gebhart/patrepeval huggingface dataset:
Bacterial Cellular Engineering by Genome Editing and Gene Silencing (2014)

Genome editing is an important technology for bacterial cellular engineering, which is commonly conducted by homologous recombination-based procedures, including gene knockout (disruption), knock-in (insertion), and allelic exchange. In addition, some new recombination-independent approaches have emerged that utilize catalytic RNAs, artificial nucleases, nucleic acid analogs, and peptide nucleic acids. Apart from these methods, which directly modify the genomic structure, an alternative approach is to conditionally modify the gene expression profile at the posttranscriptional level without altering the genomes. This is performed by expressing antisense RNAs to knock down (silence) target mRNAs in vivo. This review describes the features and recent advances on methods used in genomic engineering and silencing technologies that are advantageously used for bacterial cellular engineering.
CCNet: Criss-Cross Attention for Semantic Segmentation (2018)

Contextual information is vital in visual understanding problems, such as semantic segmentation and object detection. We propose a Criss-Cross Network (CCNet) for obtaining full-image contextual information in a very effective and efficient way. Concretely, for each pixel, a novel criss-cross attention module harvests the contextual information of all the pixels on its criss-cross path. By taking a further recurrent operation, each pixel can finally capture the full-image dependencies. Besides, a category consistent loss is proposed to enforce the criss-cross attention module to produce more discriminative features. Overall, CCNet is with the following merits: 1) GPU memory friendly. Compared with the non-local block, the proposed recurrent criss-cross attention module requires 11x less GPU memory usage. 2) High computational efficiency. The recurrent criss-cross attention significantly reduces FLOPs by about 85% of the non-local block. 3) The state-of-the-art performance. We conduct extensive experiments on semantic segmentation benchmarks including Cityscapes, ADE20K, human parsing benchmark LIP, instance segmentation benchmark COCO, video segmentation benchmark CamVid. In particular, our CCNet achieves the mIoU scores of 81.9%, 45.76% and 55.47% on the Cityscapes test set, the ADE20K validation set and the LIP validation set respectively, which are the new state-of-the-art results. The source codes are available at \url{https://github.com/speedinghzl/CCNet}.
Encoding Higher Order Ambisonics with AAC (2008)

In this work we explore a simple method for reducing the bit rate needed for transmitting and storing Higher Order Ambisonics (HOA).The HOA B-format signals are simply encoded using Advanced Audio Coding (AAC) as if they were individual mono signals.Wave field simulations show that by allocating more bits to the lower order signals than the higher the resulting error is very low in the sweet spot, but increases as function of distance from the center.Encoding the higher order signals with a low bit rate does not lead to a reduced audio quality.The spatial information is improved when higher-order channels are included, even if these are encoded with a low bit rate.
Rapid detection of Creutzfeldt‐Jakob disease and scrapie prion proteins (1990)

Creutzfeldt-Jakob disease (CJD) and Gerstmann-Sträussler syndrome (GSS) of humans as well as scrapie of animals are caused by prions. The scrapie prion protein isoform (PrPSc) is the only macromolecule identified to date which is a component of the infectious prion particle. PrPSc is converted to PrP 27-30 by limited proteolysis while the cellular isoform, designated PrPC, is completely digested under the same conditions. ELISA studies demonstrated that native PrP 27-30 bound to plastic surfaces resisted proteolysis and exhibited little or no immunoreactivity but after denaturation with guanidinium thiocyanate (GdnSCN), immunoreactivity was greatly enhanced. PrPSc bound to nitrocellulose also exhibited enhanced immunoreactivity after denaturation. PrPSc was readily detected in brain extracts from scrapie-infected hamsters, mice, and sheep by dot-blot immunoassays using limited proteolysis followed by GdnSCN denaturation. The high sensitivity and specificity of the immunoassay allowed detection of regional differences in PrPSc in sheep brain. CJD prion protein isoform (PrPCJD) was also detected in the brains of all 10 patients tested with neuropathologically confirmed CJD and in 1 patient with GSS. Enhanced immunoreactivity of PrPSc or PrPCJD after denaturation cannot only be used for immunodiagnosis of prion diseases but may also form the basis of new assays in experimental studies directed at the chemical structure of the prion particle.
Intergeneric coaggregation of oral Treponema spp. with Fusobacterium spp. and intrageneric coaggregation among Fusobacterium spp (1995)

