gebhart/patrepeval huggingface dataset:
Transcriptional Regulation of Vibrio cholerae Hemagglutinin/Protease by the Cyclic AMP Receptor Protein and RpoS (2004)

Vibrio cholerae secretes a Zn-dependent metalloprotease, hemagglutinin/protease (HA/protease), which is encoded by hapA and displays a broad range of potentially pathogenic activities. Production of HA/protease requires transcriptional activation by the quorum-sensing regulator HapR. In this study we demonstrate that transcription of hapA is growth phase dependent and specifically activated in the deceleration and stationary growth phases. Addition of glucose in these phases repressed hapA transcription by inducing V. cholerae to resume exponential growth, which in turn diminished the expression of a rpoS-lacZ transcriptional fusion. Contrary to a previous observation, we demonstrate that transcription of hapA requires the rpoS-encoded sigma(s) factor. The cyclic AMP (cAMP) receptor protein (CRP) strongly enhanced hapA transcription in the deceleration phase. Analysis of rpoS and hapR mRNA in isogenic CRP+ and CRP- strains suggested that CRP enhances the transcription of rpoS and hapR. Analysis of strains containing hapR-lacZ and hapA-lacZ fusions confirmed that hapA is transcribed in response to concurrent quorum-sensing and nutrient limitation stimuli. Mutations inactivating the stringent response regulator RelA and the HapR-controlled AphA regulator did not affect HA/protease expression. Electrophoretic mobility shift experiments showed that pure cAMP-CRP and HapR alone do not bind the hapA promoter. This result suggests that HapR activation of hapA differs from its interaction with the aphA promoter and could involve additional factors.
Diversidad malacológica en Andalucía.recurso renovable (2007)

El objetivo del estudio es la evaluacion de la diversidad malacologica andaluza como base del aprovechamiento de un recurso genetico de interes economico. Se zonifican las poblaciones de caracoles comestibles existentes en Andalucia en relacion al numero de especies y su distribucion geografica. Se observa elevada heterogeneidad que da lugar a la conformacion de tres zonas diferenciadas, en las que aparecen fundamentalmente los generos Otala, Theba, Cantareus, Iberus, Eobania, Cepaea, Pseudotachea y Sphincterochila. La Zona I comprende Sierra Morena y se caracteriza por una baja presencia de caracoles, asociados mayoritariamente a la presencia humana y representados por las especies mas comunes (O. lactea, H. aspersa, T. pisana y E. vermiculata). La Zona II comprende la Campina y Vega del Guadalquivir, donde aparecen las especies de mayor valor comercial: O. lactea y T. pisana, con gran distribucion; y H. aspersa con menor presencia. Finalmente la Zona III, que se integra por las Sierras Beticas donde aparecen, junto con las especies anteriormente citadas, gran diversidad de taxones con elevada singularidad, debido a la existencia de un numero importante de endemismos y poblaciones relictas (O. lactea murcica, O. punctata, T. pisana arietina, T. subdentata helicella, C. nemoralis, I. gualtierianus gualtierianus, I. gualtierianus alonensis, I. gualtierianus guiraoanus, etc.). La existencia de esta biodiversidad justifica la necesidad de adoptar acciones estrategicas y planes especificos de conservacion que preserven este recurso de forma eficaz.
Molecular Structures of Fructans from Agave tequilana Weber var. azul (2003)

Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.
MedRec: A Network for Personal Information Distribution (2019)

MedRec is a simple, distributed system for personal control of identity and distribution of personal information. The work is done in the context of a medical information distribution system where patients retain control over who can access their data. We present a new architecture for the MedRec project, creating a network of trusted data repositories, the access to which are determined by a set of ”smart contracts”. These contracts are stored on a distributed ledger maintained by those who generate data. The distributed nature of the system allows unified access from diverse sources in a single application with no intermediary. This increases patient control while retaining a measure of privacy of both data content and source. MedRec is amenable to extensions for decentralized messaging and distribution of information to third parties such as medical researchers, healthcare proxies, and other institutions. The system is based on a blockchain that contains smart contracts defining user identity and distribution specifics.
Cytologic diagnosis of generalized cutaneous sporotrichosis in a hunting hound (2007)

