gebhart/patrepeval huggingface dataset:
TRIADs: A new class of proteins with a novel cysteine‐rich signature (1999)

Triad1 was recently identified as a nuclear RING finger protein, which is up-regulated during retinoic acid induced granulocytic differentiation of acute leukemia cells. Here we show that a cysteine-rich domain (C6HC), present in Triad1, is conserved in at least 24 proteins encoded by various eukaryotes. The C6HC consensus pattern C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C defines this structure as the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in 22 of 24 proteins the C6HC domain is flanked by two RING finger structures. We have termed the novel C6HC motif DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (two RING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins.
Selective encryption of C2DVLC of AVS video coding standard for I &amp; P frames (2010)

In this paper, a novel method for fast protection of AVS video coding standard alongwith compression is presented. Here the problems of compression and selective encryption (SE) have been simultaneously addressed for AVS part-2 Jizhun profile. It is performed in the context-based 2D variable length coding (C2DVLC) module of video codec. SE is performed by using the Advanced Encryption Standard (AES) algorithm with the Cipher Feedback (CFB) mode on a subset of codewords. C2DVLC serves the purpose of encryption step without affecting the coding efficiency of AVS by keeping the bitrate unchanged, generating completely compliant bitstream and utilizing negligible computational power. Nine different benchmark video sequences containing different combinations of motion, texture and objects are used for experimental evaluation of the proposed algorithm.
Rectified Factor Networks (2015)

We propose rectified factor networks (RFNs) to efficiently construct very sparse, non-linear, high-dimensional representations of the input. RFN models identify rare and small events in the input, have a low interference between code units, have a small reconstruction error, and explain the data covariance structure. RFN learning is a generalized alternating minimization algorithm derived from the posterior regularization method which enforces non-negative and normalized posterior means. We proof convergence and correctness of the RFN learning algorithm. On benchmarks, RFNs are compared to other unsupervised methods like autoencoders, RBMs, factor analysis, ICA, and PCA. In contrast to previous sparse coding methods, RFNs yield sparser codes, capture the data's covariance structure more precisely, and have a significantly smaller reconstruction error. We test RFNs as pretraining technique for deep networks on different vision datasets, where RFNs were superior to RBMs and autoencoders. On gene expression data from two pharmaceutical drug discovery studies, RFNs detected small and rare gene modules that revealed highly relevant new biological insights which were so far missed by other unsupervised methods.
Identifying Source Proteins for MHC Class I-Presented Peptides (2012)

Identification of antigenic peptides recognized by cytolytic T lymphocytes (CTL) is a prerequisite for the development of targeted cancer immunotherapy approaches. This chapter provides a global approach for the identification of peptides recognized by CTL. It implies the identification of the HLA molecule presenting the peptide as well as the design and screening of a cDNA library derived from the tumor cells.
Insertion of Fluoroalkenes into Activated CH Bonds for the Preparation of Polyfluorinated Sulfanes, Alcohols, and Acyclic and Cyclic Ethers (1996)

