gebhart/patrepeval huggingface dataset:
CODEC for echo-canceling, full-rate ADSL modems (1999)

A CODEC, fabricated in 3.3-V CMOS, provides the low-voltage transmitter and receiver interfaces between the modem digital signal processing engine and the high-voltage hybrid circuitry for either the central office or the remote terminal ends of the subscriber loop, configurable by metal mask option. Extensive use of digital interpolation filters in the transmitter, decimation filters in the receiver, and oversampled data converters minimize the complexity of analog filters. On-chip filtering and 14-bit data converters support echo-canceling modems without requiring external filters. With additional external filters, frequency-division duplexing is also supported. The die area is 67.5 mm/sup 2/. The power dissipation in the central office and remote terminal are 600 and 760 mW, respectively.
Formation of the Premise of Raw-House Districts of Meiji Era. (1990)

MOST OF THE SPRAWLED DEVELOPMENTS IN THE OUTSKIRTS OF OSAKA CITY WAS TAKEN PLACE DURING THE LATTER PART OF THE MEIJI ERA. BUT, STILL, THE PROCESS OF THOSE DEVELOPMENTS HAVE NOT BEEN BROUGHT IN TO THE LIGHT. THIS STUDY BY ANALYZING THE LAND REGISTERS, IS AN ATTEMPT TO IDENTIFY THE SITUATION OF THE TANIMACHI RAW-HOUSE DISTRICT OF OSAKA BEFORE IT'S SPRAWLED DEVELOPMENTS. THE WESTERN PART OF THE DISTRICT(QUARTER) WAS DEVELOPED DURING THE EDO PERIOD BY LAND OWNERS, IN A MORE SYSTEMATIC WAY. BUT, THE OTHER PART WAS DEVELOPED DURING THE MEIJI ERA AS A RESULT OF THE SPRAWLED DEVELOPMENT, IN A MORE FRAGMENTED WAY. THUS, THE URBAN FABRIC OF THE TANIMACHI AREA, NOW POSSESSES TWO DISTINCTIVE URBAN PATTERNS.
The RIP‐like kinase, RIP3, induces apoptosis and NF‐κB nuclear translocation and localizes to mitochondria (2000)

A RIP-like protein, RIP3, has recently been reported that contains an N-terminal kinase domain and a novel C-terminal domain that promotes apoptosis. These experiments further characterize RIP3-mediated apoptosis and NF-kappaB activation. Northern blots indicate that rip3 mRNA displays a restricted pattern of expression including regions of the adult central nervous system. The rip3 gene was localized by fluorescent in situ hybridization to human chromosome 14q11.2, a region frequently altered in several types of neoplasia. RIP3-mediated apoptosis was inhibited by Bcl-2, Bcl-x(L), dominant-negative FADD, as well as the general caspase inhibitor Z-VAD. Further dissection of caspase involvement in RIP3-induced apoptosis indicated inhibition by the more specific inhibitors Z-DEVD (caspase-3, -6, -7, -8, and -10) and Z-VDVAD (caspase-2). However, caspase-1, -6, -8 and -9 inhibitors had little or no effect on RIP3-mediated apoptosis. Mutational analysis of RIP3 revealed that the C-terminus of RIP3 contributed to its apoptotic activity. This region is similar, but distinct, to the death domain found in many pro-apoptotic receptors and adapter proteins, including FAS, FADD, TNFR1, and RIP. Furthermore, point mutations of RIP3 at amino acids conserved among death domains, abrogated its apoptotic activity. RIP3 was localized by immunofluorescence to the mitochondrion and may play a key role in the mitochondrial disruptions often associated with apoptosis.
Learning Human Motion Models for Long-Term Predictions (2017)

