gebhart/patrepeval huggingface dataset:
Cloning and characterization of the Salmonella typhimurium ada gene, which encodes O6-methylguanine-DNA methyltransferase (1991)

The ada gene of Escherichia coli encodes O6-methylguanine-DNA methyltransferase, which serves as a positive regulator of the adaptive response to alkylating agents and as a DNA repair enzyme. The gene which can make an ada-deficient strain of E. coli resistant to the cell-killing and mutagenic effects of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) has been cloned from Salmonella typhimurium TA1538. DNA sequence analysis indicated that the gene potentially encoded a protein with a calculated molecular weight of 39,217. Since the nucleotide sequence of the cloned gene shows 70% similarity to the ada gene of E. coli and there is an ada box-like sequence (5'-GAATTAAAACGCA-3') in the promoter region, we tentatively refer to this cloned DNA as the adaST gene. The gene encodes Cys-68 and Cys-320, which are potential acceptor sites for the methyl group from the damaged DNA. The multicopy plasmid carrying the adaST gene significantly reduced the frequency of mutation induced by MNNG both in E. coli and in S. typhimurium. The AdaST protein encoded by the plasmid increased expression of the ada'-lacZ chromosome fusion about 5-fold when an E. coli strain carrying both the fusion operon and the plasmid was exposed to a low concentration of MNNG, whereas the E. coli Ada protein encoded by a low-copy-number plasmid increased it about 40-fold under the same conditions. The low ability of AdaST to function as a positive regulator could account for the apparent lack of an adaptive response to alkylation damage in S. typhimurium.
Macular function impairment in eyes with early age-related macular degeneration. (1997)

Macular recovery function central visual field sensitivity, and spatiotemporal contrast sensitivity are adequate and reliable indicators of macular function impairment in early AMD. Macular recovery function is the test that best reflects the ophthalmoscopic characteristics of early AMD because its deterioration parallels the worsening of typical fundus lesions. Function tests are valuable in the evaluation of patients with early AMD, particularly when interventional trials are planned.
Intraocular pressure measurement at the choroid surface: a feasibility study with implications for implantable microsystems (2001)

Small changes in IOP can be accurately measured by a sensor in contact with the surface of the choroid, for both a fixed sensor configuration and for a sensor sutured to the sclera. These results are the first step in the realisation of a surgically implantable microsensor to monitor IOP for patients suffering from low tension and other difficult to manage forms of glaucoma.
The Nordic Countries as a Cohort for Pharmacoepidemiological Research (2009)

The Nordic countries have a long tradition of registry-based epidemiological research. Many population-based health registries were established in the 1960s, with use of unique personal identifiers facilitating linkage between registries. In recent years, each country has established a national database to track prescription drugs dispensed to individuals in ambulatory care. The objectives were to present an overview of the prescription databases established in the Nordic countries, as well as to elaborate on their unique potential for record linkage and cross-national comparison of drug utilization. Five Nordic countries collect drug exposure data based on drugs dispensed at pharmacies and have the potential to link these data to health outcomes. The databases together cover 25 million inhabitants (Denmark: 5.5 million; Finland: 5.3 million; Iceland: 0.3 million; Norway: 4.8 million; and Sweden: 9.2 million). In 2007, the registries encompassed 17 million prescription drug users (68% of the total population). We provide examples of how these databases have been used for descriptive drug utilization studies and analytical pharmacoepidemiological studies linking drug exposure to other health registries. Comparisons are facilitated by many similarities among the databases, including data source, content, coverage and methods used for drug utilization studies and record linkage. There are, however, some differences in coding systems and validity, as well as in some access and technical issues. To perform cross-national pharmacoepidemiological studies, resources, networks and time are needed, as well as methods for pooling data. Interpretation of results needs to account for inter-country heterogeneity and the possibility of spurious relationships. The Nordic countries have a unique potential for collaborative high-quality cross-national pharmacoepidemiological studies with large populations. This research may assist in resolving safety issues of international interest, thus minimizing the risk of either over-reacting on possible signals or underestimating drug safety issues.
The effects of prior experience on estimating the duration of simple tasks. (2004)

