gebhart/patrepeval huggingface dataset:
Autoimmune Diseases and Sjögren's Syndrome (2007)

Autoimmune diseases include a diverse group of over 80 conditions. Sjögren's syndrome is the second most common autoimmune rheumatic disease, with an estimated prevalence in the United States of 2-4 million persons. There are prominent and consistent oral and dental findings in Sjögren's syndrome related to the autoimmune-mediated loss of normal salivary function. Additionally, nonoral clinical manifestations of Sjögren's syndrome include: dry eyes (with specific ocular surface changes termed keratoconjunctivitis sicca); other xeroses, such as dryness of the nose, throat, skin, and vagina; peripheral (and less frequently central) neuropathies; myalgias and arthralgias; thyroid disorders (particularly autoimmune thyroiditis); pulmonary disorders; renal disorders; and lymphoma. There is a significant (20- to 40-fold) increase in the incidence of malignant lymphoma, particularly in primary Sjögren's syndrome. Establishing the diagnosis of Sjögren's syndrome has been difficult in the light of its nonspecific symptoms (dry eyes and mouth), disagreement on diagnostic criteria, and a lack of both sensitive and specific laboratory markers. Many serum and salivary biomarkers for Sjögren's syndrome have been proposed although, to date, none has proven to be sufficiently specific for diagnostic purposes or has been well correlated with disease activity measures. Investigators have recently begun to apply modern genomic and proteomic approaches to identify candidate biomarkers in Sjögren's syndrome. The results of these investigations promise to provide a wealth of information on candidate biomarkers and possible etiopathological mechanisms underlying this disorder. Further, this information will improve clinical outcomes by fostering the design of new rational therapeutics and assisting in the monitoring of clinical disease.
Comparison of Increased Expression of Wild-Type and Herbicide-Resistant Acetolactate Synthase Genes in Transgenic Plants, and Indication of Posttranscriptional Limitation on Enzyme Activity (1990)

Genes encoding wild type acetolactate synthase (ALS) and a sulfonylurea herbicide-resistant form of the enzyme, isolated from Arabidopsis thaliana, were expressed in transgenic Nicotiana tabacum plants under the control of their native promoters or of the highly active cauliflower mosaic virus 35S promoter. Expression of the wild type coding region from the 35S promoter resulted in a small, threefold increase in sulfonylurea tolerance above the levels measured in tissue expressing the native wild type gene. A much larger, 300-fold increase in herbicide tolerance was conferred by the mutant gene encoding a herbicide-resistant ALS. An additional 10-fold increase in tolerance was attained by expressing this coding region from the 35S promoter. The increase in both wild type and mutant gene expression directed by the 35S promoter resulted in over 25-fold higher levels of ALS messenger RNA in some transformants as compared with those expressing the native genes. However, ALS specific activity increased at most twofold, indicating that the amount of functional enzyme and messenger RNA are not correlated.
Initial and Late Resistance to Imatinib in Advanced Gastrointestinal Stromal Tumors Are Predicted by Different Prognostic Factors: A European Organisation for Research and Treatment of Cancer–Italian Sarcoma Group–Australasian Gastrointestinal Trials Group Study (2005)

Purpose The aim of this study was to identify factors predicting initial and late resistance of GI stromal tumor (GIST) patients to imatinib and to document the dose-response relationship in the prognostic subgroups. This study is based on the European Organisation for Research and Treatment of Cancer–Italian Sarcoma Group–Australasian Gastrointestinal Trials Group randomized trial comparing two doses of imatinib in advanced disease. Patients and Methods Initial resistance was defined as progression within 3 months of randomization, and late resistance was defined as progression beyond 3 months. Investigated cofactors include imatinib dose, age, sex, performance status, original disease site, site and size of lesions at trial entry, and baseline hematologic and biologic parameters. Results Initial resistance was recorded for 116 (12%) of 934 assessable patients and was independently predicted by the presence of lung and absence of liver metastases, low hemoglobin level, and high granulocyte count. Among 818 patients who were alive and progression free at 3 months, 347 subsequent progressions were recorded, and late resistance was independently predicted by high baseline granulocyte count, primary tumor outside of the stomach, large tumor size, and low initial imatinib dose. The impact of initial dose on late resistance was mainly significant in patients with a high baseline granulocyte count (&gt; 5.10 9 /L) and in patients with tumors of GI origin outside of the stomach and small intestine. Conclusion Our study identifies patients for whom initial and/or long-term treatment needs to be improved and patients who require a high initial dose. Correlation of these results with immunohistochemistry and molecular parameters may further help to understand the biologic mechanisms of resistance.
Minimally invasive, direct, real time measurement of drug concentration in the anterior eye (2005)