We propose a new architecture for the learning of predictive spatio-temporal motion models from data alone. Our approach, dubbed the Dropout Autoencoder LSTM (DAELSTM), is capable of synthesizing natural looking motion sequences over long-time horizons1 without catastrophic drift or motion degradation. The model consists of two components, a 3-layer recurrent neural network to model temporal aspects and a novel autoencoder that is trained to implicitly recover the spatial structure of the human skeleton via randomly removing information about joints during training. This Dropout Autoencoder (DAE) is then used to filter each predicted pose by a 3-layer LSTM network, reducing accumulation of correlated error and hence drift over time. Furthermore to alleviate insufficiency of commonly used quality metric, we propose a new evaluation protocol using action classifiers to assess the quality of synthetic motion sequences. The proposed protocol can be used to assess quality of generated sequences of arbitrary length. Finally, we evaluate our proposed method on two of the largest motion-capture datasets available and show that our model outperforms the state-of-the-art techniques on a variety of actions, including cyclic and acyclic motion, and that it can produce natural looking sequences over longer time horizons than previous methods.
Genomic and functional characterization of polyunsaturated fatty acid biosynthesis in Caenorhabditis elegans (2001)

The biosynthetic pathway for polyunsaturated fatty acids in the model animal Caenorhabditis elegans was examined in the context of the completed genome sequence. The genomic organization and location of seven desaturase genes and one elongase activity, all previously identified by functional characterization, were elucidated. A pathway for the biosynthesis of polyunsaturated fatty acids in C. elegans was proposed based on these genes. The role of gene duplication in enzyme evolution and proliferation is discussed.
Strategies for the Use of Epoetin Alfa in Breast Cancer Patients (1998)

Anemia is a common complication in cancer patients undergoing chemotherapy, and its severity depends on both the type of antineoplastic drugs and the clinical status of the patient. Breast cancer patients undergoing standard chemotherapy develop clinically significant anemia in up to 25% of cases. This percentage, moreover, increases up to 63% when more intensive chemotherapy regimens are used. The therapeutic use of erythropoietin in anemic patients, i.e., in patients with hemoglobin levels below 9-10.5 g/dl, is able to correct the anemic status in nearly 40%-80% of such patients, but it does not completely eliminate the need of blood transfusions: 20%-40% of patients need to be transfused despite the erythropoietin treatment. An alternative strategy for optimizing the erythropoietin treatment is its use in the prevention of anemia, i.e., in patients with normal hemoglobin values but at high risk of becoming anemic. In a phase III study, we evaluated the role of erythropoietin in the prevention of anemia in breast cancer patients undergoing dose-intensive chemotherapy. Clinically significant anemia occurred in 52% (95% CI = 33-69) of control patients and in no patient (95% CI = 0-14) in the erythopoietin arm (p =.00001). After six cycles of chemotherapy the mean hemoglobin decrease was 3.05 g/dl (&plusmn; 1.0, 95% CI = 2.6-3.5) in the control arm and 0.8 g/dl (&plusmn; 1.4, 95% CI = 0.3-1.4) in the erythropoietin arm. Moreover, 6.4% of control patients needed blood transfusion compared to no patients in the erythropoietin arm. Erythropoietin is active in both the treatment and the prevention of anemia in cancer patients undergoing chemotherapy. Due to its high economic cost, efforts should be made to identify subsets of patients in whom the preventive use could be cost-effective. Patients undergoing chemotherapy associated with a high risk of anemia could benefit from preventive use of erythropoietin in special circumstances, such as presence of risk of myocardial or cerebral ischemia, uncommon blood group, or religious beliefs hindering blood transfusions. Moreover, anemia prevention could be considered in patients at high risk of requiring blood transfusions, such as patients with low baseline value of hemoglobin or with a hemoglobin decrease of >/=2 g/dl after the first cycle of chemotherapy.
Cytoscape: A Community-Based Framework for Network Modeling (2009)

Cytoscape is a general network visualization, data integration, and analysis software package. Its development and use has been focused on the modeling requirements of systems biology, though it has been used in other fields. Cytoscape's flexibility has encouraged many users to adopt it and adapt it to their own research by using the plugin framework offered to specialize data analysis, data integration, or visualization. Plugins represent collections of community-contributed functionality and can be used to dynamically extend Cytoscape functionality. This community of users and developers has worked together since Cytoscape's initial release to improve the basic project through contributions to the core code and public offerings of plugin modules. This chapter discusses what Cytoscape does, why it was developed, and the extensions numerous groups have made available to the public. It also describes the development of a plugin used to investigate a particular research question in systems biology and walks through an example analysis using Cytoscape.
Highly c-axis-oriented AlN film using MOCVD for 5GHz-band FBAR filter (2004)

