gebhart/patrepeval huggingface dataset:
Regulated Expression of an MHC Class II Gene from a Promoter-Inducible Retrovirus (2000)

Specific immune tolerance to fully allogeneic kidney grafts can be achieved in a miniature swine transplantation model by retrovirus-mediated transfer of allogeneic MHC class II genes into bone marrow cells (BMCs) of recipient animals. Graft survival correlated with transient expression of the somatic transgene (Tg) in the induction phase of tolerance. With the aim of investigating the effects of timing and threshold levels of Tg expression on induction of hyporesponsiveness to the grafted tissues, two recombinant retrovirus constructs containing the tetracycline binary regulatory system were used to achieve conditional expression of either the green fluorescent protein (tetGFP) as a control, or the porcine MHC class II DRβ chain (tetDRB). Effective downregulation of GFP gene transcription was demonstrated in transduced murine fibroblasts after doxycycline treatment, leading to a > 90% reduction of GFP fluorescence. Similar diminution of the DRB gene transcription was achieved in transduced pig endothelial cells (ECs). Drug-dependent downregulation of DRBc gene expression in SLAd pig ECs coincided with complete inhibition of allogeneic activation of anti-class IIc-primed SLAd T cells. These in vitro results suggest that the binary tetracycline retrovirus system may also be adequate to regulate MHC class II Tg expression in vivo.
Configuration Types and Sequence of Operations for the InfraStruXure InRow SC (2007)

The InfraStruXure ® InRow ™ SC (ACSC100 and ACSC101) is a self-contained air conditioner for server rooms and wiring closets. This application note outlines various operating modes and the impact of user configurable setting on unit component behavior.
Blue-noise halftoning for hexagonal grids (2006)

In this paper, we closely scrutinize the spatial and spectral properties of aperiodic halftoning schemes on rectangular and hexagonal sampling grids. Traditionally, hexagonal sampling grids have been shunned due to their inability to preserve the high-frequency components of blue-noise dither patterns at gray-levels near one-half, but as will be shown, only through the introduction of diagonal correlations between dots can even rectangular sampling grids preserve these frequencies. And by allowing the sampling grid to constrain the placement of dots, a particular algorithm may introduce visual artifacts just as disturbing as excess energy below the principal frequency. If, instead, the algorithm maintains radial symmetry by introducing a minimum degree of clustering, then that algorithm can maintain its grid defiance illusion fundamental to the spirit of the blue-noise model. As such, this paper shows that hexagonal grids are preferrable because they can support gray-levels near one-half with less required clustering of minority pixels and a higher principal frequency. Along with a thorough Fourier analysis of blue-noise dither patterns on both rectangular and hexagonal sampling grids, this paper also demonstrates the construction of a blue-noise dither array for hexagonal grids.
Molecular dissection of the multifunctional poliovirus RNA-binding protein 3AB. (1995)

Genome replication of poliovirus, as yet unsolved, involves numerous viral polypeptides that arise from proteolysis of the viral polyprotein. One of these proteins is 3AB, an RNA-binding protein with multiple functions, that serves also as the precursor for the genome-linked protein VPg (= 3B). Eight clustered charged amino acid-to-alanine mutants in the 3AB coding region of poliovirus were constructed and analyzed, together with three additional single-amino acid exchange mutants in VPg, for viral phenotypes. All mutants expressed severe inhibition in RNA synthesis, but none were temperature sensitive (ts). The 3AB polypeptides of mutants with a lethal phenotype were overexpressed in Escherichia coli, purified to near homogeneity, and studied with respect to four functions: (1) ribonucleoprotein complex formation with 3CDpro and the 5'-terminal cloverleaf of the poliovirus genome; (2) binding to the genomic and negative-sense RNA; (3) stimulation of 3CDpro cleavage; and (4) stimulation of RNA polymerase activity of 3Dpol. The results have allowed mapping of domains important for RNA binding and the formation of certain protein-protein complexes, and correlation of these processes with essential steps in viral genome replication.
Natural Antioxidant Extract from Fenugreek (Trigonella foenumgraecum) for Ground Beef Patties (1996)

