. (1989)

Synovial inflammation is often associated with systemic changes, such as increased levels of acute phase proteins and hypergammaglobulinemia, which cannot be explained by the cytokines described in synovial fluids and synoviocyte secretions. Interleukin 6 (IL-6) has recently been characterized as a mediator of multiple inflammatory responses. This cytokine promotes T and B lymphocyte growth and differentiation, and acute phase protein synthesis. We therefore examined IL-6 production by human synoviocytes and its presence in synovial fluids. In vitro, synoviocytes spontaneously released IL-6, which was increased by IL-1 and tumor necrosis factor-alpha. Synoviocyte-derived IL-6 activity was able to induce hybridoma-plasmacytoma proliferation, and immunoglobulin and acute-phase protein synthesis. The synovial fluids from patients with diverse arthropathies contained IL-6 activity, but higher levels were present in inflammatory arthropathies than in osteoarthritis. These results demonstrate that synoviocytes are a potent source of IL-6, which can contribute to important manifestations of inflammatory arthropathies.
Significance of Intermediate Values of Fractional Flow Reserve in Patients With Coronary Artery Disease (2016)

FFR in and around the gray zone bears a major prognostic value, especially in proximal lesions. These data confirm that FFR≤0.80 is valid to guide clinical decision making.
Synbiotics reduce allergen-induced T-helper 2 response and improve peak expiratory flow in allergic asthmatics (2010)

Four-week treatment with synbiotics had no effect on bronchial inflammation and LAR, but did significantly reduce systemic production of Th2-cytokines after allergen challenge and improved PEF.
ADAMTS-1 Protein Anchors at the Extracellular Matrix through the Thrombospondin Type I Motifs and Its Spacing Region (1998)

Cellular disintegrin and metalloproteinases (ADAMs) are a family of genes with a sequence similar to those of snake venom metalloproteinases and disintegrins. The ADAMTS-1 gene encodes a new type of ADAM protein with respect to possessing the thrombospondin (TSP) type I motifs. Expression of the gene is induced in kidney and heart by in vivo administration of lipopolysaccharide, suggesting a possible role in the inflammatory reaction. In this study, we characterized the ADAMTS-1 gene product by using a transient expression system in COS-7 cells. We found that the precursor and processed forms of ADAMTS-1 were secreted from cells. Under normal growth conditions, little or none of both forms was detected in the cell culture medium, and instead the majority was found associated with the extracellular matrix (ECM). In addition, when cells were cultured in the presence of heparin, the mature form of ADAMTS-1 protein was detected in the cell culture medium, suggesting that binding of ADAMTS-1 to the ECM is mediated through sulfated glycosaminoglycans such as heparan sulfate. Analyses of deletion mutants of the ADAMTS-1 protein revealed that the spacer region as well as three TSP type I motifs in the carboxyl-terminal region of the ADAMTS-1 protein are important for a tight interaction with the ECM. These results suggest that the ADAMTS-1 is a unique ADAM family protein that anchors at the ECM.
Rethinking Table Recognition using Graph Neural Networks (2019)

Document structure analysis, such as zone segmentation and table recognition, is a complex problem in document processing and is an active area of research. The recent success of deep learning in solving various computer vision and machine learning problems has not been reflected in document structure analysis since conventional neural networks are not well suited to the input structure of the problem. In this paper, we propose an architecture based on graph networks as a better alternative to standard neural networks for table recognition. We argue that graph networks are a more natural choice for these problems, and explore two gradient-based graph neural networks. Our proposed architecture combines the benefits of convolutional neural networks for visual feature extraction and graph networks for dealing with the problem structure. We empirically demonstrate that our method outperforms the baseline by a significant margin. In addition, we identify the lack of large scale datasets as a major hindrance for deep learning research for structure analysis and present a new large scale synthetic dataset for the problem of table recognition. Finally, we open-source our implementation of dataset generation and the training framework of our graph networks to promote reproducible research in this direction.
Soft self-consistent pseudopotentials in a generalized eigenvalue formalism (1990)

A new approach to the construction of first-principles pseudopotentials is described. The method allows transferability to be improved systematically while holding the cutoff radius fixed, even for large cutoff radii. Novel features are that the pseudopotential itself becomes charge-state dependent, the usual norm-conservation constraint does not apply, and a generalized eigenproblem is introduced. The potentials have a separable form well suited for plane-wave solid-state calculations, and show promise for application to first-row and transition-metal systems.
Aspartyl-tRNA synthetase fromEscherichia coli: cloning and characterisation of the gene, homologies of its translated amino acid sequence with asparaginyl- and lysyl-tRNA synthetases (1990)

