gebhart/patrepeval huggingface dataset:
The introns gained during divergence of protein (1998)

The similarity of intron sequences in actin gene family, especially in the same and different isoform of protein in the family is compared. The high similarities of exon sequences in whole actin show that the actin proteins were evolved from a common ancestor. The similarities of intron sequences in same isoform protein were related to the orders evolved of species. There is high similarity of intron sequences in same isoform protein between rat and mouse and between cattle and pig. These facts may indicate that the intron sequences in same isoform probably were evolved from one common ancestor; the low similarity of intron sequences in different isoforms of protein, even in same species such as human, indicates that intron sequences in different isoforms of protein were evolved from different ancestors.
Evaluation of Antibacterial Ability of Some Pure Metals (2007)

The biohazard in the medical treatment or the food industry sometimes is a matter of serious concern. Recently, the corrosion or degradation due to microbial activity is also coming to consider as one of significant problems in the industrial technology. In these biohazards, the proliferation and colonization of microbes on the material surfaces is recognized as the precursor. From a point of view of this point, the utilization of antibacterial material is considered as one of effective approach to control the activation of harmful microbes and to create a hygiene life space. Although there are so many commercial products with antibacterial ability, they are generally plastics, clothing fivers or ceramics. While, antibacterial metals (commercial products of metals with antibacterial ability) are not so popular as former. Moreover, there are some researches for antibacterial ability of silver or copper metal, the substance which is more paid attention as antibacterial agent is organic substances rather than inorganic ones. In this study, the interaction of some pure metals and microbes was examined by two experimental methods, the film contact method and the shaking flask method. Through these experiments, we evaluated the anti-bacterial ability of some pure metals and investigated the possibility of utilization for alloy element.
OS-Sommelier (2012)

Precise fingerprinting of an operating system (OS) is critical to many security and virtual machine (VM) management applications in the cloud, such as VM introspection, penetration testing, guest OS administration (e.g., kernel update), kernel dump analysis, and memory forensics. The existing OS fingerprinting techniques primarily inspect network packets or CPU states, and they all fall short in precision and usability. As the physical memory of a VM is always present in all these applications, in this paper, we present OS-Sommelier, a memory-only approach for precise and efficient cloud guest OS fingerprinting. Given a physical memory dump of a guest OS, the key idea of OS-Sommelier is to compute the kernel code hash for the precise fingerprinting. To achieve this goal, we face two major challenges: (1) how to differentiate the main kernel code from the rest of code and data in the physical memory, and (2) how to normalize the kernel code to deal with practical issues such as address space layout randomization. We have designed and implemented a prototype system to address these challenges. Our experimental results with over 45 OS kernels, including Linux, Windows, FreeBSD, OpenBSD and NetBSD, show that our OS-Sommelier can precisely fingerprint all the tested OSes without any false positives or false negatives, and do so within only 2 seconds on average.
On the Application of Energy Contours to the Recognition of Connected Word Sequences (1984)

It has recently been shown that small but consistent improvements in isolated word recognition accuracy can be obtained by supplementing the Linear Predictive Coding (LPC) features for each frame of a word by a normalized energy value for that frame. The key idea in using energy is to normalize the frame energy by the local energy maximum in time (i.e., relative to the peak energy of the spoken word). If we want to extend the concept of using frame energy as a supplement to the LPC feature set for connected word recognition, we must provide a dynamic method of energy normalization so that the peak energy within strings can closely approximate the energy contours of individual words strung together. In this paper such a dynamic energy normalization is proposed, and it is shown to provide improvements in connected word recognition applications. The normalization consists of determining a continuous peak energy contour for the speech, where the peak energy is determined over periods of time essentially corresponding to a syllable, and then modifying the actual energy contour with the peak energy contour so that absolute energy maxima occur about once per syllable. In this manner, the dynamically normalized, temporal energy contour of the word string effectively provides a set of temporal markers of high-energy events (content words) that aid the recognition of connected word sequences.
Pesticide Inactivation of Peanut Glutamate Dehydrogenase:  Biochemical Basis of the Enzyme's Isomerization (1999)

