gebhart/patrepeval huggingface dataset:
Photocatalytic oxidation of TMB with the double stranded DNA–SYBR Green I complex for label-free and universal colorimetric bioassay (2015)

We report here the newly discovered photocatalytic activity of the dsDNA-SYBR Green I (SG) complex, which can catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) under light irradiation corresponding to the excitation of the dsDNA-SG complex. The most appealing feature of the photocatalytic system here is that it can be obtained using random DNA sequences that can form a duplex. Considering the universality of the photooxidase, a label-free and universal platform was proposed for highly sensitive visual bioassays.
The design and research of high-speed channel for volume holographic data storage (2004)

The Gigabit Ethernet technology has already been maturity. Compared with other technology, Gigabit Ethernet technology possesses higher performance and more convenience realization, so in volume holographic storage (VHM) system, we choose Gigabit Ethernet as channel interface of volume holographic storage.
The emergence of stable isotopes in environmental and forensic geochemistry studies: a review (2006)

In the past decade, environmental forensics has emerged as a discipline directed toward determining parties liable for causing spills of contaminants into the environment. Such investigations, while geared toward determining the guilty parties in order to recover costs of the cleanup and remediation, require various questions to be addressed. These include determination of the nature of the product; Where did it come from?; Extent of weathering, if any; How long has it been there?; and Is it degrading naturally? Traditionally, these studies have been addressed through utilization of techniques such as gas chromatography (GC) and gas chromatography–mass spectrometry (GCMS). However, in recent years, stable isotopes, primarily determined through the use of combined gas chromatography–isotope ratio mass spectrometry (GCIRMS), have emerged as an equally important tool in environmental forensics. For relatively low molecular, volatile compounds such as MTBE, BTEX, or chlorinated solvents, the isotopes, primarily carbon and hydrogen, have been used extensively for evaluating the onset of natural attenuation. For larger molecules such as PCBs or PAHs, in which the effects of biodegradation on the isotope composition of these molecules is minimal, the isotopic fingerprints of the individual compounds can be used for correlation purposes. In this paper, a brief introduction to isotope geochemistry will be given, followed by a review of applications of stable isotopes to a variety of environmental problems. While the review may not necessarily be exhaustive, it will provide a comprehensive overview of areas where isotopes have been used and potential applications for the future. Most of the review is concerned with carbon and hydrogen isotopes, although a brief overview of the emerging area of chlorine isotopes will also be discussed.
SCCS: scalable conferencing control service (2002)

An efficient conference service facilitates the implementation and the run-time control of conference applications. Key features of a conference service are conference management, multicast communication support, application state synchronization, user data marshalling and scalability. The paper defines a conferencing service to fulfil these requirements of conferencing applications. The conference control protocol, which is used for our conferencing service, is described in its main parts like topology, reconfiguration and multipoint transfer. An object model of the service is proposed together with the resulting architecture. A multipoint platform is introduced as a case study.
Association of Plasma Levels of Tumor Necrosis Factor (TNF)–α and Its Soluble Receptors, Two Polymorphisms of the TNF Gene, with Acute Severe Pancreatitis and Early Septic Shock Due to It (2003)

The study found no association between ASP and the two polymorphisms examined, although some associations were found between TNF2 and TNFB2 alleles with the development of early septic shock in ASP. Plasma level of TNF-alpha or sTNFR was of little value in predicting the occurrence of early septic shock in ASP.
Real-Time Detection of Vehicles for Advanced Traffic Signal Control (2008)

Vehicle detection by video cameras is one of the most promising new technologies for wireless large-scale data collection and implementation of advanced traffic control and management schemes such as vehicle guidance/navigation. In this paper we propose an approach to detect and count vehicles at an intersection in real-time, using a fixed camera. After identifying moving objects images via background frame differencing, edge detection, erosion and dilation operations are performed to suppress noise. Separated and rotated properly, the denoised binary image is then used to generate a vertical projection histogram from which information about the size and coordinates of each component is utilized to compute the number of vehicles. This detection algorithm gives an approximate number of vehicles. An adaptive traffic signal control strategy controls the traffic flow. The simulating results show a great efficiency of traffic control and management scheme in practice.
In-situ Stress and Pore Pressure in the South Eugene Island Field, Gulf of Mexico (1998)

