gebhart/patrepeval huggingface dataset:
Three Mutants of Herpes Simplex Virus Type 2: One Lacking the Genes US10, US11 and US12 and Two in which RS Has Been Extended by 6 kb to 0{middle dot}91 Map Units with Loss of US Sequences between 0{middle dot}94 and the US/TRS Junction (1987)

In the process of generating restriction endonuclease site deletion mutants, we have isolated and characterized three mutants of herpes simplex virus type 2 (HSV-2), strain HG52, with large genomic deletions in Us and TRs. The deleted sequences (7.5 kb) extend from 0.94 map coordinates (m.c.) to 0.99 m.c. and are presumed to contain the HSV-2 gene equivalents of US10, 11 and 12, one copy of immediate early (IE) gene 3 and one copy of an origin of replication (ORIs). One of the mutants (HG52X163X12) has a simple deletion whereas in the two others (HG52X163X14 and HG52X163X21) the deleted sequences have been replaced by inverted duplications of Us/IRs sequences between 0.83 and 0.91 m.c. such that the molecules have short region inverted repeats extended by 6 kb on either side. All three are viable, stable and grow in tissue culture indicating that the polypeptides coded by the HSV-2 genes equivalent to US10, 11 and 12 are non-essential for lytic growth in BHK21/C13 cells. In addition the lack of one copy of the HSV-2 equivalent of IE gene 3 and ORIs in HG52X163X12 shows that only one copy of each suffices for viability. However the temperature restriction of the mutants at 38.5 degrees C suggests that one or more of the polypeptides coded by the deleted sequences may be required in conjunction with another polypeptide(s) for viral growth or stability at the higher temperature.
Flatband voltage shift in PMOS devices caused by carrier activation in p+-polycrystalline silicon and by boron penetration (2002)

After discovering that the annealing-time dependence of the flatband voltage shifts of a p/sup +/-polysilicon gate MOS diode can be attributed to boron activation in polysilicon instead of boron penetration through gate M/sub 2/, we proposed a boron activation model for polysilicon in which the carrier activation is related to the grain size of the polysilicon. Using this model, we analyzed the characteristics of pMOSFETs with polysilicon gates of different grain sizes and found that they depend on the grain size, as expected. Using the model, we quantitatively identified process windows for p/sup +/-polysilicon gate pMOSFETs, assuming that enough boron is activated in the polysilicon without the boron penetrating through the gate SiO/sub 2/.
Non-Halide Ionic Liquids for Solvation, Extraction, and Processing of Cellulosic Materials (2010)

This article gives a comprehensive overview of the relevant literature with respect to recent developments and potential uses of halide-containing and, preferably, halide-free ionic liquids (ILs) in the field of polysaccharide chemistry and engineering, and then proceeds to forthcoming concepts in industrial processing of (ligno)cellulosic materials. In addition, selected new halide-free ILs are described.
Concomitant Activation of Jasmonate and Ethylene Response Pathways Is Required for Induction of a Plant Defensin Gene in Arabidopsis (1998)

Activation of the plant defensin gene PDF1.2 in Arabidopsis by pathogens has been shown previously to be blocked in the ethylene response mutant ein2-1 and the jasmonate response mutant coi1-1. In this work, we have further investigated the interactions between the ethylene and jasmonate signal pathways for the induction of this defense response. Inoculation of wild-type Arabidopsis plants with the fungus Alternaria brassicicola led to a marked increase in production of jasmonic acid, and this response was not blocked in the ein2-1 mutant. Likewise, A. brassicicola infection caused stimulated emission of ethylene both in wild-type plants and in coi1-1 mutants. However, treatment of either ein2-1 or coi1-1 mutants with methyl jasmonate or ethylene did not induce PDF1.2, as it did in wild-type plants. We conclude from these experiments that both the ethylene and jasmonate signaling pathways need to be triggered concomitantly, and not sequentially, to activate PDF1.2 upon pathogen infection. In support of this idea, we observed a marked synergy between ethylene and methyl jasmonate for the induction of PDF1.2 in plants grown under sterile conditions. In contrast to the clear interdependence of the ethylene and jasmonate pathways for pathogen-induced activation of PDF1.2, functional ethylene and jasmonate signaling pathways are not required for growth responses induced by jasmonate and ethylene, respectively.
Role of alkaline phosphatase in colitis in man and rats (2008)

