gebhart/patrepeval huggingface dataset:
Solvent-Induced Electron Transfer and Delocalization in Mixed-Valence Complexes. Electrochemistry (1996)

For the RuIII/II couple in [(bpy)2ClOs(4,4‘-bpy)Ru(NH3)5]3+ (bpy = 2,2‘-bipyridine; 4,4‘-bpy = 4,4‘-bipyridine), E1/2 varies linearly with the donor number (DN) of the solvent with a slope of −26 ± 3 mV/DN unit ranging from nitromethane to dimethyl sulfoxide. For the OsIII/II couple, the variation is −3 ± 1 mV/DN unit. Plots of ΔE1/2 = E1/2(2) − E1/2(1) vs DN (E1/2 is the half wave potential for the first or second wave by cyclic voltammetry) undergo a change in slope at DN ∼ 14 where there is a change in oxidation states in the mixed-valence form from OsIII−RuII to OsII−RuIII. By extrapolation of these data, ΔG° for the mixed-valence equilibrium, [(bpy)2ClOsIII(4,4‘-bpy)RuII(NH3)5]4+ ⇌ [(bpy)2ClOsII(4,4‘-bpy)RuIII(NH3)5]4+, varies from +5.8 kcal/mol in nitromethane to −7.5 kcal/mol in dimethyl sulfoxide. It differs from ΔE1/2 by up to ∼20% even though it has sometimes been assumed in the literature that ΔE1/2 = −ΔG°. For [(bpy)2ClOs(pz)Ru(NH3)5]3+ (pz = pyrazine) both OsIII/II and RuIII/II couples are significantly solvent dependent for solvents of DN < 24. In these solvents oxidation states in the mixed-valence form are OsIII−RuII. The slopes of E1/2 vs DN plots are −21 ± 4 mV/DN unit (RuIII/II) and −8 ± 4 mV/DN unit (OsIII/II). At DN > 24 the oxidation states switch to OsII-RuIII and the solvent dependence reverts to being largely in RuIII/II. There is evidence in the electrochemical data, in comparisons between [(bpy)2ClOs(pz)Ru(NH3)5]3+ and [(bpy)2ClOs(4,4‘-bpy)Ru(NH3)5]3+ for significant through-bridge electronic coupling in [(bpy)2ClOsIII(pz)RuII(NH3)5]4+, but not in [(bpy)2ClOsII(pz)RuIII(NH3)5]4+. The difference in behavior is caused by extensive H-bonding to the solvent at −RuIII(NH3)53+ in [(bpy)2ClOsII(pz)RuIII(NH3)5]4+. This mixes solvent character into dπ(RuIII) which decreases electronic coupling across the bridge.
MART-1 peptide vaccination plus IMP321 (LAG-3Ig fusion protein) in patients receiving autologous PBMCs after lymphodepletion: results of a Phase I trial (2014)

Vaccination with IMP321 as an adjuvant in combination with lymphodepleting chemotherapy and adoptive transfer of autologous PBMCs induced more robust and durable cellular antitumor immune responses, supporting further development of IMP321 as an adjuvant for future immunotherapeutic strategies.
Long-Term Excitability and Fine Tuning of Nerve Pedicles Reinnervating Strap Muscles in the Dog (1998)

Contraction of paralyzed striated muscles has been restored by stimulating reinnervating pedicles with currents of low intensity. In order to allow clinical application, stable, long-term excitability must emulate the parameters necessary for the stimulation of normal motor nerves. In 6 dogs, the ansa hypoglossi nerve was implanted into the contralateral denervated sternohyoid muscle and surrounded with a bipolar cuff electrode. Three of the reinnervating pedicles were chronically paced with a Medtronic Itrel II Multiprogrammable Pulse Generator (0.5 V, 0.2 second on [30 pulses per second, 0.21-millisecond pulse width], 2.9 seconds off). At reexploration after 8 months (6 months for 1 dog), frank contraction confirmed by electromyography tracings occurred in all animals with currents in the range of 0.1 to 0.5 mA. Muscle force was further manipulated by selective release of blocking currents (600 Hz, 1.7 to 0.4 mA) superimposed over regular stimulation (50 Hz, 0.3 to 1.7 mA). Nerve and muscle vitality were histologically confirmed. Long-term, low-intensity conduction capabilities, fine tuning, good tolerance of implanted electrodes, and lack of fatigue suggest that reinnervating pedicles may be successfully used for pacing when clinically indicated.
Mapping the active-site tyrosine of vaccinia virus DNA topoisomerase I. (1989)

