gebhart/patrepeval huggingface dataset:
The Interface Between the Biological and Inorganic Worlds: Iron-Sulfur Metalloclusters (2003)

Complex iron-sulfur metalloclusters form the active sites of the enzymes that catalyze redox transformations of N2, CO, and H2, which are likely components of Earth's primordial atmosphere. Although these centers reflect the organizational principles of simpler iron-sulfur clusters, they exhibit extensive elaborations that confer specific ligand-binding and catalytic properties. These changes were probably achieved through evolutionary processes, including the fusion of small clusters, the addition of new metals, and the development of cluster assembly pathways, driven by selective pressures resulting from changes in the chemical composition of the biosphere.
One Algorithm to Match Them All: On a Generic NIPS Pattern Matching Algorithm (2007)

Today's network intrusion prevention systems (NIPS) provide an important defense mechanism against security threats. The detection of network attacks utilizes a highspeed pattern matching algorithm that can be implemented in either hardware or software. Adapting a software-based pattern matching algorithm to hardware-based device is a complicated task. This paper presents a cost effective multi-pattern matching algorithm based on Field Programmable Gate Arrays (FPGAs) and standard RAM. The algorithm achieves line-rate speed, which is several orders of magnitude faster than the current state of the art, while attaining similar accuracy of detection. The algorithm can be easily adapted to operate in hardware-based NIPS and attain even higher speed by utilizing a TCAM memory.
<title>Error analysis for CGH optical testing</title> (1999)

Computer generated holograms are widely used in optical testing and metrology. The primary role of the CGHs is to generate reference wavefront with any desired shape. Optical or electron-beam writers are commonly used for CGH fabrication. Limitations from the hologram fabrication processes cause errors in the reproduced wavefront. Errors in duty-cycle and etching depth have direct impact on both the amplitude and phase functions of the reproduced wavefront. A study using scalar diffraction model to simulate CGH fabrication errors and their effects on wavefront amplitude and phase functions are presented. Experimental analysis confirms the theoretical model. An example is given at the end to demonstrate one of the many applications of the wavefront sensitivity functions in CGH error budgeting for optical metrology.
Specific receptor sites for pyridoxal 5'-phosphate and pyridoxal 5'-deoxymethylenephosphonate at the alpha and beta NH2-terminal regions of hemoglobin. (1983)

hemoglobins have been prepared which are substituted with pyridoxal 5'-phosphate or pyridoxal 5'-deoxymethylenephosphonate at both NH2-terminal amino groups of either the alpha or the beta chains. 31P NMR titration curves of the 5' side chain show a substantial decrease in acid strength in hemoglobins pyridoxylated at the alpha chains and the reverse effect in the hemoglobins labeled in the beta chains. These changes can readily be explained by the interaction of the 5' side chains with surrounding residues which provide specific binding sites for the monoanion at the alpha chain termini and for the dianion in the case of the beta chains. Since the proportion of monoanion is at lest ten times greater for pyridoxal 5'-deoxymethylenephosphonate than for pyridoxal 5'-phosphate at neutral pH, the phosphonate reacts preferentially with the alpha chain NH2-terminal amino groups and the phosphate with the beta chain ones.
Mitogen‐activated protein kinase phosphatase‐1 modulated JNK activation is critical for apoptosis induced by inhibitor of epidermal growth factor receptor‐tyrosine kinase (2009)

Alterations resulting in enhanced epidermal growth factor receptor (EGFR) expression or function have been documented in a variety of tumors. Therefore, EGFR-tyrosine kinase is a promising therapeutic target. Although in vitro and in vivo studies have shown the anti-tumor activity of EGFR-tyrosine kinase inhibitors against various tumor types, little is known about the mechanism by which such inhibitors effect their anti-tumor action. AG1478 is known to selectively inhibit EGFR-tyrosine kinase. In this study, we showed that AG1478 caused apoptosis and apoptosis-related reactions such as the activation of caspase 3 in human non-small cell lung cancer cell line PC-9. To investigate the signaling route by which AG1478 induced apoptosis, we examined the activation of c-Jun N-terminal kinase (JNK) and mitogen-activated protein kinase p38 in AG1478-treated PC-9 cells. JNK, but not p38, was significantly activated by AG1478 as determined by both immunoblot analysis for levels of phosphorylated JNK and an in vitro activity assay. Various types of stimuli activated JNK through phosphorylation by the dual-specificity JNK kinases, but the dual-specificity JNK kinases MKK4 and MKK7 were not activated by AG1478 treatment. However, JNK phosphatase, i.e. mitogen-activated protein kinase phosphatase-1 (MKP-1), was constitutively expressed in the PC-9 cells, and its expression level was reduced by AG1478. The inhibition of JNK activation by ectopic expression of MKP-1 or a dominant-negative form of JNK strongly suppressed AG1478-induced apoptosis. These results reveal that JNK, which is activated through the decrease in the MKP-1 level, is critical for EGFR-tyrosine kinase inhibitor-induced apoptosis.
S-methyltransferases in human intestine: differential distribution of the microsomal thiol methyltransferase and cytosolic thiopurine methyltransferase along the human bowel (1993)