ABSTRACT Ground beef patties (75% lean) containing synthetic antioxidants, or Fenugreek ( Trigonella foenumgraecum ) extracts were cooked to internal temperature 70°C, and evaluated for storage stability at 4°C. Thiobarbituric acid values of raw or cooked samples containing fenugreek extracts were lower than controls (P<0.05). Fenugreek extracts delayed the induction period of oxidative rancidity. No differences were observed in psychrotrophic bacterial counts, and samples containing fenugreek extracts had lower Hunterlab “a” and higher “b” values. Samples with Fenugreek extracts had better oxidative stability and Fenugreek may be a promising natural antioxidant source.
Compiling Array Computations for the Fresh Breeze Parallel Processor (2007)

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.
Numerical Study on Shape Transformation of Silicon Trenches by High-Temperature Hydrogen Annealing (2004)

We have studied shape transformation of micron-sized trenches on Si substrates during high temperature hydrogen annealing, performing numerical simulations based on Mullins' theory. We have considered evaporation-condensation and surface diffusion as mass transport mechanisms causing shape transformation. The simulation allowing only surface diffusion reproduces well the observed micron-scale aspects of shape transformation by hydrogen annealing at 1000–1150°C.
Buoyant tower would allow deepwater platform drilling (1974)

Results of an 8-month design study by Chicago Bridge and Iron Co. for Exxon Production Research Co. indicate that a buoyant drilling-tower structure could be installed in 1350 ft of water. The tower differs from a fixed structure in that a universal joint near the ocean floor would permit the tower to tilt and oscillate when subjected to wind, current, and wave forces. The force required to prevent excessive tilting is provided by buoyancy near the water surface. If several such structures were built, they would cost about $38 to $48 million each, plus $6 to $10 million for the initial construction site.
Drug sensitivity testing for personalized lung cancer therapy. (2012)

Lung cancer is a biologically diverse disease. Non-small cell lung cancer (NSCLC), which represents about 80% of all lung cancer, is the leading worldwide cause of cancer-related death. NSCLC consists of adenocarcinoma, squamous cell carcinoma and large cell carcinoma (1). There are a number of conventional chemotherapeutic regimens available for NSCLC that, due to the heterogeneity of the disease at pathological, cellular and molecular levels, do not have the same effectiveness in individual patients. Oncologists have to decide which of the conventional regimens would potentially be optimal for a particular patient. The selection is crucial since the currently available chemo drugs are quite toxic and the toxic side effects of an ineffective regimen could preclude use of additional chemotherapy (2).
Freeform, phi-Polynomial Optical Surfaces: Optical Design, Fabrication and Assembly (2014)

Freeform optical surfaces are creating exciting new
opportunities in optics for design, fabrication, metrology, and
assembly. While the term freeform is currently being applied over a
broad range of surface shapes, in our research on imaging with
freeform optical surfaces, a freeform is a surface whose sag varies
not only with the radial component but also with the azimuthal
component, φ, also known as a φ-polynomial optical surface.
Interestingly, these surfaces are readily fabricated with
techniques like single point diamond turning; however, challenges
remain in their optimization during optical design and
characterization after fabrication. In this
dissertation, we propose a more effective optical design approach
based in nodal aberration theory that considers the aberrations
induced by a φ-polynomial optical surface up to sixth order.
Specifically, when a φ-polynomial overlay is placed on a surface
away from the aperture stop, there is both a field constant and
field dependent contribution to the net aberration field. These
findings are validated through the design, implementation, and
wavefront measurement of an aberration generating Schmidt telescope
that employs a custom fabricated φ-polynomial plate. The measured
wavefront behavior is in good agreement with the theoretical
predictions of nodal aberration theory throughout the field of
view. The design methods are also applied
to a specific example: a wide field, fast focal ratio, long wave
infrared, unobscured reflective imager. The system employs three,
tilted φ-polynomial surfaces to provide diffraction limited
performance throughout the field of view. The surfaces were
fabricated with diamond turning and a novel metrology approach
based on an inteferometric null is proposed for characterizing the
figure error of the fabricated surfaces. A mechanical design is
also presented for the housing structure that simplifies the system
assembly. The as-built optical system maintains diffraction limited
performance throughout the field of view. 
The work conducted in this dissertation provides a foundation for
the efficient design of optical systems employing freeform surfaces
and demonstrates that a system based on freeform surfaces is
realizable in the long wave infrared and may be extended to shorter
wavelength regimes.
A spectroscopic and computational study on the effects of methyl and phenyl substituted phenanthroline ligands on the electronic structure of Re(i) tricarbonyl complexes containing 2,6-dimethylphenylisocyanide (2005)