Previous research provides conflicting evidence regarding the effects of prior experience on estimates of task duration. Research supporting the planning fallacy&#13;\nsuggests that people tend to ignore information about their previous task performance, whereas other work indicates that time estimates are influenced by the duration of a&#13;\njust-completed similar task. The present research examined whether information about previous tasks was linked to temporal misestimation on subsequent tasks. Experiment 1&#13;\nrevealed that the accuracy of completion time predictions on an anagram task was influenced by the degree of misestimation in the perceived duration of the preceding&#13;\ntask. In Experiment 2, prospective estimates were found to exceed actual time, whereas the direction in which predictions were misestimated (under or overestimation) differed according to the duration of the just-completed task. These findings suggest that taskrelated information is not only used when predicting task duration but also affects temporal misestimation. This research is discussed in the context of bias in predictions of task duration and the allocation of attentional resources in dual task situations in the prospective time estimation paradigm.
Tc9 cells, a new subset of CD8+ T cells, support Th2‐mediated airway inflammation (2012)

Similar to T-helper (Th) cells, CD8(+) T cells also differentiate into distinct subpopulations. However, the existence of IL-9-producing CD8(+) T (Tc9) cells has not been elucidated so far. We show that murine CD8(+) T cells activated in the presence of IL-4 plus TGF-β develop into transient IL-9 producers characterized by specific IFN-γ and IL-10 expression patterns as well as by low cytotoxic function along with diminished expression of the CTL-associated transcription factors T-bet and Eomesodermin. Similarly to the CD4(+) counterpart, Tc9 cells required for their differentiation STAT6 and IRF4. Tc9 cells deficient for these master regulators displayed increased levels of Foxp3 that in turn suppressed IL-9 production. In an allergic airway disease model, Tc9 cells promoted the onset of airway inflammation, mediated by subpathogenic numbers of Th2 cells. This support was specific for Tc9 cells because CTLs failed to exert this function. We detected increased Tc9 frequency in the periphery in mice and humans with atopic dermatitis, a Th2-associated skin disease that often precedes asthma. Thus, our data point to the existence of Tc9 cells and to their supportive function in Th2-dependent airway inflammation, suggesting that these cells might be a therapeutic target in allergic disorders.
Various Wavelengths of Light-Emitting Diode Light Regulate the Proliferation of Human Dermal Papilla Cells and Hair Follicles via Wnt/β-Catenin and the Extracellular Signal-Regulated Kinase Pathways (2017)

Our result suggests that LED has a potential to stimulate hDPC proliferation via the activation of Wnt/β-catenin signaling and ERK pathway. To our best knowledge, this is the first report which investigated that the effect of various wavelengths of LED on hDPC proliferation and the underlying mechanisms.
Gene Structures of Low‐Neurovirulent Vaccinia Virus LC16m0, LC16m8, and Their Lister Original (LO) Strains (1985)

Vaccinia viruses LC16m0 and LC16m8 are temperature-sensitive and low-neurovirulent variants derived from the Lister (Elstree) (LO) strain. Analyses of genome DNAs by digestion with restriction endonucleases and cross-hybridization of the digested fragments revealed that LC16m0 and LC16m8 possess a new XhoI site in addition to the 14 XhoI sites of LO. This new site is located at about 12 X 10(6) daltons from the right terminal end. There was no significant difference in the genome structures between the LC16 variants and LO except the new XhoI site and their terminal fragments which were not identified in LO owing to their heterogeneity. With HindIII digested fragments, there was no difference among the three viruses. This complete mapping raised the possibility that the putative gene responsible for temperature sensitivity and neurovirulence is located at the region of the XhoI site found in LC16m0 and LC16m8.
Calorie restriction attenuates Alzheimer's disease type brain amyloidosis in Squirrel monkeys (Saimiri sciureus) (2006)

