gebhart/patrepeval huggingface dataset:
Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic BacteriumXanthomonas campestrispv. vesicatoria Revealed by the Complete Genome Sequence (2005)

The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G+C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris and a structure completely different from Xanthomonas oryzae pv. oryzae. A total of 548 coding sequences (12.2%) are unique to X. campestris pv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity, the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides.
EPIDEMIOLOGY OF COAGULATION FACTORS, INHIBITORS AND ACTIVATION MARKERS: THE THIRD GLASGOW MONICA SURVEY I. ILLUSTRATIVE REFERENCE RANGES BY AGE, SEX AND HORMONE USE (1997)

Coagulation factor activity (fibrinogen, VII, VIII and IX), coagulation inhibitor activity (antithrombin, protein C, protein S), and coagulation activation markers (prothrombin fragment F1, 2; thrombin-antithrombin complexes) were measured in 747 men and 817 women aged 25-74 years, randomly sampled from the north Glasgow population in the Third MONICA Survey. Significant effects of age, sex, menopause and hormone use were observed and specific reference ranges are presented to illustrate these effects. Significant correlations were observed between several coagulation factors and inhibitors. Increased levels of factors VII, VIII and IX and decreased levels of protein C were associated with increased coagulation activation. In general, increases in coagulation factors with age were greater than increases in coagulation inhibitors, especially in men; this imbalance may favour increased coagulation activation and hence increased thrombotic risk with age.
The Role of Apoptotic Pathways in Alzheimers Disease Neurodegeneration and Cell Death (2005)

Neuronal loss is associated with Alzheimer's disease (AD). However, it not clear what type of mechanisms underlie this neuronal loss and if neuronal loss is directly responsible for the progressive dementia of AD. This review summarizes the recent evidence for neuronal loss in AD relative to the level of cognitive impairment. It further describes the current evidence for an apoptotic mechanism in AD. Lastly, a summary of the evidence for synaptic loss being responsible for dementia rather than neuronal loss is presented. A novel hypothesis emerges from this data to explain all aspects of AD pathophysiology. This all inclusive hypothesis called the attrition hypothesis states that activation of the effector caspase-6 in AD due to one or a variety of insults is responsible for the breakdown of the cytoskeletal structure of neurites and damages proper trafficking of proteins and organelles thus resulting in the observed clinical and pathological features of AD.
Radioimaging of light chain amyloid with a fibril-reactive monoclonal antibody. (2006)

Our studies demonstrate the amyloid-imaging capability of a radiolabeled fibril-reactive mAb and provide the basis for a clinical trial designed to determine its diagnostic potential in patients with AL amyloidosis and other systemic amyloidoses.
Field Evaluation of European Corn Borer Control in Progeny of 173 Transgenic Corn Events Expressing an Insecticidal Protein from Bacillus thuringiensis (1995)

The European corn borer [ECB; Ostrinia nubilalis (Hübner)] is an economically significant pest of corn ( Zea mays L.). The ability to routinely transform corn has broadened the control options available to include the introduction of resistance genes from sexually incompatible species. In this study, microprojectile bombardment was used to introduce synthetic versions of cryIA insecticidal protein genes from Bacillus thuringiensis subsp, kurstaki (Btk) into embryogenitcis sue of the Hi‐II] (A188/B73 derivative) genotype of corn. Of 715 independent transgenic calli produced, 314 (44%) had insecticidal activity against tobacco hornworm ( Manduca sexta L.) larvae. Plants were regenerated, self‐pollinated when possible, and crossed to B73. First‐generation progeny of 173 independent Btk‐protein expressing calli were evaluated under field conditions with artificial ECB infestations in 1992 or 1993. Approximately half (89/173) segregated in single‐gene manner for resistance to first‐generation ECB leaf‐feeding damage. All of the 89 lines evaluated in 1992 or 1993 for resistance to second‐generation ECB exhibited less stalk tunneling damage than the non‐transgenic controls. In 1993, 44% (34177) of the lines tested had ≤2.5 cm of tunneling, compared to severe damage (mean = 45.7 cm) in the B73 × Hi‐II controls. Experiments are in progress to evaluate the effect of the introduced genes on yield and other agronomic properties.
Gene Silencing without DNA: RNA-Mediated Cross-Protection between Viruses (1999)