By screening of an Escherichia coli plasmidic library using antibodies against aspartyl-tRNA synthetase (AspRS) several clones were obtained containing aspS, the gene coding for AspRS. We report here the nucleotide sequence of aspS and the corresponding primary structure of the aspartyl-tRNA synthetase, a protein of 590 amino acid residues with a Mr 65,913, a value in close agreement with that observed for the purified protein. Primer extension analysis of the aspS mRNA using reverse transcriptase located its 5'-end at 94 nucleotides upstream of the translation initiation AUG; nuclease S1 analysis located the 3'-end at 126 nucleotides downstream of the stop codon UGA. Comparison of the DNA-derived protein sequence with known aminoacyl-tRNA sequences revealed important homologies with asparaginyl- and lysyl-tRNA synthetases from E.coli; more than 25% of their amino acid residues are identical, the homologies being distributed preferencially in the first part and the carboxy-terminal end of the molecule. Mutagenesis directed towards a consensus tetrapeptide (Gly-Leu-Asp-Arg) and the carboxy-terminal end showed that both domains could be implicated in catalysis as well as in ATP binding.
A Fibronectin Fragment Alters the Metabolism by Rabbit Intervertebral Disc Cells In Vitro (2005)

Treatment of NP cells in vitro with Fn-f led to changes in matrix proteins and gene expression similar to those seen during disc degeneration in vivo. This supports a possible detrimental role of the N-terminal fibronectin fragment in degenerative disc disease.
Radio frequency identification &#x2014; An innovative solution to guide dexterous prosthetic hands (2011)

Dexterous manipulation of a multi-fingered prosthetic hand requires far more cognitive effort compared to typical 1 degree of freedom hands, which hinders their acceptance clinically. This paper presents a Myoelectrically-Operated Radio Frequency Identification (RFID) Prosthetic Hand (MORPH); an implementation of RFID with a myoelectric prosthetic hand as a means to amplify the controllable degrees of freedom. Contextual information from an object equipped with an RFID tag allows automatic preshaping along with dexterous control in an attempt to reduce the cognitive effort required to operate the terminal device. The myoelectric-RFID hybrid has been demonstrated in a proof-of-concept case study where an amputee was fitted with the device and subjected to activities adapted from the Jebsen Hand Function Test and the Smith Hand Function Evaluation with RFID-tagged and untagged items. Evaluation tests revealed that the MORPH system performed significantly better in 4 of the 8 tasks, and comparable to the control in the remainder.
The Reactions of Diaminomaleonitrile with Isocyanates and Either Aldehydes or Ketones Revisited (2001)

A reinvestigation of the reactions of urea derivatives of diaminomaleonitrile 2 with aldehydes or ketones in the presence of triethylamine has established that the products of these reactions are not pyrimidino[5,4-d]pyrimidines 9 as previously reported, but 8-oxo-6-carboxamido-1,2-dihydropurines 12, which are oxidized rapidly in air to the corresponding 6-carboxamidopurines 13. Similarly, the reaction of Schiff base derivatives of DAMN 5 with isocyanates in the presence of triethylamine gives the substituted 2-oxoimidazoles 20 and not the pyrimidine derivatives 8 as previously claimed. The compounds 20 cyclize in solution and are easily oxidized to 8-oxopurine-6-carbonitriles 22, which give the same 8-oxopurine-6-carboxamides 13 upon further hydrolysis.
The development of photoreceptors in the zebrafish, Brachydanio rerio. I. Structure (1984)

Morphological development of photoreceptors in the central retina of the zebrafish, Brachydanio rerio, was studied by using light and electron microscopic techniques. Outer segments (OS) first appeared at 2.5 days postfertilization (d2.5). On d3, synaptic elaborations were seen. By d8, two OS types were present and were identified as cones. The first indication of rod formation was also evidenced at this time, when vitreally positioned nuclei were observed and rodlike cells were infrequently detected in electron micrographs. At d12, the full complement of zebrafish photoreceptors, rods and four cone types, was identified. From this time on cells grew until adult dimensions were reached at d24. These structural observations are consistent with results of functional studies which utilized physiological and behavioral techniques.
A genetic algorithm for multiprocessor scheduling (1994)

