gebhart/patrepeval huggingface dataset:
Keap1 represses nuclear activation of antioxidant responsive elements by Nrf2 through binding to the amino-terminal Neh2 domain (1999)

Transcription factor Nrf2 is essential for the antioxidant responsive element (ARE)-mediated induction of phase II detoxifying and oxidative stress enzyme genes. Detailed analysis of differential Nrf2 activity displayed in transfected cell lines ultimately led to the identification of a new protein, which we named Keap1, that suppresses Nrf2 transcriptional activity by specific binding to its evolutionarily conserved amino-terminal regulatory domain. The closest homolog of Keap1 is a Drosophila actin-binding protein called Kelch, implying that Keap1 might be a Nrf2 cytoplasmic effector. We then showed that electrophilic agents antagonize Keap1 inhibition of Nrf2 activity in vivo, allowing Nrf2 to traverse from the cytoplasm to the nucleus and potentiate the ARE response. We postulate that Keap1 and Nrf2 constitute a crucial cellular sensor for oxidative stress, and together mediate a key step in the signaling pathway that leads to transcriptional activation by this novel Nrf2 nuclear shuttling mechanism. The activation of Nrf2 leads in turn to the induction of phase II enzyme and antioxidative stress genes in response to electrophiles and reactive oxygen species.
A PCR Specific for Escherichia coli O157 Based on the rfb Locus Encoding O157 Lipopolysaccharide (1998)

A PCR was developed for the detection of Escherichia coli O157 based on the rfbE O-antigen synthesis genes. A 479-bp PCR product was amplified specifically from E. coli O157 in cell lysates containing 200 or 2 CFU following crude DNA extraction. The PCR detected < 1 CFU of E. coli O157 per ml in raw milk following enrichment.
High-speed implementations of rule-based systems (1989)

Rule-based systems are widely used in artificial intelligence for modeling intelligent behavior and building expert systems. Most rule-based programs, however, are extremely computation intensive and run quite slowly. The slow speed of execution has prohibited the use of rule-based systems in domains requiring high performance and real-time response. In this paper we explore various methods for speeding up the execution of rule-based systems. In particular, we examine the role of parallelism in the high-speed execution of rule-based systems and study the architectural issues in the design of computers for rule-based systems. Our results show that contrary to initial expectations, the speed-up that can be obtained from parallelism is quite limited, only about tenfold. The reasons for the small speed-up are: (1) the small number of rules relevant to each change to data memory; (2) the large variation in the processing requirements of relevant rules; and (3) the small number of changes made to data memory between synchronization steps. Furthermore, we observe that to obtain this limited factor of tenfold speed-up, it is necessary to exploit parallelism at a very fine granularity. We propose that a suitable architecture to exploit such fine-grain parallelism is a shared-memory multiprocessor with 32-64 processors. Using such a multiprocessor, it is possible to obtain execution speeds of about 3800 rule-firings/set. This speed is significantly higher than that obtained by other proposed parallel implementations of rule-based systems.
Detection of cancer through exhaled breath: a systematic review (2015)

Analyses of exhaled breath yielded promising results, although standardization of breath collection, sample storage and data handling remain critical issues. In order to foster breath analysis implementation into practice, larger studies should be implemented in true screening settings, paying particular attention to standardization in breath collection, consideration of covariates, and validation in independent population samples.
Insulin Across Respiratory Mucosae by Aerosol Delivery (1971)

Insulin, a protein of about 5,700 molecular weight, was delivered by aerosol inhalation to three normal volunteers and to four patients with diabetes mellitus. Direct evidence of absorption of insulin across mucosae of the respiratory tract was an increase in plasma IRI. Biologic activity of insulin absorbed by inhalation was shown by hypoglycemia temporally correlated with the increase in plasma IRI. No untoward reactions were observed.
Abstract P-557: DIAGNOSIS AND MANAGEMENT OF 60 CONGENITAL VASCULAR RINGS IN CHILDREN: A 10-YEAR EXPERIENCE (2018)

