gebhart/patrepeval huggingface dataset:
Chaxamycins A–D, Bioactive Ansamycins from a Hyper-arid DesertStreptomycessp. (2011)

Streptomyces sp. strain C34, isolated from soil collected in the Chilean hyper-arid Atacama Desert, was cultured on different media, resulting in the isolation and identification of four new ansamycin-type polyketides. The organism was selected for chemical investigation on the basis of a genome-mining PCR-based experiment targeting the gene encoding rifamycin-specific 3-amino-5-hydroxybenzoic acid synthetase (AHBA). The isolated compounds were structurally characterized using NMR and MS techniques and named chaxamycins A-D (1-4). Compounds 1-4 were tested for their antibacterial activity against Staphylococcus aureus ATCC 25923 and Escherichia coli ATCC 25922 and for their ability to inhibit the intrinsic ATPase activity of the heat shock protein 90 (Hsp90). Chaxamycin D (4), which showed a selective antibacterial activity against S. aureus ATCC 25923, was tested further against a panel of MRSA clinical isolates. In a virtual screening experiment, chaxamycins A-D (1-4) have also been docked into the ATP-binding pocket in the N-terminal domain of the Hsp90, and the observed interactions are discussed.
The degradative metabolism of l-cysteine and l-cystine in vitro by liver in cystinosis (1962)

Compounds containing N-terminal residues have been shown to be present in preparations of soluble collagen which account for most if not all the reaction of fluorodinitrobenzene with ac-amino groups.
Comprehensive computational design of ordered peptide macrocycles (2017)

Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with l-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of l- and d-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.
Fluorescence energy transfer measurements on cell surfaces: A critical comparison of steady‐state fluorimetric and flow cytometric methods (1984)

The energy transfer efficiency E was measured between fluorescein-conjugated concanavalin A (Con A) and rhodamine-conjugated Con A bound to homogeneous tissue culture cells, the HK22 murine lymphoma cell line. Results from a flow cytometric energy transfer method (FCET) and two different steady-state fluorimeter methods were compared. The data were found to be in close agreement after careful correction of the steady-state fluorimetric measurements for contributions from dissociating ligand. The biological variability of the individual cells with respect to E was calculated using an error propagation analysis and were found to be less than the variability in the absolute amount of ligand binding per cell. FCET has a number of advantages over the fluorimetric measurements using suspensions of cells: (1) relatively labile receptor-ligand complexes can be measured; (2) the analysis can be restricted to undamaged cells by gating the data collection on the light-scattering signals; (3) heterogeneous populations of cells with respect to donor and acceptor topology can be distinguished by the correlation of E with other cellular parameters derived from additional signals or combinations thereof; and (4) the dynamics of donor-acceptor redistribution on subpopulations can be measured.
Dhrystone (1984)

Reflecting current data on the use of programming language constructs in systems programming, a synthetic benchmark is constructed based on the distribution appearing in the data. The benchmark executes 100 Ada statements that are balanced in terms of the distribution of statement types, data types, and data locality. Pascal and C versions of the benchmark are discussed.
<title>Low-light-level image sensor with on-chip signal processing</title> (1993)

The design of a low-light-level CMOS active-pixel-sensor (APS) with on-chip, semi-parallel analog-to-digital (A/D) conversion is presented. The imager consists of a 128 X 128 array of active pixels at a 50 micrometers pitch. Each column of pixels shares a 10-bit A/D converter based on first-order oversampled sigma-delta ((Sigma) -(Delta) ) modulation. The 10-bit outputs of each converter are multiplexed and read out through a single set of outputs. A semi-parallel architecture is chosen to achieve 30 frames/second operation even at low light levels. The sensor is designed for less than 10 e<SUP>-</SUP> rms noise performance. A 28 X 28 active-pixel-sensor (APS) with 40 X 40 micrometers <SUP>2</SUP> pixels as well as individual elements of the sigma-delta modulator have been fabricated and tested using MOSIS* 2 micrometers CMOS technology.
Note on the Properties of a Vector Quantizer for LPC Coefficients (1983)

Vector quantization has been used in coding applications for several years. Recently, quantization of linear predictive coding (LPC) vectors has been used for speech coding and recognition. In these latter applications, the only method that has been used for deriving the vector quantizer code book from a set of training vectors is the one described by Linde, Buzo, and Gray. In this paper, we compare this algorithm to several alternative algorithms and also study the properties of the resulting code books. Our conclusion is that the various algorithms that we tried gave essentially identical code books.
Quantitative analysis of secretome from adipocytes regulated by insulin (2009)

