gebhart/patrepeval huggingface dataset:
The CCAAT box-binding factor stimulates ammonium assimilation in Saccharomyces cerevisiae, defining a new cross-pathway regulation between nitrogen and carbon metabolisms (1996)

In Saccharomyces cerevisiae, carbon and nitrogen metabolisms are connected via the incorporation of ammonia into glutamate; this reaction is catalyzed by the NADP-dependent glutamate dehydrogenase (NADP-GDH) encoded by the GDH1 gene. In this report, we show that the GDH1 gene requires the CCAAT box-binding activator (HAP complex) for optimal expression. This conclusion is based on several lines of evidence: (1) overexpression of GDH1 can correct the growth defect of hap2 and hap3 mutants on ammonium sulfate as a nitrogen source, (ii) Northern (RNA) blot analysis shows that the steady-state level of GDH1 mRNA is strongly lowered in a hap2 mutant, (iii) expression of a GDH1-lacZ fusion is drastically reduced in hap mutants, (iv) NADP-GDH activity is several times lower in the hap mutants compared with that in the isogenic wild-type strain, and finally, (v) site-directed mutagenesis of two consensual HAP binding sites in the GDH1 promoter strongly reduces expression of GDH1 and makes it HAP independent. Expression of GDH1 is also regulated by the carbon source, i.e., expression is higher on lactate than on ethanol, glycerol, or galactose, with the lowest expression being found on glucose. Finally, we show that a hap2 mutation does not affect expression of other genes involved in nitrogen metabolism (GDH2, GLN1, and GLN3 encoding, respectively, the NAD-GDH, glutamine synthetase, and a general activator of several nitrogen catabolic genes). The HAP complex is known to regulate expression of several genes involved in carbon metabolism; its role in the control of GDH1 gene expression, therefore, provides evidence for a cross-pathway regulation between carbon and nitrogen metabolisms.
Determination of the State of Strain of Large Floating Covers Using Unmanned Aerial Vehicle (UAV) Aided Photogrammetry (2017)

Floating covers used in waste water treatment plants are one of the many structures formed with membrane materials. These structures are usually large and can spread over an area measuring 470 m × 170 m. The aim of this paper is to describe recent work to develop an innovative and effective approach for structural health monitoring (SHM) of such large membrane-like infrastructure. This paper will propose a potentially cost-effective non-contact approach for full-field strain and stress mapping using an unmanned aerial vehicle (UAV) mounted with a digital camera and a global positioning system (GPS) tracker. The aim is to use the images acquired by the UAV to define the geometry of the floating cover using photogrammetry. In this manner, any changes in the geometry of the floating cover due to forces acting beneath resulting from its deployment and usage can be determined. The time-scale for these changes is in terms of weeks and months. The change in the geometry can be implemented as input conditions to a finite element model (FEM) for stress prediction. This will facilitate the determination of the state of distress of the floating cover. This paper investigates the possibility of using data recorded from a UAV to predict the strain level and assess the health of such structures. An investigation was first conducted on a laboratory sized membrane structure instrumented with strain gauges for comparison against strains, which were computed from 3D scans of the membrane geometry. Upon validating the technique in the laboratory, it was applied to a more realistic scenario: an outdoor test membrane structure and capable UAV were constructed to see if the shape of the membrane could be computed. The membrane displacements were then used to calculate the membrane stress and strain, state demonstrating a new way to perform structural health monitoring on membrane structures.
Suzuki Coupling of Aryl Chlorides with Phenylboronic Acid in Water, Using Microwave Heating with Simultaneous Cooling (2005)

[reaction: see text]. We present here a methodology for the Suzuki coupling of aryl chlorides with phenylboronic acid using Pd/C as a catalyst, water as a solvent, and microwave heating. We show that simultaneous cooling in conjunction with microwave heating prolongs the lifetime of the aryl chloride substrates during the course of the reaction and, as a result, yields of the desired biaryl as well as overall recovery of material can be increased.
Chemokines and their receptors in rheumatoid arthritis: Future targets? (2005)

No abstract.
Characterization and Biomarker Analyses of Post-COVID-19 Complications and Neurological Manifestations (2021)