The present study shows that epithelial iAP mRNA expression is reduced in patients with UC and CD. The rat model demonstrates that oral administration of active iAP enzymes in the intestinal tract results in a significant reduction of inflammation. This provides new insight on IBD pathology and a novel treatment approach to this severe inflammatory disease.
Reactions at the nitrogen atoms in azafluorene systems (1979)

Isomeric azafluorenones have been oxidized to N-oxides with H 2 O 2 in acetic acid or in the presence of Na 2 WO 4 .In the same manner monoazafluorenes have been converted into azafluorene N-oxides, but oxidation of diazafluorenes led first to diazafluorenones which then formed diazafluorenone N-oxides. Azafluorenones and azafluorenes are readily N-methylated with CH 3 I to give methiodides. The relations between the rate constants of N-methylation and structural factors have been discussed.
Amino acid precursors of monoamine neurotransmitters and some factors influencing their supply to the brain (1976)

Synopsis There is evidence that changes in the concentrations of the monoamine neurotransmitters within the brain are associated with changes in mental processes, with disorders of control of movement and with certain neuropsychiatric diseases. These neurotransmitters are synthesized in the brain from aromatic amino acid precursors that have to be obtained from the circulating blood. In this study some factors which alter the rates of entry of four amino acids (the important neurotransmitter precursors L-tyrosine and L-tryptophan, as well as L-phenylalanine and L-histidine) into the brain have been studied and the findings considered in relation to conditions in which the quantities of one or more of the monoamine neurotransmitters formed within the cerebral cells may be either too large or too small. Thus too little neurotransmitter will be formed if competition between amino acids for the carriers transporting them into the cerebral cells causes the exclusion of a large proportion of any of the aromatic amino acid precursors from the brain. For example, L-tryptophan is partially excluded from the brain if a raised level of any one of several other amino acids is maintained in the circulation. Of these, L-phenylalanine inhibits the transport of L-tryptophan into the brain most effectively, while aromatic amino acids in general exclude L-tryptophan more effectively than do other neutral amino acids. Over-production of one or more of the monoamine neurotransmitters is likely to occur when there is too much of one of the aromatic amino acid precursors in the brain cells as a result of abnormally high uptake from the blood, or as a result of their release by an excessive breakdown of the protein within these cells. Underproduction of neurotransmitters may occur in certain disease states, such as some aminoacidurias or Parkinsonism. We have listed some conditions associated with altered mental states or motor disability in which over- or under-production of monoamine neurotransmitters may occur and have tried to relate the findings in human disease with our experimental results.
On the numerical solution of heat conduction problems in two and three space variables (1956)

f(iAx
Keyless Signatures' Infrastructure: How to Build Global Distributed Hash-Trees. (2013)

Keyless Signatures Infrastructure (KSI) is a globally distributed system for providing timestamping and server-supported digital signature services. Global per-second hash trees are created and their root hash values published. We discuss some service quality issues that arise in practical implementation of the service and present solutions for avoiding single points of failure and guaranteeing a service with reasonable and stable delay. Guardtime AS has been operating a KSI Infrastructure for 5 years. We summarize how the KSI Infrastructure is built—and the lessons learned during the operational period of the service.
Abrasion as a Catalyst Deposition Technique for Carbon Nanotube Growth (2009)

Mechanical abrasion of stainless steel (SS) surfaces is demonstrated as an effective technique for the deposition of catalyst to support growth of high density layers of carbon nanotubes (CNTs) in water-assisted catalytic chemical vapor deposition. In all cases of Fe-containing materials abraded on Al(2)O(3) substrates, CNT growth is observed; the 400 series of SS appears to deposit catalyst most efficiently. We demonstrate that this simple abrasion technique enables both micro- and nanoscale accuracy in catalyst patterning as well as large area catalyst deposition for uniform, dense CNT growth. Raman spectroscopy characterization indicates high quality CNTs grown by this approach. This technique provides an inexpensive and simple route for addition of catalyst for Fe-based surface growth of CNTs.
Recent advances in DNA vaccine of hepatitis virus. (2002)