Site-directed mutagenesis of the vaccinia virus gene encoding a type I DNA topoisomerase implicates Tyr-274 as the active-site residue that forms a covalent adduct with DNA during cycles of DNA-strand breakage and reunion. Replacement of Tyr-274 by phenylalanine results in loss of the ability of the enzyme to relax negatively supercoiled DNA as well as to form the covalent DNA-protein intermediate. Substitution of phenylalanine for tyrosine at nine other sites in the protein has no apparent effect on enzyme activity. Amino acid sequence alignment reveals Tyr-274 to be homologous to Tyr-727 and Tyr-771, respectively, of the type I topoisomerases from Saccharomyces cerevisiae and Saccharomyces pombe; Tyr-727 and Tyr-771 have been shown to represent the active-site tyrosines of those enzymes. Sequence comparison of the active-site regions defines a motif Ser-Lys-Xaa-Xaa-Tyr common to the viral and cellular type I topoisomerases, including the human enzyme.
Induced β-Carotene Synthesis Driven by Triacylglycerol Deposition in the Unicellular AlgaDunaliella bardawil1 (1998)

Under stress conditions such as high light intensity or nutrient starvation, cells of the unicellular alga Dunaliella bardawil overproduce beta-carotene, which is accumulated in the plastids in newly formed triacylglycerol droplets. We report here that the formation of these sequestering structures and beta-carotene are interdependent. When the synthesis of triacylglycerol is blocked, the overproduction of beta-carotene is also inhibited. During overproduction of beta-carotene no up-regulation of phytoene synthase or phytoene desaturase is observed on the transcriptional or translational level, whereas at the same time acetyl-CoA carboxylase, the key regulatory enzyme of acyl lipid biosynthesis, is increased, at least in its enzymatic activity. We conclude that under normal conditions the carotenogenic pathway is not maximally active and may be appreciably stimulated in the presence of sequestering structures, creating a plastid-localized sink for the end product of the carotenoid biosynthetic pathway.
Replication of human papillomavirus (HPV) DNAs supported by the HPV type 18 E1 and E2 proteins (1994)

Transient replication of human papillomavirus (HPV) type 18 DNA was shown to require the viral E1 and E2 proteins. A 108-bp sequence within the long control region (nucleotides 12 to 119) was sufficient to function as the origin, but maximal replication required a region of 177 bp from positions 7800 to 7857 and 1 to 119 of HPV-18. The E1 and E2 proteins of HPV-18 also supported transient replication of plasmids containing the origins of HPV-1a and bovine papillomavirus type 1 to low levels. Interestingly, the level of replication observed with the HPV-6b origin was higher than that obtained with the homologous HPV-18 origin.
High-Density, Covalent Attachment of DNA to Silicon Wafers for Analysis by MALDI-TOF Mass Spectrometry (1997)

A method is described for the covalent attachment of DNA to a solid surface at high density for hybridization detection by mass spectrometry. A silicon wafer is functionalized to place an amino group on the surface; a heterobifunctional cross-linking agent is then reacted with the primary amine to incorporate an iodoacetamido group. An oligodeoxynucleotide containing a 3'- or a 5'-disulfide is treated with a reducing agent, resulting in a terminal free thiol, which is then coupled to the iodoacetamido surface. Analysis of the surface reveals that the amount of covalently bound oligodeoxynucleotide is 250 fmol of DNA/mm(2) with ∼40% of the immobilized oligodeoxynucleotides available for hybridization. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF MS) analysis reveals that the covalent linkage to the support remains intact, only the annealed strand is desorbed by the laser, and the amount of DNA hybridized to the array is sufficient for detection.
The Earth: A geology primer (2009)

This chapter introduces the main ideas of geology, and explains briefly the technical terms used in this book. We deal with the overall structure of the Earth, the theory of plate tectonics, the main mineral groups and rock types (igneous, sedimentary and metamorphic), the deformation of rocks into folds and faults, the processes of erosion and formation of the landscape, and the geological time scale.
Prospects on Planar Quantum Computing (2009)