Previously, it was shown that the upper leaves of plants infected with nepoviruses and caulimoviruses are symptom free and contain reduced levels of virus. These leaves are said to be recovered. Recovery is associated with RNA-mediated cross-protection against secondary virus infection. Here, by analyzing plants infected with viruses that are quite distinct from the nepovirus or caulimovirus groups, we demonstrate that this RNA-mediated defense is a general response to virus infection. Upon infection with a tobravirus, plants exhibited RNA-mediated cross-protection and recovery, as occurs in nepovirus-infected plants. However, upon infection with a potexvirus, plants exhibited RNA-mediated cross-protection without recovery. In both instances, a transient gene expression assay showed that RNA-mediated cross-protection was functionally equivalent to post-transcriptional gene silencing. Combined, these data provide direct evidence that post-transcriptional gene silencing of nuclear genes is a manifestation of a natural defense mechanism that is induced by a wide range of viruses.
Assembly-dependent maturation cleavage in provirions of a small icosahedral insect ribovirus (1988)

Extracts from nodavirus-infected Drosophila cells contained detergent-labile 140S "young" particles much richer than mature virions in their content of protein alpha, a precursor of coat proteins beta and gamma. Incorporation studies in infected cells showed that most newly synthesized alpha protein was assembled into young particles within a few minutes. Incubation of the particles, either in cytoplasmic extracts or after purification, resulted in spontaneous first-order cleavage of alpha protein to form beta-plus-gamma chains. Alpha protein that was not associated with particles failed to cleave. Cleavage was accompanied by a marked increase in detergent stability of the particles and was unaffected by a broad spectrum of protease inhibitors or by coating with precipitating antibody. We conclude (i) that alpha chains are cleaved only after assembly into provirions, (ii) that cleavage occurs internally and is likely therefore autocatalytic, and (iii) that cleavage stabilizes the mature virus particles.
Levitation and movement of human tumor cells using a printed circuit board device based on software‐controlled dielectrophoresis (2003)

In this study we describe an original, efficient, and innovative printed circuit board (PCB) device able to generate dielectrophoresis-based, software-controlled cages that can be moved to any place inside a microchamber. Depending on their dielectrophoretic properties, eukaryotic cells can be "entrapped" in cages and moved under software control. The main conclusion gathered from the experimental data reported is that the PCB device based on dielectrophoresis permits levitation and movement of different tumor cells at different dielectrophoresis conditions. The results presented herein are therefore the basis for experiments aimed at forced interactions or separation of eukaryotic cells using "lab-on-a-chip." In fact, because many cages can be controlled at the same time, and two or more cages can be forced to share the same or a different location, it is possible, in principle, either to bring in contact cells of a differing histotype or to separate them.
Hepatocyte growth factor leads to recovery from alcohol-induced fatty liver in rats (1999)

A fatty liver is characterized by the hyperaccumulation of lipids within hepatocytes and is often caused by excessive alcohol intake. Rats fed ethanol-containing diets for 37 days showed remarkable increase in hepatic lipids and lipid droplet accumulation in the hepatocytes, indicating the onset of alcoholic fatty liver. Administration of hepatocyte growth factor (HGF) for the last seven days of ethanol treatment markedly decreased hepatic lipids to a level lower than that seen before HGF treatment. In contrast, serum levels of lipids and lipoproteins increased with HGF administration. Primary cultured hepatocytes prepared from the fatty liver retained lipid droplets during a 48-hour culture. However, when cultured in the presence of HGF, intracellular lipid concentrations decreased and lipid secretion was enhanced. Consistent with these events, HGF stimulated the rate of protein synthesis of apolipoprotein B (apoB) and enhanced subsequent mobilization of lipids into the medium. These results indicate that HGF administration induced recovery from the fatty liver, at least in part, by enhancing apoB synthesis and the subsequent mobilization of lipids from hepatocytes with fatty change. The possibility that HGF can be therapeutic for subjects with an alcohol-related fatty liver warrants further attention.
Proofing of Photolithographic DNA Synthesis with 3‘,5‘-Dimethoxybenzoinyloxycarbonyl-Protected Deoxynucleoside Phosphoramidites (1998)