Recent studies from our laboratories and others suggest that calorie restriction (CR) may benefit Alzheimer's disease (AD) by preventing amyloid-beta (Abeta) neuropathology in the mouse models of AD. Moreover, we found that promotion of the NAD+-dependent SIRT1 mediated deacetylase activity, a key regulator in CR extension of life span, may be a mechanism by which CR influences AD-type neuropathology. In this study we continued to explore the role of CR in AD-type brain amyloidosis in Squirrel monkeys (Saimiri sciureus). Monkeys were maintained on the normal and CR diets throughout the entire lifespan until they died of natural causes. We found that 30% CR resulted in reduced contents of Abeta1-40 and Abeta1-42 peptides in the temporal cortex of Squirrel monkeys, relative to control (CON) fed monkeys. The decreased contents of cortical Abeta peptide inversely correlated with SIRT1 protein concentrations in the same brain region; no detectable change in total full-length amyloid-beta protein precursor (AbetaPP) level was found. Most interestingly, we found that 30% CR resulted in a select elevation of alpha- but not beta- or gamma- secretase activity which coincided with decreased ROCK1 protein content in the same brain region, relative to CON group. Collectively, the study suggests that investigation of the role of CR in non-human primates may provide a valuable approach for further clarifying the role of CR in AD.
Treatment of Ceroidosis for Cultured Flounder, Paralichthys olivaceus -Hematological characteristic of flounder with glutathione supplemented diets- (1991)

In order to investigate the effects of glutathione against ceroidosis on flounder, Paralichthys olivaceus, a serial experiment was carried out at indoor tanks in Cheju province, the southern island of R.O.Korea, from October 1 to November 4 of 1991. The choosed group of flounder for this experiment, ranged from 92 to 122g in body weight, already showed a distinct histological ceroidosis in liver, spleen, kidney about six months before this experiment. They were fed on formulated diets supplemented with glutathione of 0mg, 1mg, 2mg, 5mg, 10mg per kg of diet per day. Some flounders were fed on the decomposed diet as a control continuosuly. Two individuals fed on the experimental diets were cought at an interval 7 days for 35 days and analyzed the values of blood indexs. 1. While the values of RBC, Hb, Ht, MCHC, MCV of flounder fed on the decomposed diet and the glutathione non-supplemented diet were not changed compared with the beginning levels of experiment, those fed on the glutathione supplemented diets, showed markedly increased values from 7th day of experiment and from 21th day of experiment reached to the values of healthy flounder. 2. The variation of TP, Glu, Alp, BUN, TG, T-cho, GOT and GPT were not observed in the groups fed on the control diet and glutathione non-supplemented diet. In contrast, those values in the groups fed on the glutathione supplemented diets were markedly decreased from 7th day and become constant from 21th day. 3. The effect of glutathione supplementation with high concentration in diets showed much better improvements of symptoms concequently, compared with those of low concentration diets.
Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci (2009)

Nested Patch polymerase chain reaction (PCR) amplifies a large number (greater than 90) of targeted loci from genomic DNA simultaneously in the same reaction. These amplified loci can then be sequenced on a second-generation sequencing machine to detect single nucleotide polymorphisms (SNPs) and mutations. The reaction is highly specific: 90% of sequencing reads match targeted loci. Nested Patch PCR can be performed on many samples in parallel, and by using sample-specific DNA barcodes, these can be pooled and sequenced in a single reaction. Thus, the Nested Patch PCR protocol that is described here provides an easy workflow to identify SNPs and mutations across many targeted loci for many samples in parallel.
Mutational analysis of complementary-sense genes of African cassava mosaic virus DNA A (1991)

We have investigated the ability of African cassava mosaic virus DNA A mutants, containing disrupted complementary-sense genes, to infect Nicotiana benthamiana and to replicate in Nicotiana tabacum protoplasts. Three overlapping open reading frames (ORFs) with the capacity to encode proteins with an Mr greater than 10K (AC1, AC2 and AC3) are highly conserved between geminiviruses that infect dicotyledonous plants and one (AC4) is less well conserved. Of these, only AC1 is a prerequisite for DNA replication; disruption of this ORF rendered the DNA noninfectious in plants and prevented DNA replication in protoplasts. Disruption of ORF AC2 prevented plant infection but mutants were capable of autonomous replication and replicated DNA B in trans in protoplasts to produce DNA forms that comigrated with wild-type virus DNAs. The AC2 mutant phenotype suggests that the product of this ORF is involved in virus spread within the plant. Mutants in which ORF AC3 had been disrupted retained the ability to replicate and to infect plants systemically although symptom development was delayed and attenuated, and mutant DNA accumulated to much lower levels (10 to 20%) in comparison with wild-type infection. Typical geminate virus particles were observed in extracts of plants infected with ORF AC3 mutants indicating that this gene is not essential for coat protein synthesis or virus assembly but possibly acts by modulating virus levels in infected tissues. Disruption of ORF AC4 had no effect on infectivity or symptom development suggesting that this ORF is maintained only because it overlaps the highly conserved ORF AC1.
Pd(0)-Catalyzed 1,1-Diarylation of Ethylene and Allylic Carbonates (2013)

