gebhart/patrepeval huggingface dataset:
Insights on Alterations to the Rumen Ecosystem by Nitrate and Nitrocompounds (2016)

Nitrate and certain short chain nitrocompounds and nitro-oxy compounds are being investigated as dietary supplements to reduce economic and environmental costs associated with ruminal methane emissions. Thermodynamically, nitrate is a preferred electron acceptor in the rumen that consumes electrons at the expense of methanogenesis during dissimilatory reduction to an intermediate, nitrite, which is primarily reduced to ammonia although small quantities of nitrous oxide may also be produced. Short chain nitrocompounds act as direct inhibitors of methanogenic bacteria although certain of these compounds may also consume electrons at the expense of methanogenesis and are effective inhibitors of important foodborne pathogens. Microbial and nutritional consequences of incorporating nitrate into ruminant diets typically results in increased acetate production. Unlike most other methane-inhibiting supplements, nitrate decreases or has no effect on propionate production. The type of nitrate salt added influences rates of nitrate reduction, rates of nitrite accumulation and efficacy of methane reduction, with sodium and potassium salts being more potent than calcium nitrate salts. Digestive consequences of adding nitrocompounds to ruminant diets are more variable and may in some cases increase propionate production. Concerns about the toxicity of nitrate's intermediate product, nitrite, to ruminants necessitate management, as animal poisoning may occur via methemoglobinemia. Certain of the naturally occurring nitrocompounds, such as 3-nitro-1-propionate or 3-nitro-1-propanol also cause poisoning but via inhibition of succinate dehydrogenase. Typical risk management procedures to avoid nitrite toxicity involve gradually adapting the animals to higher concentrations of nitrate and nitrite, which could possibly be used with the nitrocompounds as well. A number of organisms responsible for nitrate metabolism in the rumen have been characterized. To date a single rumen bacterium is identified as contributing appreciably to nitrocompound metabolism. Appropriate doses of the nitrocompounds and nitrate, singly or in combination with probiotic bacteria selected for nitrite and nitrocompound detoxification activity promise to alleviate risks of toxicity. Further studies are needed to more clearly define benefits and risk of these technologies to make them saleable for livestock producers.
Modeling of Spatial Correlations in Process, Device, and Circuit Variations (2008)

We present an innovative method to model the spatial correlations in semiconductor process and device variations or in VLSI circuit variations. Without using the commonly adopted PCA technique, we give a very compact expression to represent a given spatial correlations among a set of similar statistical variables/instances located at different places on a chip/die. Our compact expression is easy for implementation in a SPICE model and is efficient in circuit simulations.
Protein SIC, a Novel Extracellular Protein of Streptococcus pyogenes Interfering with Complement Function (1996)

The human pathogen Streptococcus pyogenes possesses a chromosomal region, the mga regulon, that contains co-regulated genes important to the virulence of these bacteria. A novel gene located in the mga regulon of a S. pyogenes strain of serotype M1 was cloned and sequenced. It translates into a protein of 305 amino acid residues, including a signal sequence of 32 amino acids and a central region consisting of three tandem repeats. The sequence represents a novel structure with no significant homology to any previously published sequence. The protein was purified from the streptococcal culture media where it is present in substantial amounts. Affinity chromatography of human plasma on Sepharose coupled with the protein specifically absorbed two plasma proteins which were identified as clusterin and histidine-rich glycoprotein (HRG). The interactions between the streptococcal protein and the plasma proteins were further characterized using purified clusterin and HRG. Inhibition experiments indicated that they have affinity for overlapping or closely located sites in the streptococcal protein. Both clusterin and HRG are regulators of the membrane attack complex (C5b-C9) of complement. When the streptococcal protein was added to serum, complement-mediated lysis of sensitized sheep erythrocytes and guinea pig erythrocytes was inhibited. In addition, the streptococcal protein was incorporated into C5b-C9 in serum, indicating the location of its action. The name, protein SIC, streptococcal inhibitor of complement-mediated lysis, is therefore suggested for this novel protein. The occurrence of protein SIC and its gene was investigated in a collection of S. pyogenes strains comprising 55 different M serotypes. Only M1 and M57 strains were positive in this screening, indicating that protein SIC could be a virulence determinant. Thus, during recent years, the M1 serotype has been connected with a world-wide increase of severe and toxic S. pyogenes infections.
Analysis of the humoral response to the flagellin protein of Borrelia burgdorferi: cloning of regions capable of differentiating Lyme disease from syphilis (1993)