We have successfully developed to deposit highly c-axis-oriented aluminum nitride (AlN) film using metal-organic-chemical-vapor deposition (MOCVD). Full-width at half-maximum (FWHM) of the deposited AlN(0002) film whose thickness was 1 /spl mu/m has found to be 2.98/spl deg/. The value of FWHM means the deposited film has the electromechanical coupling coefficient (K/sup 2/) of 6.4%. The conditions of deposition were substrate temperature of 1050/spl deg/C, pressure of 20Torr, and V-III ratio of 25000. Film-bulk-acoustic resonator (FBAR) band-pass filter for 5 GHz orthogonal-frequency-division multiplexing (OFDM) wireless local area network (WLAN) system has been designed using the c-axis-oriented AlN film. The designed band-pass filter has the sufficient bandwidth of more than 100 MHz, which is evaluated from butterworth-van dyke (BVD) equivalent circuit model of FBAR.
Epoxy Sepabeads: A Novel Epoxy Support for Stabilization of Industrial Enzymes via Very Intense Multipoint Covalent Attachment (2002)

Sepabeads-EP (a new epoxy support) has been utilized to immobilize-stabilize the enzyme penicillin G acylase (PGA) via multipoint covalent attachment. These supports are very robust and suitable for industrial purposes. Also, the internal geometry of the support is composed by cylindrical pores surrounded by the convex surfaces (this offers a good geometrical congruence for reaction with the enzyme), and it has a very high superficial density of epoxy groups (around 100 micromol/mL). These features should permit a very intense enzyme-support interaction. However, the final stability of the immobilized enzyme is strictly dependent on the immobilization protocol. By using conventional immobilization protocols (neutral pH values, nonblockage of the support) the stability of the immobilized enzyme was quite similar to that achieved using Eupergit C to immobilize the PGA. However, when using a more sophisticated three-step immobilization/stabilization/blockage procedure, the Sepabeads derivative was hundreds-fold more stable than Eupergit C derivatives. The protocol used was as follows: (i) the enzyme was first covalently immobilized under very mild experimental conditions (e.g., pH 7.0 and 20 degrees C); (ii) the already immobilized enzyme was further incubated under more drastic conditions (higher pH values, long incubation periods, etc.) in order to "facilitate" the formation of new covalent linkages between the immobilized enzyme molecule and the support; (iii) the remaining epoxy groups of the support were blocked with very hydrophilic compounds to stop any additional interaction between the enzyme and the support. This third point was found to be critical for obtaining very stable enzymes: derivatives blocked with mercaptoethanol were much less stable than derivatives blocked with glycine or other amino acids. This was attributed to the better masking of the hydrophobicity of the support by the amino acids (having two charges).
Studies on the primary structure of the influenza virus hemagglutinin. (1975)

The amino-terminal sequence and composition of the subunits of the hemagglutinin (HA) of influenza virus has been determined. The hemagglutinin has been isolated by two techniques. (1) as the intact hemagglutinin after disruption of the virus in sodium dodecyl sulfate, giving 2 subunits of 58,000 daltons (HA1) and 26,000 daltons (HA2), and (2) after treatment of the virus with bromelain, giving 2 subunits of 58,000 daltons (BHA1) and 21,000 daltons (BHA2). In both preparations these subunits are linked by disulfide bonds. The aminoterminal sequences of HA1 and BHA1, and HA2 and BHA2 are the same. The composition of the 50 residue peptide associated with the membrane, which is removed from the C-terminus of HA2 by bromelain, is deduced and shown to be hydrophobic and contain 50% of the serine residues of HA2. The biosynthetic precursor of the hemagglutinin has been purified from the membranes of abortively infected chick fibroblasts and shown to have the same amino terminus as HA1. Thus the order of biosynthesis is NH2-HA1-HA2-COOH. The amino-terminal sequence of BHA2--at the cleavage site of the precursor--is shown to be a palindrome: NH2-Gly-Leu-Phe-Gly-Ala-Ile-Ala-Gly-Phe-Ile-. This sequence is conserved in representative viruses from each of the major pandemics. A region of homologous sequence is described between the hemagglutinins of influenza type A and B viruses.
Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools (2014)