A total of 22 strains of Treponema spp. including members of all four named human oral species were tested for coaggregation with 7 strains of oral fusobacteria, 2 strains of nonoral fusobacteria, and 45 strains of other oral bacteria, which included actinobacilli, actinomyces, capnocytophagae, eubacteria, porphyromonads, prevotellae, selenomonads, streptococci, and veillonellae. None of the treponemes coaggregated with any of the latter 45 oral strains or with the two nonoral fusobacteria. All treponemes, eight Treponema denticola strains, eight T. socranskii strains, four oral pectinolytic treponemes, one T. pectinovorum strain, and one T. vincentii strain coaggregated with at least one strain of the fusobacteria tested as partners. The partners consisted of one strain of Fusobacterium periodonticum, five F. nucleatum strains including all four subspecies of F. nucleatum, and a strain of F. simiae obtained from the dental plaque of a monkey. In the more than 100 coaggregations observed, the fusobacterial partner was heat inactivated (85 degrees C for 30 min), while the treponemes were unaffected by the heat treatment. Furthermore, the fusobacteria were usually inactivated by proteinase K treatment, and the treponemes were not affected. Only the T. denticola coaggregations were inhibited by lactose and D-galactosamine. None were inhibited by any of 23 other different sugars or L-arginine. Intragenic coaggregations were seen among the subspecies of F. nucleatum and with F. periodonticum, and none were inhibited by any of the sugars tested or by L-arginine. No intrageneric coaggregations were observed among the treponemes. These data indicate that the human oral treponemes show a specificity for oral fusobacteria as coaggregation partners. Such cell-to cell contact may facilitate efficient metabolic communication and enhance the proliferation of each cell in the progressively more severe stages of periodontal disease.
Wireless multicarrier communications (2000)

Relying on basic tools such as eigensignals of linear time-invariant systems, linear and circular block convolution, and fast Fourier transforms (FFTs), this article develops a systematic discrete-time framework and designs novel systems for single- and multiuser wireless multicarrier communications-a field rich in signal processing challenges that holds great potential in various applications including audio/video broadcasting, cable television, modem design, multimedia services, mobile local area networks, and future-generation wideband cellular systems. Wireless multicarrier (MC) communication systems utilize multiple complex exponentials as information-bearing carriers. MC transmissions thus retain their shape and orthogonality when propagating through linear time-dispersive media, precisely as eigensignals do when they pass through linear time-invariant (LTI) systems.
Novel bulk dynamic threshold voltage MOSFET (B-DTMOS) with advanced isolation (SITOS) and gate to shallow-well contact (SSS-C) processes for ultra low power dual gate CMOS (2002)

We have developed a high speed dynamic threshold voltage MOSFET named B-DTMOS for ultra low power operation. This was realized using a bulk wafer containing an individual trench isolated shallow-well with a high concentration buried layer sandwiched between two low concentration layers surrounded by a deep well. The B-DTMOS achieved an excellent propagation delay time of 83.6 psec at 0.6 V operation and 103.3 psec at 0.5 V operation. This was realized due to ultra low body resistance of the B-DTMOS.
Inhibition of Human Mast Cell Tryptase by Benzamidine Derivatives (1992)