Abstract Analysis of minifracs and pore pressure surveys from sand reservoirs in a Gulf of Mexico oil field show effective stress ratios, K, that scatter significantly and do not correlate with previously published fracture gradient models for this area. The lower-bound value of K is 0.33, which corresponds to the expected value for Coulomb failure for a coefficient of friction of 0.6 in normal faulting environments. However, in some sands K approaches unity, thus indicating an essentially isotropic stress field. Hence, the data indicate a highly variable state of stress that cannot be simply related to depth or pore pressure, but appears to reflect an interaction between deformational processes and material properties. Borehole breakout analysis in vertical wells reveals stress orientations that are predominantly perpendicular to normal faults and, hence, consistent with an extensional stress regime. Analysis of breakouts in inclined wells in two sand reservoirs allows to constrain the magnitude of the maximum horizontal principal stress, SHmax. and further indicates an active normal faulting environment with a clear, but small degree of horizontal stress anisotropy (i.e., Sv&gt;SHmax&gt;Shmin). P. 69
Experimental confirmation of phase encoding of instantaneous derivatives of position (1994)

Previous theoretical reports described the dependence of interpretation of the observed phase of the NMR signal on the time origin(s) of moment calculations and position's Taylor series expansion. This work provides experimental confirmation of predictions derived from that theory. For accelerative motion, experimental phase-encoded velocity measurements give instantaneous values at a time corresponding to the origin used for waveform moment calculations. For laminar flow, experimental intensity profiles agree well with theoretical simulations; new findings extend amplitude and spatial distributions of oblique flow profiles beyond previous descriptions. Experiments using sequences with controlled position of the time origins for phase and read axes show that displacement and motion artifacts are reduced when they're coincident (pulsed flow, nongated acquisitions), and virtually eliminated when combined with gating. Potentially significant clinical consequences of coincident and noncoincident time origins are demonstrated in human head MIP MRA images. These results have fundamental implications in waveform design.
Cryptographic system enhancements for the IBM System z9 (2007)

IBM has offered hardware-based cryptographic processors for its mainframe computers for nearly thirty years. Over that period, IBM has continued to update both the hardware and software, providing added features, higher performance, greater physical security, and improved management features. This commitment continues with the System z9™, as demonstrated by the two improvements described in this paper. The first part of the paper describes enhancements to the System z9 to configure and control cryptographic features. The second part describes a new method for the cryptographic coprocessors to securely manage keys which are distributed to remote devices that are not necessarily in secure or well-controlled environments
Increased Postprandial Nonesterified Fatty Acid Appearance and Oxidation in Type 2 Diabetes Is Not Fully Established in Offspring of Diabetic Subjects (2010)

Postprandial plasma NEFA intolerance observed in subjects with T2D is not fully established in non-diabetic offspring of both parents with T2D, despite the presence of increased postprandial plasma TG in the later. Elevated postprandial plasma NEFA appearance and oxidation in T2D is observed despite acute correction of the exaggerated glycemic excursion in this group.
Regulation of physiological responses to continuous and intermittent hypoxia by hypoxia‐inducible factor 1 (2006)

Hypoxia-inducible factor 1 (HIF-1) is a heterodimeric transcription factor composed of HIF-1alpha and HIF-1beta subunits that functions as a master regulator of oxygen homeostasis. Oxygen-dependent hydroxylation of HIF-1alpha provides a mechanism that allows changes in oxygenation to be transduced to the nucleus, leading to changes in gene expression. Hypoxia-inducible factor 1 plays critical roles in development, physiology and disease pathogenesis. Analyses of mice that are heterozygous for a null allele at the locus encoding the HIF-1alpha subunit have demonstrated that partial deficiency of HIF-1 is sufficient to impair multiple physiological responses to continuous and intermittent hypoxia.
Lowering the error floor of LDPC codes using cyclic liftings (2010)