Nucleic acid vaccine or DNA vaccine is a hopeful vaccine to prevent and treat viral hepatitis. Problems exist in different DNA vaccines for HBV or HCV. Optimal animal model should be established study vaccine against hepatitis. Apart from the strategy to enhance the efficiency of DNA vaccine, combined use of cytokines or chemokines, different routes of inoculation, design of optimal vector, ISS insertion in the plasmid vectors, etc to enhance the efficiency of DNA vaccine are reviewed.
A fully adaptive 19-to-56Gb/s PAM-4 wireline transceiver with a configurable ADC in 16nm FinFET (2018)

Trends in IoT and cloud computing continue to accelerate bandwidth demand, requiring technology innovation to cover 50G, 100G and 400G ports without significant increase in cost or power per bit. In order to mitigate the cost of infrastructure upgrade, the industry has proposed a standard for 56Gb/s PAM-4 interfaces [1] that can support legacy channels using Forward Error Correction (FEC). Recent publications achieve good pre-FEC BER performance using ADC-based receivers [2,3], but the power consumption (e.g. >550mW per lane at 56Gb/s excluding DSP/digital power in [2]) could be prohibitive for products with large numbers of transceivers. This paper demonstrates a fully integrated and adaptive 19-to-56Gb/s PAM-4 (9.5-to-28Gb/s in NRZ mode) transceiver implemented in 16nm FinFET technology that consumes significantly lower power.
Breath Analysis: Potential for Clinical Diagnosis and Exposure Assessment (2006)

Breath tests are among the least invasive methods available for clinical diagnosis, disease state monitoring, and environmental exposure assessment. In recent years, interest in breath analysis for clinical purposes has increased. This review is intended to describe the potential applications of breath tests, including clinical diagnosis of diseases and monitoring of environmental pollutant exposure, with emphasis on oxidative stress, lung diseases, metabolic disorder, gastroenteric diseases, and some other applications. The application of breath tests in assessment of exposure to volatile organic compounds is also addressed. Finally, both the advantages and limitations of breath analysis are summarized and discussed.
Induction of specific T-cell responsiveness to allogeneic bone. (1991)

The capacity of fresh murine allogeneic bone to induce a specific immune response in vitro was studied. T-cells stimulated by allogeneic bone in vitro were collected and were characterized for state of activation, cell-surface phenotype, and antigen specificity. The stimulating antigens were determined by genetic mapping with use of recombinant inbred strains of mice and by blocking of mixed lymphocyte cultures with use of neutralizing antibodies. Purified T-cells were cultured alone or with allogeneic or syngeneic bone. In some experiments, the bone marrow was removed before in vitro culture. Responding cells were recovered after a secondary exposure to the stimulating bone. Primed cells were used immediately or cell-lines were developed. The data demonstrated that (1) allogeneic bone activated T-cells and induced their proliferation; (2) bone-induced proliferation of T-cells was specific for antigens that map to the major histocompatibility complex of the bone donor; (3) within the major histocompatibility complex, the antigens responsible for proliferation of T-cells were apparently class-I and class-II determinants; (4) removal of bone-marrow cells had no effect on the ability of that bone to stimulate alloreactivity; and (5) all of the alloreactive T-cells had the cell-surface phenotype Thy-+ CD8+ CD4-.
The Lectin Domain of UDP-N-acetyl-d-galactosamine:PolypeptideN-acetylgalactosaminyltransferase-T4 Directs Its Glycopeptide Specificities (2000)

The initiation step of mucin-type O-glycosylation is controlled by a large family of homologous UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (GalNAc-transferases). Differences in kinetic properties, substrate specificities, and expression patterns of these isoenzymes provide for differential regulation of O-glycan attachment sites and density. Recently, it has emerged that some GalNAc-transferase isoforms in vitro selectively function with partially GalNAc O-glycosylated acceptor peptides rather than with the corresponding unglycosylated peptides. O-Glycan attachment to selected sites, most notably two sites in the MUC1 tandem repeat, is entirely dependent on the glycosylation-dependent function of GalNAc-T4. Here we present data that a putative lectin domain found in the C terminus of GalNAc-T4 functions as a GalNAc lectin and confers its glycopeptide specificity. A single amino acid substitution in the lectin domain of a secreted form of GalNAc-T4 selectively blocked GalNAc-glycopeptide activity, while the general activity to peptides exerted by this enzyme was unaffected. Furthermore, the GalNAc-glycopeptide activity of wild-type secreted GalNAc-T4 was selectively inhibited by free GalNAc, while the activity with peptides was unaffected.
A hydrogel-actuated environmentally sensitive microvalve for active flow control (2003)

