gebhart/patrepeval huggingface dataset:
Inducible production and cellular location of the epidermin biosynthetic enzyme EpiB using an improved staphylococcal expression system (1996)

The antimicrobial peptide epidermin is distinguished by thioether amino acids such as meso-lanthionine, 3-methyl-lanthionine, and 2-aminovinylcysteine. The enzyme EpiB, encoded on a plasmid of the producing strain Staphylococcus epidermidis Tü3298, is very likely involved in the formation of these unusual amino acids. In order to obtain high-level production of EpiB, an improved staphylococcal expression vector based on the xylose-inducible xylA promoter of Staphylococcus xylosus was constructed. As shown by the expression of a lipase reporter gene, the new plasmid pTX15 mediated a considerably higher expression level after induction and a lower background expression level in the uninduced state than the previously described vector pCX15. The epiB gene was inserted in pTX15 and expressed in Staphylococcus carnosus. The EpiB protein was detected both in the cytoplasmic and the membrane fraction and was partially purified in three steps.
Deep Neuroevolution: Genetic Algorithms Are a Competitive Alternative for Training Deep Neural Networks for Reinforcement Learning (2017)

Deep artificial neural networks (DNNs) are typically trained via gradient-based learning algorithms, namely backpropagation. Evolution strategies (ES) can rival backprop-based algorithms such as Q-learning and policy gradients on challenging deep reinforcement learning (RL) problems. However, ES can be considered a gradient-based algorithm because it performs stochastic gradient descent via an operation similar to a finite-difference approximation of the gradient. That raises the question of whether non-gradient-based evolutionary algorithms can work at DNN scales. Here we demonstrate they can: we evolve the weights of a DNN with a simple, gradient-free, population-based genetic algorithm (GA) and it performs well on hard deep RL problems, including Atari and humanoid locomotion. The Deep GA successfully evolves networks with over four million free parameters, the largest neural networks ever evolved with a traditional evolutionary algorithm. These results (1) expand our sense of the scale at which GAs can operate, (2) suggest intriguingly that in some cases following the gradient is not the best choice for optimizing performance, and (3) make immediately available the multitude of neuroevolution techniques that improve performance. We demonstrate the latter by showing that combining DNNs with novelty search, which encourages exploration on tasks with deceptive or sparse reward functions, can solve a high-dimensional problem on which reward-maximizing algorithms (e.g.\ DQN, A3C, ES, and the GA) fail. Additionally, the Deep GA is faster than ES, A3C, and DQN (it can train Atari in ${\raise.17ex\hbox{$\scriptstyle\sim$}}$4 hours on one desktop or ${\raise.17ex\hbox{$\scriptstyle\sim$}}$1 hour distributed on 720 cores), and enables a state-of-the-art, up to 10,000-fold compact encoding technique.
In vitro selection of DNA binding sites for ABF1 protein from <i>Saccharomyces cerevisiae</i> (2005)

The autonomously replicating sequence-binding factor 1 (ABF1) from Sacchramoyces cerevisiae is known as a multifunctional DNA binding protein that is involved in transcriptional regulation, DNA-replication, and in restructuring of chromatin via nucleosome remodelling. ABF1 binds to DNA sequences found in ARS elements and in various transcriptional regulatory elements. This led to the early definition of the consensus motive 5'-CGTnnnnnnnGA(G/C)-3'. We have used a SELEX approach to expand and better characterize the DNA sequence requirements of ABF1. Starting from a pool of oligonucleotides randomized at a sequence of 30 nucleotides, we used EMSA to select for sequences with high affinity for ABF1. We obtained the sequences of 106 aptamers after the 15th SELEX round. A 16 nucleotide consensus was derived from this pool by analysis with the motif search programme MEME. Quantitative EMSA experiments verified our experimental approach since binding sequences which were bound with high affinity occurred more often in the pool and resembled the derived consensus to a higher degree. We found DNA sequences that are bound by ABF1 with nearly two-magnitude higher affinity as compared to the hitherto accepted ABF1 consensus sequence. This led us to postulate a strong recognition motive: 5'-TnnCGTnnnnnnTGAT-3'.
Identification of a second hemolysin (HlyII) in Actinobacillus pleuropneumoniae serotype 1 and expression of the gene in Escherichia coli (1992)