High-fidelity planar quantum circuits have been recently experimentally demonstrated, enabling a new generation of quantum computing, based on reliable, monolithically integrated planar optical devices. The present paper is a contribution to the development of this new concept, giving a general and at most comprehensive overview of quantum algorithms that can be implemented using planar optics devices. Starting from the four postulates of quantum mechanics, the complete set of quantum-gate operations is described using only planar 1-qubit rotations and CNOT gates, both in universal and non-deterministic forms. Both single-photon and coherent-states quantum computing are considered, and the effects of photon losses and phase noise are investigated.
Plasma DNA microsatellites as tumor-specific markers and indicators of tumor progression in melanoma patients. (1999)

Multiple DNA microsatellites with frequent loss of heterozygosity (LOH) in melanomas have been demonstrated. The finding that free DNA is enriched in blood of melanoma patients prompted studies to determine whether tumor-specific DNA, such as DNA microsatellites exhibiting LOH, can be detected in blood and have clinical use. In this study, 57 advanced and 19 early clinically staged melanoma patients were assessed using 10 microsatellite markers on six chromosomes. Matched plasma and melanoma tissues from 40 patients showed significant concordance of LOH (P < 0.0001). The frequency of LOH microsatellite markers detected in plasma significantly increased in more advanced-staged patients. At locus D3S1293, LOH detection showed significant correlation to clinical disease progression (P = 0.02). Additionally, the combination of LOH microsatellite markers D9S157 and D3S1293 (P = 0.01), D9S157 and D1S228 (P = 0.05), and D11S925 and D3S1293 (P = 0.01) were significantly correlated to progression of different clinical stages of disease. These studies indicate that tumor-specific LOH markers in plasma have a potential clinical use as diagnostic and prognostic markers in melanoma patients.
Cells isolated from adult human skeletal muscle capable of differentiating into multiple mesodermal phenotypes. (1999)

Wound healing is the response of tissue to injury that results in scar formation. Tissue regeneration would be a more ideal response. Previously, we have isolated a population of cells from avian, rodent, and rabbit skeletal muscle capable of differentiating into multiple mesodermal phenotypes. The present experiments were designed to determine whether a similar population of cells exist in human skeletal muscle. Separate cell preparations from skeletal muscle on an amputated leg of a 75-year-old female and the pectoralis muscle of a 27-year-old male were enzymatically dissociated and cultured to confluence in Eagle's minimal essential medium with 10 per cent preselected horse serum, then trypsinized, filtered, and slowly frozen in 7.5 per cent dimethylsulfoxide to -80 degrees C. The cells were thawed and plated with the same media plus dexamethasone (a nonspecific differentiation agent) at 10(-10) - 10(-6) M concentrations for up to 6 weeks. Immunological and histochemical staining assays were performed. Phenotypes observed included stem cells with typical stellate morphology (control), skeletal myotubes (anti-myosin), smooth muscle (anti-a-actin), bone (von Kossa stain), cartilage (Alcec blue), and fat (Sudan black B). These experiments establish the existence of a population of mesenchymal stem cells in human skeletal muscle capable of differentiating into multiple mesodermal phenotypes. The possibility exists of manipulating the mesenchymal stem cells to achieve appropriate regeneration of mesenchymal tissues in the injured patient.
Evaluation of the semiautomated Abbott LCx Mycobacterium tuberculosis assay for direct detection of Mycobacterium tuberculosis in respiratory specimens (1997)

Five hundred twenty processed respiratory specimens from 326 patients received for the diagnosis of tuberculosis or other mycobacterial infections were tested by means of the LCx Mycobacterium tuberculosis Assay from Abbott Laboratories, which uses ligase chain reaction technology for the direct detection of M. tuberculosis complex in respiratory specimens. The results of the LCx M. tuberculosis Assay were compared with the results of culture and staining techniques. After a combination of culture results and the patient's clinical data, a total of 195 specimens were collected from 110 patients who were positively diagnosed as having pulmonary tuberculosis. Twenty-three of these 195 specimens which corresponded to 10 patients with a history of pulmonary tuberculosis (TB) and anti-TB treatment ranging from 1 to 6 months were culture negative. The other 172 specimens were culture positive for M. tuberculosis. With an overall positivity rate of 37.5% (195 of 520 specimens), the sensitivity, specificity, and positive and negative predictive values were 90.8, 100, 100, and 94.7%, respectively, for the LCx M. tuberculosis Assay; 88.2, 100, 100, and 93.4%, respectively, for culture; and 82.6, 92, 72.9, and 97.6%, respectively, for acid-fast staining. For 161 specimens (82.6%) from patients smear positive for the disease and 34 specimens (17.4%) from patients smear negative for the disease, the sensitivity values for the LCx M. tuberculosis Assay were 98.8 and 53%, respectively. There were no statistically significant differences in the sensitivities and specificities between the LCx M. tuberculosis Assay and culture (P > 0.05). Conclusively, the LCx M. tuberculosis Assay has proved to have an acceptable sensitivity and a high specificity in detecting M. tuberculosis and has the potential of reducing the diagnosis time to an 8-h working day.
Why hunter-gatherer populations do not show signs of Pleistocene demographic expansions (1999)