Adipocyte is not only a central player involved in storage and release of energy, but also in regulation of energy metabolism in other organs via secretion of peptides and proteins. During the pathogenesis of insulin resistance and type 2 diabetes, adipocytes are subjected to the increased levels of insulin, which may have a major impact on the secretion of adipokines. We have undertaken cleavable isotope-coded affinity tag (cICAT) and label-free quantitation approaches to identify and quantify secretory factors that are differentially secreted by 3T3-L1 adipocytes with or without insulin treatment. Combination of cICAT and label-free results, there are 317 proteins predicted or annotated as secretory proteins. Among these secretory proteins, 179 proteins and 53 proteins were significantly upregulated and down-regulated, respectively. A total of 77 reported adipokines were quantified in our study, such as adiponectin, cathepsin D, cystatin C, resistin, and transferrin. Western blot analysis of these adipokines confirmed the quantitative results from mass spectrometry, and revealed individualized secreting patterns of these proteins by increasing insulin dose. In addition, 240 proteins were newly identified and quantified as secreted proteins from 3T3-L1 adipocytes in our study, most of which were up-regulated upon insulin treatment. Further comprehensive bioinformatics analysis revealed that the secretory proteins in extracellular matrix-receptor interaction pathway and glycan structure degradation pathway were significantly upregulated by insulin stimulation.
Components of the IFN-gamma signaling pathway in tumorigenesis. (2002)

Many features of the interferon gamma (IFN-gamma) signaling pathway would suggest that it is anti-tumorigenic. The IFN-gamma signaling pathway leads to apoptosis and to the expression of immune function proteins that could cooperate with T cells in the destruction of tumor. Various lines of experimental approach have, in general, supported the hypothesis that the IFN-gamma signaling pathway is anti-tumorigenic. However, data also indicate that the idea that the IFN-gamma signaling pathway is exclusively anti-tumorigenic is too simplistic. Also, to date, very little of the knowledge regarding the anti-tumor effects of the IFN-gamma pathway has been useful in the prognosis or therapy of cancer. This review summarizes the current state of knowledge regarding the IFN-gamma signaling pathway in tumorigenesis, with an emphasis on MHC class II induction in tumor cells and the induction of apoptosis in tumor cells. The review also indicates some future areas of investigation that offer hope for applying this knowledge in reducing cancer mortality.
Differentiation of T Regulatory Cells by Immature Dendritic Cells (2001)

The induction of antigen-specific tolerance is critical for the prevention of autoimmunity and maintenance of immune homeostasis. The immune system's ability to distinguish between self and non-self and between innocuous and harmful foreign antigens is controlled by mechanisms of central and
Modeling the Semantics of Contextual and Content-specific Research Metadata using Ontology Languages: issues on combining CERIF and OWL (2012)

Current Research Information Systems (CRISs) enable the maintenance of information related to research activities of organizations and their members, including outputs or products from these activities. Such contextual information is of uttermost importance for the processing of datasets and with the retrieval of scientific documents, providing e.g. the key information on provenance and characteristics of research activities that are needed when searching for data or scholarly content. In the context of the expanding initiative of the Web of Linked Data, translating that information into semantic languages enables new ways of querying benefitting from the reuse of domain ontologies. In that direction, this paper reports on the engineering of an ontology based version of the CERIF standard for CRISs using the OWL language and a proposed mapping to research datasets.
Stable in vivo expression of the cystic fibrosis transmembrane conductance regulator with an adeno-associated virus vector. (1993)

Adeno-associated virus (AAV) vectors expressing the normal cystic fibrosis transmembrane conductance regulator (CFTR) cDNA complement the cystic fibrosis (CF) defect in vitro. Unlike other DNA virus vectors, AAV is a stably integrating virus, which could make possible long-term in vivo complementation of the CF defect in the airway epithelium. We report AAV-CFTR gene transfer and expression after infection of primary CF nasal polyp cells and after in vivo delivery of AAV-CFTR vector to one lobe of the rabbit lung through a fiberoptic bronchoscope. In the rabbit, vector DNA could be detected in the infected lobe up to 6 months after administration. A 26-amino acid polypeptide sequence unique to the recombinant AAV-CFTR protein was used to generate both oligonucleotide probes and a polyclonal antibody which allowed the unambiguous identification of vector RNA and CFTR protein expression. With these reagents, CFTR RNA and protein were detected in the airway epithelium of the infected lobe for up to 6 months after vector administration. AAV vectors do, therefore, efficiently promote in vivo gene transfer to the airway epithelium which is stable over several months. These findings indicate that AAV-CFTR vectors could potentially be very useful for gene therapy.
Generation of large numbers of dendritic cells from mouse bone marrow cultures supplemented with granulocyte/macrophage colony-stimulating factor. (1992)