Aims & Objectives: To summarize the clinical features, diagnosis and treatment of congenital vascular ring (VR) in chldren. Methods Retrospective study of 60 patients with diagnosis of congenital VR. All the children were given CTA, Echocardiography, Gastrointestinal barium meal, Fiberoptic bronchoscopy. Results Sixty cases including 40 males and 20 females, aged from 1 day to 6 years, were enrolled in our study. The most frequent diagnosis was pulmonary artery sling (25 cases, 41.67 %), followed by double aorta arch (21 cases, 35 %). Twenty-eight cases (46.7%) combined with heart malformations. Forty five cases (46.7%) combined with tracheobronchial stenosis, 10 cases combined with esophageal stricture. The sensitivity of CTA to diagnose vascular ring was 81.82%, while echocardiographic diagnosis rate was 53.33%. 52 cases (87%) had a history of respiratory symptoms. Forty patient who underwent surgery included left pulmonary artery transplantation(15 cases), double aortic arch devascularization(12 cases), cut off the artery catheter/ligament(12 cases), left subclavian artery occlusion (1 case).Seven patients died in sixty cases. Vascular ring combined with complete tracheal ring was a risk factor in patients undergoing surgery (P<0.05). The underwent surgery children remained respiratory symptoms for up to 6 months, however, they had significant improvement in the postoperative period. Conclusions The children with recurrent respiratory symptoms such as recurrent respiratory tract infections, chronic cough and wheeze, dysphagia should be examined for the presence of congenital VR. Echocardiography combined with CTA was the best way to diagnose vascular ring. Early correct diagnosis and timely surgical treatment is the key to children vascular rings survival.
High-mobility strained-Si PMOSFET's (1996)

Operation and fabrication of a new high channel mobility strained-Si PMOSFET are presented. The growth of high-quality strained Si layer on completely relaxed, step-graded, SiGe buffer layer is demonstrated by gas source MBE. The strained-Si layer is characterized by double crystal X-ray diffraction, photoluminescence, and transmission electron microscopy. The operation of a PMOSFET is shown by device simulation and experiment. The high-mobility strained-Si PMOSFET is fabricated on strained-Si, which is grown epitaxially on a completely relaxed step-graded Si/sub 0.82/Ge/sub 0.18/ buffer layer on Si(100) substrate. At high vertical fields (high |V/sub g/|), the channel mobility of the strained-Si device is found to be 40% and 200% higher at 300 K and 77 K, respectively, compared to those of the bulk Si device. In the case of the strained-Si device, degradation of channel mobility due to Si/SiO/sub 2/ interface scattering is found to be more pronounced compared to that of the bulk Si device. Carrier confinement at the type-II strained-Si/SiGe-buffer interface is clearly demonstrated from device transconductance and C-V measurements at 300 K and 77 K.
Double-Blind Treatment of Major Depression With Dehydroepiandrosterone (1999)

These results suggest that DHEA treatment may have significant antidepressant effects in some patients with major depression. Further, larger-scale trials are warranted.
Cefazolin-Gentamicin versus Vancomycin-Ceftazidime Eye Drops for Bacterial Corneal Ulcers;a Randomized Clinical Trial. (2009)

Vancomycin-ceftazidime eye drops seem to be more effective than cefazolin-gentamicin eye drops for the treatment of bacterial corneal ulcers and are probably better tolerated locally.
Current and Future Role of Interferon Beta in the Therapy of Multiple Sclerosis (2010)

Interferon beta was the first specific disease-modifying therapy licensed for multiple sclerosis (MS) and in its many forms remains the most commonly prescribed agent worldwide. It, however, has a modest effect in reducing relapse rates, magnetic resonance imaging activity, and disability, and many patients are unable to tolerate it because of the associated side effects or mode of administration. With the licensing of glatiramer acetate, natalizumab and mitoxantrone as disease-modifying therapies for MS alternative options are available to people with MS. Many exciting new therapies are also in the pipeline, namely, the monoclonal antibodies alemtuzumab, rituximab, and daclizumab and the promising oral agents BG00012, cladribine, fingolimod, laquinimod, and teriflunomide. In this article we review the immunopathology of MS and the proposed mechanisms of action of currently available and anticipated treatments. We also review the efficacy of each drug, use of combination therapy strategies, and the potential role of the interferon beta preparations in the future.
Field Demonstration of a Pilot-Scale Plasma Reactor for the Rapid Removal of Poly- and Perfluoroalkyl Substances in Groundwater (2021)