Hemolysin genes of the reference strains of Actinobacillus pleuropneumoniae serotypes 1 and 2 were identified, cloned, and expressed in Escherichia coli by using polymerase chain reaction amplification with oligonucleotides derived from the DNA sequence of the corresponding appA gene from A. pleuropneumoniae serotype 5. The three genes from serotypes 1, 2, and 5 have identical restriction maps and appear to encode a hemolysin which was previously identified in serotype 2 and designated HlyII. Gene appA is different from hlyIA encoding the major hemolysin type I (HlyI) which was identified earlier in serotype 1. Polymerase chain reaction amplification with oligonucleotides derived from the DNA sequence of hlyIA of serotype 1 showed that the gene encoding HlyI is present in serotype 1 but not in serotype 2, in contrast to the gene encoding HlyII that was present in both serotypes. This was confirmed by Western blot (immunoblot) experiments using monoclonal antibodies specific for either recombinant HlyI or recombinant HlyII, which showed that A. pleuropneumoniae serotype 1 strain 4074 produces both HlyI and HlyII, whereas serotype 2 strain S1536 produces only HlyII. The expression of both hemolysins was investigated in all serotypes by the use of monoclonal antibodies. HlyI was shown to be expressed by the reference strains of serotypes 1, 5a, 5b, 9, 10, and 11, whereas HlyII was shown to be expressed by the reference strains of all 12 serotypes tested except serotype 10. A. pleuropneumoniae serotype 1 strain 4074 is the first bacterium which has been shown to contain two different actively expressed RTX toxin genes. Comparison of our data with those from other groups shows that the originally described strongly hemolytic hemolysin type I (HlyI) corresponds to cytolysin I (ClyI) which was recently described by others, while the weakly hemolytic hemolysin type II (HlyII) seems to be identical to ClyII and AppA.
Coupling of regional activations in a human brain during an object and face affect recognition task (2000)

Magnetic field tomography (MFT) was used to extract estimates for distributed source activity from average and single trial MEG signals recorded while subjects identified objects (including faces) and facial expressions of emotion. Regions of interest (ROIs) were automatically identified from the MFT solutions of the average signal for each subject. For one subject the entire set of MFT estimates obtained from unaveraged data was also used to compute simultaneous time series for the single trial activity in different ROIs. Three pairs of homologous areas in each hemisphere were selected for further analysis: posterior calcarine sulcus (PCS), fusiform gyrus (FM), and the amygdaloid complex (AM). Mutual information (MI) between each pair of the areas was computed from all single trial time series and contrasted for different tasks (object or emotion recognition) and categories within each task. The MI analysis shows that through feed-forward and feedback linkages, the "computation" load associated with the task of identifying objects and emotions is spread across both space (different ROIs and hemispheres) and time (different latencies and delays in couplings between areas)-well within 200 ms, different objects separate first in the right hemisphere PCS and FG coupling while different emotions separate in the right hemisphere FG and AM coupling, particularly at latencies after 200 ms.
Exact accumulation of floating-point numbers (2002)

The authors present a new idea for designing a chip which computes the exact sum of arbitrarily many floating-point numbers, i.e. it can accumulate the floating-point numbers without cancellation. Such a chip is needed to provide a fast implementation of Kulisch arithmetic. This is a new theory of floating-point arithmetic which makes it possible to compute least significant bit accurate solutions to even ill-conditioned numerical problems. The proposed approach avoids the disadvantages of previously suggested designs which are too large, too slow, or consume too much power. The crucial point is a technique for a fast carry resolution in a long accumulator. It can also be implemented in software.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
THE FATAL TOXIC MANIFESTATIONS OF THE THIOCYANATES (1939)

The purpose of this report is to draw attention to the fatal toxic manifestations of the thiocyanates. Ever since the first pharmacologic investigation of the thiocyanates in 1857 by Claude Bernard<sup>1</sup>there have been numerous references to the toxic properties of this drug. However, the observations of Pauli<sup>2</sup>in 1903 that thiocyanates were effective in reducing high blood pressure caused the use of the drug to gain favor. Untoward symptoms occurred so frequently, however, that the drug fell into disrepute until it was reintroduced in the treatment of hypertension by Westphal<sup>3</sup>in 1925. Since that time some investigators have felt that the thiocyanates were valuable drugs;<sup>4</sup>others have felt that they were not only useless but dangerous.<sup>5</sup> The published work of others and personal observations would indicate that in many instances the continued administration of thiocyanates leads to lowering of the blood pressure. There is
Expression of miRNA-29a in U937 macrophages infected with Mycobacterium tuberculosis and its regulation of target genes (2018)

Objective
To analyze the expression of miRNA-29a in U937 macrophages infected with Mycobacterium tuberculosis and its regulation of target genes.