This device has the potential to allow repeated measurements of drug concentrations in the anterior eye provided the drug has suitable absorption or fluorescence characteristics.
Immunological Abnormalities in Autism Spectrum Disorders (2013)

Secondary to clinical features indicating chronic inflammation and immune dysregulation, the immune system has long been suspected to have a role in autism spectrum disorders (ASD). Studies of postmortem autistic brains indicate the presence of immun
Microglia-targeting nanotherapeutics for neurodegenerative diseases (2020)

Advances in nanotechnology have enabled the design of nanotherapeutic platforms that could address the challenges of targeted delivery of active therapeutic agents to the central nervous system (CNS). While the majority of previous research studies on CNS nanotherapeutics have focused on neurons and endothelial cells, the predominant resident immune cells of the CNS, microglia, are also emerging as a promising cellular target for neurodegeneration considering their prominent role in neuroinflammation. Under normal physiological conditions, microglia protect neurons by removing pathological agents. However, long-term exposure of microglia to stimulants will cause sustained activation and lead to neuronal damage due to the release of pro-inflammatory agents, resulting in neuroinflammation and neurodegeneration. This Perspective highlights criteria to be considered when designing microglia-targeting nanotherapeutics for the treatment of neurodegenerative disorders. These criteria include conjugating specific microglial receptor-targeting ligands or peptides to the nanoparticle surface to achieve targeted delivery, leveraging microglial phagocytic properties, and utilizing biocompatible and biodegradable nanomaterials with low immune reactivity and neurotoxicity. In addition, certain therapeutic agents for the controlled inhibition of toxic protein aggregation and for modulation of microglial activation pathways can also be incorporated within the nanoparticle structure without compromising stability. Overall, considering the multifaceted disease mechanisms of neurodegeneration, microglia-targeted nanodrugs and nanotherapeutic particles may have the potential to resolve multiple pathological determinants of the disease and to guide a shift in the microglial phenotype spectrum toward a more neuroprotective state.
Freezing of homogenized sputum samples for intermittent storage (2001)

Our results indicate that the freezing of sputum samples at different stages of processing does not alter sputum morphology to an extent that affects the results of differential cell counts.
Simple/rapid test devices for anti-HIV screening: Do they come up to the mark?© Crown copyright 1999. Reproduced with the permission of the Controller of Her Majesty's Stationary Office. (1999)

Thirteen simple/rapid test devices (S/RTDs) for the detection of antibodies to HIV 1 and HIV 2 were assessed. Ninety-two specimens in four categories were used and results with the thirteen S/RTDs were compared with those obtained with six currently available commercial laboratory-based anti-HIV 1/2 EIAs. Seven of the 13 S/RTDs scored all 26 blood donors' specimens as unreactive, and 11 correctly identified all the 25 “straightforward” anti-HIV positive specimens. False negative results arose when testing by Uni-Gold HIV and SeroCard HIV, which gave 72 and 68 correct positive observations, respectively, out of 75. No S/RTD detected seroconversion earlier than the most sensitive EIAs, but four S/RTDs performed similarly to most of the EIAs. On the low-titre panel specimens, six S/RTDs were less sensitive than the least sensitive EIA and, in contrast to four of the six EIAs, only one S/RTD was able correctly to identify all the positive specimens. A manufacturing problem was identified that allowed the HIV antigen-sensitised area on the membrane of two SeroCard HIV devices to be misaligned with the device's reading window so that the reaction was almost entirely obscured. As long as small numbers of specimens were involved, most S/RTDs required considerably less time and less equipment than EIAs, but overall they were slightly less sensitive. Their use in various health settings and for confirmatory procedures is discussed. J. Med. Virol. 59:104–109, 1999. Published 1999 Wiley-Liss, Inc.
Depolarisation and field transmittances in indoor communications (1991)