Selected regions of the Borrelia burgdorferi flagellin gene (fla) that exhibit high or low homology with related genes from other bacterial species were amplified by the polymerase chain reaction and expressed as fusion proteins in Escherichia coli. Purified fusion proteins were assayed for antibody reactivity in a microtiter plate enzyme-linked immunosorbent assay with sera from Lyme disease patients as well as syphilitic and normal sera. Immunoglobulin G antibody from Lyme disease patient sera reacted predominantly with the central portion of the protein. The region of the flagellin protein encompassing amino acids 64 to 311 detected nearly all of the immunoglobulin G-positive Lyme sera and only reacted with 1 of 26 syphilis patient serum samples. In contrast, 12 of 26 syphilis patient serum samples and 2 of 47 normal serum samples reacted with the amino terminus of the flagellin protein, whereas 4 of 26 syphilis patient serum samples and 7 of 47 normal serum samples reacted with the carboxyl terminus. The central region containing amino acids 64 to 311 may be employed diagnostically to differentiate antibodies to B. burgdorferi from antibodies to Treponema pallidum. In addition, this region also was recognized by immunoglobulin M in the Lyme patient sera, indicating its potential usefulness as a marker for early Lyme disease.
A non-contact biopotential sensing system with motion artifact suppression (2013)

This paper describes a wearable sensing system to monitor biopotentials via noncontact capacitive sensors that are suitable for long-term and ambulatory monitoring applications. To overcome motion-induced measurement artifacts typically encountered in such systems, a motion artifact suppression technique is introduced. Specifically, a sensor that consists of a pair of physically-interleaved capacitive channels is designed to have different amounts of parasitic input capacitance, creating channel-specific outputs that depend on the input coupling capacitance itself. Differences in output channel results can then be placed through a digital reconstruction filter to re-create the original biopotential with attenuated motion artifacts. To validate the system concept, a wireless ECG sensing system is designed. Simulation results indicate that motion-induced signal distortion is reduced by over 14X after reconstruction.
Potent and Specific Inhibition of NTCP-Mediated HBV/HDV Infection and Substrate Transporting by a Novel, Oral-Available Cyclosporine A Analogue (2020)

Analogues of the natural product cyclosporine A (CsA) were developed and assessed as antivirals against infection of hepatitis B virus (HBV) and its satellite hepatitis D virus (HDV). An analogue termed <b>27A</b> exhibits potent inhibition of HBV/HDV infection by specifically blocking viral engagement to its cellular receptor NTCP, while it lacks immunosuppressive activity found in natural CsA. Intraperitoneal injection or oral intake of <b>27A</b> protects HDV-susceptible mouse model from HDV infection. <b>27A</b> serves as a promising lead for the development of novel anti-HDV/HBV agents.
2D Focal Plane Steerable and Scalable Cortical Filters (1999)

We describe a 25&amp;times;25 pixel image sensor which spatially filters a set of input currents supplied by an array of phototransistors by two orientation selective image filters. The filters are similar to even and odd Gabor filters, which have been used to model the receptive fields of neurons in the visual cortex. The circuit architecture implementing the image filter consists of two resistive networks which are coupled by transconductance amplifiers. The tuned orientation can be steered and the filter response scaled by adjusting the conductances of the resistors and gains of the transconductance amplifiers. The architecture implemented here is a 2D extension of a previous 1D architecture with some modifications which enable one chip to implement filters of arbitrary orientation.
Lignin valorization through integrated biological funneling and chemical catalysis (2014)