Free radical addition reactions of tetrahydrothiophene, pentamethylene sulfide, and 1,4-thioxane with various cyclic and acyclic per- and polyfluorinated olefins are readily initiated by di-tert-butyl peroxide, providing a convenient route for synthesizing cyclic sulfanes with fluorinated side groups. Tetrahydrothiophene reacts with hexafluoropropene, perfluoroallylbenzene, perfluorocyclobutene, and 1,2-dichlorotetrafluorocyclobutene in the presence of catalytic amounts of the peroxide to give the corresponding addition products CH(2)CH(2)CH(2)SCHCF(2)CHFCF(3) (1), CH(2)CH(2)CH(2)SCHCF(2)CHFCF(2)C(6)F(5) (2), CH(2)CH(2)CH(2)SCHCFCHFCF(2)CF(2) (3), and CH(2)CH(2)CH(2)SCHCClCHClCF(2)CF(2) (4), respectively. Pentamethylene sulfide reacts analogously with hexafluoropropene to give CH(2)CH(2)CH(2)CH(2)SCHCF(2)CHFCF(3) (8). Reaction of 1,4-thioxane with hexafluoropropene or perfluoroallylbenzene gives a mixture of two products, OCH(2)CH(2)SCH(2)CHCF(2)CHFCF(3) (9) and SCH(2)CH(2)OCH(2)CHCF(2)CHFCF(3) (10) or OCH(2)CH(2)SCH(2)CHCF(2)CHFCF(2)C(6)F(5) (11) and SCH(2)CH(2)OCH(2)CHCF(2)CHFCF(2)C(6)F(5) (12), respectively. Fluorinated alcohols C(6)F(5)CF(2)CHFCF(2)C(CH(3))(2)OH (15), C(6)F(5)CF(2)CHFCF(2)CH(CH(3))OH (16), and C(6)F(5)CF(2)CHFCF(2)CH(2)OH (17) are prepared by reacting perfluoroallylbenzene with the corresponding alcohols. When 15 is reacted with pentafluorobenzonitrile in the presence of potassium carbonate, an unexpected cyclic ether 19 is obtained as the major product in addition to C(6)F(5)CF(2)CHFCF(2)C(CH(3))(2)OC(6)F(5)CN (18). Alcohols 15-17 can be cyclized by heating with potassium carbonate to give fluorinated cyclic ethers 19-21. The X-ray crystal structures of acyclic ether 18 and cyclic ether 19 are given. Compound 18 crystallizes in the tetragonal system, space group P4(2)/n, with a = 18.471(0) Å, b = 18.471(0) Å, c = 11.702(0) Å, V = 3992.5(9) Å(3), D(calc) = 1.768 mg/m(3), Z = 8, and R = 0.0617. Compound 19 crystallizes in the triclinic system, space group P&onemacr;, with a = 8.103(3) Å, b = 8.790(3) Å, c = 9.832(3) Å, alpha = 66.25(4) degrees, beta = 72.01(3) degrees, gamma = 80.19(4) degrees, V = 608.7(4) Å(3), D(calc) = 1.845 mg/m(3), Z = 2, and R = 0.0346.
Protection of sheep against experimental footrot by vaccination with pili purified from<i>Bacteroides</i>nodosus (1982)

Merino sheep vaccinated with either whole Bacteroides nodosus organisms, a crude surface antigen preparation or highly purified pili (>99% homogeneity) in oil adjuvant, developed significant resistance to artificial footrot infection when compared with unvaccinated control sheep inoculated with saline-in-oil emulsion (Freund;s incomplete adjuvant) alone. The pili-vaccinated sheep generally had higher K-agglutinating antibody titres than sheep vaccinated with whole B. nodosus. These results confirmed the role of B. nodosus pilus protein both as a protective antigen and the K-agglutinogen. Vaccines prepared with Freund;s incomplete adjuvant containing either purified pili, crude pili or B. nodosus whole cells did not produce significantly different injection-site reactions.
An evolutionary fuzzy neural network approach for short-term electric power load forecasting (2006)

A hybrid evolutionary programming and fuzzy neural network (HEFNN) for load forecasting is presented in this paper. A fuzzy hyper-rectangular composite neural networks (FHRCNNs) was used for the initial load forecasting. Evolutionary programming (EP) was then used to find the optimal solution for the parameters of FHRCNNs (including parameters such as synaptic weights, biases, membership functions, sensitivity factor in membership functions and adjustable synaptic weights). The EP generates a set of feasible solution parameters The EP has good global optimal search capabilities. The HEFNN was used to see if it could improve the solution quality and reduce the load forecasting error.
Liquefaction and storage of thermal treatment off-gases (1992)

A fluidized bed catalytic oxidation unit is being developed for use in the destruction of mixed waste at the Rocky Flats Plant. Cyclones, filters, in situ neutralization of acid gases, and a catalytic converter are used to meet emission standards. Because there is concern by the public that these measures may not be adequate, two off-gas capture systems were evaluated. Both systems involve liquefaction of carbon dioxide produced in the oxidation process. The carbon dioxide would be released only after analysis proved that all appropriate emission standards are met.
Vitronectin gene expression in vivo. Evidence for extrahepatic synthesis and acute phase regulation. (1994)