This paper reports on the fabrication and test of a hydrogel-actuated microvalve that responds to changes in the concentration of specific chemical species in an external liquid environment. The microvalve consists of a thin hydrogel, sandwiched between a stiff porous membrane and a flexible silicone rubber diaphragm. Swelling and deswelling of the hydrogel, which results from the diffusion of chemical species through the porous membrane is accompanied by the deflection of the diaphragm and hence closure and opening of the valve intake orifice. A phenylboronic-acid-based hydrogel was used to construct a smart microvalve that responds to the changes in the glucose and pH concentrations. The fastest response time (for a pH concentration cycle) achieved was 7 min using a 30-μm-thick hydrogel and a 60-μm-thick porous membrane with 0.1 μm pore size and 40% porosity.
The NGFI-B protein, an inducible member of the thyroid/steroid receptor family, is rapidly modified posttranslationally. (1990)

The NGFI-B gene is rapidly activated by a variety of stimuli that induce cells to differentiate or proliferate. It encodes a protein with a predicted molecular mass of congruent to 61 kDa and is a member of the thyroid/steroid hormone receptor gene family. To characterize this protein, monoclonal antibodies were raised against a bacterial TrpE-NGFI-B fusion protein that encompasses a large portion (Glu-410 to Leu-527) of the carboxy-terminal domain of NGFI-B. These antibodies detected a protein that was rapidly synthesized in response to nerve growth factor (NGF) and migrated as a broad band on sodium dodecyl sulfate-polyacrylamide gels with an apparent molecular mass that ranged from 63 to 88 kDa. Pulse-chase analysis demonstrated that NGFI-B was rapidly posttranslationally modified and was a short-lived protein. NGFI-B was found to be a phosphorylated protein, and the multiple NGFI-B species coalesced into a single, more rapidly migrating species when treated with alkaline phosphatase. PC12 cells grown in the absence of NGF contained low levels of NGFI-B that was underphosphorylated. Epidermal growth factor, phorbol ester, and the calcium ionophore A23187 stimulated the synthesis of NGFI-B that was composed largely of underphosphorylated, rapidly migrating species. In contrast, basic fibroblast growth factor, which promotes differentiation of PC12 cells, induced the synthesis of NGFI-B species similar to those synthesized in response to NGF treatment. The underphosphorylated NGFI-B found in uninduced PC12 cells was found only in the nucleus, whereas NGFI-B in NGF-stimulated PC12 cells was present in approximately equal quantities in the cytoplasm and nucleus. Consistent with the cellular distribution observed in nonstimulated PC12 cells, the highly phosphorylated species were predominantly cytoplasmic whereas the more rapidly migrating forms were nuclear.
Role of bulky polysiloxanylalkyi methacrylates in oxygen‐permeable hydrogel materials (1995)

Abstract Polysiloxanylalkyl methacrylates, such as methacryloxypropyl tris(trimethylsiloxy)silane (TRIS), have been used extensively in rigid gas‐permeable contact lens materials due to their ability to produce high oxygen permeability in the resulting polymeric material. In this study, the role of TRIS was evaluated as a component in silicone hydrogel materials based on polysiloxane‐based prepolymers. It was found that it not only gave high oxygen permeability, but also gave hydrogels with better tear strength and lower modulus. These changes in properties are all favorable for applications such as oxygen‐permeable hydrogel lenses. © 1995 John Wiley &amp; Sons, Inc.
The pig as a model for excisional skin wound healing: characterization of the molecular and cellular biology, and bacteriology of the healing process. (2001)