Glutamate dehydrogenase (GDH) isomerizes in response to pesticides and environmental chemicals, but the biochemical basis of the isomerization is not known. Clearer understanding of the isomerization would permit expansion of its utility in the diagnosis of the responses of plant tissues to challenged environments. Peanut plants were treated with different rates of Basagran (3-(1-methylethyl)-1H-2,1,3-benzothiadiazin-4(3H)-one 2,2-dioxide), Bravo 720 (tetrachloroiso-phthalonitrile), and Sevin XLR Plus (1-naphthyl N-methylcarbamate). Free solution isoelectric focusing, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) fractionated the peanut seed GDH to its constituent subunits and degradation polypeptides. After western transfer to nitrocellulose membrane, the GDH subunits and degradation polypeptides were immunodetected with anti-GDH. The pesticide treatments did not induce increased proteolytic activity, but induced about 50% degradation of the GDH, whereas the GDH of the control peanut suffered only about 25% degradation, thus showing that the degradation rate was about double the rate of de novo synthesis in the pesticide treatments. The heavy displacement of the GDH subunit equilibrium toward degradation explains the biochemical basis of the isomerization reaction.
<i>Neisseria gonorrhoeae</i> secretes chromosomal DNA via a novel type IV secretion system (2005)

The process of DNA donation for natural transformation of bacteria is poorly understood and has been assumed to involve bacterial cell death. Recently in Neisseria gonorrhoeae we found that mutations in three genes in the gonococcal genetic island (GGI) reduced the ability of a strain to act as a donor in transformation and to release DNA into the culture. To better characterize the GGI and the process of DNA donation, the 57 kb genetic island was cloned, sequenced and subjected to insertional mutagenesis. DNA sequencing revealed that the GGI has characteristics of a horizontally acquired genomic island and encodes homologues of type IV secretion system proteins. The GGI was found to be incorporated near the chromosomal replication terminus at the dif site, a sequence targeted by the site-specific recombinase XerCD. Using a plasmid carrying a small region of the GGI and the associated dif site, we demonstrated that this model island could be integrated at the dif site in strains not carrying the GGI and was spontaneously excised from that site. Also, we were able to delete the entire 57 kb region by transformation with DNA from a strain lacking the GGI. Thus the GGI was likely acquired and integrated into the gonococcal chromosome by site-specific recombination and may be lost by site-specific recombination or natural transformation. We made mutations in six putative type IV secretion system genes and assayed these strains for the ability to secrete DNA. Five of the mutations greatly reduced or completely eliminated DNA secretion. Our data indicate that N. gonorrhoeae secretes DNA via a specific process. Donated DNA may be used in natural transformation, contributing to antigenic variation and the spread of antibiotic resistance, and it may modulate the host immune response.
Study of Blockchain-as-a-Service Systems with a Case Study of Hyperledger Fabric Implementation on Kubernetes (2020)

Blockchain is a shared, immutable, decentralized ledger to record the transaction history. Blockchain technology has changed the world, changed the way we do the business. It has transformed the commerce across every industry, which may be supply chain, IoT, financial services, banking, healthcare, agriculture and many more. It had introduced a new way of transactional applications that bring trust, security, transparency and accountability. To develop any blockchain use case, the main task is to develop an environment for creating and deploying the application. In our case, we created an environment on IBM Cloud Kubernetes service using Kubernetes, a container orchestration tool and implemented Hyperledger Fabric network to create and deploy blockchain applications. Implementing Hyperledger Fabric business blockchain network on IBM Cloud Kubernetes service provides several advantages. We can have multiple users work on the same setup. Moreover, this setup can be used and reused for many different blockchain applications as well as for deploying chaincodes and smart contracts. Fabric components can accomplish high availability by deploying on Kubernetes. We can execute several isolated Fabric instances on our Kubernetes platform as it supports multi-tenancy. This makes it easier for us to develop and test the blockchain applications. Hyperledger Fabric and Kubernetes, both if used together delivers a powerful and secure platform for processing blockchain transactions.
Mechanical Properties of Magnetic Attachments for Removable Prostheses on Teeth and Implants (2008)