As the SARS-CoV-2 pandemic continues, reports have demonstrated neurologic sequelae following COVID-19 recovery. Mechanisms to explain long-term neurological sequelae are unknown and need to be identified. Plasma from 24 individuals recovering from COVID-19 at 1 to 3 months after initial infection were collected for cytokine and antibody levels and neuronal-enriched extracellular vesicle (nEV) protein cargo analyses. Plasma cytokine IL-4 was increased in all COVID-19 participants. Volunteers with self-reported neurological problems (nCoV, <i>n</i> = 8) had a positive correlation of IL6 with age or severity of the sequalae, at least one co-morbidity and increased SARS-CoV-2 antibody compared to those COVID-19 individuals without neurological issues (CoV, <i>n</i> = 16). Protein markers of neuronal dysfunction including amyloid beta, neurofilament light, neurogranin, total tau, and p-T181-tau were all significantly increased in the nEVs of all participants recovering from COVID-19 compared to historic controls. This study suggests ongoing peripheral and neuroinflammation after COVID-19 infection that may influence neurological sequelae by altering nEV proteins. Individuals recovering from COVID-19 may have occult neural damage while those with demonstrative neurological symptoms additionally had more severe infection. Longitudinal studies to monitor plasma biomarkers and nEV cargo are warranted to assess persistent neurodegeneration and systemic effects.
Retroviral vector-mediated gamma-interferon gene transfer into tumor cells generates potent and long lasting antitumor immunity. (1990)

Retroviral vectors were used to introduce the gamma-interferon (IFN-gamma) gene into CMS-5 cells, a weakly immunogenic tumor of BALB/c origin. After selection in G418-containing medium, colonies were isolated, cloned, and expanded to cell lines. IFN-gamma secretion was assessed using a bioassay and enzyme-linked immunosorbent assay, and high (25 units/ml) and low (5 units/ml) IFN-gamma producers were isolated. Tumor growth was followed after intradermal injection, and spleen cells were isolated at different time points. IFN-gamma secretion by tumor cells abrogated their tumorigenicity and induced a persistent and specific antitumor immunity. In contrast to the normally observed cellular immunosuppression in unmodified CMS-5 tumor-bearing mice, IFN-gamma-producing tumors induced a long lasting state of T-cell immunity, as judged by rejection of a CMS-5 tumor challenge and persistence of specific cytotoxic activity in the spleen cell population. High levels of tumor-specific cytotoxic activity could also be detected if IFN-gamma-secreting tumor cells, but not unmodified CMS-5 cells, were used as targets at a time point when immunosuppression was usually seen. These studies highlight the potential advantages of localized IFN-gamma secretion to induce potent antitumor immune responses.
Fast phase reconstruction in white light diffraction phase microscopy (2012)

In off-axis interferometry, we usually have to deal with the unwrapping process, which is very computationally intensive and prevents us from real time phase reconstruction. The wrapping problem usually occurs when imaging thick objects, which introduce phase shifts of more than 2π radians. However, in off-axis interferometry, the nonzero angle of interference of the two beams creates a ramp in the phase across the image that can produce phase wrapping errors. In this paper, we propose a simple technique that avoids the need for the unwrapping step in reconstructing quantitative phase images in white light diffraction phase microscopy of thin samples. We show that this approach can improve significantly the phase reconstruction speed and allow high impact applications, such as real-time blood testing.
Intracellular Trafficking of Adeno-Associated Virus Vectors: Routing to the Late Endosomal Compartment and Proteasome Degradation (2001)

The early steps of adeno-associated virus (AAV) infection involve attachment to a variety of cell surface receptors (heparan sulfate, integrins, and fibroblast growth factor receptor 1) followed by clathrin-dependent or independent internalization. Here we have studied the subsequent intracellular trafficking of AAV particles from the endosomal compartment to the nucleus. Human cell lines were transduced with a recombinant AAV (rAAV) carrying a reporter gene (luciferase or green fluorescent protein) in the presence of agents that affect trafficking. The effects of bafilomycin A(1), brefeldin A, and MG-132 were measured. These drugs act at the level of endosome acidification, early-to-late endosome transition, and proteasome activity, respectively. We observed that the transducing virions needed to be routed as far as the late endosomal compartment. This behavior was markedly different from that observed with adenovirus particles. Antiproteasome treatments with MG-132 led to a 50-fold enhancement in transduction efficiency. This effect was accompanied by a 10-fold intracellular accumulation of single-stranded DNA AAV genomes, suggesting that the mechanism of transduction enhancement was different from the one mediated by a helper adenovirus, which facilitates the conversion of the rAAV single-stranded DNA genome into its replicative form. MG-132, a drug currently in clinical use, could be of practical use for potentializing rAAV-mediated delivery of therapeutic genes.
A Preliminary Trial of Lamivudine for Chronic Hepatitis B Infection (1995)