Methods
The target genes of miRNA-29a were predicted with softwares miRnada, RNAhybrid and targetscan. The differentiation of U937 macrophages was induced by phorbol ester (PMA), the induced U937 cells were infected with bacilli calmette guerin (BCG). The expression levels of miRNA-29a and its target genes in U937 cells were detected with real-time fluorescence quantitative PCR (RT-fqPCR). The miRNA-29a over- and low-expression U937 macrophage cell lines were constructed and the levels of miRNA-29a and its garget genes were detected. The SPSS 18.0 software was used to analyze the data.


Results
As predicted by relevant softwares, the miRNA-29a regulate the expression of VEGFA, NFATC3 and TSC22D3 genes. After BCG infection, the expression of miRNA-29a increased to 1.33 fold (P<0.05), and the expression levels of VEGFA, NFATC3 and TSC22D3 were increased to 5.34, 99.25 and 2.12 fold, respectively (P<0.01). In the miRNA-29a over-expressing U937 macrophages, the expression levels of VEGFA, NFATC3 and TSC22D3 were up-regulated to 1.35, 1.29 and 3.38 fold, respectively (P<0.05 or <0.01). While in the U937 macrophages with miRNA-29a knock-down, the expression levels of VEGFA, NFATC3 and TSC22D3 were down-regulated to 0.07, 0.08 and 0.55 fold, respectively (P<0.01).


Conclusion
The results suggest that Mycobacterium tuberculosis infection can increase the expression of miRNA-29a in U937 macrophages, further targeting the regulation of VEGFA, NFATC3 and TSC22D3 gene expression, which may participate in the pathogenesis and development of tuberculosis.


Key words: 
Mycobacterium tuberculosis; miRNA-29a; BCG vaccine; Macrophages
Dendritic Metallophthalocyanines—Synthesis, Electrochemical Properties, and Catalytic Activities (1999)

A new dendritic cobalt phthalocyanine has been prepared from a phthalocyanine core by a combination of convergent and divergent synthetic approaches. The dendritic cobalt phthalocyanine serves as an effective catalyst for the thiol oxidation, and the stability of the catalyst is enhanced by the encapsulation with the dendritic branches.
Fast VQ encoding by an efficient kick-out condition (2000)

A new fast approach to the nearest codeword search using a single kick-out condition is proposed. The nearest codeword found by the proposed approach is identical to the one found by the full search, although the processing time is much shorter. The principle is to bypass those codewords which satisfy the proposed kick-out condition without the actual (and time-consuming) computation of the distortions from the bypassed codewords to the query vector. Due to the efficiency and simplicity of the proposed condition, a considerable saving of the central processing unit time needed to encode a data set (using a given codebook) can be achieved. Moreover, the memory requirement is low. Comparisons with some previous works are included to show these two benefits.
Functional Identification of the Product of the <i>Bacillus subtilis yvaL</i> Gene as a SecG Homologue (1999)

Protein export in Escherichia coli is mediated by translocase, a multisubunit membrane protein complex with SecA as the peripheral subunit and the SecY, SecE, and SecG proteins as the integral membrane domain. In the gram-positive bacterium Bacillus subtilis, SecA, SecY, and SecE have been identified through genetic analysis. Sequence comparison of the Bacillus chromosome identified a potential homologue of SecG, termed YvaL. A chromosomal disruption of the yvaL gene results in mild cold sensitivity and causes a beta-lactamase secretion defect. The cold sensitivity is exacerbated by overexpression of the secretory protein alpha-amylase, whereas growth and beta-lactamase secretion are restored by coexpression of yvaL or the E. coli secG gene. These results indicate that the yvaL gene codes for a protein that is functionally homologous to SecG.
Daily Rhythmicity of Serum Testosterone Concentration in the Male Laboratory Rat* (1978)