The mitochondrial DNA diversity of 62 human population samples was examined for potential signals of population expansions. Stepwise expansion times were estimated by taking into account heterogeneity of mutation rates among sites. Assuming an mtDNA divergence rate of 33% per million years, most populations show signals of Pleistocene expansions at around 70,000 years (70 KY) ago in Africa and Asia, 55 KY ago in America, and 40 KY ago in Europe and the Middle East, whereas the traces of the oldest expansions are found in East Africa (110 KY ago for the Turkana). The genetic diversity of two groups of populations (most Amerindian populations and present-day hunter-gatherers) cannot be explained by a simple stepwise expansion model. A multivariate analysis of the genetic distances among 61 populations reveals that populations that did not undergo demographic expansions show increased genetic distances from other populations, confirming that the demography of the populations strongly affects observed genetic affinities. The absence of traces of Pleistocene expansions in present-day hunter-gatherers seems best explained by the occurrence of recent bottlenecks in those populations, implying a difference between Pleistocene (approximately 1,800 KY to 10 KY ago) and Holocene (10 KY to present) hunter-gatherers demographies, a difference that occurred after, and probably in response to, the Neolithic expansions of the other populations.
Nav2/NaG Channel Is Involved in Control of Salt-Intake Behavior in the CNS (2000)

Na(v)2/NaG is a putative sodium channel, whose physiological role has long been an enigma. We generated Na(v)2 gene-deficient mice by inserting the lacZ gene. Analysis of the targeted mice allowed us to identify Na(v)2-producing cells by examining the lacZ expression. Besides in the lung, heart, dorsal root ganglia, and Schwann cells in the peripheral nervous system, Na(v)2 was expressed in neurons and ependymal cells in restricted areas of the CNS, particularly in the circumventricular organs, which are involved in body-fluid homeostasis. Under water-depleted conditions, c-fos expression was markedly elevated in neurons in the subfornical organ and organum vasculosum laminae terminalis compared with wild-type animals, suggesting a hyperactive state in the Na(v)2-null mice. Moreover, the null mutants showed abnormal intakes of hypertonic saline under both water- and salt-depleted conditions. These findings suggest that the Na(v)2 channel plays an important role in the central sensing of body-fluid sodium level and regulation of salt intake behavior.
Genomic comparisons among Escherichia coli strains B, K-12, and O157:H7 using IS elements as molecular markers (2002)

These data reveal a high level of IS activity since E. coli B, K-12, and O157:H7 diverged from a common ancestor, including IS association with deletions and incorporation of horizontally acquired genes as well as transpositions. These findings indicate the important role of IS elements in genome plasticity and divergence.
Activation of the Notch pathway in the hair cortex leads to aberrant differentiation of the adjacent hair-shaft layers (2000)

Little is known about the mechanisms underlying the generation of various cell types in the hair follicle. To investigate the role of the Notch pathway in this process, transgenic mice were generated in which an active form of Notch1 (Notch(DeltaE)) was overexpressed under the control of the mouse hair keratin A1 (MHKA1) promoter. MHKA-Notch(DeltaE) is expressed only in one precursor cell type of the hair follicle, the cortex. Transgenic mice could be easily identified by the phenotypes of curly whiskers and wavy, sheen pelage hair. No effects of activated Notch on proliferation were detected in hair follicles of the transgenic mice. We find that activating Notch signaling in the cortex caused abnormal differentiation of the medulla and the cuticle, two neighboring cell types that did not express activated Notch. We demonstrate that these non-autonomous effects are likely caused by cell-cell interactions between keratinocytes within the hair follicle and that Notch may function in such interactions either by directing the differentiation of follicular cells or assisting cells in interpreting a gradient emanating from the dermal papilla.
Scheduling processes with release times, deadlines, precedence and exclusion relations (1990)