Abstract1. The activities of the microsomal thiol methyltransferase and the cytosolic thiopurine methyltransferase were measured with 2-mercaptoethanol and 6-mercaptopurine as substrates in human ileum, ascending colon, transverse colon, descending colon and liver.2. Thiol methyltransferase activity (pmol/min per mg) (mean±SD) was 495±280 (ileum), 786±454 (ascending colon), 1791±233 (transverse colon), 964±484 (descending colon) and 4800±1194 (liver).3. Thiopurine methyltransferase (pmol/min per mg) (mean±SD) was 53.5±15.4 (ileum), 34.6±11.4 (ascending colon), 64.3±12.1 (transverse colon), 57.0±10.1 (descending colon) and 106±20.4 (liver).4. Transferases in intestinal mucosa followed non-Michaelis-Menten kinetics, and two phases representing high and low affinity forms, for the acceptor methyl substrates were observed.5. Comparison of intestinal with hepatic activities showed that thiopurine methyltransferase is better expressed than thiol methyltransferase in the human intestine, at least with the substrates studied.
Intravenous immunoglobulin in primary and secondary chronic progressive multiple sclerosis: a randomized placebo controlled multicentre study (2007)

In patients with relapsing-remitting multiple sclerosis (MS), IVIG was shown to reduce the relapse rate and progression of disability. In patients with chronic progressive MS, a beneficial effect of IVIG was not documented in placebo controlled studies. This trial investigated the influence of IVIG in primary (PPMS) and secondary (SPMS) chronic progressive MS. Two-hundred and thirty-one patients stratified for PPMS (n=34) and SPMS (n=197) were randomly assigned to IVIG 0.4 g/kg per month or to placebo for 24 months. Primary endpoints were 1) the time to sustained progression of disease identified as worsening of the expanded disability status scale (EDSS) sustained for 3 months, and 2) the improvement of neurological functions defined by a patient's best EDSS score. Secondary endpoints were the proportion of patients with sustained progression, the relapse rate, the assessment of fine motor skills, visual evoked potentials, contrast sensitivity, depression and quality of life. Analysis of the intention-to-treat (ITT) population of combined PPMS and SPMS patients showed that the mean time to sustained progression was 74 weeks in the IVIG compared with 62 weeks in the placebo group (P=0.0406). When PPMS and SPMS patients were analysed separately, the time to sustained progression was also longer in the IVIG group, but the difference was not significant. There was no IVIG-mediated improvement in neurological functions. In the combined per protocol (PP) treated patients, IVIG treatment prolonged time to sustained progression by 13 weeks (P=0.0396). PPMS patients, but not SPMS patients showed a slight favourable IVIG effect on the best EDSS score. In the combined ITT population there were less patients with sustained progression in the IVIG than in the placebo group (P=0.028). The difference was significant in PPMS (P=0.016), but not in SPMS patients. In the combined PP population, there was a trend for a favorable IVIG effect on the rates of patients with sustained progression. In patients with PPMS, this IVIG effect reached significance (P=0.036). Other secondary endpoints did not show significant differences between treatment groups. Eighteen patients with PPMS and 102 patients with SPMS withdrew from the study for various reasons. Treatment was generally well tolerated. It was concluded that monthly IVIG infusion could delay progression of disease in patients with PPMS, and that there was a trend in favour of IVIG treatment in patients with SPMS.
Divergence of Apoptosis-Inducing and Preventing Signals in Bacteria-Faced Macrophages Through Myeloid Differentiation Factor 88 and IL-1 Receptor-Associated Kinase Members (2002)