[Re(CO)3(CNx)(L)]+, where CNx = 2,6-dimethylphenylisocyanide, forms complexes with L = 1,10-phenanthroline (1), 4-methyl-1,10-phenanthroline (2), 4,7-dimethyl-1,10-phenanthroline (3), 3,4,7,8-tetramethyl-1,10-phenanthroline (4), 2,9-dimethyl-1,10-phenanthroline (5) and 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (6). The metal-ligand-to-ligand charge transfer transition (MLLCT) absorption bands follow the series: (27800 cm(-1)) > 1, 2, 4 and 5(27500 cm(-1)) > 6 (26600 cm(-1)). Density functional theory (DFT) geometry optimizations reveal elongated Re-N (L) distances of 2.28 and 2.27 A for 5 and 6, respectively, compared to 2.23 A for 1-4. The reversible reduction potentials (E(1/2(red))) of 1-4 are linearly dependent on the B3LYP calculated LUMO energies. Time-dependent (TD) DFT and conductor-like polarizable continuum model (CPCM) calculated singlet excited states deviate by 700 cm(-1) or less from the experimental absorption maxima and aid in the spectral assignments. The (3)MLLCT emitting state energies are within 900 cm(-1) of the experimental 77 K emission energies for 1-6. The 77 K emission energies, E(1/2(red)), and the room temperature emission quantum yields (phi(LUMO)(em)) decrease in the order 1 >2 >3 >4 whereas E(LUMO) and the room temperature emission energies follow the opposite trend. The emission lifetimes (tau(em)) decrease in the order 3 > 4 >2 >1 >5 with 3 having the highest emission lifetime values of 26.9 micros at room temperature and 384 micros at 77 K and complex 5 having the lowest emission lifetimes of 4.6 micros at room temperature and 61 micros and 77 K.
<i>Cichorium intybus</i>: Traditional Uses, Phytochemistry, Pharmacology, and Toxicology (2013)

The genus Cichorium (Asteraceae) is made up of six species with major geographical presence in Europe and Asia. Cichorium intybus, commonly known as chicory, is well known as a coffee substitute but is also widely used medicinally to treat various ailments ranging from wounds to diabetes. Although this plant has a rich history of use in folklore, many of its constituents have not been explored for their pharmacological potential. Toxicological data on C. intybus is currently limited. This review focuses on the economic and culturally important medicinal uses of C. intybus. Traditional uses, scientific validation, and phytochemical composition are discussed in detail.
The effects of long term administration of prazosin on the microcirculation in skeletal muscles (1989)

The effect on the microcirculation of long term administration of the alpha 1 blocker prazosin, which increases peripheral blood flow, was studied in skeletal muscles with differing metabolic profiles. Prazosin (50 mg.litre-1), given ad libitum for 5 weeks in the drinking water, resulted in an increase in capillarity in both fast glycolytic tibialis anterior cortex and slow oxidative soleus muscles of the rat. In tibialis anterior, the velocity of red blood cells through capillaries was increased, a smaller proportion of capillaries had intermittent flow, less time was spent stationary by red blood cells, and hence the calculated volume flow per capillary was increased. In soleus, capillary diameters were larger, but velocity, intermittency and calculated volume flow were unchanged. Therefore, suggested mechanisms for capillary growth induced by prazosin are different for the two muscles studied: increased shear stress and blood/endothelial cell interaction in the case of tibialis anterior, and increased capillary wall tension in the soleus.
pH-Triggered, Macromolecule-Sized Poration of Lipid Bilayers by Synthetically Evolved Peptides (2016)