In a preliminary trial, 12 weeks of lamivudine therapy was well tolerated, and daily doses of 100 mg and 300 mg reduced HBV DNA to undetectable levels.
Domperidone (2012)

Because domperidone has placebo-like benefits but is associated with increased SCD and a narrow safety margin, it should not be used in medicine.
Stressors in the primary caregivers of traumatic head injured persons. (1996)

This study was designed to identify the intrapersonal, interpersonal and extrapersonal stressors of primary caregivers caring for a traumatic-head-injured person. Betty Neuman's (1989) theoretical model provides a conceptual framework for studying the relationship between stressors and the changing stress level of primary caregivers caring for a traumatic-head-injured person. The Appraisal Caregiving Scale and the Burden Interview were administered to 23 caregivers. Intrapersonal, interpersonal and extrapersonal stressors are identified. Caregivers differed in the changing stress level they experienced. Positive correlations were found between the intrapersonal stressors and the changing stress level and the interpersonal stressors and the changing stress level.
Binding of human factor VII and VIIa to monocytes. (1982)

Human coagulation Factors VII and VIIa bind with equal affinity to monocytes stimulated with endotoxin. Equilibrium binding studies performed at 0 degrees C using 125I-labeled Factor VII and VIIa showed the dissociation constant (Kd) to be congruent to 82 pM with congruent to 3,600 binding sites/monocyte. Ca++ was required for Factor VII and VIIa interaction with monocytes (optimal CaC12 concentration greater than or equal to 2.5 mM) and binding was reversed by the addition of EDTA. The rate of conversion of Factor X to Xa in mixtures containing Factor VIIa and monocytes was directly related to the quantity of Factor VIIa bound to the monocyte surface. Thus the monocyte binding sites appear to represent tissue factor. Competition experiments showed that Factor VII and VIIa bind to the same monocyte sites and further, that unlabeled Factor VII and VIIa have the same affinity for the binding sites as the 125I-labeled proteins.
Assigning function tags to parsed text (2000)

It is generally recognized that the common nonterminal labels for syntactic constituents (NP, VP, etc.) do not exhaust the syntactic and semantic information one would like about parts of a syntactic tree. For example, the Penn Treebank gives each constituent zero or more &amp;apos;function tags&amp;apos; indicating semantic roles and other related information not easily encapsulated in the simple constituent labels. We present a statistical algorithm for assigning these function tags that, on text already parsed to a simplelabel level, achieves an F-measure of 87%, which rises to 99% when considering &amp;apos;no tag&amp;apos; as a valid choice.
Epidermal Growth Factor Receptor Dimerization and Activation Require Ligand-Induced Conformational Changes in the Dimer Interface (2005)

Structural studies have shown that ligand-induced epidermal growth factor receptor (EGFR) dimerization involves major domain rearrangements that expose a critical dimerization arm. However, simply exposing this arm is not sufficient for receptor dimerization, suggesting that additional ligand-induced dimer contacts are required. To map these contributions to the dimer interface, we individually mutated each contact suggested by crystallographic studies and analyzed the effects on receptor dimerization, activation, and ligand binding. We find that domain II contributes >90% of the driving energy for dimerization of the extracellular region, with domain IV adding little. Within domain II, the dimerization arm forms much of the dimer interface, as expected. However, a loop from the sixth disulfide-bonded module (immediately C-terminal to the dimerization arm) also makes a critical contribution. Specific ligand-induced conformational changes in domain II are required for this loop to contribute to receptor dimerization, and we identify a set of ligand-induced intramolecular interactions that appear to be important in driving these changes, effectively "buttressing" the dimer interface. Our data also suggest that similar conformational changes may determine the specificity of ErbB receptor homo- versus heterodimerization.
Dynamic molecular linkers of the genome: the first decade of SMC proteins (2005)

