gebhart/patrepeval huggingface dataset:
ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space (1999)

We investigate the space of all protein sequences in search of clusters of related proteins.Our aim is to automatically detect these sets, and thus obtain a classification of all protein sequences.Our analysis, which uses standard measures of sequence similarity as applied to an all-vs.allcomparison of SWISSPROT, gives a very conservative initial classification based on the highest scoring pairs.The many classes in this classification correspond to protein subfamilies.Subsequently we merge the subclasses using the weaker pairs in a two-phase clustering algorithm.The algorithm makes use of transitivity to identify homologous proteins; however, transitivity is applied restrictively in an attempt to prevent unrelated proteins from clustering together.This process is repeated at varying levels of statistical significance.Consequently, a hierarchical organization of all proteins is obtained.The resulting classification splits the protein space into well-defined groups of proteins, which are closely correlated with natural biological families and superfamilies.Different indices of validity were applied to assess the quality of our classification and compare it with the protein families in the PROSITE and Pfam databases.Our classification agrees with these domain-based classifications for between 64.8% and 88.5% of the proteins.It also finds many new clusters of protein sequences which were not classified by these databases.The hierarchical organization suggested by our analysis reveals finer subfamilies in families of known proteins as well as many novel relations between protein families.Pro-
Identification of a cis‐regulatory element for L1 layer‐specific gene expression, which is targeted by an L1‐specific homeodomain protein (2001)

The Arabidopsis thaliana PROTODERMAL FACTOR1 (PDF1) gene encoding a putative extracellular proline-rich protein is exclusively expressed in the L1 layer of shoot apices and the protoderm of organ primordia. In order to identify essential cis-regulatory sequences required for the L1 layer-specific expression, a series of 5' deletions of the PDF1 promoter were fused to the beta-glucronidase (GUS) gene and introduced into Arabidopsis plants. Our analysis revealed that the minimum region necessary to confer L1-specific expression of PDF1 is confined within a 260-bp fragment upstream of the transcription start site. We identified an 8-bp motif in this region that is conserved between promoter regions of all the L1-specific genes so far cloned, and we designated it the L1 box. Electrophoretic mobility shift assays demonstrated that the L1-specific homeodomain protein ATML1 can bind to the L1 box sequence in vitro. The GUS expression in transgenic plants disappeared when a mutation that abolishes binding of ATML1 was introduced into the PDF1 l1 box sequence of the construct. These results suggest that the L1 box plays a crucial role in the regulation of PDF1 expression in L1 cells and that ATML1 could cooperate to drive L1-specific expression.
Photochromotropism of gamma-(2,4-Dinitrobenzyl)-Pyridine in Solution (1960)

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Alternative treatment for secretory diarrhea revealed in a new class of CFTR inhibitors (2002)

NKCC); yellow fluorescent protein
Conformational flexibility facilitates self-assembly of complex DNA nanostructures (2008)

Molecular self-assembly is a promising approach to the preparation of nanostructures. DNA, in particular, shows great potential to be a superb molecular system. Synthetic DNA molecules have been programmed to assemble into a wide range of nanostructures. It is generally believed that rigidities of DNA nanomotifs (tiles) are essential for programmable self-assembly of well defined nanostructures. Recently, we have shown that adequate conformational flexibility could be exploited for assembling 3D objects, including tetrahedra, dodecahedra, and buckyballs, out of DNA three-point star motifs. In the current study, we have integrated tensegrity principle into this concept to assemble well defined, complex nanostructures in both 2D and 3D. A symmetric five-point-star motif (tile) has been designed to assemble into icosahedra or large nanocages depending on the concentration and flexibility of the DNA tiles. In both cases, the DNA tiles exhibit significant flexibilities and undergo substantial conformational changes, either symmetrically bending out of the plane or asymmetrically bending in the plane. In contrast to the complicated natures of the assembled structures, the approach presented here is simple and only requires three different component DNA strands. These results demonstrate that conformational flexibility could be explored to generate complex DNA nanostructures. The basic concept might be further extended to other biomacromolecular systems, such as RNA and proteins.
Pd-Catalyzed Enantioselective Aerobic Oxidation of Secondary Alcohols: Applications to the Total Synthesis of Alkaloids (2008)