Cyclic liftings are proposed to lower the error floor of low-density parity-check (LDPC) codes. The liftings are designed to eliminate dominant trapping sets of the base code by removing the short cycles which form the trapping sets. We derive a necessary and sufficient condition for the cyclic permutations assigned to the edges of a cycle c of length ℓ(c) in the base graph such that the inverse image of c in the lifted graph consists of only cycles of length strictly larger than ℓ(c). The proposed method is universal in the sense that it can be applied to any LDPC code over any channel and for any iterative decoding algorithm. It also preserves important properties of the base code such as degree distributions. The proposed method is applied to both structured and random codes over the binary symmetric channel (BSC). The error floor improves consistently by increasing the lifting degree, and the results show significant improvements in the error floor compared to the base code, a random code of the same degree distribution and block length, and a random lifting of the same degree. Similar improvements are also observed when the codes designed for the BSC are applied to the additive white Gaussian noise (AWGN) channel.
Novel Fiber-Dependent Entry Mechanism for Adenovirus Serotype 5 in LacrimalAcini (2006)

The established mechanism for infection of most cells with adenovirus serotype 5 (Ad5) involves fiber capsid protein binding to coxsackievirus-adenovirus receptor (CAR) at the cell surface, followed by penton base capsid protein binding to alpha(v) integrins, which triggers clathrin-mediated endocytosis of the virus. Here we determined the identity of the capsid proteins responsible for mediating Ad5 entry into the acinar epithelial cells of the lacrimal gland. Ad5 transduction of primary rabbit lacrimal acinar cells was inhibited by excess Ad5 fiber or knob (terminal region of the fiber) but not excess penton base. Investigation of the interactions of recombinant Ad5 penton base, fiber, and knob with lacrimal acini revealed that the penton base capsid protein remained surface associated, while the knob domain of the fiber capsid protein was rapidly internalized. Introduction of rabbit CAR-specific small interfering RNA (siRNA) into lacrimal acini under conditions that reduced intracellular CAR mRNA significantly inhibited Ad5 transduction, in contrast to a control (nonspecific) siRNA. Preincubation of Ad5 with excess heparin or pretreatment of acini with a heparinase cocktail each inhibited Ad5 transduction by a separate and apparently additive mechanism. Functional and imaging studies revealed that Ad5, fiber, and knob, but not penton base, stimulated macropinocytosis in acini and that inhibition of macropinocytosis significantly reduced Ad5 transduction of acini. However, inhibition of macropinocytosis did not reduce Ad5 uptake. We propose that internalization of Ad5 into lacrimal acini is through a novel fiber-dependent mechanism that includes CAR and heparan sulfate glycosaminoglycans and that the subsequent intracellular trafficking of Ad5 is enhanced by fiber-induced macropinocytosis.
Development of Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification for Detection of SARS-CoV-2 and Influenza Viral RNA (2021)

The ongoing pandemic has demonstrated the utility of widespread surveillance and diagnostic detection of the novel SARS-CoV-2. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) has enabled broader testing, but current LAMP tests only detect single targets and require separate reactions for controls. With flu season in the Northern Hemisphere, the ability to screen for multiple targets will be increasingly important, and the ability to include internal controls in RT-LAMP allows for improved efficiency. Here we describe multiplexed RT-LAMP with four targets (SARS-CoV-2, influenza A, influenza B, human RNA) in a single reaction using real-time and end point fluorescence detection. Such increased functionality of RT-LAMP will enable even broader adoption of this molecular testing approach and aid in the fight against this public health threat.
The potency and effect of phytotoxins within yellow split-pea <i>(Pisum sativum)</i> and adzuki bean <b>(Vigna angularis)</b> on survival and reproductive potential of <i>Sitophilus oryzae</i> (L.) (Coleoptera: Curculionidae) (1986)