A pilot-scale plasma-based water treatment system containing two enhanced contact plasma reactors was deployed to a fire training area at Wright-Patterson Air Force Base to treat poly- and perfluoroalkyl substances (PFAS) in aqueous film-forming foam-impacted groundwater from two monitoring wells, wells B and C. Extracted water from both wells was treated through the plasma trailer in a semibatch mode at flow rates ranging from 2.4 to 8.4 L/min. Long-chain perfluoroalkyl acids (PFAAs; fluorocarbon chain of ≥6) and PFAS precursors were reduced by ≥90% for all flow rates in a single cycle through the reactors. Combined perfluorooctanoic acid and perfluorooctanesulfonic acid concentrations lower than the U.S. Environmental Protection Agency’s health advisory level of 70 ng/L were achieved in fewer than three cycles through the reactors. Short-chain PFAAs (fluorocarbon chain of ≤5) were removed to a lesser extent (0–95%) due to their generation during plasma treatment of long-chain PFAAs and PFAS precursors and limited accumulation at the plasma–liquid interface of the reactor. To improve the destruction of short-chain PFAAs, batch mode experiments were performed with the addition of a cationic surfactant (cetrimonium bromide), resulting in an 88% reduction of all short-chain PFAAs within 120 min of treatment.
Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering (2015)

Cholera, caused by the facultative pathogen Vibrio cholerae, remains a serious public health threat. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) provide prokaryotes with sequence-specific protection from invading nucleic acids, including bacteriophages. In this work, we show that one genomic feature differentiating sixth pandemic (classical biotype) strains from seventh pandemic (El Tor biotype) strains is the presence of a CRISPR-Cas system in the classical biotype. We demonstrate that the CRISPR-Cas system from a classical biotype strain can be transferred to a V. cholerae El Tor biotype strain and that it is functional in providing resistance to phage infection. Finally, we show that this CRISPR-Cas system can be used as an efficient tool for the editing of V. cholerae lytic phage genomes.
Molecular cloning and characterization of the aroD gene encoding 3-dehydroquinase from Salmonella typhi (1991)

The aroD gene from Salmonella typhi, encoding 5-dehydroquinate hydrolyase (3-dehydroquinase), has been cloned into Escherichia coli and the DNA sequence determined. The aroD gene was isolated from a cosmid gene bank by complementation of an S. typhimurium aroD mutant. Analysis of the DNA sequence revealed the presence of an open reading frame capable of encoding a protein of 252 amino acids with a calculated Mr of 27706. Comparison of the deduced S. typhi 3-dehydroquinase protein sequence with that elucidated for E. coli revealed 69% homology. Alignment of the S. typhi sequence and equivalent Aspergillus nidulans and Saccharomyces cerevisiae sequences showed that homology was lower, at 24%, but still significant. Use of a minicell expression system demonstrated that a polyclonal antibody raised against E. coli 3-dehydroquinase cross-related with its S. typhi counterpart.
Plant type ferredoxins and ferredoxin‐dependent metabolism (2012)

Ferredoxin (Fd) is a small [2Fe-2S] cluster-containing protein found in all organisms performing oxygenic photosynthesis. Fd is the first soluble acceptor of electrons on the stromal side of the chloroplast electron transport chain, and as such is pivotal to determining the distribution of these electrons to different metabolic reactions. In chloroplasts, the principle sink for electrons is in the production of NADPH, which is mostly consumed during the assimilation of CO2 . In addition to this primary function in photosynthesis, Fds are also involved in a number of other essential metabolic reactions, including biosynthesis of chlorophyll, phytochrome and fatty acids, several steps in the assimilation of sulphur and nitrogen, as well as redox signalling and maintenance of redox balance via the thioredoxin system and Halliwell-Asada cycle. This makes Fds crucial determinants of the electron transfer between the thylakoid membrane and a variety of soluble enzymes dependent on these electrons. In this article, we will first describe the current knowledge on the structure and function of the various Fd isoforms present in chloroplasts of higher plants and then discuss the processes involved in oxidation of Fd, introducing the corresponding enzymes and discussing what is known about their relative interaction with Fd.
A case of malignant mastocytosis with circulating mast cell precursors: biologic and phenotypic characterization of the malignant clone. (1996)