A 1-year-old male Foxhound/Walker Hound mix was presented to the small animal internal medicine service at Louisiana State University School of Veterinary Medicine with a 6-week history of progressive, multifocal, ulcerative and draining, well-circumscribed lesions in a generalized distribution. Prior to referral, a presumptive diagnosis was made of sterile pyogranulomatous disease; immunosuppressive therapy was instituted but resulted in clinical deterioration. At presentation, the dog had marked neutropenia (1100 neutrophils/microL), and a mild toxic left shift (400 bands/microL). Cytologic findings in the exudates from a draining skin lesion included high numbers of markedly degenerate neutrophils (about 95% of nucleated cells) as well as low numbers of macrophages, small mature lymphocytes, and eosinophils. Low numbers of intracellular (within neutrophils and macrophages) and extracellular, pleomorphic, cigar-to-ovoid shaped organisms ( approximately 3x9 microm) consistent with Sporothrix were observed. Histopathologic examination of a skin biopsy showed marked, chronic, active, ulcerative, pyogranulomatous dermatitis and panniculitis, with intralesional yeast consistent with Sporothrix sp. The etiologic agent was confirmed as Sporothrix schenckii by macerated tissue fungal culture. The patient was treated with itraconazole, enrofloxacin, and clindamycin, with clinical resolution occurring over a 3-month period. This case is a rare example of the cytologic diagnosis of Sporothrix schenckii in a canine patient. Diagnosis of canine sporotrichosis is often challenging and usually requires tissue culture, as infected dogs typically harbor very few organisms. The patient's prior immunosuppressive therapy likely contributed to higher numbers of organisms in exudates from the cutaneous lesions, facilitating cytologic diagnosis.
PREVENTION OF ORTHOTOPIC LIVER ALLOGRAFT REJECTION IN RATS WITH A SHORT-TERM BREQUINAR SODIUM THERAPY (1994)

Brequinar sodium (BQR) is a new immunosuppressive drug that is highly effective in preventing graft rejection in several different experimental settings, including primary allografts and xenografts. A short course of BQR treatment during the onset of allograft rejection can induce the permanent survival of liver and kidney allografts in rats. To study the molecular basis of BQR-induced prolongation of allograft survival, we analyzed the intragraft pattern of IL-1 alpha, IL-2, IL-2R, IL-4, IL-6, IL-10, and TNF gene expression in the ACI-to-LEW liver allograft model. A semiquantitative polymerase chain reaction was developed to measure cytokine gene expression in control and BQR-treated liver graft recipients at various days after transplantation. Untreated control liver allografts expressed all of the cytokines analyzed. There was a marked increase in the steady state level of transcripts for each cytokine as graft rejection proceeded. The treatment of liver graft recipients with 12 mg/kg/day of BQR on days 6, 7, and 8 after transplantation suppressed the expression of all these cytokines within 24 hr of administration. The early suppression of cytokine expression was associated with a modest but distinct reduction in the infiltration of inflammatory cells into the liver grafts. The reduction in the level of transcripts for IL-4, IL-6, and IL-10 persisted in long-term survivors (30 days after transplantation). In contrast, there was a significant increase in the level of transcripts for IL-1 alpha, IL-2, and IL-2R in these long-term survivors. Our results demonstrated clearly that the pattern of cytokine gene expression during allograft rejection is significantly altered by a 3-day course of therapy with BQR. The temporary down-regulation of cytokine gene expression may be responsible for an altered immunological state that results in the prolonged survival of liver allografts.
Metabolic inhibition by transition metal ions in a slow-growing, toluene-enriched microbial population (1998)