Abstract Sitophilus oryzae (L.) is a serious pest of stored cereal grains, but recently a few populations have been found able to feed and breed on certain legumes also. Legumes contain many toxic phytochemicals. A technique is described to generate data suitable for probit analysis, enabling a dose- response line to a toxic food to be constructed. The toxic effects of two legumes, yellow split-pea and adzuki bean, on adult survival and reproduction in three geographical strains of S. oryzae were examined. The strains were shown to vary in their abilities to tolerate legume phytotoxins, but there was no correlation between the abilities to survive on different legumes in the same strain. Yellow split-pea was shown to have residual effects on adult survival and reproduction, but performance was enhanced rather than impaired. It is suggested that improved performance results from induction of certain enzymes by substances within yellow split-pea. The use of legumes mixed with cereals as a control measure against S. oryzae is also discussed.
Activated Carbon Produced from Charcoal Obtained by Vacuum Pyrolysis of Softwood Bark Residues (2001)

Vacuum pyrolysis of softwood bark residues yields besides oil, charcoal as second valuable product. The activation behavior of the vacuum pyrolysis charcoal was compared to charcoal produced during conventional, atmospheric carbonization process. Steam activation of charcoal obtained by vacuum pyrolysis yields an activated carbon with a higher surface area than by using charcoal produced during atmospheric carbonization process. This can be related to the more open pore structure of the vacuum pyrolysis charcoal. Steam activation of the vacuum pyrolysis charcoal was studied at temperatures ranging from 760 to 850 °C. Activated carbons with surface areas above 1200 m2/g and micropore volumes above 0.40 cm2/g were obtained. Depending on the activation conditions, carbons with properties (surface area, pore volume, pore structure and methylene blue value) similar to commercial grades were produced.
Bi-gram based Query Expansion Technique for Amharic Information Retrieval System (2015)

Information retrieval system has been using to connect users of the information and information repository corpora. Even though the task of information retrieval systems is to retrieve relevant information, it is very difficult to find a perfect information retrieval system which is capable of retrieving relevant and only relevant documents as per user's query. The aim of this research is to increase precision of an Amharic information retrieval system while preserving the original recall. In order to achieve this bi-gram technique has been adopted for the query expansion. The main reason for performing query expansion is to provide relevant documents as per users' query that can satisfy their information need. Because users are not fully knowledgeable about the information domain area, they mostly formulate weak queries to retrieve documents. Thus, they end up frustrated with the results found from an information retrieval system. Amharic language has many meaning for a single word and also the word can be found in different form. These are some of the challenges that made the information retrieval system performing at very low level. Query expansion methods outperform in differentiating the various meanings of a polysemous term and find synonymous terms for reformulating users' query. Bi-gram technique uses the underling theory of expanding a query; using terms that appear adjacent to a query term frequently. The proposed technique was integrated to an information retrieval system. Then the retrieval system is tested with and without using bi-gram technique query expansion. The test result showed that bi-gram based method outperformed the original query based retrieval, and scored 8% improvement in total Fmeasure. This is an encouraging result to design an applicable search engine, for Amharic language.
Dopamine Deficiency Contributes to Early Visual Dysfunction in a Rodent Model of Type 1 Diabetes (2014)

