gebhart/patrepeval huggingface dataset:
Electroreductive formation of polysilanes (1990)

Electroreduction of dichlorosilanes, such as 1,1-dichlorodialkylsilanes, 1,2-dichlorotetra-alkyldisilanes, and 1,4-bis(chlorodialkylsilyl)benzenes, with Mg electrodes in a single-compartment cell was found to yield the corresponding polysilanes.
Isolation of the Arabidopsis ABI3 gene by positional cloning. (1992)

Arabidopsis abi3 mutants are altered in various aspects of seed development and germination that reflect a decreased responsiveness to the hormone abscisic acid. The ABI3 gene has been isolated by positional cloning. A detailed restriction fragment length polymorphism (RFLP) map of the abi3 region was constructed. An RFLP marker closely linked to the abi3 locus was identified, and by analyzing an overlapping set of cosmid clones containing this marker, the abi3 locus was localized within a 35-kb region. An 11-kb subfragment was then shown to complement the mutant phenotype in transgenic plants, thereby further delimiting the position of the locus. A candidate ABI3 gene was identified within this fragment as being expressed in developing fruits. The primary structure of the encoded protein was deduced from sequence analysis of a corresponding cDNA clone. In the most severe abi3-4 allele, the size of this predicted protein was reduced by 40% due to the presence of a point mutation that introduced a premature stop codon. The predicted ABI3 protein displays discrete regions of high similarity to the maize viviparous-1 protein.
Functional Characterization of Complement Proteases C1s/Mannan-binding Lectin-associated Serine Protease-2 (MASP-2) Chimeras Reveals the Higher C4 Recognition Efficacy of the MASP-2 Complement Control Protein Modules (2005)

C1s and mannan-binding lectin-associated serine protease-2 (MASP-2) are the proteases that trigger the classical and lectin pathways of complement, respectively. They have identical modular architectures and cleave the same substrates, C2 and C4, but show markedly different efficiencies toward C4. Multisite-directed mutagenesis was used to engineer hybrid C1s/MASP-2 molecules where either the complement control protein (CCP) modules or the serine protease (SP) domain of C1s were swapped for their MASP-2 counterparts. The resulting chimeras (C1s(MASP-2 CCP1/2) and C1s(MASP-2 SP), respectively) were expressed and characterized chemically and functionally. Whereas C1s(MASP-2 SP) was recovered as an active enzyme, C1s(MASP-2 CCP1/2) was produced in a proenzyme form and was susceptible to activation by C1r, indicating that the activation properties of the chimeras were dictated by the nature of their SP domain. Similarly, each activated chimera had an esterolytic activity characteristic of its own SP domain and cleaved C2 with an efficiency comparable with that of their parent C1s and MASP-2 proteases. Both chimeras cleaved C4, but whereas C1s(MASP-2 SP) and C1s had Km values in the micromolar range, C1s(MASP-2 CCP1/2) and MASP-2 had Km values in the nanomolar range, resulting in 21-27-fold higher kcat/Km ratios. Thus, the higher C4 cleavage efficiency of MASP-2 arises from a higher substrate recognition efficacy of its CCP modules. Remarkably, C1s(MASP-2 CCP1/2) retained C1s ability to associate with C1r and C1q to form a pseudo-C1 complex and to undergo activation within this complex, indicating that the C1s-CCP modules have no direct implication in either function.
Voids, Layers, and the First Sharp Diffraction Peak inZnCl2 (1998)

The origin of the first-sharp diffraction peak (FSDP) in supercooled liquid ${\mathrm{ZnCl}}_{2}$ (a network-forming, intermediate strength fluid) is studied by computer simulation. Measures are introduced to characterize voids in the spatial distribution of cations and the existence of transient layered structures and to clarify their role in producing the FSDP. It is shown that the position of the FSDP is set by the mean intervoid separation and that its intensity is due to density fluctuations with a layered character even well above the glass transition.
Timing of activity in early visual cortex as revealed by transcranial magnetic stimulation (1999)

To determine the timing of visual processing in the early visual cortex, we applied single pulse transcranial magnetic stimulation to the occipital pole of healthy subjects while they were engaged in a forced-choice visual letter-identification task. We found two separate periods of activity, the first ranging from 20 to 60 ms after the onset of the visual stimulus, and the second ranging from 100 to 140 ms after the onset of the visual stimulus. We suggest that these two periods reflect necessary activity in V1, before and after re-entry.
Phase II Trial of Intratumoral Administration of ONYX-015, a Replication-Selective Adenovirus, in Patients With Refractory Head and Neck Cancer (2001)

ONYX-015 can be safely administered via intratumoral injection to patients with recurrent/refractory SCCHN. ONYX-015 viremia is transient. Evidence of modest antitumoral activity is suggested.
Immunization of adult hamsters against Clostridium difficile-associated ileocecitis and transfer of protection to infant hamsters (1987)