The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches.
Characterization of the Proteases in the Crude Mite Extract (1989)

Characterization of the proteases was performed in the crude mite extract fractionated by Sephacryl S-200 gel filtration. Three peaks of protease activities were detected in the fractions. From the results of substrate specificity and susceptibility to the inhibitors, PK.1 protease (about 60 kD) is suggested to be a trypsin-like protease of mites. From the results of susceptibility to various agents, PK.2 (about 30 kD) and PK.3 (about 20 kD) proteases may be cysteine proteases, e.g., papain and cathepsin B. PK.3 protease existed in the precipitate of 60% ammonium sulfate fractionation. The data in the present study suggest the possibility that Dermatophagoides farinae I allergen might be a cysteine protease probably derived from the gastrointestinal tract of the house dust mite.
A user interface for distributed multimedia database querying with mediator supported refinement (2003)

The Delaunay/sup MM/ system supports an interactive, customizable interface for querying multimedia distributed databases, such as digital libraries. Through this interface, users select virtual document styles that cater the display of query results to their needs, while also offering transparent preand post-query refinement and querying. Delaunay/sup MM/'s virtual documents preserve context by maintaining a single customizable interface for result viewing. The advanced transparent query features rely on mediation to provide adept access to information. In this paper, we present the framework for Delaunay/sup MM/, its architecture, the user interface, and results of the first usability study.
Delayed hypersensitivity skin testing as a prognostic indicator in patients with small cell lung cancer (1983)

The prognostic importance of pretreatment delayed hypersensitivity skin test reactivity was determined in 154 newly diagnosed, carefully staged and aggressively treated small cell lung cancer patients. One hundred twenty-one patients were reactive to at least 1 of 5 skin test antigens and 33 were anergic. Skin test reactive patients survived significantly longer than anergic patients. This result was expected since there was a significant trend for reactive patients to have good performance status (P = 0.005) and low tumor burden (P = 0.005) compared to anergic patients. The principal finding of this study was that skin test reactivity was of prognostic utility primarily in otherwise good prognosis patients, i.e., individuals with good performance status and low tumor burden. In this group anergy was associated with significantly shortened survival (P = 0.025). In poor prognosis (poor performance status and high tumor burden) or intermediate prognosis (either poor performance status or high tumor burden) patients skin test reactivity or anergy had no significant influence on survival.
Immunogenicity ofMycobacterium tuberculosisAntigens inMycobacterium bovisBCG-Vaccinated andM. bovis-Infected Cattle (2006)

The development of novel vaccine strategies supplementing Mycobacterium bovis BCG (BCG) constitutes an urgent research challenge. To identify potential subunit vaccine candidates, we have tested a series of eight recently identified Mycobacterium tuberculosis antigens in M. bovis-infected and BCG-vaccinated cattle. These antigens were characterized on the basis of their ability to induce in vitro gamma interferon responses in infected or BCG-vaccinated calves. We were able to establish a hierarchy of these antigens based on how frequently they were recognized in both groups of animals. In particular, we were able to prioritize frequently recognized proteins like Rv0287, Rv1174, and Rv1196 for future evaluation as subunit vaccines to be used in BCG-protein heterologous prime-boost vaccination scenarios. In addition, the antigen most dominantly recognized in M. bovis-infected cattle in this study, Rv3616c, was significantly less frequently recognized by BCG vaccinees and could be a target to improve BCG, for example, by increasing its secretion, in a recombinant BCG vaccine.
Identification of the Peptides That Stimulate the Phosphoinositide Hydrolysis in Lymphocyte Cell Lines from Peptide Libraries (1996)