The induction of apoptosis in host cells is a common strategy by which pathogenic bacteria interfere with the host immune response. The Yersinia enterocolitica outer protein P (YopP) inhibits activation of transcription factor NF-kappa B in macrophages, which suppresses NF-kappa B-dependent antiapoptotic activities. The simultaneous initiation of proapoptotic signaling by yersiniae infection or LPS treatment results in macrophage apoptosis. In this study, we used YopP as a tool to dissect survival- and death-inducing pathways in bacteria-faced macrophages. We cotransfected J774A.1 macrophages with expression plasmids for YopP and dominant-negative mutants of signal transmitters of the NF-kappa B cascade downstream from the LPS receptor complex. Dominant-negative myeloid differentiation factor 88 (MyD88) or IL-1R-associated kinase (IRAK) 2 diminished LPS-induced apoptosis in YopP-transfected macrophages, suggesting implication of MyD88 and IRAK2 in signaling cell death. In contrast, dominant-negative IRAK1 and TNFR-associated factor 6 (TRAF6) did not provide protection, but augmented LPS-mediated apoptosis in the absence of YopP, which indicates roles of IRAK1 and TRAF6 in the antiapoptotic signal relay of the NF-kappa B cascade. The distinct functions of IRAK members in macrophage survival were reflected by opposing effects of dominant-negative IRAK1 and IRAK2 on Y. enterocolitica-mediated apoptosis. Yersiniae- and LPS-dependent cell death were substantially attenuated by a specific caspase-8 inhibitory peptide or by dominant negative Fas-associated death domain protein (FADD). This suggests, that Yersinia-induced apoptosis involves a proapoptotic signal relay through MyD88 and IRAK2, which potentially targets the Fas-associated death domain protein/caspase-8 apoptotic pathway, whereas IRAK1 and TRAF6 counteract the bacteria-induced cytotoxic response by signaling macrophage survival.
Creatine kinase B-subunit activity in human sera: temporal aspects of its sensitivity after myocardial infarction. (1981)

We assessed the changes in sensitivity and specificity of creatine kinase (CK) isoenzymes at various times after acute myocardial infarction. CK-B was measured by an immunoinhibition technique. CK-MB was measured both by column chromatography on Sephadex DEAE A-50 and by electrophoresis on agarose gel. For CK-B, the sensitivity in detecting infarct varied from 11% in the first 8 h after onset of symptoms to 80% at 32 h after the infarct. Sensitivities for CK-MB by column and by electrophoresis were 25 and 45% for the first 8-h period and 80 and 89% at the 32nd hour, respectively. Comparison of values for CK-B with values for CK-MB by column and by electrophoresis gave correlation coefficients of 0.935 and 0.896, respectively. Patients having macro CK-BB exhibit anomalously high values for CK-B with respect to total CK. Patients having a mild infarct may show no increase in CK-isoenzymes.
Serum Inhibin Levels in Polycystic Ovary Syndrome: Basal Levels and Response to Luteinizing Hormone-Releasing Hormone Agonist and Exogenous Gonadotropin Administration* (1988)

Serum inhibin levels were measured by RIA twice weekly for 4 weeks in 5 women with the polycystic ovary syndrome (PCOS). These were compared to those in 10 women with normal menstrual cycles. Serum inhibin levels were similar in the 5 PCOS women (mean, 199; range, 126-266 U/L) and were not significantly different from those in the normal women during the early follicular phase (227; 100-485 U/L) or midfollicular phase (243; 143-412 U/L) of their cycles. Inhibin levels were higher (P less than 0.001) in the late follicular phase (408; 227-732 U/L), at midcycle (623; 367-1058 U/L), and during the midluteal phase (1245; 898-1727 U/L) in the normal women compared to those in the PCOS group. Serum inhibin levels were also measured in PCOS (n = 8) and infertile (n = 14) women after the rise and subsequent diminished gonadotropin secretion that occurred during LHRH agonist administration. In both groups, serum LH and FSH increased after initiation of LHRH agonist administration; this increase was accompanied by parallel rises in serum estradiol and inhibin before suppression (PCOS women: r = 0.71; P less than 0.001; n = 108; infertile women: r = 0.42; P less than 0.05; n = 163). All hormone levels, including inhibin, decreased during continued LHRH administration. Five PCOS women underwent ovulation induction using combined LHRH agonist and human menopausal gonadotropin administration. Serum estradiol and inhibin rose in parallel in response to exogenous gonadotropins (r = 0.92; P less than 0.001; n = 77). In conclusion, we found no evidence of a primary defect in ovarian inhibin physiology in women with PCOS in terms of either basal or gonadotropin-stimulated (exogenous or endogenous) secretion.
Convergence of the SMI and the diagonally loaded SMI algorithms with weak interference (adaptive array) (1990)