Enantioselective syntheses of the alkaloids (-)-aurantioclavine, (+)-amurensinine, (-)-lobeline, and (-)- and (+)-sedamine are described. The syntheses demonstrate the effectiveness of the Pd-catalyzed asymmetric oxidation of secondary alcohols in diverse contexts and the ability of this methodology to set the absolute configuration of multiple stereocenters in a single operation. The utility of an aryne C-C insertion reaction in accessing complex polycyclic frameworks is also described.
Surface Stimulation Techniques for Bladder Management in the Spinal Dog (1989)

Electrical stimulation of the bladder wall or sacral nerves may be effective for bladder management in the spinal cord injured patient. However, extensive surgery has been required for electrode implantation. We compared urodynamic responses using surface and minimally invasive epidural stimulating techniques in the chronic spinal male dog. Various surface stimulating techniques were effective: 1) sacral monopolar electrical stimulation with negative electrodes over S2 sacral foramina and positive electrodes on the legs, 2) sacral bipolar electrical stimulation with electrodes only over sacral foramina, 3) perineal monopolar electrical stimulation, and 4) perineal tactile stimulation. Urodynamic responses were similar to those for sacral epidural electrodes implanted adjacent to sacral nerves. Voiding was obtained both during stimulation and poststimulation. Stimulating parameters that were effective for daily voiding with sacral surface electrodes were 10 pps, 30 to 45 ma, 0.6 ms pulse duration, and 2 to 5 sec stimulation train duration.
Functional dysbiosis within the gut microbiota of patients with constipated‐irritable bowel syndrome (2012)

Summary Background The role of the gut microbiota in patho‐physiology of irritable bowel syndrome ( IBS ) is suggested by several studies. However, standard cultural and molecular methods used to date have not revealed specific and consistent IBS ‐related groups of microbes. Aim To explore the constipated‐IBS (C‐IBS) gut microbiota using a function‐based approach. Methods The faecal microbiota from 14 C‐IBS women and 12 sex‐match healthy subjects were examined through a combined strictly anaerobic cultural evaluation of functional groups of microbes and fluorescent in situ hybridisation (16S rDNA gene targeting probes) to quantify main groups of bacteria. Starch fermentation by C‐IBS and healthy faecal samples was evaluated in vitro . Results In C‐ IBS , the numbers of lactate‐producing and lactate‐utilising bacteria and the number of H 2 ‐consuming populations, methanogens and reductive acetogens, were at least 10‐fold lower ( P &lt; 0.05) compared with control subjects. Concomitantly, the number of lactate‐ and H 2 ‐utilising sulphate‐reducing population was 10 to 100 fold increased in C‐ IBS compared with healthy subjects. The butyrate‐producing Roseburia – E. rectale group was in lower number (0.01 &lt; P &lt; 0.05) in C‐ IBS than in control. C‐ IBS faecal microbiota produced more sulphides and H 2 and less butyrate from starch fermentation than healthy ones. Conclusions A major functional dysbiosis was observed in constipated‐irritable bowel syndrome gut microbiota, reflecting altered intestinal fermentation. Sulphate‐reducing population increased in the gut of C‐ IBS and were accompanied by alterations in other microbial groups. This could be responsible for changes in the metabolic output and enhancement in toxic sulphide production which could in turn influence gut physiology and contribute to IBS pathogenesis.
Design issues of a cooperative cache with no coherence problems (1997)

In this paper, we examine some of the important problems observed in the design of cooperative caches. Solutions to the coherence, load-balancing and fault-tolerance problems are presented. These solutions have been implemented as a part of PAFS, a parallel/distributed file system, and its performance has been compared to the one achieved by xFS. Using the comparison results, we have observed that the proposed ideas not only solve the main problems of cooperative caches, but also increase the overall system performance. Although the solutions presented in this paper were targeted to a parallel machine, reasonable good results have also been obtained for networks of workstations.
A New PAPR Reduction Technique for OFDM-WLAN in 802.11a Systems (2008)