A competitive polymerase chain reaction (PCR) assay was developed to quantitate vitronectin (Vn) mRNA in murine tissues using a synthetic RNA as an external standard. Although the liver contained the highest concentration of Vn mRNA, significant levels were also detected in the brain (25-fold less) and in adipose tissue, heart, and skeletal muscle (100-fold less than liver). Lower concentrations also were detected in the lung, uterus, testis, and thymus, and little or no Vn mRNA could be detected in kidney, spleen, and blood. These results indicate that significant amounts of Vn mRNA are produced in extrahepatic organs. The regulation of Vn gene expression in vivo was studied in a murine model system in which acute systemic inflammation was induced by endotoxin administration. Plasma Vn levels increased 2- to 3-fold within 16 h after endotoxin administration and remained elevated for up to 72 h. This increase appeared to result from increased synthesis in the liver since the steady-state level of hepatic Vn mRNA increased 4-fold after endotoxin administration. Moreover, Vn mRNA levels in heart, lung, and brain were not significantly increased by endotoxin. These results suggest that Vn gene expression in vivo is regulated in a tissue-specific manner and identify Vn as a novel acute phase reactant.
Results of the First Pilot‐Scale Controlled Cohort Epidemiological Investigation into the Possible Health Effects of Bathing in Seawater at Langland Bay, Swansea (1991)

Abstract A pilot study was conducted to investigate the feasibility of using adult volunteers to examine the possible health effects of bathing in UK seawaters which passed the EC bathing waters Directive. Langland Bay, near Swansea, was chosen for this experiment, which was conducted on 2 September 1989. Adult volunteers were recruited from the City of Swansea and randomly divided into bather and non‐bather groups. All volunteers were given medical examinations and medical questionnaire interviews before and after 2 September. Water quality on the day of the test was relatively unpolluted, as indexed by the commonly‐employed bacterial and viral indicator species. The detailed medical questionnaire resulted in higher reported attack rates of perceived illness in both bather and non‐bather groups than those published in previous studies, which have commonly employed a single telephone interview to acquire disease perception data. Statistically‐significant differences in the bather and non‐bather cohorts were found for the following perceived symptoms: sore throat, ear symptom, eye symptom at 3 d after 2 September, and for diarrhoea at three weeks after the experiment. The clinical tests employed failed to confirm these significant perceived symptom attack rate differentials. The significance of these results is discussed in the context of previous research protocols to demonstrate the feasibility of this novel prospective controlled cohort approach for the acquisition of scientifically robust data on the health effect of recreational water use. If taken to a full‐scale study, it is argued that this research protocol could offer considerable advantages over past methods and lead to scientifically valid water‐quality standards for recreational waters.
ChemInform Abstract: BIPHENYLENES. XXXI. CONDENSATION OF BENZOCYCLOBUTENE‐1,2‐DIONE WITH ALIPHATIC C AND HETEROCYCLIC 1,2‐DIAMINES AND THE SYNTHESIS OF CIS‐2‐CYANO‐3‐(2′‐CYANOVINYL)1,4‐DIAZABIPHENYLENE (1979)

Abstract Das Dion (I) wird mit den 1,2‐Diaminen (II), (IV), (VI), (VIII), (X) und (XII) zu den entsprechenden Verbindungen (III), (V), (VII), (IX), (XI) und (XIII) kondensiert.
Detection of specific mRNAs in single nephron segments by use of the polymerase chain reaction (1990)

We have developed a procedure to detect specific mRNAs in single renal nephron segments. This approach combines microdissection, reverse transcription (RT) of the target mRNA, and amplification of the resulting cDNA using the polymerase chain reaction (PCR). After microdissection, the sample is placed in a tube where it is permeabilized and where all reactions are performed directly without the need for isolation of the RNA. Our model target was the mRNA for aldose reductase. This enzyme catalyzes the conversion of glucose to sorbitol. Its expression is modulated by changes in extracellular osmolality in the renal medulla. RT-PCR of inner medullary collecting duct (1 mm) and glomeruli (6-10) yielded a product of the predicted length (670 base pairs) defined by the PCR primers. Its identity was confirmed by a specific oligonucleotide probe that differed from the primers. RT-PCR of proximal tubules (1 mm) resulted in no aldose reductase-specific amplification product. RT-PCR is generally applicable for measuring specific gene expression in single nephron segments or small numbers of cultured cells. Utility, limitations, and refinements of this approach are discussed.
A CAD System for Color Design of a Car (1992)