Measurements of copolar and crosspolar field amplitudes in an indoor cordless communications environment are presented. Measurements of narrowband and wideband transmittance magnitude are also presented for vertical and horizontal polarisations. An important longitudinal component is identified and the general concepts of co- and crosspolar (transversal and longitudinal) frequency/distance transmittance H{jω, d) are introduced and defined.
Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III (1983)

Sites on an fd DNA template which terminate synthesis catalyzed by each of four forms of Escherichia coli DNA polymerase III have been identified at single nucleotide resolution. Results were obtained by comparing the products made by forms of DNA polymerase III with products generated from the same 3'-terminus by using the dideoxynucleotide sequencing method, on high-resolution polyacrylamide gel electrophoresis. Each form of DNA polymerase III generates products of distinct lengths ending at a limited number of preferred sites of synthesis termination. The addition of auxiliary subunits to the DNA polymerase III core form of the enzyme has a distinct functional effect on primer elongation and specificity of polymerase pausing. Most sites (65%) can be correlated to positions of potential secondary structure in the template arising via local hydrogen-bonding interactions. The proximity of polymerase pausing to sites adjacent to hairpin stems was related to the size of the enzyme since the smaller core form of DNA polymerase III generally paused at sites which were closer to the base of these structures than the larger holoenzyme. The occurrence of termination sites is markedly affected by the inclusion of spermidine or Escherichia coli single-stranded DNA binding protein in the reaction mixtures. Additionally, a nucleotide composition specificity of pause sites has been observed.
An Evaluation of Intranasal Sufentanil and Dexmedetomidine for Pediatric Dental Sedation (2014)

Conscious or moderate sedation is routinely used to facilitate the dental care of the pre- or un-cooperative child. Dexmedetomidine (DEX) has little respiratory depressant effect, possibly making it a safer option when used as an adjunct to either opioids or benzodiazepines. Unlike intranasal (IN) midazolam, IN application of DEX and sufentanil (SUF) does not appear to cause much discomfort. Further, although DEX lacks respiratory depressive effects, it is an α2-agonist that can cause hypotension and bradycardia when given in high doses or during prolonged periods of administration. The aim of this feasibility study was to prospectively assess IN DEX/SUF as a potential sedation regimen for pediatric dental procedures. After IRB approval and informed consent, children (aged 3-7 years; n = 20) from our dental clinic were recruited. All patients received 2 μg/kg (max 40 μg) of IN DEX 45 min before the procedure, followed 30 min later by 1 μg/kg (max 20 μg) of IN SUF. An independent observer rated the effects of sedation using the Ohio State University Behavior Rating Scale (OSUBRS) and University of Michigan Sedation Scale (UMSS). The dentist and the parent also assessed the efficacy of sedation. Dental procedures were well tolerated and none were aborted. The mean OSUBRS procedure score was 2.1, the UMSS procedure score was 1.6, and all scores returned to baseline after the procedure. The average dentist rated quality of sedation was 7.6 across the 20 subjects. After discharge, parents reported one child with prolonged drowsiness and one child who vomited at home. The use of IN DEX supplemented with IN SUF provided both an effective and tolerable form of moderate sedation. Although onset and recovery are slower than with oral (PO) midazolam and transmucosal fentanyl, the quality of the sedation may be better with less risk of respiratory depression. Results from this preliminary study showed no major complications from IN delivery of these agents.
Neuroprotective Effect of a CNTF-Expressing Lentiviral Vector in the Quinolinic Acid Rat Model of Huntington's Disease (2001)