There were differences between magnetic attachments for both the initial retentive capabilities and the characteristic curves. Recently introduced products provided relatively high initial retentive forces despite their small size. The measured retentive forces and the manufacturer's information differed in the majority of magnetic systems evaluated.
Sensor for the measurement of the level and volume of conductive liquids (1980)

A sensor for the measurement of the level and volume of liquids is described. The device employs an array of point sensors, each of which is sensitive to the large changes in impedance between a conductive liquid and the gas above it. The device, in principle, will function in any liquid medium that can conduct an electric current without significantly perturbing that medium. It has in fact been successfully tested in aqueous solutions with conductivity ranging from 9.0×10−7 Ω−1 cm−1 to 0.38 Ω−1 cm−1. The sensor is activated with either AC or DC applied voltage and used with electronic circuits having linear outputs. The sensor’s output is solution independent and a function of the number of conducting electrodes. The precision of the sensor is controlled by the spacing of its electrode array. The linear output of the sensor has been correlated linearly to solution volume regardless of the shape of the solution tank by the use of unequal spacing between the array electrodes. Several designs of sensors with fixed and adjustable precision are described.
Nerve Regeneration and Functional Recovery after a Sciatic Nerve Gap Is Repaired by an Acellular Nerve Allograft Made through Chemical Extraction in Canines (2007)

The purpose of the present study is to test whether chemically extracted acellular nerve segments can be used to repair the sciatic nerve gap. Fifteen canines were divided into acellular nerve allografting group (ANG, six canines), autografting group (AG, six canines), and fresh nerve allografting group (FNG, three canines). The sciatic nerves on the right side of the animals were exposed, and 5-cm-long segments of the nerves were removed from the midthigh level and replaced by the three types of grafts. At 6 months after grafting, all animals in the ANG and AG had similar patterns of right posterior limb gait cycle and right ankle movements. Moreover, the animals in the ANG and AG had similar nerve regeneration, with dense regeneration fibers in the distal tibial nerves and obvious motor end plates in the target muscle. But in FNG, the area surrounding the graft was scarred as the result of inflammation, and there was a brown central area where there was little nerve regeneration. All of the above shows that chemical acellular nerve allografting can be used to repair a gap as long as 5 cm in the continuity of the sciatic nerve in canines and has similar effects to autografting.
Targeting the MHC Ligandome by Use of TCR-Like Antibodies (2019)

Monoclonal antibodies (mAbs) are valuable as research reagents, in diagnosis and in therapy. Their high specificity, the ease in production, favorable biophysical properties and the opportunity to engineer different properties make mAbs a versatile class of biologics. mAbs targeting peptide-major histocompatibility molecule (pMHC) complexes are often referred to as "TCR-like" mAbs, as pMHC complexes are generally recognized by T-cell receptors (TCRs). Presentation of self- and non-self-derived peptide fragments on MHC molecules and subsequent activation of T cells dictate immune responses in health and disease. This includes responses to infectious agents or cancer but also aberrant responses against harmless self-peptides in autoimmune diseases. The ability of TCR-like mAbs to target specific peptides presented on MHC allows for their use to study peptide presentation or for diagnosis and therapy. This extends the scope of conventional mAbs, which are generally limited to cell-surface or soluble antigens. Herein, we review the strategies used to generate TCR-like mAbs and provide a structural comparison with the analogous TCR in pMHC binding. We further discuss their applications as research tools and therapeutic reagents in preclinical models as well as challenges and limitations associated with their use.
Down-Sampling Based Video Coding Using Super-Resolution Technique (2011)