Antigen-presenting, major histocompatibility complex (MHC) class II-rich dendritic cells are known to arise from bone marrow. However, marrow lacks mature dendritic cells, and substantial numbers of proliferating less-mature cells have yet to be identified. The methodology for inducing dendritic cell growth that was recently described for mouse blood now has been modified to MHC class II-negative precursors in marrow. A key step is to remove the majority of nonadherent, newly formed granulocytes by gentle washes during the first 2-4 d of culture. This leaves behind proliferating clusters that are loosely attached to a more firmly adherent "stroma." At days 4-6 the clusters can be dislodged, isolated by 1-g sedimentation, and upon reculture, large numbers of dendritic cells are released. The latter are readily identified on the basis of their distinct cell shape, ultrastructure, and repertoire of antigens, as detected with a panel of monoclonal antibodies. The dendritic cells express high levels of MHC class II products and act as powerful accessory cells for initiating the mixed leukocyte reaction. Neither the clusters nor mature dendritic cells are generated if macrophage colony-stimulating factor rather than granulocyte/macrophage colony-stimulating factor (GM-CSF) is applied. Therefore, GM-CSF generates all three lineages of myeloid cells (granulocytes, macrophages, and dendritic cells). Since > 5 x 10(6) dendritic cells develop in 1 wk from precursors within the large hind limb bones of a single animal, marrow progenitors can act as a major source of dendritic cells. This feature should prove useful for future molecular and clinical studies of this otherwise trace cell type.
Androgen receptor gene mutations in hormone‐refractory prostate cancer (1999)

Prostate cancer is considered to be one of the most hormone-dependent human malignancies. As a key mediator of hormonal response, the androgen receptor (AR) is believed to have an important role in the progression of prostate cancer. Mutations in the coding region of the AR gene have been found in both untreated and hormone-refractory prostate cancer, but the frequency of such mutations at different stages of the disease is poorly documented and even contradictory results have been published. In the present study, the frequency of AR gene mutations was determined in 30 locally recurrent and two metastatic hormone-refractory prostate tumours using the polymerase chain reaction (PCR), non-radioactive single strand conformation polymorphism (SSCP), and sequencing. The length of the polymorphic CAG repeat, which is inversely correlated with the ability of the AR to activate transcription, was also analysed as well as the GGC repeat. Twelve samples were known to contain an AR gene amplification. Altogether, one point mutation (Gly674→Ala) and one microsatellite mutation (CAG20→CAG18) were found, both in cancers containing the AR gene amplification. The mean lengths of the polymorphic CAG and GGC repeats were similar to those observed in the normal population. These results favour the view that mutations in the AR gene are rare in hormone-refractory prostate cancer and do not play an important role, at least, in local relapse. Instead, the amplification and consequent overexpression of the wild-type AR gene seem to be the most common alteration involving the AR in hormone-refractory prostate cancer. Copyright © 1999 John Wiley & Sons, Ltd.
Characterization of Molecularly Cloned Human 5-Aminoimidazole-4-Carboxamide Ribonucleotide Transformylase (1997)

The cDNA encoding human 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase has been cloned from a placenta cDNA library, utilizing a PCR-derived probe. It encodes a peptide of 592 amino acids. The amino (N)-terminal sequence of this enzyme, purified from HeLa cells and CCRF-CEM cells, was found to be APGQLALF-. Both sequencing results revealed a difference of six N-terminal residues when compared to the reported sequence of cloned cDNA from a hepatoma cDNA library. Northern-blot analysis of human AICAR transformylase mRNA showed the expression of a single 2.0 kb mRNA in all tissues examined. With the cloned cDNA fragment, we constructed expression vectors for mature and GST-fused AICAR transformylase. Both recombinant molecules possessing AICAR transformylase activity were overproduced in Escherichia coli. GST-AICAR transformylase can be purified to homogeneity by a single-step affinity procedure with glutathione Sepharose. Mutational analysis, utilizing this expression system, showed that His213 and His267 were essential for AICAR transformylase activity.
The potential for elemental analysis in biotechnology (2002)

The ICP-MS brings particular attributes to the method that distinguishes it from organic mass spectrometry: relative insensitivity to concomitant organic or metallic species, equivalent sensitivity to all similarly-tagged complexes, inherent ability to provide absolute quantitation and linearity of response. All these positive features fit the requirements of modern-day biotechnology. In this work, the potential of ICP-MS is discussed in the context of several urgent problems of biotechnology including: the determination of the state of phosphorylation of proteins, quality control of biologically active materials and control of efficiency of cell line transfections.
Modeling Multi-speaker Latent Space to Improve Neural TTS: Quick Enrolling New Speaker and Enhancing Premium Voice (2018)