We have evaluated in a microchip format the photochemical solid-phase phosphoramidite DNA synthesis method we previously developed. A set of nucleoside building blocks with “easy-off” base protecting groups was prepared bearing photolabile 5‘-O-dimethoxybenzoincarbonate (DMBOC) groups. Photolysis rates and cycle yields for these DMBOC-protected nucleotides covalently attached to planar, derivatized glass surfaces were determined by fluorescence imaging-based methods earlier developed by McGall et al. and described in detail elsewhere. Data were obtained for both 280/310 and 365/400 nm irradiation in a range of solvents. Deprotection of the DMBOC occurs fastest in a nonpolar medium or without solvent. The coupling efficiency of these amidites in the synthesis of homopolymers was determined to be in the range 80−97%, with purines generally showing lower efficiency than pyrimidines. These DMBOC-protected monomers were used to prepare a 4 × 4 array of 16 decanucleotides of the sequence 5‘-AAXTAXCTAC−chip, where X = A, C, G, or T. The array was hybridized with a target deoxyeicosanucleotide of the sequence fluorescein-5‘-CTGAACGGTAGCATCTTGAC. Surface fluorescence imaging demonstrated sequence-specific hybridization to this probe.
Thermal conductivities of thin, sputtered optical films (1993)

The normal component of thin-film thermal conductivity has been measured for the first time, to the best of our knowledge, for several advanced sputtered optical materials. Included are data for single layers of boron nitride, silicon aluminum nitride, silicon aluminum oxynitride, silicon carbide, and for dielectricenhanced metal reflectors of the form Al(SiO(2)/Si(3)N(4))(n) and Al(Al(2)O(3)/AlN)(n). Sputtered films of more conventional materials such as SiO(2), Al(2)O(3), Ta(2)O(5), Ti, and Si have also been measured. The data show that thin-film thermal conductivities are typically 10 to 100 times lower than conductivities for the same materials in bulk form. Structural disorder in the amorphous or fine-grained films appears to account for most of the conductivity difference. Conclusive evidence for a film-substrate interface contribution is presented.
Targeting of HIV- and SIV-Infected Cells by CD4-Chemokine Receptor Pseudotypes (1997)

Retroviral vectors containing CD4 and an appropriate chemokine receptor were evaluated for the ability to transduce cells infected with human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). These CD4-chemokine receptor pseudotypes were able to target HIV- and SIV-infected cell lines and monocyte-derived macrophages in a manner that corresponded to the specificity of the viral envelope glycoprotein for its CD4-chemokine receptor complex. This approach could offer a way to deliver antiviral genes directly to HIV-infected cells in vivo and could provide an additional treatment strategy in conjunction with existing antiviral therapies.
Detection of Individual Differences in Radiation-Induced Apoptosis of Peripheral Blood Lymphocytes in Normal Individuals, Ataxia Telangiectasia Homozygotes and Heterozygotes, and Breast Cancer Patients after Radiotherapy (2000)