Lignin is an energy-dense, heterogeneous polymer comprised of phenylpropanoid monomers used by plants for structure, water transport, and defense, and it is the second most abundant biopolymer on Earth after cellulose. In production of fuels and chemicals from biomass, lignin is typically underused as a feedstock and burned for process heat because its inherent heterogeneity and recalcitrance make it difficult to selectively valorize. In nature, however, some organisms have evolved metabolic pathways that enable the utilization of lignin-derived aromatic molecules as carbon sources. Aromatic catabolism typically occurs via upper pathways that act as a "biological funnel" to convert heterogeneous substrates to central intermediates, such as protocatechuate or catechol. These intermediates undergo ring cleavage and are further converted via the β-ketoadipate pathway to central carbon metabolism. Here, we use a natural aromatic-catabolizing organism, Pseudomonas putida KT2440, to demonstrate that these aromatic metabolic pathways can be used to convert both aromatic model compounds and heterogeneous, lignin-enriched streams derived from pilot-scale biomass pretreatment into medium chain-length polyhydroxyalkanoates (mcl-PHAs). mcl-PHAs were then isolated from the cells and demonstrated to be similar in physicochemical properties to conventional carbohydrate-derived mcl-PHAs, which have applications as bioplastics. In a further demonstration of their utility, mcl-PHAs were catalytically converted to both chemical precursors and fuel-range hydrocarbons. Overall, this work demonstrates that the use of aromatic catabolic pathways enables an approach to valorize lignin by overcoming its inherent heterogeneity to produce fuels, chemicals, and materials.
&#x201C;RegionCut&#x201D; &#x2014; Interactive multi-label segmentation utilizing cellular automaton (2013)

This paper addresses the problem of interactive image segmentation. We propose an extension of the GrowCut framework which follows Cellular Automaton theory and is comparable to a label propagation algorithm. Therefore, user labels are propagated according to Cellular Automaton until convergency. A common problem of GrowCut is the time consuming user initialization which requires distributed seeds. Our main contribution focuses on determining such an initialization utilizing GMMs and spherical coordinates. Furthermore we propose a new weight function based on the mean image gradient. According to our evaluation, our extensions result in a simplified user interaction and in better results in terms of accuracy and running time. Our experiments show that our method can compete with state-of-the-art energy minimization frameworks.
Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers (2016)

This study detailed the genome mapping of three cotton phytochrome genes with newly developed CAPS and dCAPS markers. The proximity of these loci to fiber quality and other cotton QTL was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers will be valuable for marker-assisted selection (MAS) programs to rapidly introgress G. barbadense phytochromes and/or HY5 gene (s) into G. hirsutum cotton genotypes or vice versa.
Min-Delay Margin/Error Detection and Correction for Flip-Flops and Pulsed Latches in 10-nm CMOS (2019)

Min-delay (MID) error rates increase dramatically under aggressive voltage and technology scaling, limiting VMIN. Pulsed latches offer significant clocking power savings over flip-flops but further aggravate MID failures. This letter proposes MID margin/error detection and correction (M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /EDAC) for flip-flops and pulsed latches to reduce VMIN guard bands for voltage noise, temperature variation, and aging, and to detect and correct rare MID failures. Statistical data collection from a prototype in 10-nm tri-gate CMOS shows up to 122-mV VMIN reduction. Reliable pulsed latches enabled by M <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /EDAC offer 12%-18% total dynamic power savings for logic blocks in 10-nm CMOS.
Raman Chemical Imaging Spectroscopy Reagentless Detection and Identification of Pathogens:  Signature Development and Evaluation (2007)