Approximations for the power levels at the output of an adaptive array that uses the diagonally loaded sample matrix inversion (SMI) algorithm are derived. Diagonal loading is a technique where the diagonal of the covariance matrix is augmented with a positive or negative constant prior to inversion. The authors examine how the signal-to-interference-plus-noise ratio (SINR) and signal-to-interference ratio (SIR) at the array output vary with the number of samples taken when the input signals are continuous wave. It is shown that positive loading produces more rapid convergence with a reduction in output SIR. Negative loading provides an improved SIR level, but it is shown that positive loading produces more rapid convergence with a reduction in output SIR. Negative loading provides an improved SIR level, but it is shown that the output power levels are erratic and slow to converge. Simulation results which verify the theoretical procedure are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Distributed Model of Human Learning and Memory (1986)

This chapter contains sections titled: A Distributed Model of Memory, Simulations of Experimental Results, Extensions of the Model, Augmenting the Model with Hidden Units, Conclusion, Acknowledgments
The role of pulsed light and heat energy (LHE<sup>TM</sup>) in acne clearance (2004)

ClearTouch pulsed light and heat energy (LHE) technology is effective and safe for the treatment of acne vulgaris.
Cryptographic security evaluation of MD4 hash function (2002)

Cryptography is the only powerful tool for achieving high levels of information security in a computer networks environment. The ISO have proposed five security service groups including, confidentiality, authentication, data integrity, non-repudiation, and access control. Cryptography can support implementation of all these security services, by using various cryptographic techniques, which include among other things conventional secret key algorithms, public-key algorithms, authentication procedures, and different digital signature schemes. Hash functions, in cryptography, are used for digital signature applications and authentication procedures. It is advisable, for cryptographic reasons, to sign only hashed messages. A secure hash function must be a one-way and collision-free function. Cryptographic security of hash functions could be evaluated, so far, either by conducting detailed cryptanalysis, or by using computational complexity theory. Each of these methods has its own shortcomings. A new scheme for evaluating the cryptographic security of hash functions is proposed. The proposed scheme is simple, fast, and based on a solid mathematical model offered by Markov process. The proposed scheme is used to evaluate the cryptographic security of the Message Digest MD-4 algorithm. The results are in accordance with what was conjectured and published.
Channel Estimation in OFDM Systems Based on Mismatched-Sequence (2010)

A new approach which using mismatched-sequence to channel estimation in OFDM systems is proposed.In the scheme,mismatched-sequence is added to OFDM signal as a training sequence at sender,the receiver calculates the cross-correlation between the received mismatched sequence with CP removed and the circular shifted mismatched filter coefficient.By making use of the auto-correlation property of the mismatched-sequence the channel impulse response can be estimated and then the channel frequency response can be acquired.Theoretical analysis and simulation results show that the new algorithm has good property of low-complexity, accurate estimation and better BER performance.
Systems Biology Approaches to Understand Natural Products Biosynthesis (2015)

Actinomycetes populate soils and aquatic sediments that impose biotic and abiotic challenges for their survival. As a result, actinomycetes metabolism and genomes have evolved to produce an overwhelming diversity of specialized molecules. Polyketides, non-ribosomal peptides, post-translationally modified peptides, lactams, and terpenes are well-known bioactive natural products with enormous industrial potential. Accessing such biological diversity has proven difficult due to the complex regulation of cellular metabolism in actinomycetes and to the sparse knowledge of their physiology. The past decade, however, has seen the development of omics technologies that have significantly contributed to our better understanding of their biology. Key observations have contributed toward a shift in the exploitation of actinomycete's biology, such as using their full genomic potential, activating entire pathways through key metabolic elicitors and pathway engineering to improve biosynthesis. Here, we review recent efforts devoted to achieving enhanced discovery, activation, and manipulation of natural product biosynthetic pathways in model actinomycetes using genome-scale biological datasets.
CERTAIN THEORETICAL ASPECTS OF RADIATION DUE TO SUPERLUMINAL MOTION IN A MEDIUM (1960)