Neurodegenerative diseases represent promising targets for gene therapy approaches provided effective transfer vectors. In the present study, we evaluated the effectiveness of LacZ-expressing lentiviral vectors with two different internal promoters, the mouse phosphoglycerate kinase 1 (PGK) and cytomegalovirus (CMV), to infect striatal cells. The intrastriatal injection of lenti-beta-Gal vectors lead to 207, 400 +/- 11,500 and 303,100 +/- 4,300 infected cells in adult rats, respectively. Importantly, the beta-galactosidase activity was higher in striatal extracts from PGK-LacZ-injected animals as compared to CMV-LacZ animals. The efficacy of the system was further examined with a potential therapeutic gene for the treatment of Huntington's disease, the human ciliary neurotrophic factor (CNTF). PGK-LacZ- or PGK-CNTF-expressing viruses were stereotaxically injected into the striatum of rats, 3 weeks later the animals were unilaterally lesioned with 180 nmol of quinolinic acid (QA). Control animals displayed 148 +/- 43 apomorphine-induced rotations ipsilateral to the lesion 5 days postlesion as compared to 26 +/- 22 turns/45 min in the CNTF-treated group. The extent of the striatal damage was significantly diminished in the CNTF-treated rats as indicated by the 52 +/- 9.7% decrease of the lesion volume and the sparing of DARPP-32, ChAT and NADPH-d neuronal populations. These results further establish that lentiviruses may represent an efficient gene delivery system for the screening of therapeutic molecules in Huntington's disease.
A bipartite nuclear localization signal in the retinoblastoma gene product and its importance for biological activity. (1993)

The retinoblastoma gene product, p110RB1, appears to regulate cell growth by modulating the activities of nuclear transcription factors. The elements that specify the transport of p110RB1 into the nucleus have not yet been explored. We now report the identification of a basic region, KRSAEGGNPPKPLKKLR, in the C terminus of p110RB1, which has sequence similarity to known bipartite nuclear localization signals (NLSs). A two-amino-acid mutation introduced into this putative NLS [to give mutant NLS(NQ)] or deletion of the entire NLS (delta NLS) abrogated exclusive nuclear localization, yielding proteins which were distributed either equally throughout the cell or predominantly in the cytoplasm. A mutant protein [NLS(NQ)/delta 22] containing both the mutated NLS and a deletion of exon 22, previously shown to disrupt the interaction of p110RB1 with several cellular transcription factors and oncoproteins, accumulated only in the cytoplasm. When fused to the C terminus of Escherichia coli beta-galactosidase, the RB1 NLS directed this protein to the nucleus, indicating that the motif is not only necessary but also sufficient for nuclear transport. Neither NLS(NQ) nor delta NLS was hyperphosphorylated in vivo, but both retained their abilities to interact, in vitro, with simian virus 40 large T antigen, adenovirus E1a, and the cellular transcription factor E2F. When transfected at multiple copy number, the NLS mutant alleles displayed reduced biological activity, measured by inhibition of growth of the osteogenic sarcoma cell line Saos-2, which has no wild-type RB1. Naturally occurring mutations and deletions in exon 25 of RB1 which disrupt the NLS may lead to partial or complete inactivation of p110RB1 and may be responsible for some retinoblastoma and other tumors.
The Fibroblast-Populated Collagen Microsphere Assay of Cell Traction Force—Part 2: Measurement of the Cell Traction Parameter (1995)

In Part 1 of this work, we formulated and analyzed a mathematical model for our fibroblast-populated collagen microsphere (FPCM) assay of cell traction forces (Moon and Tranquillo, 1993). In this assay, the FPCM diameter decreases with time as the cells compact the gel by exerting traction on collagen fibrils. In Part 1 we demonstrated that the diameter reduction profiles for varied initial cell concentration and varied initial FPCM diameter are qualitatively consistent with the model predictions. We show here in Part 2 how predictions of a model similar to that of Part 1, along with the determination of the growth parameters of the cells and the viscoelastic parameters of the gel, allow us to estimate the magnitude of a cell traction parameter, the desired objective index of cell traction forces. The model is based on a monophasic continuum-mechanical theory of cell-extracellular matrix (ECM) mechanical interactions, with a species conservation equation for cells (1), a mass conservation equation for ECM (2), and a mechanical force balance for the cell/ECM composite (3). Using a constant-stress rheometer and a fluids spectrometer in creep and oscillatory shear modes, respectively, we establish and characterize the linear viscoelastic regime for the reconstituted type 1 collagen gel used in our FPCM traction assay and in other assays of cell-collagen mechanical interactions. Creep tests are performed on collagen gel specimens in a state resembling that in our FPCM traction assay (initially uncompacted, and therefore nearly isotropic and at a relatively low collagen concentration of 2.1 mg/ml), yielding measurements of the zero shear viscosity, mu 0 7.4 x 10(6) Poise), and the steady-state creep compliance, J0e. The shear modulus, G (155 dynes/cm2), is then determined from the inverse of J0e in the linear viscoelastic regime. Oscillatory shear tests are performed in strain sweep mode, indicating linear viscoelastic behavior up to shear strains of approximately 10 percent. We discuss the estimation of Poisson's ratio, v, which along with G and mu 0 specifies the assumed isotropic, linear viscoelastic stress tensor for the cell/collagen gel composite which appears in (3). The proliferation rate of fibroblasts in free floating collagen gel (appearing in (1)) is characterized by direct cell counting, yielding an estimate of the first-order growth rate constant, k (5.3 x 10(-6) s-1). These independently measured and estimated parameter values allow us to estimate that the cell traction parameter, tau 0, defined in the active stress tensor which also appears in (3), is in the range of 0.00007-0.0002 dyne.cm4/mg collagen.cell.(ABSTRACT TRUNCATED AT 400 WORDS)
Autocloning and Amplification of LIP2 in Yarrowia lipolytica (2000)