An efficient protocol for the one-step synthesis of biologically relevant 1,1-diarylalkanes has been described. This reaction introduces two different aryl groups across the terminal end of simple feedstock alkenes such as ethylene and allylic carbonates. The propensity to generate π-benzylpalladium intermediates dictates the exclusive 1,1-regioselectivity observed in the product.
The Human Cationic Peptide LL-37 Induces Activation of the Extracellular Signal-Regulated Kinase and p38 Kinase Pathways in Primary Human Monocytes (2004)

LL-37 is a cationic peptide that is found in the granules of neutrophils and is secreted by epithelial cells from a variety of tissues. Levels of LL-37 in vivo increase upon infection, and its production and secretion are increased upon stimulation with proinflammatory mediators. It has been postulated that LL-37 modulates the immune response by interacting with the effector cells of innate immunity; however, the mechanism of this interaction is unknown. LL-37 induced phosphorylation and activation of the mitogen-activated protein kinases, extracellular signal-regulated kinase 1/2 (ERK1/2) and p38, in human peripheral blood-derived monocytes and a human bronchial epithelial cell line, but not in B or T lymphocytes. Phosphorylation was not dependent on the G protein-coupled formyl peptide-like receptor 1, which was previously proposed to be the receptor for LL-37-induced chemotaxis on human monocytes and T cells. Activation of ERK1/2 and p38 was markedly increased by the presence of GM-CSF, but not M-CSF. Exposure to LL-37 also led to the activation of Elk-1, a transcription factor that is downstream of and activated by phosphorylated ERK1/2, the up-regulation of various Elk-1-controlled genes, and the transcription and secretion of IL-8. Inhibition of either p38 or ERK1/2 kinases led to a reduction in LL-37-induced IL-8 secretion and inhibition of the transcription of various chemokine genes. The ability of LL-37 to signal through these pathways has broad implications in immunity, monocyte activation, proliferation, and differentiation.
Plasmid vehicles for direct cloning of Escherichia coli promoters (1979)

A multicopy plasmid cloning vehicle, pGA22, which carries genes for ampicillin resistance (Apr), tetracycline resistance (Tcr), chloramphenicol resistance (Cmr), and kanamycin resistance (Kmr) has been constructed. This plasmid has five unique sites for restriction endonucleases EcoRI, PstI, XhoI, SmaI, and SalI within antibiotic resistance genes. pGA22, which is 5.1 megadaltons in size, has a low copy number (probably fewer than 10 per genome), is capable of relaxed replication, and is mobilized by F-factor at a frequency of 10(-5). A series of promoter-cloning vehicles, pGA24, pGA39, and pGA46, has been developed from pGA22. In these plasmids the natural promoter for Tcr has been removed and has been replaced by small deoxyribonucleic acid fragments carrying unique sites for several restriction endonucleases. Cells carrying these vectors are sensitive to tetracycline unless insertional activation of the Tcr occurs by cloning a promoter-carrying deoxyribonucleic acid fragment in one of the unique sites adjacent to the 5' end of Tcr. In this way, promoters carried on a HindIII-generated deoxyribonucleic acid fragment can be inserted at the HindIII site of plasmid pGA24, pGA39, or pGA46. A promoter in fragments generated by digestion with restriction endonuclease XmaI or PstI or by any restriction endonucleases which generate flush ends, such as SmaI, PvuII, HpaI, HincII, or HaeIII, can be clones in plasmid pGA39. Plasmid pGA46 can be used to detect a promoter fragment carried on a BglII, BamHI, MboI, or PstI fragment. We also describe a plasmid, pGA44, with a unique KpnI site in the rifampin resistance gene rpoB.
Identification of T-Cell Antigens Specific for Latent Mycobacterium Tuberculosis Infection (2009)

Our findings further support the hypothesis that the latency-associated antigens can be exploited as biomarkers for LTBI.
Secure pattern matching using somewhat homomorphic encryption (2013)