An optical detection method, Raman chemical imaging spectroscopy (RCIS), is reported, which combines Raman spectroscopy, fluorescence spectroscopy, and digital imaging. Using this method, trace levels of biothreat organisms are detected in the presence of complex environmental backgrounds without the use of amplification or enhancement techniques. RCIS is reliant upon the use of Raman signatures and automated recognition algorithms to perform species-level identification. The rationale and steps for constructing a pathogen Raman signature library are described, as well as the first reported Raman spectra from live, priority pathogens, including Bacillus anthracis, Yersinia pestis, Burkholderia mallei, Francisella tularensis, Brucella abortus, and ricin. Results from a government-managed blind trial evaluation of the signature library demonstrated excellent specificity under controlled laboratory conditions.
Connecting Separate Computers to a Common Bus (1984)

Network bus adapter (NBA) handles protocols for computer-tocomputer communications. NBA does all protocol handling and communications with bus for its host computer, that processor of different speeds sends data to each other continuously at maximum speed. Any host can communicate with any other, or several or with all.
Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases (2016)

High-throughput linked-read sequencing followed by maternal plasma-based relative haplotype dosage analysis represents a streamlined approach for noninvasive prenatal testing of inherited single gene diseases. The approach bypasses the need for mutation-specific assays and is not dependent on the availability of DNA from other affected family members. Thus, the approach is universally applicable to pregnancies at risk for the inheritance of a single gene disease.
Highly electronegative contacts to compound semiconductors (1977)

Gold contacts to most III–V and II–VI compounds position the Fermi level at the interface well into the energy gaps of the semiconductors. To position the Fermi level closer to a conduction-band edge, particularly in the more ionic semiconductors, one may substitute a more electropositive element like Al for the Au contact. To position the Fermi level closer to a valence-band edge, however, there are no further possibilities among the elemental metals, since Au is the most electronegative of these. Two contact materials, (SN)x and HgSe, which overcome this limitation have recently been reported. Barriers produced by these contacts on many compound semiconductors will be reported and shown to exhibit the well-known ionic–covalent transition. Device use and suggestions for further research are mentioned.
Sound Detection of Stored-Product Insects That Feed Inside Kernels of Grain1 (1988)

A system for acoustically detecting internal-feeding insect larvae in grain is described. Larvae of the lesser grain borer, Rhyzopertha dominica (F.); rice weevil, Sitophilus oryzae (L.); and Angoumois grain moth, Sitotroga cerealella (Olivier), produced sounds loud enough to be detected 13-19 d after oviposition, depending upon the species. After first detection, larvae produced detectable sounds 71-90% of the time until pupation. Infestation rates could be estimated, at least in the range of 1-20 infested kernels per 100 ml of grain, where the infestation rate was strongly correlated to number of sounds as counted by a frequency counter.
Fourier domain mode locked optoelectronic oscillator based on the deamplification of stimulated Brillouin scattering (2018)

A fast frequency scanning optoelectronic oscillator (OEO) based on Fourier domain mode locking (FDML) and the deamplification of stimulated Brillouin scattering (SBS) is proposed and experimentally demonstrated. The SBS is used to realize a fast frequency scanning microwave photonics filter (MPF). By synchronizing the scanning period of the MPF to the cavity round-trip time, the OEO can be made to operate in the FDML regime. Tunable linearly chirped microwave waveforms are generated in the experiment with a chirp rate up to 0.85 GHz/μs and a time-bandwidth product as large as 23,850. The proposed fast frequency scanning FDML OEO can find applications in modern radar and communication systems.
Determining Tumor Load and Biallelic Mutation in Patients with CALR Mutation Using Peripheral Blood Plasma (2014)