Structural maintenance of chromosomes (SMC) proteins are chromosomal ATPases, highly conserved from bacteria to humans, that play fundamental roles in many aspects of higher-order chromosome organization and dynamics. In eukaryotes, SMC1 and SMC3 act as the core of the cohesin complexes that mediate sister chromatid cohesion, whereas SMC2 and SMC4 function as the core of the condensin complexes that are essential for chromosome assembly and segregation. Another complex containing SMC5 and SMC6 is implicated in DNA repair and checkpoint responses. The SMC complexes form unique ring- or V-shaped structures with long coiled-coil arms, and function as ATP-modulated, dynamic molecular linkers of the genome. Recent studies shed new light on the mechanistic action of these SMC machines and also expanded the repertoire of their diverse cellular functions. Dissecting this class of chromosomal ATPases is likely to be central to our understanding of the structural basis of genome organization, stability, and evolution.
Filter Response of Nonuniform Almost-Periodic Structures (1976)

The filter response of nonuniform, almost-periodic structures, such as corrugated optical waveguides, is investigated theoretically. The filter process, leading to reflection of a band of frequencies near the Bragg frequency, is treated as a contradirectional coupled-wave interaction and shown to obey a Riccati differential equation. The nonuniformity of the structure is represented by a tapering in the coupling strength (e.g., the depth of the corrugation) and by a chirp in the period of the structure. For small reflectivities, the filter response is a Fourier transform of the taper function. For large reflectivities, the Riccati equation was evaluated numerically and plots are given for the response of filters with linear and quadratic tapers and with linear and quadratic chirps.
Health Promotion Dissemination and Systems Thinking: Towards an Integrative Model (2003)

Systems thinking has potential to improve synthesis, translation, and dissemination of research findings in other health promotion initiatives.
Diabetes Mellitus Associated with Atypical Anti-Psychotic Medications (2003)

Diabetes or hyperglycemia associated with the use of atypical anti-psychotic agents is a subject of growing concern among health care providers and the patients who use the drugs. Although much attention has been relegated to this topic in the mental health literature, there has been little attention devoted to it in the diabetes literature. The purpose of this report is to review the problem of diabetes mellitus associated with atypical anti-psychotic use from an endocrinology perspective. This paper will specifically present (a) a review of the increased prevalence of diabetes in the setting of schizophrenia, (b) a compilation and critical assessment of the existing publications that have documented the association of hyperglycemia and atypical anti-psychotic use, (c) a discussion of the potential mechanisms through which antipsychotics may lead to disturbances in glucose homeostasis, and (d) recommendations for the effective monitoring and treatment of affected patients.
Chip‐Based Free‐Flow Electrophoresis with Integrated Nanospray Mass‐Spectrometry (2015)

Free-flow electrophoresis is an ideal tool for preparative separations in continuous microflow. With the approach presented herein for coupling free-flow electrophoresis and mass spectrometry it is now also possible to trace non-fluorescent compounds and identify them by means of mass spectrometry. The functionality of the method and its potential as an integrated separation unit for microflow synthesis is demonstrated by application to a multicomponent [3+2]-cycloannulation.
Optimizing the MALDI-TOF-MS observation of peptides containing disulfide bonds. (2003)

The observation of peaks corresponding to both disulfide-bonded and reduced peptides in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra of disulfides could suggest that the samples are either mixtures prior to analysis or that the measurement process has converted single compounds into mixtures. This is an important distinction when characterizing potentially disulfide-bonded peptides obtained from proteolyzed proteins or from oxidized synthetic peptides. It is well documented that disulfides can undergo in-source decay (ISD) when using a 337-nm laser. However, the mixed matrix 2-(4-hydroxyphenylazo)benzoic acid:alpha-cyano-4-hydroxycinnamic acid (1:10) not only suppresses the ISD reduction of disulfides to thiols but allows the same low threshold laser power generally used with alpha-cyano-4-hydroxycinnamic acid to be applied.
Intelligent controller for a stand-alone hybrid generation system (2006)