pH-triggered membrane-permeabilizing peptides could be exploited in a variety of applications, such as to enable cargo release from endosomes for cellular delivery, or as cancer therapeutics that selectively permeabilize the plasma membranes of malignant cells. Such peptides would be especially useful if they could enable the movement of macromolecules across membranes, a rare property in membrane-permeabilizing peptides. Here we approach this goal by using an orthogonal high-throughput screen of an iterative peptide library to identify peptide sequences that have the following two properties: (i) little synthetic lipid membrane permeabilization at physiological pH 7 at high peptide concentration and (ii) efficient formation of macromolecule-sized defects in synthetic lipid membranes at acidic pH 5 and low peptide concentration. The peptides we selected are remarkably potent macromolecular sized pore-formers at pH 5, while having little or no activity at pH 7, as intended. The action of these peptides likely relies on tight coupling between membrane partitioning, α-helix formation, and electrostatic repulsions between acidic side chains, which collectively drive a sharp pH-triggered transition between inactive and active configurations with apparent pK<sub>a</sub> values of 5.5-5.8. This work opens new doors to developing applications that utilize peptides with membrane-permeabilizing activities that are triggered by physiologically relevant decreases in pH.
Voltage stability assessment of a power system incorporating FACTS controllers using unique network equivalent (2013)

Voltage instability is considered as a main threat to stability, security, and reliability in the modern power systems. Prediction of voltage stability limit of multi-bus system through its two-bus equivalent model is a hot topic of the research in the field of power system operation and control. This paper presents a novel method to assess voltage stability status using a unique two-bus π-network equivalent derived with OPF solution of the actual system at different operating conditions. As the FACTS controllers are now an ineluctable part of power system, this paper considers an SVC and a TCSC in OPF formulation to assess voltage stable states of any interconnected power system in terms of its reduced two-bus integrated π-equivalent system. Simulation results for a practical power system establish that the proposed methodology is highly promising to assess voltage stability in a better way as compared to existing series equivalent model.
Novel Oxazolidinone-Based Peroxisome Proliferator Activated Receptor Agonists: Molecular Modeling, Synthesis, and Biological Evaluation (2015)

A series of new peroxisome proliferator activated receptors (PPARs) chiral ligands have been designed following the accepted three-module structure comprising a polar head, linker, and hydrophobic tail. The majority of the ligands incorporate the oxazolidinone moiety as a novel polar head, and the nature of the hydrophobic tail has also been varied. Docking studies using the crystal structure of an agonist bound to the ligand binding domain of the PPARα receptor have been performed as a tool for their design. Suitable synthetic procedures have been developed, and compounds with different stereochemistries have been prepared. Evaluation of basal and ligand-induced activity proved that several compounds showed agonist activity at the PPARα receptor, thus validating the oxazolidinone template for PPAR activity. In addition, two compounds, 2 and 4, showed dual PPARα/PPARγ agonism and interesting food intake reduction in rats.
Visualizing parallel execution of FORTRAN programs (1991)

As a first step toward the parallel execution analysis of FORTRAN programs, a tool called the Parallel Execution Profiler has been designed and implemented for the graphical postexecution analysis of parallel programs using the Parallel FORTRAN environment as a vehicle for both implementing parallel programs and tracing parallel events. The dynamic behavior of parallel execution is observed interactively in color graphs, which can be displayed concurrently with the source code, and in statistical summaries. This paper describes the implementation of our tool for parallel performance analysis with the aid of a parallelized application program from plasma physics.
Study of complement-mediated anaphylaxis in humans. The role of IgG subclasses (IgG1 and/or IgG4) in the complement-activating capacity of immune complexes (1996)

The role of Ig classes and subclasses in complement activation has been investigated both in vitro and in experimental animals, but not in humans. This study was conducted to determine the immunologic events of post-transfusion anaphylaxis in humans, and the effects of immune complexes of different IgG subclass compositions on complement activation. The ability of immune complexes containing mixed IgG1 and IgG4 or IgG4 Ab only to activate complement was investigated in two patients with von Willebrand's disease (a congenital bleeding disorder). This disease was complicated by precipitating IgG alloantibodies to von Willebrand factor (vWF), which triggered complement-mediated anaphylaxis after infusion of vWF-containing preparations. Complement activation was greater in the presence of mixed IgG1- and IgG4-vWF complexes than with IgG4-vWF alone. In one patient, the generation of large amounts of C4a, C3a, and terminal complement complexes following the formation of mixed IgG1- and IgG4-vWF was associated with life-threatening anaphylaxis. In this patient, IgG4 appeared to have no inhibitory effect on antigen-bound IgG1-mediated complement activation. In the other patient, formation of IgG4-vWF led to a lesser degree of complement activation and was associated with moderately severe anaphylaxis. Since neither patient showed any biochemical alterations indicating the involvement of mast cells or the contact phase of coagulation at any time, it is probable that the pathogenetic mechanism of the clinical syndrome was a direct effect of complement anaphylatoxins on vascular permeability and smooth muscle contraction. In both patients, IgG-vWF bound C4 and C3 (IgG4-vWF to a lesser extent than mixed IgG1- and IgG4-vWF), and this probably prevented serum sickness as a complication.
Excited-state properties and photosensitization behaviour of bis(2,4-dihydroxyphenyl)squaraine (1993)