Barber, J. B. P., West, C. M. L., Kiltie, A. E., Roberts, S. A. and Scott, D. Detection of Individual Differences in Radiation-Induced Apoptosis of Peripheral Blood Lymphocytes in Normal Individuals, Ataxia Telangiectasia Homozygotes and Heterozygotes, and Breast Cancer Patients after Radiotherapy.Quantification of radiation-induced apoptosis in peripheral blood lymphocytes (PBLs) has been proposed as a possible screening test for cancer-prone individuals and also for the prediction of normal tissue responses after radiotherapy. We have used the TUNEL assay (terminal transferase nick-end labeling) 24 h after irradiation with 4 Gy at high dose rate to assess interindividual differences in radiation-induced apoptosis between (1) a panel of normal individuals, (2) ataxia telangiectasia (AT) homozygotes and heterozygotes, and (3) breast cancer patients who had received radiotherapy 8–13 years ago, including a number of patients who had suffered adverse responses to radiation. With this protocol, we show clear differences in radiation-induced apoptosis between individuals, and good reproducibility in the assay. In agreement with previous reports using EBV-transformed lymphoblasts, we show a very poor induction of apoptosis in AT homozygotes and a reduced level in AT heterozygotes compared to normal individuals. A similar reduced level compared to normal individuals was seen in the breast cancer patients. Despite a wide range of values in the breast cancer patients and good reproducibility on repeat samples, there was no correlation of rates of apoptosis with the severity of breast fibrosis, retraction or telangiectasia. The reduced rate of apoptosis observed in the breast cancer cases may be associated with genetic predisposition to breast cancer; however, we conclude that assays of lymphocyte apoptosis are unlikely to be of use in predicting normal tissue tolerance to radiotherapy.
Decoration of lipopolysaccharide with phosphorylcholine: a phase-variable characteristic of Haemophilus influenzae (1997)

Choline, although not a nutritional requirement for Haemophilus influenzae, is taken up from the growth medium and incorporated into its lipopolysaccharide (LPS). Incorporated choline is in the form of phosphorylcholine (ChoP) based on the reactivity with the monoclonal antibody with specificity for this structure, TEPC-15. Incorporation of [3H]choline from the growth medium and expression of the TEPC-15 epitope undergo high-frequency phase variation, characteristic of other LPS structures in this species. The expression and phase variation of ChoP require a previously identified locus involved in LPS biosynthesis, lic1. The first gene in lic1, licA, contains a translational switch based on variation in the number of intragenic tandem repeats of the sequence 5'-CAAT-3'. The full-length LicA polypeptide resembles choline kinases of eucaryotes, suggesting that the pathway for choline incorporation into the H. influenzae glycolipid has similarities to the pathway for choline incorporation in eucaryotic lipid synthesis. The display of ChoP, a host-like structure, renders the organism more rather than less susceptible to the bactericidal activity of human serum. The increased serum sensitivity of variants with ChoP correlates with higher serum immunoglobulin G titers to LPS containing this structure. ChoP appears to be a cell surface feature common to a number of pathogens of the human respiratory tract, including Streptococcus pneumoniae and mycoplasmas. In the case of H. influenzae, its primary contribution to pathogenesis does not appear to be antigenic variation to evade host humoral clearance mechanisms.
Are autoantibodies active players or epiphenomena? (1998)

Autoantibodies have the potential of pathogenicity in several diseases. In rheumatoid arthritis (RA), however, this has not been ultimately proven. RA is characterized by a variety of autoantibodies. Newer insights into characteristics of rheumatoid factors indirectly suggest their pathogenetic involvement. In contrast, antibodies to collagen, despite the availability of an experimental model, do not appear to be pathogenetic in man. Anti-hnRNP antibodies, particularly anti-A2/RA33, are present in RA and experimental models of RA, and therefore, aside from their diagnostic value in established and early RA, could also be involved in the disease process. The nature of Sa, another target antigen in RA, has not yet been elucidated. Filaggrin is the antigen recognized by antikeratin antibodies and antiperinuclear factor; however, citrullin is the target amino acid in filaggrin, and anticitrullin antibodies have a high predictive value. Among a series of cartilage proteins, most have not yet been characterized sufficiently; one, gp39, appears to be of particular interest. Whether or not these antibodies are involved in RA pathogenesis is not yet known. It can be speculated that autoimmunity to some, if not all, of these autoantigens mirrors events important in the development of RA, but further studies on T-cell reactivities and in experimental models are needed to fully understand the involvement.
Leptin deficiency, not obesity, protects mice from Con A-induced hepatitis (2002)