Neural TTS has shown it can generate high quality synthesized speech. In this paper, we investigate the multi-speaker latent space to improve neural TTS for adapting the system to new speakers with only several minutes of speech or enhancing a premium voice by utilizing the data from other speakers for richer contextual coverage and better generalization. A multi-speaker neural TTS model is built with the embedded speaker information in both spectral and speaker latent space. The experimental results show that, with less than 5 minutes of training data from a new speaker, the new model can achieve an MOS score of 4.16 in naturalness and 4.64 in speaker similarity close to human recordings (4.74). For a well-trained premium voice, we can achieve an MOS score of 4.5 for out-of-domain texts, which is comparable to an MOS of 4.58 for professional recordings, and significantly outperforms single speaker result of 4.28.
Comparisons of phenotype and immunomodulatory capacity among rhesus bone‐marrow‐derived mesenchymal stem/stromal cells, multipotent adult progenitor cells, and dermal fibroblasts (2014)

Extensive phenotypic similarities exist among each cell type, although immunosuppressive potencies are distinct. MAPCs are most potent, and fibroblasts are the least potent cell type. All three cell types demonstrated immunomodulatory capacity such that each may have potential therapeutic applications such as in organ transplantation, where reduced local immune response is desirable.
ShahriJat andPahari Jatni: Gendered Ethnicity in an Urbanizing Jat Village in North India (2001)

This paper discusses women’s changing roles in Shahargaon - a rapidly urbanizing Jat village in New Delhi, India. The paper traces the change in women’s identity and roles in the context of shift in subsistence strategy from agriculture to an urban economy and examines how Jat women maintain rural-urban network ties and traditional Jat identity in an urban context. As the Shahargaon Jat community experiences social change brought about by urban expansion and assimilation, cultural practices associated with the traditional peasant Jat identity are now idealized as a means of maintaining ethnic boundaries between the Jats and the surrounding multi ethnic urban population. Recent changes in Shahargaon have created new sets of conditions that further marginalize women by excluding them from public income-generating activities. In Shahargaon, like in several other urbanizing communities, women’s economic roles as agricultural laborers have been replaced by their roles within the household and as carriers of traditions, customs, and practices associated with the community’s agrarian past.
A screen of approved drugs and molecular probes identifies therapeutics with anti–Ebola virus activity (2015)

Currently, no approved therapeutics exist to treat or prevent infections induced by Ebola viruses, and recent events have demonstrated an urgent need for rapid discovery of new treatments. Repurposing approved drugs for emerging infections remains a critical resource for potential antiviral therapies. We tested ~2600 approved drugs and molecular probes in an in vitro infection assay using the type species, Zaire ebolavirus. Selective antiviral activity was found for 80 U.S. Food and Drug Administration-approved drugs spanning multiple mechanistic classes, including selective estrogen receptor modulators, antihistamines, calcium channel blockers, and antidepressants. Results using an in vivo murine Ebola virus infection model confirmed the protective ability of several drugs, such as bepridil and sertraline. Viral entry assays indicated that most of these antiviral drugs block a late stage of viral entry. By nature of their approved status, these drugs have the potential to be rapidly advanced to clinical settings and used as therapeutic countermeasures for Ebola virus infections.
Third-order cascaded sigma-delta modulators (1991)

A sigma-delta modulator architecture wherein third-order noise shaping is achieved with relatively modest constraints on device matching is explored. The architecture is based on a cascade of a second-order modulator stage followed by a first-order stage, both using 1-b quantization. To improve the dynamic range, the input to the second stage is generated as an asymmetrically weighted error signal from the first stage. An analytical model for assessing the performance and device matching requirements of cascaded architectures is introduced, and computer simulations are used to verify the approximations made in this model. The analytical model is used to show that the proposed architecture offers performance comparable to other third-order cascaded sigma-delta modulator topologies, while being less sensitive to device matching errors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Staphylococcus Biofilm Components as Targets for Vaccines and Drugs (2007)

Staphylococci have become the most common cause of nosocomial infections, especially in patients with predisposing factors such as indwelling or implanted foreign polymer bodies. The pathogenesis of foreign-body associated infections with S.aureus and S. epidermidis is mainly related to the ability of these bacteria to form thick, adherent multilayered biofilms. In a biofilm, staphylococci are protected against antibiotic treatment and attack from the immune system, thus making eradication of the infections problematic. This necessitates the discovery of novel prophylactic and therapeutic strategies to treat these infections. In this review, we provide an overview of staphylococcal biofilm components and discuss new possible approaches to controlling these persistent biofilm-dwelling bacteria.