We synthesized a Yarrowia lipolytica strain overproducing lipase for industrial applications by using long terminal repeat (zeta) of the Y. lipolytica retrotransposon Ylt1 and an allele of URA3 with a promoter deletion to construct JMP3. JMP3 is a derivative of plasmid pHSS6 carrying a NotI-NotI cassette which contains a defective URA3 allele, a polylinker sequence, and the zeta region for targeting to multiple sites in the genome of the recipient. We inserted the LIP2 gene (encoding extracellular lipase) under the control of the strong POX2 promoter into JMP3 to generate JMP6. The pHSS6 region was removed by NotI digestion prior to transformation. Two Y. lipolytica strains transformed with the JMP6 LIP2 cassette had a mean of 10 integrated copies devoid of the Escherichia coli region, corresponding to an autocloning event. The copy number in the transformants was stable even after 120 generations in nonselective and lipase-inducing conditions. The resulting strains could produce 0.5 g of active lipase per liter in the supernatant, 40 times more than the single-copy strain with the LIP2 promoter. This work provides a new expression system in Y. lipolytica that results in strains devoid of bacterial DNA and in strains producing a high level of lipase for industrial uses, waste treatment, and pancreatic insufficiency therapy.
Molecular analysis of SCARECROW function reveals a radial patterning mechanism common to root and shoot (2000)

Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. Analysis of the shoot phenotype of scr mutants revealed that both hypocotyl and shoot inflorescence also have a radial pattern defect, loss of a normal starch sheath layer, and consequently are unable to sense gravity in the shoot. Analogous to its expression in the endodermis of the root, SCR is expressed in the starch sheath of the hypocotyl and inflorescence stem. The SCR expression pattern in leaf bundle sheath cells and root quiescent center cells led to the identification of additional phenotypic defects in these tissues. SCR expression in a pin-formed mutant background suggested the possible origins of the starch sheath in the shoot inflorescence. Analysis of SCR expression and the mutant phenotype from the earliest stages of embryogenesis revealed a tight correlation between defective cell divisions and SCR expression in cells that contribute to ground tissue radial patterning in both embryonic root and shoot. Our data provides evidence that the same molecular mechanism regulates the radial patterning of ground tissue in both root and shoot during embryogenesis as well as postembryonically.
Molecular structure and mechanisms of action of cyclic and linear ion transport antibiotics (1996)

As a direct result of the vision, determination, and magnetic personality of Yuri Ovchinnikov a collaboration between the Shemyakin Institute of Bioorganic Chemistry and the Medical Foundation of Buffalo was begun in the early 1970's. The collaboration generated valuable insight into the structural basis for the capture, transport, and release of ions by ion transport antibiotics and the basis for the ion selectivity of these compounds. The collaboration produced dozens of joint publications on the structure and function of cyclic and linear ion transport antibiotics, fostered fruitful exchange visits between scientists in the two Research Institutes and has been a major source of creativity in my scientific career and those of many of my colleagues in Buffalo. This review summarizes major accomplishments of the collaboration.