Considerable circumstantial evidence has been provided by in vitro studies that tryptase (EC 3.4.21.59), a neutral serine proteinase stored in large amounts in mast cell granules, may play an important pathogenetic role in mast cell-dependent diseases. However, a definitive role has not yet been ascribed to this trypsin-like enzyme with restricted substrate specificity as natural or synthetic inhibitors of tryptase applicable for in vivo studies are not available so far. Therefore, we have studied structure-activity relationships for inhibition of tryptase by benzamidine derivatives, compounds known to be potent inhibitors of various trypsin-like enzymes. Among the benzamidine derivatives 4-amidinophenylpyruvic acid exerts a striking inhibitory activity with a Ki of 0.71 mumol/l. Several additional inhibitors of tryptase with Ki values in the micromolar range were found among bis-benzamidines. Derivatives of N alpha-arylsulfonyl-omega-amidinophenyl-alpha-aminoalkylcarboxylic acids are only weak inhibitors of tryptase, although members of this group are potent and selective inhibitors of several other trypsin-like enzymes. Comparison of the inhibition of tryptase and trypsin revealed that the affinities of the benzamidine derivatives to both proteinases are closely correlated (correlation coefficient r = 0.702; n = 37; p < 0.001). These results demonstrate that 4-amidinophenylpyruvic acid may be useful as a pharmacologic tool for the investigation of the (patho)physiological role of tryptase. In addition, benzamidine derivatives may be applicable to probe the active site topography of tryptase isoenzymes.
The complement system in myocardial ischaemia/reperfusion injury (1994)

Journal Article The complement system in myocardial ischaemia/reperfusion injury Get access Kenneth S Kilgore, Kenneth S Kilgore University of Michigan Medical School, Department of Pharmacology, M6322 Medical Sciences Building I, Ann Arbor, Michigan 48109-0626, USA: K S Kilgore, G S Friedrichs, J W Homeister, B R Lucchesi. Correspondence to Professor Lucchesi. Search for other works by this author on: Oxford Academic PubMed Google Scholar Gregory S Friedrichs, Gregory S Friedrichs University of Michigan Medical School, Department of Pharmacology, M6322 Medical Sciences Building I, Ann Arbor, Michigan 48109-0626, USA: K S Kilgore, G S Friedrichs, J W Homeister, B R Lucchesi. Search for other works by this author on: Oxford Academic PubMed Google Scholar Jonathon W Homeister, Jonathon W Homeister University of Michigan Medical School, Department of Pharmacology, M6322 Medical Sciences Building I, Ann Arbor, Michigan 48109-0626, USA: K S Kilgore, G S Friedrichs, J W Homeister, B R Lucchesi. Search for other works by this author on: Oxford Academic PubMed Google Scholar Benedict R Lucchesi Benedict R Lucchesi University of Michigan Medical School, Department of Pharmacology, M6322 Medical Sciences Building I, Ann Arbor, Michigan 48109-0626, USA: K S Kilgore, G S Friedrichs, J W Homeister, B R Lucchesi. Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 28, Issue 4, April 1994, Pages 437–444, https://doi.org/10.1093/cvr/28.4.437 Published: 01 April 1994 Article history Received: 28 September 1993 Accepted: 07 December 1993 Published: 01 April 1994
Imaging of hemoglobin oxygen saturation variations in single vessels in vivo using photoacoustic microscopy (2007)

Photoacoustic microscopy was used to noninvasively image variations in hemoglobin oxygen saturation (SO2) in the subcutaneous microvasculature of rats in vivo. In phantom tests, the calculated concentration fractions of red ink in double-ink mixtures matched the actual values with a 1% error. In ex vivo studies, the calculated SO2 in bovine blood agreed with the standard spectrophotometric measurements within a 4% systematic difference. In in vivo studies, arteries and veins were separated based on the measured SO2 values and variations in SO2 between different physiological states (hyperoxia, normoxia, and hypoxia) were imaged in single blood vessels.
Optimum Combining in Digital Mobile Radio with Cochannel Interference (1984)

This paper studies optimum signal combining for space diversity reception in cellular mobile radio systems. With optimum combining, the signals received by the antennas are weighted and combined to maximize the output signal-to-interference-plus-noise ratio. Thus, with cochannel interference, space diversity is used not only to combat Rayleigh fading of the desired signal (as with maximal ratio combining) but also to reduce the power of interfering signals at the receiver. We use analytical and computer simulation techniques to determine the performance of optimum combining when the received desired and interfering signals are subject to Rayleigh fading. Results show that optimum combining is significantly better than maximal ratio combining even when the number of interferers is greater than the number of antennas. Results for typical cellular mobile radio systems show that optimum combining increases the output signalto-interference ratio at the receiver by several decibels. Thus, systems can require fewer base station antennas and/or achieve increased channel capacity through greater frequency reuse. We also describe techniques for implementing optimum combining with least mean square (LMS) adaptive arrays.
TiProD: the Tissue-specific Promoter Database (2005)