We studied the effects of common first-row transition metal ions, Mn(II), Fe(III), Co(II), Cu(II), Zn(II), on the respiration of a mixed microbial population enriched for toluene degradation. Dissolved oxygen consumption, i.e., respiration rate, was used to measure metabolic activity of a slow-growing consortium of toluene-enriched microorganisms. Respiration rates decreased within 30 s of exposure to the metal ions and did not measurably recover during observation times (<80 min.). Metal ion toxicity increased with metal-phosphate binding affinities, consistent with cell damage by conformational changes in the phospholipid bilayer membrane to accommodate geometry requirements of complexes with transition metal ions. Changes in normalized metabolic activity (AN) with aqueous composition were compared with an equilibrium free-ion toxicity mechanism relating the fraction of membrane phosphatic ligands affected by metal ion chemisorption to diminished metabolic activity. AN measurements agreed with model predictions that the toxicity function (AN−1−1) is proportional to the free metal ion concentration when hydrogen ions do not compete with metal ions for the phosphatic membrane sites and proportional to the square root of the free metal ion concentration if hydrogen ions effectively compete with metal ions for membrane phosphate ligands. Transition metal ion uptake and toxicity were diminished by concentrations of competing Ca(II) and Mg(II) metal ion concentrations an order of magnitude larger than concentrations of transition metal ion. The Cu(II)-EDTA complex was nontoxic compared to Cu(II) ions. Metabolic inhibition produced by Cu(II) ions was not significantly reversed by sequestering Cu(II) ions using EDTA, suggesting that membrane damage is irreversible. Published 1998 John Wiley & Sons, Inc. Environ Toxicol Water Qual 13: 249–261, 1998
Transverse flows in rapidly oscillating elastic cylindrical shells (2006)

We analyse the flows in fluid-conveying tubes whose elastic walls perform small-amplitude high-frequency oscillations. We show that the velocity perturbations induced by the wall motion are dominated by their transverse components and use numerical simulations to analyse the two-dimensional flows that develop in the tube's cross-sections. Asymptotic methods are then employed to derive explicit predictions for the flow fields and for the total viscous dissipation, whose magnitude plays an important role in the development of self-excited oscillations. We show that in cases with fluid–structure interaction, the coupled oscillations are controlled by the ratio of the fluid and wall densities, and by a material parameter that is equivalent to the Womersley number, and indicates the importance of fluid inertia and wall elasticity relative to the fluid's viscosity. We present numerical simulations of the coupled oscillations and use asymptotic techniques to derive explicit predictions for their period and decay rate. Finally, we discuss the implications of our results for the development of self-excited oscillations in three-dimensional collapsible tubes.
A Novel Fully Automated CAD System for Left Ventricle Volume Estimation (2018)

Left ventricular (LV) volumes, and emptying and filling function remain important indices in conditions such as heart failure. These parameters are derived from the volume curve contained by the inner border of the LV of the heart, throughout the emptying and filling phases of the cardiac cycle, and the peak emptying and filling rates. The gold standard uses the Simpson rule to estimate volume from stacks of short axis images acquired using cine MRI. In this study, a deep learning, automated supervised approach to estimate ventricular volumes is introduced. Unlike prior methods that required hand-crafted image features to segment the inner contour, the proposed approach uses an automatically selected region of interest (ROI), and intelligently determines the optimum features directly from the ROI information. These derived features are then inputted into a deep learning regression model, with the estimated volume as the output results.
Morphology and Film Properties of Composite Carboxylated Latexes (1999)

Abstract In industrial applications, such as paints or adhesives, composite latex particles are very common. Most of the properties which are obtained from composite latexes and their films cannot be achieved by physical blending of different polymer components. Therefore it becomes crucial to examine the morphology of composite latexes formed by a multiple-stage polymerization process. The latexes for this study have been examined by transmission electron microscopy (TEM) and atomic force microscopy (AFM). Various staining methods were used such as ruthenium tetroxide (RuO4), cesium hydroxide (CsOH), and uranyl acetate (UAc) as a negative stain. The poly(n-butyl acrylate/ poly(methylmethacrylate) (PBA/PMMA) composite latex particles consist of a soft core phase and a hard second phase with varying amounts of acrylic acid in the core, the shell and in both core and shell. The latexes were examined before and after cleaning by a centrifugation technique with 100,000 molecular weight filters.
Analyzing and improving the IEEE 802.11-MAC protocol for wireless LANs (2002)