Dopamine (DA) functions as an essential neuromodulator in the brain and retina such that disruptions in the dopaminergic system are associated with common neurologic disorders such as Parkinson's disease. Although a reduction in DA content has been observed in diabetes, its effects in the development of diabetes-induced neuropathy remains unknown. Because the retina is rich in DA and has a well known diabetes-induced pathology (diabetic retinopathy or DR), this study was designed to examine the role of retinal DA deficiency in early visual defects in DR. Using rodent models of type 1 diabetes mellitus, we investigated whether diabetes caused a reduction in retinal DA content in both rats and mice and determined whether restoring DA levels or activating specific DA receptor pathways could improve visual function (evaluated with optokinetic tracking response) of diabetic mice, potentially via improvement of retinal function (assessed with electroretinography). We found that diabetes significantly reduced DA levels by 4 weeks in rats and by 5 weeks in mice, coincident with the initial detection of visual deficits. Treatment with l-DOPA, a DA precursor, improved overall retinal and visual functions in diabetic mice and acute treatment with DA D1 or D4 receptor agonists improved spatial frequency threshold or contrast sensitivity, respectively. Together, our results indicate that retinal DA deficiency is an underlying mechanism for early, diabetes-induced visual dysfunction and suggest that therapies targeting the retinal dopaminergic system may be beneficial in early-stage DR.
Specific immunological test for the rapid identification of members of the genus Histoplasma (1976)

A sensitive and specific immunological method was developed for rapid identification of the mycelial forms of Histoplasma capsulatum var. capsulatum, H. capsulatum var. duboisii, and H. farciminosum and for separation of these pathogenic fungi from morphologically similar hyphomycetes and other fungal pathogens. This method is based on the fact that all of the Histoplasma spp. produce H and M histoplasmin antigens, whereas the other fungi do not. Inocula consisting of heavy mycelial growth from a pure, full-grown culture were transferred into flasks containing small volumes of brain heart infusion broth. These cultures were placed on a shaker and grown at 25 C. Using the micro-immunodiffusion technique and antisera containing antibodies to H and M precipitinogens, we detected exoantigens in 3-day-old brain heart infusion culture supernatants concentrated 25 and 50 times. The ability of the procedure to identify Histoplasma spp. was evaluated by testing 96 unknown mycelial cultures that grossly or microscopically resembled Histoplasma spp. Three- and six-day-old concentrated culture supernatants prepared from each unknown were tested against rabbit anti-Arthroderma tuberculatum, Chrysosporium keratinophilum, H. capsulatum var. duboisii, and Corynascus (Thielavia) sepedonium sera and human histoplasmosis case serum. Each unknown was also identified by conventional laboratory procedures involving cultural and, where necessary, in vivo studies. In the comparative evaluation the immunological test was observed to be 100% sensitive. It permitted the accurate generic identification of the Histoplasma spp. within 5 days, in contrast to the average of 33 days required by the routine mycological procedure.
Flavivirus-Mosquito Interactions (2014)

The Flavivirus genus is in the family Flaviviridae and is comprised of more than 70 viruses. These viruses have a broad geographic range, circulating on every continent except Antarctica. Mosquito-borne flaviviruses, such as yellow fever virus, dengue virus serotypes 1-4, Japanese encephalitis virus, and West Nile virus are responsible for significant human morbidity and mortality in affected regions. This review focuses on what is known about flavivirus-mosquito interactions and presents key data collected from the field and laboratory-based molecular and ultrastructural evaluations.
Subgingival temperature and microbiota in initial periodontitis (1998)

The association between subgingival temperature, other clinical characteristics, and the subgingival microbiota was examined in adult subjects with initial periodontitis and differing levels of gingival inflammation. 43 subjects were measured at 6 sites per tooth for pocket depth, attachment level, presence of plaque, gingival redness, bleeding on probing and subgingival temperature at 3-month intervals for 1 year. Subgingival plaque was sampled from 15 initial active periodontitis sites (10 subjects), 121 gingivitis, sites (20 subjects) and 202 healthy sites (13 subjects), and included the 5 hottest and 5 coldest sites in each subject. Plaque samples were analyzed for 13 subgingival species using whole-genomic DNA probes. The major influences on the subgingival microbiota were the clinical status of sites, pocket depth, and the presence of supragingival plaque. No significant association between species and site temperature was observed. Initial active sites were associated with Bacteroides forsythus and Campylobacter rectus, and had a higher mean subgingival temperature and deeper mean pocket depth than inactive sites. A weak association between pocket depth and site temperature was noted. The major influence on subgingival temperature of sites was the anterior to posterior anatomical temperature gradient in the mandible and maxilla.