Daily rhythmicity of serum testosterone concentration in the mature male laboratory rat was examined under various lighting schedules. In rats living in a standard light cycle (12-h light, 12-h dark; lights on at 0600 h), a trimodal rhythm was predominant, with elevations near 0200, 1200, and 1800 h. This pattern was reasonably stable in seven different studies, despite differences in experimental design, method of blood collection, anesthesia, and whether individual rats were sampled once or repeatedly, and was found both in groups of animals and in individuals, including a study using 40-day-old rats. In constant illumination, the pattern was disrupted, but in constant darkness the trimodal pattern was maintained, indicating that the rhythm is endogenous. In a reversed light cycle (12-h dark, 12-h light; lights on at 1800 h), the “midday” elevation was reversed; in an altered light cycle (12-h dark, 12-h light; lights on at 2300 h), the time of the “midday” elevation was shifted. Serum testosterone concentration was higher during the light phase than the dark phase, and was higher in constant light than in constant darkness. A seasonal shift in the daily rhythmicity of serum testosterone concentration is suggested. The trimodal rhythmicity contrasts with the circadian rhythmicity of other hormones. Its functional role in the life of the animal is unknown.
A quantitative tear fluids determination of therapeutic efficacy for allergic conjunctivitis. (1984)

A provocation test was conducted with volunteers in 10 cases with seasonal cedar pollinosis during a quiescent stage to determine quantitatively the therapeutic effect of 0.08% Ketotifen eye drops. The efficacy rate of this preparation was found to be 80%.
Improved Durability of WO3 Nanocomposite Films Using Atomic Layer and Vapor Deposited Coatings (2012)

The durability of mesoporous films comprised of tungsten oxide nanoparticles was studied by monitoring their electrochromic performance during extended cycling in lithium perchlorate solution. Standard films rapidly lost charge capacity as nanoparticles detached from the film and were lost to solution. This issue was mitigated through the use of protection layers including evaporated LiAlF4 and alumina applied by atomic layer deposition (ALD). Three ALD cycles offered superior protection to 100 nm of LiAlF4, enabling >2500 cycles with no appreciable change in electrochromic performance. Moreover, the addition of these protection layers did not degrade the switching time as evidenced by their transient response to potential step changes.
Structure–property relation in polyvinyl alcohol/starch composites (2003)

Abstract A series of polyvinyl alcohol (PVA)/starch films were cast by the solvent method. Mechanical, optical, wide‐angle X‐ray scattering (WAXS), and biodegradation studies of starch‐filled PVA films were carried out. With the addition of starch there was an increase in haze and diffusion of light, whereas there was only slight change associated with tensile behavior and burst strength of the PVA film. Microstructural parameters, such as crystal size (〈 N 〉) and lattice distortion ( g , in %) were estimated using one‐dimensional Hosemann's paracrystalline model along with WAXS data. These parameters quantify the changes in the PVA/starch systems, which resulted in the observed physical properties. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 12: 630–635, 2004
Radiation-Induced Change in Serum and Urinary Amylase Levels in Man (1973)

Serum and urinary amylase levels in cancer patients were studied before and after radiation treatment. Fourteen patients received radiation to the whole body, 2 to the upper body (above the xiphoid...
The History of Staining Cochineal Dyes (1928)

Of the dyes used in early histological work, none was so highly prized as carmin. Even today biologists would be loath to part with it. It is still valuable to the histologist and embryologist as a bulk stain of great permanency, and for the preparation of in toto mounts. To the cytologist, also, it is invaluable as a medium for the rapid staining and examination of chromosomes in fresh material. Its permanence has always been a great advantage. To the early histologists, however, it was the dye, par excellence.
An Implementation of Concurrency Control between Batch Update and Online Entries (2014)