Introduction 874 1. Characteristic Features of Radiation Due to Superlight Motion (Classical Theory) 874 2. Quantum Theory of Radiation and Absorption Due to Superlight Motion 876 3. Radiation Reaction Force for Motion of a Charge in a Medium 880 4. Cerenkov Radiation and Absorption of Waves in an Isotropic Magnetoactive Plasma 883 5. Cerenkov Radiation of Dipole Moments in a Continuous Medium and in Channels and Slits 87 Literature References 891
Nickel‐Catalyzed Amination of Aryl Pivalates by the Cleavage of Aryl CO Bonds (2010)

Catalytic amination: The title reaction demonstrates the use of aryl carboxylates as suitable electrophilic coupling substrates in catalytic amination reactions. N-heterocyclic carbene ligands and NaOtBu promote the amination of aryl pivalates through the cleavage of normally unreactive aryl carbon-oxygen bonds (see scheme; cod=cyclooctadiene).
Rapid colorimetric detection of COVID-19 coronavirus using a reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic platform: iLACO (2020)

Abstract The recent outbreak of a novel coronavirus SARS-CoV-2 (also known as 2019-nCoV) threatens global health, given serious cause for concern. SARS-CoV-2 is a human-to-human pathogen that caused fever, severe respiratory disease and pneumonia (known as COVID-19). By press time, more than 70,000 infected people had been confirmed worldwide. SARS-CoV-2 is very similar to the severe acute respiratory syndrome (SARS) coronavirus broke out 17 years ago. However, it has increased transmissibility as compared with the SARS-CoV, e.g. very often infected individuals without any symptoms could still transfer the virus to others. It is thus urgent to develop a rapid, accurate and onsite diagnosis methods in order to effectively identify these early infects, treat them on time and control the disease spreading. Here we developed an isothermal LAMP based method-iLACO ( i sothermal LA MP based method for CO VID-19) to amplify a fragment of the ORF1ab gene using 6 primers. We assured the species-specificity of iLACO by comparing the sequences of 11 related viruses by BLAST (including 7 similar coronaviruses, 2 influenza viruses and 2 normal coronaviruses). The sensitivity is comparable to Taqman based qPCR detection method, detecting synthesized RNA equivalent to 10 copies of 2019-nCoV virus. Reaction time varied from 15-40 minutes, depending on the loading of virus in the collected samples. The accuracy, simplicity and versatility of the new developed method suggests that iLACO assays can be conveniently applied with for 2019-nCoV threat control, even in those cases where specialized molecular biology equipment is not available.
Business and society in transformation (1976)

Although most of us have to be concerned primarily with the welfare of our own organizations, we recognize that these organizations prosper only as the society as a whole prospers. Society presently faces a set of complex problems, and neither the bureaucratic process of executive decision‐making nor the adversary process of political decision‐making seems well adapted to their resolution. What appears to be required is a process for developing new perceptions of the situation, the facts, and the action possibilities .
Measuring the Degree of Synonymy between Words Using Relational Similarity between Word Pairs as a Proxy (2012)

Two types of similarities between words have been studied in the natural language processing community: synonymy and relational similarity. A high degree of similarity exist between synonymous words. On the other hand, a high degree of relational similarity exists between analogous word pairs. We present and empirically test a hypothesis that links these two types of similarities. Specifically, we propose a method to measure the degree of synonymy between two words using relational similarity between word pairs as a proxy. Given two words, first, we represent the semantic relations that hold between those words using lexical patterns. We use a sequential pattern clustering algorithm to identify different lexical patterns that represent the same semantic relation. Second, we compute the degree of synonymy between two words using an inter-cluster covariance matrix. We compare the proposed method for measuring the degree of synonymy against previously proposed methods on the Miller-Charles dataset and the WordSimilarity-353 dataset. Our proposed method outperforms all existing Web-based similarity measures, achieving a statistically significant Pearson correlation coefficient of 0.867 on the Miller-Charles dataset.