TiProD is a database of human promoter sequences for which some functional features are known. It allows a user to query individual promoters and the expression pattern they mediate, gene expression signatures of individual tissues, and to retrieve sets of promoters according to their tissue-specific activity or according to individual Gene Ontology terms the corresponding genes are assigned to. We have defined a measure for tissue-specificity that allows the user to discriminate between ubiquitously and specifically expressed genes. The database is accessible at http://tiprod.cbi.pku.edu.cn:8080/index.html.
IL-15 and IL-15R in leucocytes from patients with systemic lupus erythematosus (2005)

Our data indicate that there is enhanced synthesis of IL-15 by immune cells from SLE patients, with a poor response to this cytokine by different leucocyte subsets. This abnormal function of IL-15/IL-15Ralpha may contribute significantly to the pathogenesis of SLE.
Absolute stability of a class of neural networks with unbounded delay: Research Articles (2004)

In this paper, the existence and uniqueness of the equilibrium point and absolute stability of a class of neural networks with partially Lipschitz continue activation functions are investigated. The neural networks contain both variable and unbounded delays. Using the matrix property, the necessary and sufficient condition for the existence and uniqueness of the equilibrium point of the neural networks is obtained. By constructing proper vector Liapunov functions and non-linear integro-differential inequalities involving both variable delays and unbounded delay, the sufficient conditions for absolute stability (global asymptotic stability) are obtained. Copyright © 2004 John Wiley & Sons, Ltd.
Validation of A Fully Integrated Microfluidic Array Device for Influenza A Subtype Identification and Sequencing (2006)

Rapid detection and identification of influenza virus is becoming increasingly important in the face of concerns over an influenza pandemic. A fully integrated and self-contained microfluidic device has been developed to rapidly identify influenza A hemagglutinin and neuraminidase subtypes and sequence portions of both genes. The device consists of a DNA microarray with 12 000 features and a microfluidic cartridge that automates the fluidic handling steps required to carry out a genotyping assay for pathogen identification and sequencing. The fully integrated microfluidic device consists of microfluidic pumps, mixers, valves, fluid channels, reagent storage chambers, and DNA microarray silicon chip. Microarray hybridization and subsequent fluidic handling and reactions were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. A micromixing technique based on gas bubbling generated by electrochemical micropumps was developed. Low-cost check valves were implemented in the cartridge to prevent cross talk of the stored reagents. The genotyping results showed that the device identified influenza A hemagglutinin and neuraminidase subtypes and sequenced portions of both genes, demonstrating the potential of integrated microfluidic and microarray technology for multiple virus detection. The device provides a cost-effective solution to eliminate labor-intensive and time-consuming fluidic handling steps and allows the detection and identification of influenza virus in a rapid and automated fashion.
Immunopotentiation by a new antitumor polysaccharide, DMG, a degraded D-manno-D-glucan from Microellobosporia grisea culture fluid. (1984)

The immunopharmacological behavior of DMG, an antitumor polysaccharide, was studied in mice. DMG administered ip or sc stimulated peritoneal macrophages to produce high levels of interleukin-1 activity, which can amplify successive immune responses. DMG dose-dependently and schedule-dependently increased the cellular immune response against allogeneic tumor cells and the humoral immune response to sheep erythrocytes. DMG also enhanced nonspecific antitumor effector functions, such as natural killer activity of spleen and peritoneal cells, and the cytostatic activity of peritoneal macrophages. Peritoneal macrophages activated by ip or sc injection of DMG exhibited high cytostatic activity, especially after exposure in vitro to lymphokine supernatants containing macrophage activation factor. Moreover, granulocyte/macrophage colony-stimulating activity in the serum increased 2-10 hr after DMG administration. Thus, DMG potentiated antigen-specific immunological functions and nonspecific functions of host defense systems against cancer both qualitatively and quantitatively.
Activating Antibodies to the Calcium-Sensing Receptor in Two Patients with Autoimmune Hypoparathyroidism (2004)