Abstract Databases of business systems are generally updated by two methods: the online entries reflect the input from a lot of terminals immediately; the batch update updates a great deal of data in a lump. Here, the batch update usually takes time. So, in the case where it is performed as a single transaction by using the lock, the conflicting online entries wait for a long while. For this problem, we had proposed the temporal update method, and showed the both can be executed concurrently by it. However, to process them by a serializable schedule, the execution timing of the online entries has to be divided by the batch update. So, it raises a problem that there are still latencies of some online entries by this. In this article, we propose four concurrency control methods to shorten this wait. And, we show their implementations and evaluation results. Moreover, we show the appropriate method should be chosen based on the operational requirements
Intel® Software Guard Extensions (Intel® SGX) Architecture for Oversubscription of Secure Memory in a Virtualized Environment (2017)

As workloads and data move to the cloud, it is essential that software writers are able to protect their applications from untrusted hardware, systems software, and co-tenants. Intel® Software Guard Extensions (SGX) enables a new mode of execution that is protected from attacks in such an environment with strong confidentiality, integrity, and replay protection guarantees. Though SGX supports memory oversubscription via paging, virtualizing the protected memory presents a significant challenge to Virtual Machine Monitor (VMM) writers and comes with a high performance overhead. This paper introduces SGX Oversubscription Extensions that add additional instructions and virtualization support to the SGX architecture so that cloud service providers can oversubscribe secure memory in a less complex and more performant manner.
Statistical evidence about the mechanism of action of the Yuzpe regimen of emergency contraception*1 (1999)

The Yuzpe regimen could not be as effective as it appears to be if it worked only by preventing or delaying ovulation.
<i>Anaplasma phagocytophilum p44</i> mRNA Expression Is Differentially Regulated in Mammalian and Tick Host Cells: Involvement of the DNA Binding Protein ApxR (2007)

The natural life cycle of Anaplasma phagocytophilum, an obligatory intracellular bacterium that causes human granulocytic anaplasmosis, consists of alternate infection of two distinct hosts, ticks and mammals, in which bacterial surface proteins are expected to have a critical role. The present study investigated regulation of A. phagocytophilum p44 genes, which encode the P44 major surface proteins. Quantitative real-time reverse transcription-PCR analysis revealed that the amount of p44 mRNA obtained from spleens of A. phagocytophilum-infected SCID mice was approximately 10-fold greater than the amount obtained from salivary glands of A. phagocytophilum-infected Ixodes scapularis nymphs. Similarly, the amount of p44 mRNA obtained from A. phagocytophilum-infected HL-60 cells per bacterium was significantly greater than the amount obtained from infected ISE6 tick cells. The relative amount of p44 mRNA was approximately threefold higher in A. phagocytophilum-infected HL-60 cells cultured at 37 degrees C than in A. phagocytophilum-infected HL-60 cells cultured at 28 degrees C. Although there are more than 100 p44 paralogs, we observed expression mainly from the p44 expression locus (p44E) in various host environments. Interestingly, transcription of the A. phagocytophilum gene encoding the DNA binding protein ApxR was also significantly greater in A. phagocytophilum-infected HL-60 cells than in infected ISE6 tick cells. Gel mobility shift and DNase I protection assays revealed recombinant ApxR binding to the promoter regions of p44E and apxR. ApxR also transactivated the p44E and apxR promoter regions in a lacZ reporter assay. These results indicate that p44 genes and apxR are specifically up-regulated in the mammalian host environment and suggest that ApxR not only is positively autoregulated but also acts as a transcriptional regulator of p44E.
Twelve Random Characters: Passwords in the Era of Massive Parallelism (2013)

Passwords are an old-fashioned authentication mechanism that remains ubiquitous, but modern processing hardware with massive parallelism has suddenly undercut the security of the traditional eight-character password. Administrators and users need to understand the increased risks and to find ways to use and protect longer passwords.
A convergent algorithm for solving polynomial equations. (1967)

Zeros of polynomials with real or complex coefficients determined, using steepest descent method in convergent procedure
Common anorectal disorders. (2014)

Anorectal disorders result in many visits to healthcare specialists. These disorders include benign conditions such as hemorrhoids to more serious conditions such as malignancy; thus, it is important for the clinician to be familiar with these disorders as well as know how to conduct an appropriate history and physical examination. This article reviews the most common anorectal disorders, including hemorrhoids, anal fissures, fecal incontinence, proctalgia fugax, excessive perineal descent, and pruritus ani, and provides guidelines on comprehensive evaluation and management.