In this investigation, the role of antibodies against Clostridium difficile toxins A and B in protecting hamsters against C. difficile-associated ileocecitis was examined. We also studied the transfer of protection against C. difficile-associated intestinal disease from immunized female hamsters to their infants. Adult female hamsters immunized parenterally with toxoid A or a mixture containing both toxoids A and B were protected against clindamycin-induced C. difficile-associated fatal ileocecitis. On the other hand, hamsters immunized with toxoid B or a broth filtrate from a nontoxigenic strain of C. difficile were not protected against C. difficile-induced ileocecitis. Antibody against the immunizing toxoid could be demonstrated in both the serum and the cecal contents of hamsters. Some infant hamsters from mothers immunized with toxoid A or AB were protected against C. difficile-associated ileocecitis, while infant hamsters from mothers immunized with toxoid B or a nontoxigenic broth filtrate were not protected against disease. Neutralizing antibodies to toxins A and B could be demonstrated in both maternal milk and serum, as well as in infant serum and intestinal contents. Foster-mothering experiments demonstrated that maternal protection of infants against C. difficile-associated ileocecitis was transferred to infant hamsters through breast milk. These results suggest that toxin A may play a more important role in the pathogenesis of C. difficile-associated ileocecitis in hamsters than toxin B. Furthermore, variations in the severity of C. difficile-associated illness in infants and adults may reflect the lack or presence of passively or actively acquired immunity against C. difficile toxins.
Steady Flow of Gas-oil-water Mixtures through Unconsolidated Sands (1941)

The dynamic behavior of a multiple fluid system is completely describable interms of driving forces and resistances to flow. The latter are proportional tothe viscosity of the fluid under consideration and inversely proportional to aproperty of the system termed the" effective permeability" to thatfluid, a property therefore defined by this relation. Since three phases are usually present in oil reservoirs, it is essential toknow the effective permeabilities to the several fluid phases, and therelationship between the composition of the fluid in the pore space and that ofthe flowing stream, in order to handle satisfactorily certain problems of oilproduction. In this regard, there are many unknown factors and parameters, andmany that can be evaluated only indirectly. However, it is expected that workalong lines similar to this present undertaking will help materially in solvingthese problems. Previous workers in this field have investigated the two-phase systems, water-gas, water-oil in unconsolidated sands, and water-gas in consolidatedsands. The extension of the study of the flow of heterogeneous fluid systemsfrom two to three phases involved only slight changes in technique. Theapparatus used in the present work, except for slight changes to be described, was that used by Leverett in his water-oil experiments. Correlation andinterpretation of data were made by methods analogous to those used in two-phase work. The relative permeability to a phase-the effective permeabilitydivided by the permeability of the system to a homogeneous fluid-was employedthroughout in correlating the rate of flow of that phase with the compositionof the pore space. Quantitative measurements of two independent physical properties of the systemwere required to determine the composition of the pore space. As in thetwo-phase work, the fraction of water was determined electrically. The gasfraction was determined by measuring changes in volume accompanying measuredpressure changes. Suitable account was taken of the solubility of the gas inthe liquid phases, and of the vapor pressure of the water phase. Since thiswork was exploratory in nature, no attempt was made to obtain highly accuratenumerical results. Reasonable precision and reproducibility were sought. Experimental Procedure Variables Considered.-Of the properties of the fluids, the oil viscosity ismost likely in practice to vary widely. Variations in oil viscosity weretherefore included in this work, but variations in other properties of thefluids are as yet unexplored. It appears unlikely that the normally encounteredvariations will produce significant changes. The observations were made atfairly high pressure gradients, no attempt being made to detect a variation ofthe relative permeabilities with pressure gradient. T.P. 1206
New Criteria for Alzheimer Disease and Mild Cognitive Impairment (2012)

These new criteria are immediately helpful to the practicing clinician, providing more accurate and specific guidelines for the diagnosis of AD dementia and MCI due to AD. As new diagnostic tools and new treatments for AD become available, diagnosis using these criteria will enable patients with this disorder to receive the best possible care.
Receive Side Processing for Automotive Hands-Free Systems (2008)

In the sending path of automotive hands-free systems several subunits - such as acoustic echo cancellation (AEC) and noise reduction (NR) - improve the quality of the outgoing signal. These units are usually realized in the frequency or subband domain in order to reduce the computational complexity. In the receiving path, however, only a few signal processing stages - such as bandwidth extension (BWE) [1] or gain adjustment - are realized in recent systems [2, 3]. These units are implemented in most cases in the time domain, since two analysis-synthesis schemes (one in the sending and one in the receiving path) would introduce more delay than allowed by ITU- or VDA-recommendations [4]. According to the best knowledge of the authors linking of conventional processing schemes in the sending path (AEC and NR) with those of the receiving path has not yet been addressed in research on hands-free systems. For the car environment some amplifier manufacturers perform a volume control in dependence of the driving speed of the car. Some have even the possibility of placing a microphone in the cabin for measuring the noise level within the car [2, 5]. But this does not apply to hands-free telephony. The estimated power spectral density (PSD) of the background noise (already estimated within the NR unit) can be used to adjust the BWE unit. Since in high noise conditions, artifacts introduced by a BWE scheme are less audible a stronger extension can be used compared to stand-still operation. Taking also the estimated echo spectrum into account (beside the noise PSD) an estimate for the SNR within the car cabin can be obtained. Using this estimate one could perform an automatic gain control of the receive signal for retaining a particular SNR within the car while the noise or the speaking level of the remote partner is changing. This can also be done in a frequency specific manner, resulting in a frequency selective adaptive equalization. No further microphone has to be placed in the cabin and the volume can be controlled independent of the amplifier using the resources (AEC, NR) already available.
Ellipsometric spectra and growth of MgO thin films by pulsed laser deposition (2003)