The phenotypic and biologic properties of malignant cells in a case of aggressive mastocytosis with multi-organ involvement, circulating mast cell precursors and absence of skin infiltrates were analyzed. Circulating mast cell precursors were detected by immunostaining using antibodies against mast cell tryptase as well as by electron microscopy. These progenitors were tryptase+/chymase- (MCT) and accounted for 10 to 20% of nucleated mononuclear blood cells (MNC). A subset of them contained metachromatic granules. As assessed by combined toluidine blue/immunofluorescence staining, the granulated mast cell precursors were found to express CD9 (P24), CD33 (gp67) and CD44 (Pgp-1), but not basophil-related markers (CD11b (C3biR), CDw17 (lactosylceramide), CD123 (il-3R alpha))or monocyte-related antigens (CD14, CD15). Expression of the mast cell growth factor (MGF) receptor, c-kit(CD117), was also demonstrable, whereas the skin mast cell marker C5aR (CD88) could not be detected on mast cell precursors. The ligand of c-kit, recombinant human (rh) stem cell factor (SCF = MGF), induced histamine release from circulating mast cell progenitors, whereas rhC5a, a potent skin mast cell-/basophil-agonist, was ineffective over the dose-range (10(-9) to 10(-7(M)) tested. Analysis of mast cell antigens in malignant mastocytosis or mast cell leukemias may be helpful to establish a diagnosis and to determine the phenotype of the clone.
Simvastatin Reduces Graft Vessel Disease and Mortality After Heart Transplantation (1997)

In comparison with dietary measures alone, the combination of a low-cholesterol diet and simvastatin after heart transplantation led to a significant reduction in cholesterol levels, a significantly higher long-term survival rate, and a lower incidence of GVD.
Genetic heterogeneity of the NS3 protease gene in hepatitis C virus genotype 1 from untreated infected patients (2005)

NS3 protease is essential for hepatitis C Virus (HCV) replication, and is one of the most promising targets for specific anti-HCV therapy. Its natural polymorphism has not been studied at the quasispecies level. In the present work, the genetic heterogeneity of the NS3 protease gene was analyzed in 17 HCV genotype 1 (5 subtypes 1a and 12 subtypes 1b) samples collected from infected patients before anti-viral therapy. A total of 294 clones were sequenced. Although the protease NS3 is considered to be one of the less variable genes in the HCV genome, variability of both nucleotide and amino acid sequences was found. In variants belonging to 1a and 1b subtypes, 224 and 267 of 543 positions showed one or more nucleotide substitutions, respectively. Forty and 74 of the 181 NS3 amino acid positions showed at least one mutation in HCV-1a and HCV-1b isolates, respectively. Most substitutions were conservative. This substantial polymorphism of the NS3 protease produced by HCV-1a and HCV-1b suggests that, despite the numerous functional and structural constraints, the enzyme is sufficiently flexible to tolerate substitutions.
Cross-Clade Protection Induced by Human Immunodeficiency Virus-1 DNA Immunogens Expressing Consensus Sequences of Multiple Genes and Epitopes From Subtypes A, B, C, and FGH (2005)

The correlate of protection in human immunodeficiency virus (HIV) infection is not known, but preclinical and clinical studies support the involvement of both antibodies and cellular immunity. In addition, the existence of multiple HIV clades makes HIV vaccine design especially challenging. We have constructed a vaccine platform with an HIV-1 subtype B DNA immunogen expressing full length consensus sequences from HIV-1 rev, nef, tat, and gag with additional cellular epitope clusters from the env and pol regions. Furthermore, this platform has been extended to three additional plasmids expressing the same immunogens but originating from subtypes A or C consensus or FGH ancestral sequences. Immunogenicity in BALB/c mice, by gene gun or intramuscular delivery, revealed strong IFN-gamma production in response to in vitro re-stimulation with a H-2d restricted gag peptide (AMQMLKETI) or even stronger toward an env epitope (RGPGRAFVTI). Weak humoral immunity was detected. Gene gun immunization with a cocktail of all four plasmids induced pre-challenge cellular immunity in C57Bl6/A2.01 mice and subsequently a robust frequency of protection (11/12 animals) after experimental challenge with subtype A or B HIV-1/Murine Leukemia Virus (HIV-1/MuLV). The cross-clade protection observed in this challenge experiment demonstrates that these multigene/multiepitope HIV DNA immunogens are likely to be potent immunogens also against the HIV-infection of human beings.
Human Activities and Vegetation (2005)