Autoimmune hypoparathyroidism is thought to result from immune-mediated destruction of the parathyroid glands. We encountered two patients with hypoparathyroidism and other autoimmune conditions (Graves' disease and Addison's disease, respectively) in whom autoimmune destruction of the parathyroid glands had not taken place. In the first, a histologically normal parathyroid gland was observed at the time of subtotal thyroidectomy; and in the second, the hypoparathyroidism remitted spontaneously. Both patients had antibodies that reacted with the cell surface of bovine parathyroid cells and human embryonic kidney (HEK293) cells transfected with the extracellular calcium-sensing receptor (CaR) but not with nontransfected HEK293 cells. The antibodies also reacted with the same bands on Western analysis of extracts of bovine parathyroid tissue and CaR-transfected HEK293 cells that were identified by an authentic, polyclonal, anti-CaR antiserum and reacted with several peptides with sequences from the CaR's extracellular domain. These anti-CaR antibodies activated the receptor based on their ability to increase inositol phosphate accumulation, activate MAPK, and inhibit PTH secretion. These results, therefore, demonstrate that patients with the biochemical findings of primary hypoparathyroidism can harbor activating antibodies to the CaR, which, in the two cases studied here, did not produce irreversible destruction of the parathyroid glands.
The use of topical glycopyrrolate in the treatment of hyperhidrosis (1998)

The use of an aqueous solution of 0.5% topical glycopyrollate was effective in the treatment of hyperhidrosis of the scalp and forehead after other treatments had proved ineffective; this appears to be the first report of its use in this condition.
Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov. (2009)

We isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic, motile or non-motile and Gram-positive rods. Some of the strains formed spores. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms could be placed within clostridial cluster IV as defined by Collins et al. [(1994). Int J Syst Bacteriol 44, 812-826] and shared more than 99 % sequence similarity with Clostridium orbiscindens DSM 6740(T) and Eubacterium plautii DSM 4000(T). Together, they formed a distinct cluster, with Bacteroides capillosus ATCC 29799(T) branching off from this line of descent with sequence similarities of 97.1-97.4 %. The next nearest neighbours of these organisms were Clostridium viride, Oscillibacter valericigenes, Papillibacter cinnamivorans and Sporobacter termitidis, with sequence similarities to the respective type strains of 93.1-93.4, 91.2-91.4, 89.8-90 and 88.7-89.3 %. On the basis of biochemical properties, phylogenetic position, DNA G+C content and DNA-DNA hybridization, it is proposed to unify Clostridium orbiscindens and Eubacterium plautii in a new genus as Flavonifractor plautii gen. nov., comb. nov., with the type strain Prévot S1(T) (=ATCC 29863(T) =VPI 0310(T) =DSM 4000(T)), and to reassign Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov., with the type strain CCUG 15402A(T) (=ATCC 29799(T) =VPI R2-29-1(T)).
Human Retinoblastoma Susceptibility Gene: Cloning, Identification, and Sequence (1987)

Recent evidence indicates the existence of a genetic locus in chromosome region 13q14 that confers susceptibility to retinoblastoma, a cancer of the eye in children. A gene encoding a messenger RNA (mRNA) of 4.6 kilobases (kb), located in the proximity of esterase D, was identified as the retinoblastoma susceptibility (RB) gene on the basis of chromosomal location, homozygous deletion, and tumor-specific alterations in expression. Transcription of this gene was abnormal in six of six retinoblastomas examined: in two tumors, RB mRNA was not detectable, while four others expressed variable quantities of RB mRNA with decreased molecular size of about 4.0 kb. In contrast, full-length RB mRNA was present in human fetal retina and placenta, and in other tumors such as neuroblastoma and medulloblastoma. DNA from retinoblastoma cells had a homozygous gene deletion in one case and hemizygous deletion in another case, while the remainder were not grossly different from normal human control DNA. The gene contains at least 12 exons distributed in a region of over 100 kb. Sequence analysis of complementary DNA clones yielded a single long open reading frame that could encode a hypothetical protein of 816 amino acids. A computer-assisted search of a protein sequence database revealed no closely related proteins. Features of the predicted amino acid sequence include potential metal-binding domains similar to those found in nucleic acid-binding proteins. These results provide a framework for further study of recessive genetic mechanisms in human cancers.