In this paper, we proposed a new PAPR reduction technique using selective mapping (SLM) cascade with adaptive peak power reduction (APPR) methods. This technique is used in a system based on Orthogonal Frequency Division Multiplexing (OFDM). OFDM has many orthogonally modulated sub-carriers which unexpectedly produce high peak to average power ratio (PAPR). The high PAPR will occasionally reach the amplifier saturation region and therefore result in signal distortion, which causes bit error rate (BER) degradation. The proposed method, a sequence of input data is rearranged by SLM for the reduction of PAPR and then fed into the APPR process in the proposed system. The APPR method controls the peak levels of the modulation signal by an adaptive algorithm. It reduces modulation signals over a predefined range. The parameter for simulation used standard WLAN in IEEE 802.11a system. In simulation results, the proposed method shows the improvement on PAPR, power spectrum density (PSD) and high performance BER compared with conventional APPR.
[Effects of bone morphogenetic protein-2 on proliferation of tongue cancer Tca8113]. (2011)

Ad-BMP-2 gene can inhibit the proliferation of Tca8113 cells in vitro.
Atmospheric chemistry and environmental impact of the use of amines in carbon capture and storage (CCS) (2012)

This critical review addresses the atmospheric gas phase and aqueous phase amine chemistry that is relevant to potential emissions from amine-based carbon capture and storage (CCS). The focus is on amine, nitrosamine and nitramine degradation, and nitrosamine and nitramine formation processes. A comparison between the relative importance of the various atmospheric sinks for amines, nitrosamines and nitramines is presented.
Interactions Between Drug Resistance Mutations in Human Immunodeficiency Virus Type 1 Reverse Transcriptase (1994)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Aeromonas popoffii sp. nov., a Mesophilic Bacterium Isolated from Drinking Water Production Plants and Reservoirs (1997)

We examined the taxonomic position of seven Aeromonas isolates, recovered from Flemish and Scottish drinking water production plants and reservoirs, which were previously recognized by numerical analysis of genomic AFLP fingerprints as members of an unknown Aeromonas taxon that most closely resembled the species Aeromonas bestiarum (DNA hybridization group [HG] 2). The new phenotypic and DNA-DNA hybridization data obtained in this study show that the A. bestiarum-like strains constitute a separate Aeromonas species, for which the name Aeromonas popoffii sp. nov. is being proposed. The new species exhibited an internal DNA relatedness ranging from 79 to 100% and was 22 to 63% related to the type or reference strains of other Aeromonas spp. The highest DNA binding values were determined with A. bestiarum (51 to 63%), followed by Aeromonas hydrophila sensu stricto (HG1; 50 to 60%) and Aeromonas salmonicida (HG3; 39 to 55%). Although fingerprints generated by ribotyping and cellular fatty acid analysis often were highly similar, minor differences between the respective fingerprints were of significance for the differentiation of A. popoffii from its closest taxonomic neighbors, HG1, HG2, and HG3. Phenotypically, all seven strains of A. popoffii were positive for acid and gas production from D-glucose and glycerol, growth in KCN broth, arginine dihydrolase, DNase, Voges-Proskauer reaction, and resistance to vibriostatic agent O/129 and ampicillin but displayed negative reactions for production of urease, tryptophan deaminase, ornithine decarboxylase, and lysine decarboxylase (LDC). None of the strains displayed strong hemolytic activity. The lack of D-sucrose fermentation and LDC production and the ability to utilize DL-lactate as the sole energy and carbon source were useful characteristics for the biochemical separation of A. popoffii from A. bestiarum. Other Aeromonas spp. could be differentiated phenotypically from the new species by at least two features. The chromosomal G+C content of A. popoffii ranges from 57.7 to 59.6 mol%. Strain LMG 17541 is proposed as the type strain.
Anthracnose Development on Pepper Fruits Inoculated withColletotrichum gloeosporioides (1995)