Peptides which stimulate the formation of inositol phosphates (InoPs) in lymphocyte cell lines were identified by screening synthetic peptide libraries composed of random sequences of hexapeptides. The peptides containing the consensus sequence XKYX(P/V)M were found to be most active in the phospholipase C (PLC)-mediated formation of InoPs in a human B myeloma cell line, U266. The peptides also stimulated the phosphoinositide hydrolysis and the release of [Ca2+]i in HL60 and U937 cell lines. On the other hand, these peptides showed no effect in the following cell lines: NIH3T3, PC12, Daudi, Sp2, Jurkat, H9, Molt-4, SupT-1, K562, and RBL-2H3. The result suggests the possibility that the peptides may have cell type specificity. Experiments with one of the active peptides, WKYMVM-NH2 showed that its action mimics the effect of AlF4- which is a G-protein activator in the InoPs generation, and pertussis toxin partially blocked the InoPs accumulation and [Ca2+]i release induced by the peptide in the U266 cells. Binding assays with the peptide labeled with 125I showed that U266 cells have a saturable number of binding sites for the peptide. Taken together, these results suggest that the peptides could activate PLC-mediated signal transduction via a pertussis toxin-sensitive G-protein coupled receptor in certain cell types.
Allogeneic bone marrow transplantation with a fixed low number of T cells in the marrow graft [see comments] (1994)

Despite prophylaxis with immunosuppressive drugs, severe acute graft-versus-host disease (GVHD) remains a major cause of morbidity and mortality in patients transplanted with unmodified bone marrow (BM) grafts from HLA-identical siblings. Although T-cell depletion of the BM graft has evolved as the most effective method to prevent severe acute GVHD, this beneficial effect is counterbalanced by an increased rate of graft failure and relapse of the disease. To find an approach to T-cell depletion that may avoid these extreme risks, we gave BM recipients a fixed low number of 1 x 10(5) donor T cells per kilogram of recipient's body weight in the graft. This corresponds with 99% T-cell depletion and is achieved by the addition of T cells to the graft that was previously depleted of T cells. A total of 70 patients with hematologic malignancies or aplastic anemia, including 40 patients with standard-risk leukemias, received BM grafts, depleted of T cells according to this approach, from HLA-identical siblings. The preparative regimen consisted of cyclophosphamide and total body irradiation. The patients also received a short course of cyclosporine posttransplant. Graft failure did not occur. Acute GVHD, only grade I or II, was seen in 70% of the patients and was limited to the skin in all patients. Chronic GVHD occurred in 31% of the patients and, with the exception of 1 patient, was limited to the skin as well. Relapse occurred in 3 of 40 (8%) patients with standard-risk leukemias, resulting in a projected survival at 5 years of 80%. Patients with standard-risk diseases had a procedure-related mortality of 11%. Quality of life, determined 1 year after BM transplant, was good in almost all patients with standard-risk diseases. Thus, this approach of T-cell depletion may be an approach that avoids the development of severe acute and chronic GVHD without damaging the function or antileukemic effect of the graft and that has a low transplant-related morbidity and mortality.
Immunological Aspects of Allergic Asthma (1994)

Asthma is a chronic obstructive disease of the lower airways. It is characterized by episodic exacerbations of at least partially reversible airflow limitation, along with bronchial hyperreactivity and airway inflammation. This latter characteristic, airway inflammation, is now a major focus of investigation, in large part because of a growing body of evidence to support its critical role in the pathogenesis of this disorder. Investigations of the histopathologic, cytologic, and chemical events accompanying fatal and nonfatal asthma, as well as experimental allergen-induced allergic reactions of the lower airways, have confirmed that a wide variety of immunologic phenomena occur, including local release of preformed mediators, newly synthesized metabolites of arachidonic acid, and soluble pro-inflammatory proteins including kinins and cytokines; alterations in vascular permeability and the development of airways edema; leukocyte activation and accumulation; and immune-mediated neurogenic responses that affect airway smooth muscle and other local responses. This information has led to new pharmacologic approaches designed to antagonize each of these elements of the asthmatic diathesis, with varying degrees of success. Nevertheless, the development of novel antagonists of mediators, pro-inflammatory proteins, cells, adhesion molecules, neuropeptides, and their respective receptors have begun to yield additional insight into their relative importance in the immunologic basis of asthma.
Characterization of Protein Glycosylation by MALDI-TOFMS (2003)

Glycosylation is one of the most common modifications in proteins. Among all characterized proteins, more than 50% are glycoproteins. During the last two decades, extensive knowledge about functional aspects of the glycans attached to the glycoproteins has been obtained (,). Structural characterization of glycoproteins, including glycan structure elucidation, is important for understanding their functions. Furthermore, characterization of glycosylation patterns of recombinant glycoproteins is of importance for both industry and pharmaceutical research.