An algorithm that finds an optimal schedule on a single processor for a given set of processes is presented. Each process starts executing after its release time and completes its computation before its deadline and a given set of precedence relations and exclusion relations defined on ordered pairs of process segments are satisfied. This algorithm can be applied to the important and previously unsolved problem of automated pre-run-time scheduling of processes with arbitrary precedence and exclusion in hard-real-time systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
New Molecular and Biological Mechanism of Antitumor Activities of KW-2478, a Novel Nonansamycin Heat Shock Protein 90 Inhibitor, in Multiple Myeloma Cells (2010)

These results suggest that targeting such diverse pathways by KW-2478 could be a promising strategy for the treatment of MM with various cytogenetic abnormalities.
Biosynthetic Modulation of Sialic Acid-dependent Virus-Receptor Interactions of Two Primate Polyoma Viruses (1995)

Sialic acids are essential components of the cell surface receptors of many microorganisms including viruses. A synthetic, N-substituted D-mannosamine derivative has been shown to act as precursor for structurally altered sialic acid incorporated into glycoconjugates in vivo (Kayser, H., Zeitler, R., Kannicht, C., Grunow, D., Nuck, R., and Reutter, W. (1992) J. Biol. Chem. 267, 16934-16938). In this study we have analyzed the potential of three different sialic acid precursor analogues to modulate sialic acid-dependent virus receptor function on different cells. We show that treatment with these D-mannosamine derivatives can result in the structural modification of about 50% of total cellular sialic acid content. Treatment interfered drastically and specifically with sialic acid-dependent infection of two distinct primate polyoma viruses. Both inhibition (over 95%) and enhancement (up to 7-fold) of virus binding and infection were observed depending on the N-acyl substitution at the C-5 position of sialic acid. These effects were attributed to the synthesis of metabolically modified, sialylated virus receptors, carrying elongated N-acyl groups, with altered binding affinities for virus particles. Thus, the principle of biosynthetic modification of sialic acid by application of appropriate sialic acid precursors to tissue culture or in vivo offers new means to specifically influence sialic acid-dependent ligand-receptor interactions and could be a potent tool to further clarify the biological functions of sialic acid, in particular its N-acyl side chain.
Development of a second‐generation oncolytic Herpes simplex virus expressing TNFα for cancer therapy (2007)

This approach is therefore beneficial in increasing localised TNFalpha expression as compared to the use of non-replicative approaches, and combines the effects of TNFalpha with oncolytic virus replication which is expected to further enhance the efficacy of radiotherapy in a combined treatment approach.
Integration of human immunodeficiency virus type 1 DNA in vitro. (1990)

A highly efficient cell-free system for the integration of human immunodeficiency virus type 1 DNA is described. Linear viral DNA synthesis occurs in the cytoplasm of newly infected cells, reaching peak levels 4 hr after infection. The linear viral DNA molecules present in cytoplasmic extracts are capable of integrating into heterologous DNA targets in vitro. The viral DNA resides in a high molecular weight nucleoprotein structure that can be separated from the bulk of cellular protein and nucleic acid without a detectable decrease in the ability to integrate in vitro.
Pressure Derivative Matching Method for Two Phase Fluid Flow in Heterogeneous Reservoir (2000)

Abstract Automatic history matching method for simultaneous matching at pressure and its derivatives for two phase fluid flow in heterogeneous reservoir was developed. Adjoint method was used for calculating gradients of new objective function which consists of two parts; one is the original term and the other is the sum of differences between calculated pressure change rate and observed change rate. A set of two phase fluid flow equations which includes capillary pressure are used for calculating pressures and its change rate in the objective function. Quasi-Newton method (Self Scaling Variable Metric Method) was used as optimization algorithm. The one dimensional heterogeneous permeability distribution was estimated with the proposed method for a simple numerical model case. With this method, transient flow behavior in heterogeneous reservoir with multiple phase condition was applied for automatic history matching without too much computing time.