The MAC-part of the upcoming IEEE 802.11 standard for wireless LANs-named DFWMAC is based on a CSMA/CA-type access protocol with a rotating backoff window and an optional RTS/CTS message exchange. In this paper, following a short presentation of DFWMAC we present the results of our simulative analysis of DFWMAC focussing on analysis and improvements of the basic key mechanisms-the RTS/CTS message exchange and the backoff algorithm.
Multiple mRNA species for the precursor to an adenovirus-encoded glycoprotein: identification and structure of the signal sequence. (1980)

Early region 3 of the adenovirus type 2 genome encodes three proteins with molecular weights of 16,000, 14,500, and 14,000 (E2/16, E3/14.5, and E3/14). The E3/16 protein is the precursor to the E3/19 glycoprotein and is around 1500 daltons larger than the unglycosylated E3/19O protein. The E3/14.5 and E3/14 proteins are structurally related to each other but different from E3/16. Three mRNA species were identified for E3/16; all have common 5' ends with the same spliced region but with different 3' ends. E3/14 was translated from a 13S mRNA with the same 5' structure as the E3/16 mRNA but followed by a second spliced region with a different 3' end. A partial amino acid sequence was determined for E3/16 after radioactive labeling in vitro and this sequence can be aligned with a known DNA sequence. It contains a hydrophobic signal sequence, two presumptive glycosylation sites, and a hydrophobic region close to the COOH terminus.
Single tone parameter estimation from discrete-time observations (1974)

Estimation of the parameters of a single-frequency complex tone from a finite number of noisy discrete-time observations is discussed. The appropriate Cramér-Rao bounds and maximum-likelihood (MI.) estimation algorithms are derived. Some properties of the ML estimators are proved. The relationship of ML estimation to the discrete Fourier transform is exploited to obtain practical algorithms. The threshold effect of one algorithm is analyzed and compared to simulation results. Other simulation results verify other aspects of the analysis.
Melanoma thickness measurement in two-layer tissue phantoms using pulsed photothermal radiometry (PPTR) (2009)

Melanoma is a malignant tumor of melanocytes which are found predominantly in skin. Melanoma is one of the rarer types of skin cancer but causes the majority of skin cancer related deaths. The staging of malignant melanoma using Breslow thickness is important because of the relationship to survival rate after five years. Pulsed photothermal radiometry (PPTR) is based on the time-resolved acquisition of infrared (IR) emission from a sample after pulsed laser exposure. PPTR can be used to investigate the relationship between melanoma thickness and detected radiometric temperature using two-layer tissue phantoms. We used a Monte Carlo simulation to mimic light transport in melanoma and employed a three-dimensional heat transfer model to obtain simulated radiometric temperature increase and, in comparison, we also conducted PPTR experiments to confirm our simulation results. Simulation and experimental results show similar trends: thicker absorbing layers corresponding to deeper lesions produce slower radiometric temperature decays. A quantitative relationship exists between PPTR radiometric temperature decay time and thickness of the absorbing layer in tissue phantoms.
Dicarbonyl Stress and Apoptosis of Vascular Cells: Prevention by αB‐Crystallin (2005)

Methylglyoxal (MGO) is an alpha-dicarbonyl compound produced from triose phosphate intermediates of glycolysis. It reacts rapidly with proteins to produce advanced glycation products. We have studied the effect of MGO modification of fibronectin on retinal capillary cell viability. Our studies show that pericytes grown on MGO-modified fibronectin (FN) undergo enhanced apoptosis through the p38MAPK-mediated oxidative pathway and that alphaB-crystallin, a stress protein present in pericytes, can protect them from MGO-mediated apoptosis. Our studies with vascular endothelial cells show that hyperglycemia-induced apoptosis is inhibited by overexpression of alphaB-crystallin. These observations suggest a novel role of alphaB-crystallin in hyperglycemia-mediated damage to vascular cells in diabetes.
Response of disseminated breast cancer to combined modality treatment with chemotherapy and levamisole with or without Bacillus Calmette-Guérin. (1978)