The basic pattern matching problem is to find the locations where a pattern occurs in a text. Recently, secure pattern matching has been received much attention in various areas, including privacy-preserving DNA matching and secure biometric authentication. The aim of this paper is to give a practical solution for this problem using homomorphic encryption, which is public key encryption supporting some operations on encrypted data.
Multiple Lateral Polysilicon Diodes as Temperature Sensors for Chemical Microreaction Systems (2003)

Lateral polysilicon P+–N–N+ and P+–P–N+ diodes were fabricated and their reverse current was measured at various temperatures in the range of 50°C to 150°C. The reverse current at a constant bias was characterized and used as a parameter to determine temperature by a method proposed in this work for possible application in a chemical microreaction system. Polysilicon diodes in a series combination of 2 or 3 were also fabricated and their electronic properties such as ON resistance, reverse current and ideality factor were studied. The ON resistance and the ideality factor increased linearly with the number of diodes in series, owing to the effect of the series combination of diodes. The multiple diodes also showed a lower reverse current than the individual single diodes in the series. Hence, it is beneficial to use these multiple diodes as temperature sensors, since they give the least error in temperature determination.
The Staphylococcal Transferrin-Binding Protein Is a Cell Wall Glyceraldehyde-3-Phosphate Dehydrogenase (1999)

Staphylococcus aureus and Staphylococcus epidermidis possess a 42-kDa cell wall transferrin-binding protein (Tpn) which is involved in the acquisition of transferrin-bound iron. To characterize this protein further, cell wall fractions were subjected to two-dimensional sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis blotted, and the N-terminus of Tpn was sequenced. Comparison of the first 20 amino acid residues of Tpn with the protein databases revealed a high degree of homology to the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Analysis of staphylococcal cell wall fractions for GAPDH activity confirmed the presence of a functional enzyme which, like Tpn, is regulated by the availability of iron in the growth medium. To determine whether Tpn is responsible for this GAPDH activity, it was affinity purified with NAD+ agarose. Both S. epidermidis and S. aureus Tpn catalyzed the conversion of glyceraldehyde-3-phosphate to 1,3-diphosphoglycerate. In contrast, Staphylococcus saprophyticus, which lacks a Tpn, has no cell wall-associated GAPDH activity. Native polyacrylamide gel electrophoresis of the affinity-purified Tpn revealed that it was present in the cell wall as a tetramer, consistent with the structures of all known cytoplasmic GAPDHs. Furthermore, the affinity-purified Tpn retained its ability to bind human transferrin both in its native tetrameric and SDS-denatured monomeric forms. Apart from interacting with human transferrin, Tpn, in common with the group A streptococcal cell wall GAPDH, binds human plasmin. Tpn-bound plasmin is enzymatically active and therefore may contribute to the ability of staphylococci to penetrate tissues during infections. These studies demonstrate that the staphylococcal transferrin receptor protein, Tpn, is a multifunctional cell wall GAPDH.
Biocompatibility of a Biodegradable, Controlled-Release Polymer in the Rabbit Brain (1989)

The biodegradable polyanhydrides are a new class of controlled release polymers developed for the interstitial delivery of drugs to their target site in the brain or other organs over periods ranging from days to years. These polymers can release molecules of any size in a predictable fashion. Their degradation products are non-cytotoxic and biocompatible. The biocompatibility of a biodegradable polyanhydride, the copolymer of poly[bis(p-carboxyphenoxy)propane] anhydride and sebacic acid (PCPP-SA) in a 50:50 formulation, was studied in the rabbit brain. Twenty adult New Zealand White male rabbits underwent implantation of PCPP-SA in a frontal lobe and absorbable gelatin sponge (Gelfoam) in the other frontal lobe. The animals were evaluated daily until the time of sacrifice. Groups of four animals were sacrificed sequentially on post-operative days 1, 3, 7, 21, and 60, and the brains processed for histological evaluation. None of the animals showed behavioral changes or neurological deficits suggestive of toxicity and all that received implants survived to their date of sacrifice. The histological examination showed no significant differences between the tissue reaction from PCPP-SA compared to Gelfoam. The polymers were also tested in the rabbit cornea bioassay and did not induce an inflammatory response. We conclude that PCPP-SA (50:50), a new biodegradable polymeric matrix that can be surgically implanted for the interstitial delivery of drugs in the brain, is biocompatible in the rabbit brain.