Abstract We have developed a color CAD system which enables a color designer to evaluate and create body colors of a car on a graphic display and put this system into practical use. The system has three features; generating realistic images comparable to photography to satisfy the car designer's needs, through close analysis of the physical phenomena taking place in the real environment, reproducing the desired colors very accurately on a CRT monitor, through analysis of the CRT colorimetric characteristics of reproducing the specified colors in response to the input signals, and utilizing a parallel computer to generate realistic images at a high speed and to control colors through interactive operation. Application of the CAD system reported here to the field of color design made it possible to fully evaluate and create body colors by means of computer graphics, replacing the conventional method which requires the painting of clay models or prototype cars.
Ensuring the integrity of the E-court process (2006)

This paper considers possible implications of information protection within Australia's e-court processes. While judgements on the directed use of courtroom technologies during proceedings and current practice directions provide some indication of the thoughts that underlie the use of IT in court proceedings, a literature review conducted by the research team has revealed that there is a distinct lack of formal research and more work is required to fully address the issue of information protection and e-courts.
Generation of 50-fsec pulses from a pulse-compressed, cw, passively mode-locked Ti:sapphire laser (1991)

Stable pulses of less than 150 fsec are generated directly from a tunable cw passively mode-locked Ti:sapphire laser, through a balance of self-phase modulation in the Ti:sapphire rod and negative group-velocity dispersion produced by a prism pair. After external fiber compression, 50-fsec pulses are obtained at approximately 750 nm.
PRA: A PERSPECTIVE ON STRENGTHS, CURRENT LIMITATIONS, AND POSSIBLE IMPROVEMENTS (2014)

Probabilistic risk assessment (PRA) has been used in various technological fields to assist regulatory agencies, managerial decision makers, and systems designers in assessing and mitigating the risks inherent in these complex arrangements. Has PRA delivered on its promise? How do we gage PRA performance? Are our expectations about value of PRA realistic? Are there disparities between what we get and what we think we are getting form PRA and its various derivatives? Do current PRAs reflect the knowledge gained from actual events? How do we address potential gaps? These are some of the questions that have been raised over the years since the inception of the field more than forty years ago. This paper offers a brief assessment of PRA as a technical discipline in theory and practice, its key strengths and weaknesses, and suggestions on ways to address real and perceived shortcomings.
Characterization of the Structural Gene Encoding Nisin F, a New Lantibiotic Produced by a <i>Lactococcus lactis</i> subsp. <i>lactis</i> Isolate from Freshwater Catfish ( <i>Clarias gariepinus</i> ) (2007)

Lactococcus lactis F10, isolated from freshwater catfish, produces a bacteriocin (BacF) active against Staphylococcus aureus, Staphylococcus carnosus, Lactobacillus curvatus, Lactobacillus plantarum, and Lactobacillus reuteri. The operon encoding BacF is located on a plasmid. Sequencing of the structural gene revealed no homology to other nisin genes. Nisin F is described.
The interaction of novolak oligomers with hydrogen bond acceptors. (1994)

Hydrogen bonding between several novolak oligomers as donors and phenylsulfoxide as acceptor was investigated as a model for the interaction of inhibitors with o-o-connected phenolic blocks in practical novolak resins. It was found that the attraction of the novolak dimer for the acceptor was more than twice as strong as that of the corresponding monomeric phenol.
Bystander Effects: Intercellular Transmission of Radiation Damage Signals (2002)

Biological effects were examined in confluent cultures of fibroblasts and epithelial cells exposed to very low mean doses of alpha radiation, doses by which only 1-2% of the cells were actually traversed by an alpha particle. Enhanced frequencies of sister chromatid exchanges and HPRT mutations occurred in the non-irradiated, 'bystander' cells associated with a similar increase in the frequency of micronuclei, indicating the induction of DNA damage in these cells. In order to gain information concerning molecular pathways, changes in gene expression were examined in bystander cells by western analysis and in situ immunofluorescence staining. The expression levels of p53, p21 and MDM2 were significantly modulated in bystander cells; the damage signals leading to these changes were transmitted from irradiated to bystander cells by gap junction mediated intercellular communication. The bystander response was suppressed by incubation with superoxide dismutase as well as an inhibitor of NADPH oxidase, suggesting the effect may be mediated by oxidative stress. To examine other signalling pathways responsive to oxidative stress, the activation of stress-related kinases and their downstream transcription factors were analysed in bystander cells by western blotting and electrophoretic mobility shift assays; a 2-4-fold increase in the phosphorylation levels of JNK, ERK1/2, p90RSK, Elk-1 and ATF2 was observed. These changes were detected by 15 min after irradiation and persisted for at least 1 h. These findings indicate the activation of multiple signal transduction pathways in bystander cells, involving signals arising from the plasma membrane as well as from DNA damage.
Training deep neural-networks based on unreliable labels (2016)