One hundred and fourteen evaluable patients with measurable metastatic breast cancer were treated with a combination chemoimmunotherapy program (5-fluorouracil, adriamycin, and cyclophosphamide [FAC-levamisole [LSM]). An additional 117 patients with similar characteristics were treated with the same program with the addition of bacillus Calmette-Guérin (BCG) by scarification (FAC-BCG-LMS). The results were compared to those observed in 44 evaluable patients treated with FAC chemotherapy alone. Overall remission rates were identical in the three studies (72%, 73%, and 72%). The median duration of remission was 9 months for FAC, 13 months for FAC-LMS (P = 0.07), and 14 months for FAC-BCG-LMS (P = 0.05). The median duration of survival was 17 months for FAC and 28.6 months for FAC-LMS (P = 0.01). Although the median survival for the FAC-BCG-LMS group has not been reached, it is significantly superior to FAC alone (P = 0.009). These three sequential studies suggest that the addition of nonspecific immunotherapy with LMS or the combination of BCG and LMS prolongs the duration of remission and survival of responding patients treated with chemotherapy. Combination immunotherapy with BCG and LMS did not seem superior to LMS alone in this study.
Phomanolides A and B from the Fungus Phoma sp.: Meroterpenoids Derived from a Putative Tropolonic Sesquiterpene via Hetero-Diels–Alder Reactions (2015)

Phomanolides A (1) and B (2), unique meroterpenoids with new pentacyclic and tetracyclic skeletons, respectively, and phomanoxide (3), the double-epoxidation product of a putative biosynthetic precursor of 1 and 2, were isolated from the solid substrate fermentation cultures of the fungus Phoma sp., along with the known compound eupenifeldin (4). The structures of 1-3 were elucidated based on NMR spectroscopic data and electronic circular dichroism calculations and further secured by X-ray crystallography. Biogenetically, compounds 1 and 2 could be derived from a hypothetical monotropolonic sesquiterpene intermediate via hetero-Diels-Alder reactions. Compound 4 showed potent antiproliferative effects against three human glioma cell lines, with IC50 values of 0.08-0.13 μM.
Low-capacitance PbTe photodiodes (1977)

Thin-film PbTe photodiodes have been operated at 80 K with significantly reduced capacitance. The technique is based upon limitation of the voltage-induced change of the depletion-layer volume by the presence of an insulating substrate. Capacitances as low as 64 pF for a 9-mil-square diode and 35 pF for a 28-mil-square diode have been achieved with retention of background-limited detectivities, which were typically about 1.7×1011 cm Hz1/2 W−1 for peak wavelength near 5 μm.
In vitroAntioxidant, Antifungal and Antibacterial Activities of Essential Oil ofMorina longifoliaWall. Leaves (2013)

Essential oil isolated from the leaves of Morina longifolia, a perennial aromatic herb of medicinal value distributed in the temperate and alpine region of the Himalayas from Kashmir to Bhutan, was screened for in vitro antioxidant, antifungal and antibacterial activities. Compared to the reference antioxidant compounds, the oil showed antioxidant capacity comparable to BHT and ⟨-tocopherol and higher than BHA in Oxygen Radical Absorbance Capacity (ORAC) assay. The oil exhibited pronounced antifungal and varied antibacterial activities against four fungi (Alternaria alternata, Aspergillus flavus, A. fumigatus and Fusarium solani) and six bacteria (Escherichia coli, Staphylococcus aureus, Proteus vulgaris, Klebsiella pneumonia, Bacillus subtilis and Pseudomonas aeruginosa determined using spore germination and disc diffusion method, respectively. The inhibitory activity of the oil in Gram positive bacteria was higher than the Gram negative bacteria. Our findings indicate that the essential oil isolated from M. longifolia leaves could be used as an antioxidant and antimicrobial agent in food, pharmaceutical and pesticide industries.
Supplementary Table 1 from Novel Oral mTORC1/2 Inhibitor TAK-228 Has Synergistic Antitumor Effects When Combined with Paclitaxel or PI3Kα Inhibitor TAK-117 in Preclinical Bladder Cancer Models (2023)

&lt;p&gt;Mutation status of bladder cancer cell lines&lt;/p&gt;