Leptin-deficient ob/ob mice are protected from Con A-induced hepatitis. However, it is unclear whether leptin deficiency or obesity itself is responsible for this protection. To address this question, wild-type (WT) obese mice with high serum leptin levels were generated by injection of gold thioglucose (WT GTG). Both Con A-injected WT and WT GTG mice developed hepatitis, whereas no hepatic damage was observed in ob/ob mice. Moreover, TNF-alpha and IFN-gamma levels as well as expression of the activation marker CD69 were elevated in liver mononuclear cells of WT and WT GTG mice, but not in ob/ob mice following administration of Con A. The liver of WT and WT GTG mice had the same percentage of NK T cells, a lymphocyte population involved in Con A-induced hepatitis. This population decreased equally in both WT and WT GTG mice after Con A injection. In contrast, the liver of ob/ob mice contained 50% less NK T cells compared to WT and WT GTG mice. Furthermore, no decrease in NK T cells was observed in Con A-injected ob/ob mice. We conclude that leptin-deficiency, not obesity, is responsible for protection from Con A-induced hepatitis.
Novel CXCR2‐dependent liver regenerative qualities of ELR‐containing CXC chemokines (1999)

Severe acute liver injury due to accidental or intentional acetaminophen overdose presents a major clinical dilemma often requiring liver transplantation. In the present study, liver regeneration after profound liver injury in mice challenged with acetaminophen was facilitated by the exogenous addition of ELR-containing CXC chemokines such as macrophage inflammatory protein-2 (MIP-2), epithelial neutrophil-activating protein-78 (ENA-78), or interleukin 8. Intravenous administration of ELR-CXC chemokines or N-acetyl-cysteine (NAC) immediately after acetaminophen challenge in mice significantly reduced histological and biochemical markers of hepatic injury. However, when the intervention was delayed until 10 h after acetaminophen challenge, only ELR-CXC chemokines significantly reduced liver injury and mouse mortality. The delayed addition of ELR-CXC chemokines to cultured hepatocytes maintained the proliferation of these cells in a CXCR2-dependent fashion after acetaminophen challenge whereas delayed NAC treatment did not. These observations demonstrate that ELR-CXC chemokines represent novel hepatic regenerative factors that exhibit prolonged therapeutic effects after acetaminophen-induced hepatotoxicity.
Respiratory Syncytial Virus G Protein and G Protein CX3C Motif Adversely Affect CX3CR1+ T Cell Responses (2006)

Interactions between fractalkine (CX3CL1) and its receptor, CX3CR1, mediate leukocyte adhesion, activation, and trafficking. The respiratory syncytial virus (RSV) G protein has a CX3C chemokine motif that can bind CX3CR1 and modify CXCL1-mediated responses. In this study, we show that expression of the RSV G protein or the G protein CX3C motif during infection is associated with reduced CX3CR1+ T cell trafficking to the lung, reduced frequencies of RSV-specific, MHC class I-restricted IFN-gamma-expressing cells, and lower numbers of IL-4- and CX3CL1-expressing cells. In addition, we show that CX3CR1+ cells constitute a major component of the cytotoxic response to RSV infection. These results suggest that G protein and the G protein CX3C motif reduce the antiviral T cell response to RSV infection.
Remote Sensing for Vital Information Based on Spectral-Domain Harmonic Signatures (2019)

In this paper, we propose an efficient and robust non-contact heart rate estimation algorithm. The key idea is to recover the fundamental heartbeat frequency from its higher-order spectral features. Our contributions are threefold: 1) carefully review and examine possible approaches in vital signs detection with ultra-wide band (UWB) impulse radar; 2) numerically and experimentally show an important result that, in the spectral domain, the fundamental heartbeat signal is respiration-interference-limited, whereas its higher-order harmonics are noise-limited; and 3) implement an adaptive heart rate monitoring algorithm based on the proposed theory, which is feasible with continuous monitoring. To justify the proposed theory, we perform a spectral analysis of the harmonics of vital signs signal. We validate the proposed algorithm using a controlled vital sign simulator. We experimentally demonstrate the effectiveness of the harmonics-based heart rate estimation algorithm and compare it against existing methods. For completeness, we also provide a limitation analysis of the proposed algorithm.