A pig model of wound healing was developed by excision of 2-cm-diameter full thickness skin in young Yorkshire pigs. The results indicated that wound re-epithelialization in this animal model took an average of 20 days. Analysis of cellular change was assessed by use of DNA quantification and determination of apoptotic cells in tissue sections. The results indicate that RNA and DNA contents paralleled each other throughout the healing process, and observed changes in the pattern of RNA and DNA content of the scar tissues were consistent with cell loss due to apoptosis in this model. Expression of mRNA for relevant genes was assessed by use of semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis, using porcine specific primer sets and RNA isolated from normal skin and specimens obtained at various times after wounding. The mRNA values for tumor necrosis factor-alpha (TNF-alpha), connective tissue growth factor (CTGF), insulin-like growth factor II (IGF-II), and decorin were significantly high at specific times after wounding, but mRNA values for the transcription factors (c-fos and c-jun) were significantly decreased. Quantitative bacteriologic results indicated that the total bacterial count in this animal model reached 10(9) colony-forming units (CFU)/g, with the highest value at post-wounding day 7, and Pseudomonas aeruginosa and Staphylocococci aureus were the most common bacteria detected in this model. Further definition of this model should identify unique points in the healing process, and such information could lead to development of therapeutic interventions to improve skin wound healing.
Lumbar Interbody Cages (1998)

Interbody cage devices, used to assist interbody fusion, are rapidly gaining popularity in the surgical management of chronic low back pain. This update provides a structural classification of commonly used devices and assesses them against a set of clearly defined surgical goals, including ability to correct the existing mechanical deformation, ability to provide mechanical stability, ability to provide a suitable environment for arthrodesis, and ability to limit "built-in" morbidity. In addition, the materials used in the devices are examined regarding their biomechanical, biologic, and radiographic characteristics.
Uplink Nonorthogonal Multiple Access Technologies Toward 5G: A Survey (2018)

Owing to the superior performance in spectral efficiency, connectivity, and flexibility, nonorthogonal multiple access (NOMA) is recognized as the promising access protocol and is now undergoing the standardization process in 5G. Specifically, dozens of NOMA schemes have been proposed and discussed as the candidate multiple access technologies for the future radio access networks. This paper aims to make a comprehensive overview about the promising NOMA schemes. First of all, we analyze the state‐of‐the‐art NOMA schemes by comparing the operations applied at the transmitter. Typical multiuser detection algorithms corresponding to these NOMA schemes are then introduced. Next, we focus on grant‐free NOMA, which incorporates the NOMA techniques with uplink uncoordinated access and is expected to address the massive connectivity requirement of 5G. We present the motivation of applying grant‐free NOMA, as well as the typical grant‐free NOMA schemes and the detection techniques. In addition, this paper discusses the implementation issues of NOMA for practical deployment. Finally, we envision the future research challenges deduced from the recently proposed NOMA technologies.
Rescue of Infectious Rift Valley Fever Virus Entirely from cDNA, Analysis of Virus Lacking the NSs Gene, and Expression of a Foreign Gene (2006)

Rift Valley fever virus (RVFV) (genus Phlebovirus, family Bunyaviridae) has a tripartite negative-strand genome, causes a mosquito-borne disease that is endemic in sub-Saharan African countries and that also causes large epidemics among humans and livestock. Furthermore, it is a bioterrorist threat and poses a risk for introduction to other areas. In spite of its danger, neither veterinary nor human vaccines are available. We established a T7 RNA polymerase-driven reverse genetics system to rescue infectious clones of RVFV MP-12 strain entirely from cDNA, the first for any phlebovirus. Expression of viral structural proteins from the protein expression plasmids was not required for virus rescue, whereas NSs protein expression abolished virus rescue. Mutants of MP-12 partially or completely lacking the NSs open reading frame were viable. These NSs deletion mutants replicated efficiently in Vero and 293 cells, but not in MRC-5 cells. In the latter cell line, accumulation of beta interferon mRNA occurred after infection by these NSs deletion mutants, but not after infection by MP-12. The NSs deletion mutants formed larger plaques than MP-12 did in Vero E6 cells and failed to shut off host protein synthesis in Vero cells. An MP-12 mutant carrying a luciferase gene in place of the NSs gene replicated as efficiently as MP-12 did, produced enzymatically active luciferase during replication, and stably retained the luciferase gene after 10 virus passages, representing the first demonstration of foreign gene expression in any bunyavirus. This reverse genetics system can be used to study the molecular virology of RVFV, assess current vaccine candidates, produce new vaccines, and incorporate marker genes into animal vaccines.