This paper aims at the modeling and power flow analysis of a stand-alone hybrid generating system (SAHGS) comprising of wind and photovoltaic systems. The wind driven self-excited induction generator (SEIG), photovoltaic array and other network components are modeled and simulated using Matlab/Simulink. The variable voltage and frequency of a generator is first rectified and controlled by a DC/DC converter before being fed to a common DC bus. The variable output voltage of the photovoltaic module is also controlled by a DC/DC converter. The DC bus collects the total power from the wind and photovoltaic systems and uses it partly to supply the required load demand and partly to charge the battery bank. The individual systems are simulated for varying wind velocities and solar intensities respectively and the results are used to identify the operating modes. A neuro controller is designed to adjust the duty ratios of the choppers and the firing angle of the converter at which the maximum power generation occurs.
Comparative prophylactic efficacies of ciprofloxacin, ofloxacin, cefazolin, and vancomycin in experimental model of staphylococcal wound infection (1994)

Recent shifts in the species and antibiotic resistance patterns of bacteria causing nosocomial infections present new challenges for providing effective prophylaxis in surgery. Traditional regimens lack activity against methicillin-resistant staphylococci and many gram-negative species causing nosocomial infections. The new fluoroquinolones exhibit in vitro activity against many emerging surgical wound pathogens. To determine the potential of this class of antimicrobial agents for use in surgery, we compared the prophylactic efficacies of ciprofloxacin and ofloxacin with those of cefazolin and vancomycin in a guinea pig model of abscess formation. Four Staphylococcus aureus strains, one Staphylococcus epidermidis strain, and one Staphylococcus haemolyticus strain were evaluated. Vancomycin was the most effective prophylactic agent, exhibiting in vivo activity against all strains which was superior or equivalent to those of all other agents tested. Cefazolin was the least effective agent and surpassed the two quinolones in prophylactic efficacy against only one organism, a quinolone- and methicillin-resistant strain of S. aureus. The two quinolones provided excellent protection against infection with all but the quinolone-resistant isolate. The in vivo emergence of quinolone resistance among quinolone-susceptible isolates was not detected. The methicillin-resistant, quinolone-susceptible S. epidermidis and S. haemolyticus isolates were extremely susceptible to prophylaxis, exhibiting 50% infective doses above 4 x 10(6) CFU for seven of the eight antibiotic-strain combinations. We conclude that ciprofloxacin and ofloxacin may be effective antistaphylococcal agents in surgery. The role of these agents remains to be defined, and the definition should include consideration of an adverse effect upon antibiotic resistance patterns of organisms causing nosocomial infections.
ARC-1, a sequence element complementary to an internal 18S rRNA segment, enhances translation efficiency in plants when present in the leader or intercistronic region of mRNAs (2004)

The sequences of different plant viral leaders with known translation enhancer ability show partial complementarity to the central region of 18S rRNA. Such complementarity might serve as a means to attract 40S ribosomal subunits and explain in part the translation-enhancing property of these sequences. To verify this notion, we designed beta-glucuronidase (GUS) mRNAs differing only in the nature of 10 nt inserts in the center of their 41 base leaders. These were complementary to consecutive domains of plant 18S rRNA. Sucrose gradient analysis revealed that leaders with inserts complementary to regions 1105-1114 and 1115-1124 ('ARC-1') of plant 18S rRNA bound most efficiently to the 40S ribosomal subunit after dissociation from 80S ribosomes under conditions of high ionic strength, a treatment known to remove translation initiation factors. Using wheat germ cell-free extracts, we could demonstrate that mRNAs with these leaders were translated more than three times more efficiently than a control lacking such a complementarity. Three linked copies of the insert enhanced translation of reporter mRNA to levels comparable with those directed by the natural translation enhancing leaders of tobacco mosaic virus and potato virus Y RNAs. Moreover, inserting the same leaders as intercistronic sequences in dicistronic mRNAs substantially increased translation of the second cistron, thereby revealing internal ribosome entry site activity. Thus, for plant systems, the complementary interaction between mRNA leader and the central region of 18S rRNA allows cap-independent binding of mRNA to the 43S pre-initiation complex without assistance of translation initiation factors.