The influence of human activities on vegetation is sometimes so great. However, the history of vegetation and the human impact on it is not so clear. Here the relation between the vegetation of the first half of Meiji era and human activities has been inferred from some good materials such as topographical maps, photographs and literatures which have much more information about vegetation and related human activities than those before the era. Studied areas are the suburbs of Kyoto and the rural areas of Kanto region. As the result, it was found that there was deep relation between the vegetation and the human activities in Meiji era. It was also found that some types of vegetation seemed to have been deeply influenced by the human activities before. Dwarf pine tree areas and few vegetation parts of the hills around Kyoto at that time were examples of such vegetation types.
Disulfide-Linked Antibody−Maytansinoid Conjugates: Optimization of In Vivo Activity by Varying the Steric Hindrance at Carbon Atoms Adjacent to the Disulfide Linkage (2011)

In this report, we describe the synthesis of a panel of disulfide-linked huC242 (anti-CanAg) antibody maytansinoid conjugates (AMCs), which have varying levels of steric hindrance around the disulfide bond, in order to investigate the relationship between stability to reduction of the disulfide linker and antitumor activity of the conjugate in vivo. The conjugates were first tested for stability to reduction by dithiothreitol in vitro and for plasma stability in CD1 mice. It was found that the conjugates having the more sterically hindered disulfide linkages were more stable to reductive cleavage of the maytansinoid in both settings. When the panel of conjugates was tested for in vivo efficacy in two human colon cancer xenograft models in SCID mice, it was found that the conjugate with intermediate disulfide bond stability having two methyl groups on the maytansinoid side of the disulfide bond and no methyl groups on the linker side of the disulfide bond (huC242-SPDB-DM4) displayed the best efficacy. The ranking of in vivo efficacies of the conjugates was not predicted by their in vitro potencies, since all conjugates were highly active in vitro, including a huC242-SMCC-DM1 conjugate with a noncleavable linkage which showed only marginal activity in vivo. These data suggest that factors in addition to intrinsic conjugate potency and conjugate half-life in plasma influence the magnitude of antitumor activity observed for an AMC in vivo. We provide evidence that bystander killing of neighboring nontargeted tumor cells by diffusible cytotoxic metabolites produced from target cell processing of disulfide-linked antibody-maytansinoid conjugates may be one additional factor contributing to the activity of these conjugates in vivo.
Detection, location, and severity assessment of left anterior descending coronary artery stenoses by means of contrast-enhanced transthoracic harmonic echo Doppler (2009)

Blood flow velocity evaluation in the LAD by means of transthoracic ED is feasible and reliable in detecting, locating, and assessing the severity of LAD stenosis.
Mutation of the Alzheimer's Disease Amyloid Gene in Hereditary Cerebral Hemorrhage, Dutch Type (1990)

An amyloid protein that precipitates in the cerebral vessel walls of Dutch patients with hereditary cerebral hemorrhage with amyloidosis is similar to the amyloid protein in vessel walls and senile plaques in brains of patients with Alzheimer's disease, Down syndrome, and sporadic cerebral amyloid angiopathy. Cloning and sequencing of the two exons that encode the amyloid protein from two patients with this amyloidosis revealed a cytosine-to-guanine transversion, a mutation that caused a single amino acid substitution (glutamine instead of glutamic acid) at position 22 of the amyloid protein. The mutation may account for the deposition of this amyloid protein in the cerebral vessel walls of these patients, leading to cerebral hemorrhages and premature death.
Effective ultraviolet irradiation of platelet concentrates in teflon bags (1990)

Several plastic materials used in blood storage were evaluated for their ability to transmit ultraviolet B (UVB) light. A plastic bag manufactured from sheets of transparent Teflon efficiently (78-86%) transmitted UVB light and was employed in subsequent functional studies of lymphocytes and platelets exposed to UVB light while contained in these bags. In vitro experiments showed a UVB dose-dependent abrogation of lymphocyte responder and stimulator functions, with concurrent preservation of platelet aggregation responses. In a phase I pilot study, UVB-treated platelet concentrates were administered to four bone marrow transplant recipients. Adverse effects attributable to the transfusions were not observed, and patients showed clinically effective transfusion responses. No patient developed lymphocytotoxic HLA or platelet antibodies. These studies suggest that platelets can be effectively irradiated with UVB light in a closed system. However, numerous variables, including container material, volume and composition of contents, steady exposure versus agitation, and exact UV wavelength, must be considered.