Colletotrichum gloeosporioides caused anthracnose on pepper fruits of line PBC 510 when inoculated with a microdrop spore suspension on immature fruits one-half the normal size up to fully mature ripe red fruits. Incidence of anthracnose was greater on inoculated purple and ripe red fruits than on fruits at other developmental stages. Cuticle and exocarp thicknesses varied by fruit maturity. Disease incidence differed among eight pepper lines based on the number of days to fruit lesion development. Over 50% of the fruits in lines PBC 452, PBC 454, and PBC 595 had lesions less than 5 days after inoculation, whereas it took 6 days for fruits in three lines (PBC 365, PBC 371, and PBC 518), 8 days for fruits in line PBC 370, and 11 days for fruits in line PBC 495. Fruits of PBC 595 had the largest lesions, while fruits of PBC 518 had the smallest lesions. Conidial production was lowest on fruit lesions of PBC 495 and highest on fruit lesions of PBC 595. Disease incidence was correlated to cuticle and exocarp thicknesses. Cuticle thickness was significantly negatively correlated to conidial production (r = -0.45) and lesion expansion (r = -0.46). C. gloeosporioides infected more fruits of var. Szechwan 90714 in a given period than did C. capsici, whether or not fruits were chloroform-dipped. Anthracnose was detected more on incubated fruits that were chloroform-dipped than water-dipped prior to inoculation.
Autophagy induction by trehalose counter-acts cellular prion-infection (2009)

Prion diseases are fatal neurodegenerative and infectious disorders for which no therapeutic or prophylactic regimens exist. In search of cellular mechanisms that play a role in prion diseases and have the potential to interfere with accumulation of intracellular pathological prion protein (PrP(Sc)), we investigated the autophagic pathway and one of its recently published inducers, trehalose. Trehalose, an alpha-linked disaccharide, has been shown to accelerate clearance of mutant huntingtin and alpha-synuclein by activating autophagy, mainly in an mTOR-independent manner. Here, we demonstrate that trehalose can significantly reduce PrP(Sc) in a dose- and time-dependent manner while at the same time it induces autophagy in persistently prion-infected neuronal cells. Inhibition of autophagy, either pharmacologically by known autophagy inhibitors like 3-methyladenine, or genetically by siRNA targeting Atg5, counteracted the anti-prion effect of trehalose. Hence, we provide direct experimental evidence that induction of autophagy mediates enhanced cellular degradation of prions. Similar results were obtained with rapamycin, a known inducer of autophagy, and imatinib, which has been shown to activate autophagosome formation. While induction of autophagy resulted in reduction of PrP(Sc), inhibition of autophagy increased the amounts of cellular PrP(Sc), suggesting that autophagy is involved in the physiological degradation process of cellular PrP(Sc). Preliminary in vivo studies with trehalose in intraperitoneally prion-infected mice did not result in prolongation of incubation times, but demonstrated delayed appearance of PrP(Sc) in the spleen. Overall, our study provides the first experimental evidence for the impact of autophagy in yet another type of neurodegenerative disease, namely prion disease.
Isolation and Properties of a Macromolecular, Water-Soluble, Immuno-Adjuvant Fraction from the Cell Wall of Mycobacterium smegmatis (1972)

Trypsin- and chymotrypsin-treated delipidated cell walls of Mycobacterium smegmatis were digested overnight with lysozyme. The water-soluble products thus obtained were filtered on a column of Sephadex G-50; the first peak, excluded from the column, has immunological adjuvant activity. The material of the excluded peak is obtained after lyophilization as a snow-white, fluffy material, soluble in water and insoluble in organic solvents. It behaves as a slightly polydisperse macromolecule in an ultracentrifuge, with an approximate molecular weight of 20,000. All the constituents of this material are typical bacterial cell-wall constituents; thus, the water-soluble adjuvant is considered to be an "oligomer" of the cell wall. When added to Freund's incomplete adjuvant with an antigen (e.g., ovalbumin) and injected into hind-foot pads of guinea pigs, this water-soluble adjuvant increases the amount of precipitating antibodies and induces hypersensitivity to ovalbumin and the biosynthesis of gamma(2)-type precipitating antibodies. The water-soluble material has a stronger adjuvant activity than equal amounts of whole bacteria, cell walls, or wax D, and seems to be the first well-defined, water-soluble, adjuvant-active fraction isolated from Mycobacteria.
Sensitivities of monolayers and spheroids of the human bladder cancer cell line MGH-U1 to the drugs used for intravesical chemotherapy. (1989)