Two protonation equilibria (pKa at 3.7 and 7.4) have been identified for the dye, bis(2,4-dihydroxyphenyl)-squaraine in the ground state. These various protonation forms exhibit widely different absorption properties. The singlet excited-state behaviour of this dye has been characterized by picosecond laser flash photolysis. The fluorescence quantum yield and the excited singlet lifetime of the unprotonated dye (ϕf= 0.092, τs= 740 ps) are considerably higher than that of the neutral (ϕf= 0.037, τs= 130 ps) or the protonated (ϕf= 0.01, τs⩽ 100 ps) forms of the dye. The triplet excited state has been characterized by both direct excitation and T–T energy transfer methods. The triplet excited state has an absorption maximum around 430 nm and a lifetime of ca. 100 µs in ethanol. Photosensitization of a thin microporous TiO2 semiconductor film has been carried out by adsorbing the squaraine dye from an ethanolic solution and exciting it with visible light. An incident photon-to-current conversion efficiency of 0.05% at 500 nm has been obtained for the dye-modified TiO2 electrode.
A complex Polycomb issue: the two faces of EZH2 in cancer (2012)

In the April 1, 2012, issue of Genes & Development, Simon and colleagues (pp. 651-656) demonstrated that the disruption of Ezh2 in mice is sufficient to cause T-acute lymphoblastic leukemia (T-ALL). Moreover, in concert with concurrent studies, the authors revealed that similar mechanisms are involved in human T-ALL. These data contrast with previous findings showing that increased EZH2 activity promotes cancer.
Zur Biochemie und Physiologie der Kollagentypen (1990)

Zusammenfassung Kollagene stellen eine Gruppe von Proteinen des Bindegewebes dar, die als gemeinsames Merkmal eine charakteristische Dreikettenstruktur aufweisen. Voraussetzung für ihre Ausbildung ist, daß in jeder der drei Ketten jede dritte Position mit Glyzin besetzt ist. Außerdem sind Prolin und Hydroxyprolin häufig vorkommende Aminosäuren. Diese gestreckte, verhältnismäßig steife Tripelhelix bestreitet bei den interstitiellen Kollagenen vom Typ I in Haut, Sehnen oder Knochen, Typ II im Knorpel oder Typ III in der Aortenwand über 90% des Monomerenmoleküls. In Vorstufen dieser Monomeren sind sowohl an der N-terminalen wie an der C-terminalen Seite zusätzliche globuläre Domänen angebracht, die bei der Reifung abgestoßen werden. Endständige globuläre Domänen finden sich auch in anderen Kollagenen, z.B. in Typ VI, das in verschiedenen Geweben, darunter der Aorta, in Form von Mikrofibrillen vorkommt. Die Monomeren der interstitiellen Kollagene lagern sich in einer versetzten parallelen Anordnung zusammen und bilden Fibrillen, die durch kovalente Vernetzung zwischen den einzelnen Monomeren verfestigt werden. Das fadenförmige Kollagenmolekül vom Typ IV, das nur am C-Terminus eine globuläre Domäne trägt, bildet dagegen netzartige flächenförmige Strukturen. Dieselben stellen das Grundgerüst von Basalmembranen, an das sich andere Komponenten wie Laminin, Nidogen, Heparansulfatproteoglykan oder das Protein BM-40 anlagern. Die netzartige Struktur kommt dadurch zustande, daß das Molekül nur am N-Terminus in einem kurzen tripelhelikalen Bereich und am C-Terminus mit der globulären Domäne mit Nachbarmolekülen vom Typ IV assoziiert. Besondere Aufgaben haben die Kollagentypen VII und IX, die für eine Verankerung von Basalmembranen (VII) oder von Kollagenfasern des Knorpels (IX) mit ihrer Umgebung sorgen.