It has been reported that oversampling a still image before compression does not guarantee a good image quality. Similarly, down-sampling before video compression in low bit rate video coding may alleviate the blocking effect and improve peak signal-to-noise ratio of the decoded frames. When the number of discrete cosine transform coefficients is reduced in such a down-sampling based coding (DBC), the bit budget of each coefficient will increase, thus reduce the quantization error. A DBC video coding scheme is proposed in this paper, where a super-resolution technique is employed to restore the down-sampled frames to their original resolutions. The performance improvement of the proposed DBC scheme is analyzed at low bit rates, and verified by experiments.
gltB gene and regulation of nitrogen metabolism by glutamine synthetase in Escherichia coli (1978)

A mutant (gltB) of Escherichia coli lacking glutamate synthase (GOGAT) was unable to utilize a wide variety of compounds as sole nitrogen source (e.g., arginine, proline, gamma-aminobutyrate, and glycine). Among revertants of these Asm- strains selected on one of these compounds (e.g., arginine, proline, or gamma-aminobutyrate) were those that produce glutamine synthetase (GS) constitutively (GlnC phenotype). These revertants had a pleiotropically restored ability to grow on compounds that are metabolized to glutamate. This suggested that the expression of the genes responsible for the metabolism of these nitrogen sources was regulated by GS. An examination of the regulation of proline oxidase confirmed this hypothesis. The differential sensitivities of GlnC and wild-type strains to low concentrations (0.1 mM) of the glutamine analog L-methionine-DL-sulfoximine supported the conclusion that the synthesis of a glutamine permease was also positively controlled by GS. During the course of this study we found that the reported position of the locus (gltB) for glutamate synthase is incorrect. We have relocated this gene to be 44% linked to the argG locus by P1 transduction. Further mapping has shown that the locus previously called aspB is in reality the gltB locus and that the "suppressor" of the aspB mutation (A. M. Reiner, J. Bacteriol. 97:1431-1436, 1969) is the locus for glutamate dehydrogenase (gdhA).
Alteplase for the treatment of acute ischaemic stroke: a single technology appraisal (2009)

This paper presents a summary of the evidence review group report into the clinical effectiveness and cost-effectiveness of alteplase for the treatment of acute ischaemic stroke, in accordance with the licensed indication, based upon the evidence submission from the manufacturer to the National Institute for Health and Clinical Excellence (NICE) as part of the single technology appraisal (STA) process. The submitted clinical evidence included several randomised controlled trials indicating that, in highly selected patients, alteplase administered at a licensed dose within 3 hours of the onset of acute ischaemic stroke is associated with a statistically significant reduction in the risk of death or dependency at 3 months compared with placebo, despite a significantly increased risk of symptomatic intracranial haemorrhage within the first 7–10 days. Data from the National Institute of Neurological Disorders and Stroke (NINDS) trial suggest that the benefit of treatment is sustained at 6 and 12 months. However, data from observational studies suggest that few patients with acute ischaemic stroke will be eligible for alteplase therapy under the terms of the current licensing agreement. In particular, many patients will be excluded by virtue of their age, and many more by the restriction of therapy to patients in whom treatment can be initiated within 3 hours of symptom onset. The manufacturer’s submission included a state transition model evaluating the impact of treatment with alteplase within 3 hours of onset of stroke symptoms compared to standard treatment reporting that, in the base-case analysis, alteplase was both less costly and more effective than standard treatment. This increased to a maximum of approximately £4000 upon one-way sensitivity analysis of the parameters. The probabilistic sensitivity analysis presented within the submission suggests that the probability that alteplase has a cost-effectiveness ratio greater than £20,000 per quality-adjusted life-year (QALY) gained is close to 1 (0.99). The results of the short-term model demonstrate that alteplase is cost-effective over a 12-month period, with an incremental cost-effectiveness ratio of £14,026 per QALY gained. This increased to a maximum of £50,000 upon one-way sensitivity analysis of the parameters. At 12 months, the probabilistic sensitivity analysis presented within the submission suggests that the probability that alteplase has a cost-effectiveness ratio greater than £20,000 per QALY gained is approximately 0.7. The guidance issued by NICE in April 2007 as a result of the STA states that alteplase is recommended for the treatment of acute ischaemic stroke only when used by physicians trained and experienced in the management of acute stroke and in centres with the required facilities.
The Zodiac Policy Subsystem: A Policy-Based Management System for a High-Security MANET (2009)