The problem of multiprocessor scheduling can be stated as finding a schedule for a general task graph to be executed on a multiprocessor system so that the schedule length can be minimized. This scheduling problem is known to be NP-hard, and methods based on heuristic search have been proposed to obtain optimal and suboptimal solutions. Genetic algorithms have recently received much attention as a class of robust stochastic search algorithms for various optimization problems. In this paper, an efficient method based on genetic algorithms is developed to solve the multiprocessor scheduling problem. The representation of the search node is based on the order of the tasks being executed in each individual processor. The genetic operator proposed is based on the precedence relations between the tasks in the task graph. Simulation results comparing the proposed genetic algorithm, the list scheduling algorithm, and the optimal schedule using random task graphs, and a robot inverse dynamics computational task graph are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Distinct but Overlapping Epitopes for the Interaction of a CC-Chemokine with CCR1, CCR3, and CCR5 (1997)

Chemokines play an important role in inflammation. The mechanism via which they bind to more than one receptor and activate them is not well understood. The chemokines are thought to interact with their receptors via two distinct sites, one necessary for binding and the other for activation of signal transduction. In this study we have used alanine scanning mutagenesis to identify residues on RANTES that specifically interact with its receptors CCR1, CCR3, and CCR5 for binding and activation. Residues within a potential receptor binding site known as the N-loop (residues 12-20) and near the N-terminus of RANTES were individually mutated to alanine. The results of this study show that, within the N-loop, the side chain of R17 is necessary for RANTES binding to CCR1, F12 for binding to CCR3, and F12 and I15 for binding to CCR5, thus forming distinct but overlapping binding epitopes. In addition, our finding that P2 is necessary for binding to CCR5 is the first to show that a residue near the N-terminus of a CC-chemokine is involved in binding to a receptor. We have also found that P2, D6, and T7 near the N-terminus are involved in activating signal transduction via CCR1, P2 and Y3 via CCR3, and Y3 and D6 via CCR5. These results indicate that RANTES interacts with each of its receptors in a distinct and specific manner and provide further evidence to support the two-site model of interaction between chemokines and their receptors.
An open-label, phase II trial of nanoparticle albumin bound paclitaxel (nab-paclitaxel), carboplatin, and bevacizumab in first-line patients with advanced non-squamous non-small cell lung cancer (NSCLC) (2007)

7610 Background: The development of nab-paclitaxel has circumvented many of the infusion difficulties that are associated with standard solvent based paclitaxel (in cremophor). In this open label, phase II trial, patients with advanced (stage IIIB or IV) nonsquamous NSCLC received the combination of nab-paclitaxel, carboplatin and bevacizumab. Methods: 50 patients were enrolled between October 2005 and April 2006. Patients received intravenous (IV) nab-paclitaxel 300 mg/m 2 , carboplatin IV AUC=6, and bevacizumab 15 mg/kg on day 1 of each 21-day cycle. Responding patients received at least 4 cycles of treatment; however, therapy was discontinued for patients with progression or intolerable toxicity. The primary endpoint was response rate based on RECIST. Results: The median patient age was 67 years; 80% were white and 56% were female. Patients received a median of 4 cycles (range, &lt;1–6). The preliminary efficacy results are PR 30% and SD 48%; no complete responses were noted. Median progression-free survival was 7.1 months (range, &lt;1–10.6); median survival has not yet been reached. Grade 3–4 treatment related toxicities were neutropenia (52%); fatigue (19%); neuropathy (15%); thrombocytopenia (10%) dyspnea (6%), anorexia, constipation, febrile neutropenia, hemoptysis, and nausea and/or vomiting (4% each). 64% of patients are currently alive. 32 patients have come off study, prior to 4 cycles due to disease progression (12%), adverse event (10%), investigator request (8%), sudden death (6%), and withdrawal of consent (2%); 16 patients had normal study completion (completed 4 cycles of therapy). Conclusions: This combination of nab-paclitaxel, carboplatin and bevacizumab was well tolerated, with moderate neutropenia. Adverse events were manageable. The preliminary analysis from this study indicates that this combination has promising activity in first-line patients with non-squamous NSCLC. This research was supported, in part, by a research grant from Abraxis BioScience, Inc., Santa Monica, CA. No significant financial relationships to disclose.
Mta, a global MerR‐type regulator of the Bacillus subtilis multidrug‐efflux transporters (1999)