Abstract Background: CALR gene is frequently mutated in patients with myeloproliferative neoplasmas (MPN). Almost all mutations are indel - some with large (>50 bp) deletion. Detecting this type of mutations with acceptable sensitivity is difficult by sequencing. Fragment length analysis (FLA) is a reliable technique in detecting this type of mutations. Furthermore, FLA allows quantifying the mutant DNA and better evaluation of tumor load. Determining tumor load can be confusing and difficult when the mutation is biallelic. Distinguishing between patients with single allele mutation from those with biallelic mutations might add another dimension in predicting clinical behavior and determining the tumor load. We explored using cell free DNA in peripheral blood plasma to test for CALR mutations and determining tumor load. Methods: Using Direct bidirectional sequencing and FLA, we detected CALR indel mutations in 71 of 522 (14%) patients suspected of having MPN and referred for testing for CALR mutation. No sample showed point mutation. DNA from cells and cell free DNA in plasma was available from 31 of the 71 cases. The mutant DNA peak was quantified and the relative percentage of mutant DNA was calculated in both cellular DNA and cell free plasma DNA. FLA and Sanger sequencing data were compared between cellular DNA and cell free plasma DNA. Any ratio >55% was considered as evidence of biallelic mutation. Results: As expected all positive samples by cellular DNA testing also showed the indel mutation in cell free plasma by FLA. However, four of the 31 (13%) positive samples by FLA failed to show the mutation on Sanger sequencing. The most likely cause for failing to detect the mutation by Sanger is low level mutation load and the lower sensitivity of Sanger sequencing. When we compared ratios of mutant peak (tumor load) between cellular DNA and cell free DNA in plasma, mutant CALR DNA was significantly higher (P=0.0002, Wilcoxon matched pairs test) in cell free DNA in plasma than in cellular DNA. More importantly, we were able to determine the presence of homozygous mutation (>55% mutant DNA) in 5 of 31 (16%) patients when cell free DNA in plasma is used. In contrast, only 1 of 31 (3%) patients showed evidence of biallelic mutation when cellular DNA is used. Most of the mutations (25 of 31, 81%) were deletions. As deletions results in smaller size amplicon on the FLA and better amplification efficiency, we set 55% as a cut-off for biallelic mutation to account for the more efficient amplification of the deleted peak. Conclusion: Cell free DNA in plasma is more reliable than cellular DNA for the detection of CALR mutations and for determining tumor load. Testing for CALR must include fragment length analysis. More importantly, biallelic CALR mutation is frequent and the clinical relevance of biallelic CALR mutation needs to be investigated. Disclosures No relevant conflicts of interest to declare.
Interoperable Credentials Management for Wholesale Banking (2011)

A gap exists between wholesale-banking business practices and security best practices: wholesale banks operate within the boundaries of contract law, while security best practices often relies upon a benevolent trusted party outside the scope of straightforward contracts. While some business domains may be able to bridge this gap, the ultra-high-value transactions used in business-to-business banking substantially increase the size of the gap. The gap becomes most apparent when regarded from the perspective of interoperability. If a single user applies the same credential to sign high-value transactions at multiple banks, then the trusted-party model becomes overly cumbersome and conflicts with an acceptable concept of liability. This paper outlines the business complexities of wholesale banking and proposes a solution called Partner Key Management (PKM). PKM technology manages the credentials required to authenticate users and sign transactions. This paper presents PKM technology by describing an interoperable protocol, requisite data structures, and an interoperable XML definition. The paper uses formal methods to demonstrate a security equivalence between revocation options within PKM against the security offered by the traditional Public Key Infrastructure (PKI), a technology that features the benevolent trusted party.
Practical and Secure Substring Search (2018)

In this paper we address the problem of outsourcing sensitive strings while still providing the functionality of substring searches. While security is one important aspect that requires careful system design, the practical application of the solution depends on feasible processing time and integration efforts into existing systems. That is, searchable symmetric encryption (SSE) allows queries on encrypted data but makes common indexing techniques used in database management systems for fast query processing impossible. As a result, the overhead for deploying such functional and secure encryption schemes into database systems while maintaining acceptable processing time requires carefully designed special purpose index structures. Such structures are not available on common database systems but require individual modifications depending on the deployed SSE scheme.