Zodiac (zero outage dynamic intrinsically assurable communities) is an implementation of a high-security MANET, resistant to multiple types of attacks, including Byzantine faults. The Zodiac architecture poses a set of unique system security, performance, and usability requirements to its policy-based management system (PBMS). In this paper, we identify theses requirements, and present the design and implementation of the Zodiac policy subsystem (ZPS), which allows administrators to securely specify, distribute and evaluate network control and system security policies to customize Zodiac behaviors. ZPS uses the Keynote language for specifying all authorization policies with simple extension to support obligation policies.
Impact of Membrane Phospholipid Alterations in Escherichia coli on Cellular Function and Bacterial Stress Adaptation (2017)

Bacteria have evolved multiple strategies to sense and rapidly adapt to challenging and ever-changing environmental conditions. The ability to alter membrane lipid composition, a key component of the cellular envelope, is crucial for bacterial survival and adaptation in response to environmental stress. However, the precise roles played by membrane phospholipids in bacterial physiology and stress adaptation are not fully elucidated. The goal of this study was to define the role of membrane phospholipids in adaptation to stress and maintenance of bacterial cell fitness. By using genetically modified strains in which the membrane phospholipid composition can be systematically manipulated, we show that alterations in major <i>Escherichia coli</i> phospholipids transform these cells globally. We found that alterations in phospholipids impair the cellular envelope structure and function, the ability to form biofilms, and bacterial fitness and cause phospholipid-dependent susceptibility to environmental stresses. This study provides an unprecedented view of the structural, signaling, and metabolic pathways in which bacterial phospholipids participate, allowing the design of new approaches in the investigation of lipid-dependent processes involved in bacterial physiology and adaptation.<b>IMPORTANCE</b> In order to cope with and adapt to a wide range of environmental conditions, bacteria have to sense and quickly respond to fluctuating conditions. In this study, we investigated the effects of systematic and controlled alterations in bacterial phospholipids on cell shape, physiology, and stress adaptation. We provide new evidence that alterations of specific phospholipids in <i>Escherichia coli</i> have detrimental effects on cellular shape, envelope integrity, and cell physiology that impair biofilm formation, cellular envelope remodeling, and adaptability to environmental stresses. These findings hold promise for future antibacterial therapies that target bacterial lipid biosynthesis.
Modeling, Fabrication, and Characterization of Piezoelectric Micromachined Ultrasonic Transducer Arrays Based on Cavity SOI Wafers (2015)

This paper presents high fill-factor piezoelectric micromachined ultrasonic transducer (PMUT) arrays fabricated via a novel process using cavity SOI wafers. The simple three-mask fabrication process enables smaller diameter PMUTs (25 μm) and finer pitch than previous processes requiring through-wafer etching. PMUTs were fabricated with diameters from 25 to 50 μm, resulting in center frequencies from 13 to 55 MHz in air. Two types of devices, having different piezoelectric layers, lead zirconium titanate (PZT), and aluminum nitride (AlN), were fabricated and characterized. Comparing 50-μm diameter devices, the PZT PMUTs show large dynamic displacement sensitivity of 316 nm/V at 11 MHz in air, which is ~20x higher than that of the AlN PMUTs. Electrical impedance measurements of the PZT PMUTs show high electromechanical coupling k <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> = 12.5% and 50-Ω electrical impedance that is well-matched to typical interface circuits. Immersion tests were conducted on PZT PMUT arrays. The fluid-immersed acoustic pressure generated by an unfocused 9 × 9 array of 40-μm diameter, 10-MHz PZT PMUTs, measured with a needle hydrophone 1.2 mm away from the array, was 58 kPa with a 25 Vpp input. Beam forming based on electronic phase control produced a narrow, 150-μm diameter, focused beam over a depth of focus >0.2 mm and increased the pressure to 450 kPa with 18 Vpp input.