Little is known about the natural functions of multidrug-efflux transporters expressed by bacteria. Although identified as membrane proteins actively extruding exogenous toxins from the cell, they may actually be involved in the transport of as yet unidentified specific natural substrates. The expression of two highly similar multidrug transporters of Bacillus subtilis, Bmr and Blt, is regulated by specific transcriptional activators, BmrR and BltR, respectively, which respond to different inducer molecules, thus suggesting distinct functions for the two transporters. Here, we describe an alternative mechanism of regulation, which involves a global transcriptional activator, Mta, a member of the MerR family of bacterial regulatory proteins. The individually expressed N-terminal DNA-binding domain of Mta interacts directly with the promoters of bmr and blt and induces transcription of these genes. Additionally, this domain stimulates the expression of the mta gene itself and at least one more gene, ydfK, which encodes a hypothetical membrane protein. These results and the similarity of Mta to the thiostrepton-induced protein TipA of Streptomyces lividans strongly suggest that Mta is an autogenously controlled global transcriptional regulator, whose activity is stimulated by an as yet unidentified inducer. This stimulation is mimicked by the removal of the C-terminal inducer-binding domain. The fact that both Bmr and Blt are controlled by this regulator demonstrates that some of their functions are either identical or, at least, related. Further analysis of Mta-mediated regulation may reveal the natural function of the system of multidrug transporters in B. subtilis and serve as a paradigm for similar systems in other bacteria.
Software support for distributed and parallel computing (1996)

This dissertation addresses creating portable and efficient parallel programs for scientific computing. Both of these aspects are important. Portability means the program can execute on any parallel machine. Efficiency means there is little or no penalty for using our solution instead of hand-coded, architecture-specific programs. Although parallel programming is necessarily more difficult than sequential programming, it is currently more complicated than it has to be. The Filaments package provides fine-grain parallelism and a shared memory programming model. It can be viewed as a "least common denominator" for parallel scientific computing. Fine-grain parallelism supports any number (even thousands) of threads, and shared memory provides a natural programming model. Consequently, the combination allows the programmer to concentrate on the application and not the architecture of the target machine. The Filaments package makes extensive use of run-time decision making. Run-time decision making has several advantages. First, it is often possible to make a better decision because more information is available at run time. Second, run-time decision making can obviate the need for complex, often intractable, static analysis. Moreover, run-time decision making leads to much of the package's efficiency.
Genetic progression model for head and neck cancer: implications for field cancerization. (1996)

A genetic progression model of head and neck squamous cell carcinoma has not yet been elucidated, and the genetic basis for "field cancerization" of the aerodigestive tract has also remained obscure. Eighty-seven lesions of the head and neck, including preinvasive lesions and benign lesions associated with carcinogen exposure, were tested using microsatellite analysis for allelic loss at 10 major chromosomal loci which have been defined previously. The spectrum of chromosomal loss progressively increased at each histopathological step from benign hyperplasia to dysplasia to carcinoma in situ to invasive cancer. Adjacent areas of tissue with different histopathological appearance shared common genetic changes, but the more histopathologically advanced areas exhibited additional genetic alterations. Abnormal mucosal cells surrounding preinvasive and microinvasive lesions shared common genetic alterations with those lesions and thus appear to arise from a single progenitor clone. Based on these findings, the local clinical phenomenon of field cancerization seems to involve the expansion and migration of clonally related preneoplastic cells.
Granulocyte colony-stimulating factor crosses the placenta and stimulates fetal rat granulopoiesis (1993)

We studied the effect of recombinant human granulocyte colony-stimulating factor (rhG-CSF) administration to pregnant rats upon fetal and neonatal myelopoiesis. Pregnant rats were treated with rhG-CSF twice daily for 2, 4, and 6 days before parturition. rhG-CSF crossed the placenta and reached peak fetal serum concentrations 4 hours after administration. Peak fetal serum levels were 1,000-fold lower than levels detected in the dam. Hematopoietic effects of rhG-CSF were assessed by cytologic analysis of the newborn blood, spleen, bone marrow, thymus, and liver. White blood cell counts were increased twofold to fourfold in newborns. This increase was due to circulating numbers of polymorphonuclear cells (PMN). rhG-CSF induced a myeloid hyperplasia in the newborn marrow consisting of immature and mature myeloid cells in the day-2 and day-4 treated pups. Bone marrow of pups treated for 6 days contained mostly hyper-segmented PMN with little or no increase in myeloid precursors. An increase in the number of postmitotic (PMN, bands, and metamyelocytes) and mitotic (promyeloblasts, myeloblasts, and metamyeloblasts) myeloid cells in the spleen of neonates was observed. No change was detected in splenic lymphocytes or monocytes. No effect of rhG-CSF was noted in the newborn liver or thymus. These results demonstrate that maternally administered rhG-CSF crosses the placenta and specifically induces bone marrow and spleen myelopoiesis in the fetus and neonate. The significant myelopoietic effects of rhG-CSF at low concentrations in the fetus suggest an exquisite degree of developmental sensitivity to this cytokine and may provide enhanced defense mechanisms to the neonate.