In this study we address the problem of training a neural network based on data with unreliable labels. We introduce an extra noise layer by assuming that the observed labels were created from the true labels by passing through a noisy channel whose parameters are unknown. We propose a method that simultaneously learns both the neural network parameters and the noise distribution. The proposed method is compared to standard back-propagation neural-network training that ignores the existence of wrong labels. The improved classification performance of the method is illustrated on several standard classification tasks. In particular we show that in some cases our approach can be beneficial even when the labels are set manually and assumed to be error-free.
Genomic Sequence of Bacteriophage ATCC 8074-B1 and Activity of Its Endolysin and Engineered Variants against Clostridium sporogenes (2012)

Lytic bacteriophage ATCC 8074-B1 produces large plaques on its host Clostridium sporogenes. Sequencing of the 47,595-bp genome allowed the identification of 82 putative open reading frames, including those encoding proteins for head and tail morphogenesis and lysis. However, sequences commonly associated with lysogeny were absent. ORF 22 encodes an endolysin, CS74L, that shows homology to N-acetylmuramoyl-L-alanine amidases, and when expressed in Escherichia coli, the protein causes effective lysis of C. sporogenes cells when added externally. CS74L was also active on Clostridium tyrobutyricum and Clostridium acetobutylicum. The catalytic domain expressed alone (CS74L(1-177)) exhibited a similar activity and the same host range as the full-length endolysin. A chimeric endolysin consisting of the CS74L catalytic domain fused to the C-terminal domain of endolysin CD27L, derived from Clostridium difficile bacteriophage ΦCD27, was produced. This chimera (CSCD) lysed C. sporogenes cells with an activity equivalent to that of the catalytic domain alone. In contrast, the CD27L C-terminal domain reduced the efficacy of the CS74L catalytic domain when tested against C. tyrobutyricum. The addition of the CD27L C-terminal domain did not enable the lysin to target C. difficile or other CD27L-sensitive bacteria.
Case Report: Emergent Resistance in a Treatment-Naive Person With Human Immunodeficiency Virus Under Bictegravir-Based Therapy (2021)

Few instances of treatment-emergent resistance to bictegravir have been reported in the literature. We describe a case of treatment-emergent resistance to bictegravir in a person recently diagnosed with human immunodeficiency virus who developed M184V and R263K mutations while on therapy.
Three Timing Synchronization Methods Based on Two Same Preambles for OFDM Systems (2012)

Abstract The purpose of this paper is to propose two fast timing synchronization methods of OFDM System which has two preamble symbols, the two preamble symbols are used for SNR estimation for OFDM systems. The synchronization techniques are examined in Multipath fading environments for comparison. The results of the performance comparison are presented in terms of mean obtained by simulations.
Serum and urinary biomarkers in acute kidney transplant rejection (2011)

The discovery of surrogate biomarkers in kidney transplantation is an evolving field of crucial importance that may change the way we practice transplant nephrology in the future.
Investigation of reflective electrochromic all-solid-state devices by Nuclear Reaction Analysis (1990)

Electrochromic all-solid-state devices (ASSD) produced by reactive evaporation have been investigated by iaeans of reflectance measurements in the VIS/NIR range and cyclovoltammetry. Hydrogen depth proil were then by a NRA-technique employing the resonant reaction H( N, ar) C. Two different types of designs have been characterized. The electrochromic behaviour of ASSD's can not be described by models based on H transport for devices containing only W03 layers as active materials. Using NiOXH films as electrochromic substances, the injected/ejected charge corelates with changes in the H content.