The in vitro cytotoxicities of the four drugs most frequently used for intravesical chemotherapy (Adriamycin, epodyl, mitomycin C, Thiotepa) and epirubicin were compared using monolayers and multicellular tumor spheroids of the human bladder cancer cell line, MGH-U1. Adriamycin and epirubicin were most cytotoxic against monolayer cultures, whereas mitomycin C killed more cells in spheroids. Epodyl was least cytotoxic against both two- and three-dimensional cultures. Thiotepa was the only drug more cytotoxic to three- than two-dimensional cultures. Topographic analysis of bromodeoxyuridine-stained nuclei using image analysis indicated that Adriamycin selectively removed or killed superficial cells in multicellular tumor spheroids, but had little effect on DNA synthesis within the spheroids. In contrast Thiotepa killed cells throughout the spheroids. These in vitro data appear to reflect clinical experience using intravesical chemotherapy to treat superficial bladder cancer.
Diffraction-specific fringe computation for electro-holography (1994)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1994.
De Novo Design of Potent Antimicrobial Peptides (2004)

Lipopolysaccharide (LPS), shed by gram-negative bacteria during infection and antimicrobial therapy, may lead to lethal endotoxic shock syndrome. A rational design strategy based on the presumed mechanism of antibacterial effect was adopted to design cationic antimicrobial peptides capable of binding to LPS through tandemly repeated sequences of alternating cationic and nonpolar residues. The peptides were designed to achieve enhanced antimicrobial potency due to initial bacterial membrane binding with a reduced risk of endotoxic shock. The peptides designed displayed binding affinities to LPS and lipid A (LA) in the low micromolar range and by molecular modeling were predicted to form amphipathic beta-hairpin-like structures when they bind to LPS or LA. They also exhibited strong effects against gram-negative bacteria, with MICs in the nanomolar range, and low cytotoxic and hemolytic activities at concentrations significantly exceeding their MICs. Quantitative structure-activity relationship (QSAR) analysis of peptide sequences and their antimicrobial, cytotoxic, and hemolytic activities revealed that site-directed substitutions of residues in the hydrophobic face of the amphipathic peptides with less lipophilic residues selectively decrease the hemolytic effect without significantly affecting the antimicrobial or cytotoxic activity. On the other hand, the antimicrobial effect can be enhanced by substitutions in the polar face with more polar residues, which increase the amphipathicity of the peptide. On the basis of the QSARs, new analogs that have strong antimicrobial effects but that lack hemolytic activity can be proposed. The findings highlight the importance of peptide amphipathicity and allow a rational method that can be used to dissociate the antimicrobial and hemolytic effects of cationic peptides, which have potent antimicrobial properties, to be proposed.
Overview of Serological Techniques for Influenza Vaccine Evaluation: Past, Present and Future (2014)

Serological techniques commonly used to quantify influenza-specific antibodies include the Haemagglutination Inhibition (HI), Single Radial Haemolysis (SRH) and Virus Neutralization (VN) assays. HI and SRH are established and reproducible techniques, whereas VN is more demanding. Every new influenza vaccine needs to fulfil the strict criteria issued by the European Medicines Agency (EMA) in order to be licensed. These criteria currently apply exclusively to SRH and HI assays and refer to two different target groups-healthy adults and the elderly, but other vaccine recipient age groups have not been considered (i.e., children). The purpose of this timely review is to highlight the current scenario on correlates of protection concerning influenza vaccines and underline the need to revise the criteria and assays currently in use. In addition to SRH and HI assays, the technical advantages provided by other techniques such as the VN assay, pseudotype-based neutralization assay, neuraminidase and cell-mediated immunity assays need to be considered and regulated via EMA criteria, considering the many significant advantages that they could offer for the development of effective vaccines.