2002-2003 > Academic research: refereed > Publication in refereed journal
Command shaping for residual vibration free crane maneuvers (2005)

Cranes used in the construction and transportation industries are generally devices with multiple degrees of freedom including variable load-line length, variable jib length (usually via a trolley), and variable boom angles. Point-to-point payload maneuvers using cranes are performed so as not to excite the spherical pendulum modes of their cable and payload assemblies. Typically, these pendulum modes, although time-varying, exhibit low frequencies. Current crane maneuvers are therefore performed slowly contributing to high construction and transportation costs. This investigation details a general method for applying command shaping to various multiple degree of freedom cranes such that the payload moves to a specified point without residual oscillation. A dynamic programming method is used for general command shaping for optimal maneuvers. Computationally, the dynamic programming approach requires order M calculations to arrive at a solution, where M is the number of discretizations of the input commands. This feature is exploited for the crane command shaping problem allowing for rapid calculation of command histories. Fast generation of commands is a necessity for practical use of command shaping for the applications described in this work. These results are compared to near-optimal solutions where the commands are linear combinations of acceleration pulse basis functions. The pulse shape is required due to hardware requirements. The weights on the basis functions are chosen as the solution to a parameter optimization problem solved using a recursive quadratic programming technique. Simulation results and experimental verification for a variable load-line length rotary crane are presented using both design procedures.
Intramolecular Reactions of Alkynes with Furans and Electron Rich Arenes Catalyzed by PtCl2:  The Role of Platinum Carbenes as Intermediates (2003)

5-(2-Furyl)-1-alkynes react, with PtCl(2) as catalyst, to give phenols. On the basis of DFT calculations, a cyclopropyl platinacarbene complex was found as the key intermediate in the process. The cyclopropane and dihydrofuran rings of this intermediate open to form a carbonyl compound, which reacts with the platinum carbene to form an oxepin, which is in equilibrium with an arene oxide. When the reaction is carried out in the presence of water, dicarbonyl compounds are obtained, which support the proposed mechanism. Other cyclizations of alkynes with furans or electron-rich arenes give products of apparent Friedel-Crafts-type reactions, although these processes could also proceed by pathways involving the formation of cyclopropyl platinum carbenes.
Cancer-Associated Carbonic Anhydrases and Their Inhibition (2008)

Cells of the growing tumor tissue are exposed to physiological stresses connected with insufficient delivery of oxygen (hypoxia) and accumulation of acidic products of the glycolytic metabolism (acidosis). Adaptation to these microenvironmental stresses involves remodeling of the cellular expression program mediated by hypoxia-inducible factor (HIF), which activates broad array of genes functionally involved in angiogenesis, anaerobic glycolysis, de-adhesion, invasion etc. This leads to increased aggressiveness of tumors, metastatic spread and poor response to therapy. Genes coding for transmembrane carbonic anhydrase (CA) isoforms IX and XII are induced in response to low oxygen as a part of the hypoxic transcriptome. Moreover, CA IX is a direct target of HIF and serves as a surrogate marker of hypoxia and prognostic indicator. Its expression is strongly linked to different types of tumors with the HIF pathway activated due to genetic defect or physiological hypoxia. CA IX (and possibly also CA XII) is participates in pH regulation, which is important for survival of hypoxic cells. Both enzymes are therefore promising therapeutic molecules targetable by inhibitors of CA activity. Some of these sulfonamide compounds and their derivatives are capable to block CA-mediated pH regulation in hypoxia. This review summarizes research data related to distribution, regulation and functional aspects of CA IX and CA XII, and describes emerging possibilities for clinical exploitation of CA inhibitors as imaging tools and anticancer drugs.
Influenza A Virus Coding Regions Exhibit Host-Specific Global Ordered RNA Structure (2012)

Influenza A is a significant public health threat, partially because of its capacity to readily exchange gene segments between different host species to form novel pandemic strains. An understanding of the fundamental factors providing species barriers between different influenza hosts would facilitate identification of strains capable of leading to pandemic outbreaks and could also inform vaccine development. Here, we describe the difference in predicted RNA secondary structure stability that exists between avian, swine and human coding regions. The results predict that global ordered RNA structure exists in influenza A segments 1, 5, 7 and 8, and that ranges of free energies for secondary structure formation differ between host strains. The predicted free energy distributions for strains from avian, swine, and human species suggest criteria for segment reassortment and strains that might be ideal candidates for viral attenuation and vaccine development.
Molecular Cloning, DNA Sequence Analysis, and Biochemical Characterization of a Novel 65-kDa FK506-binding Protein (FKBP65) (1995)

We have identified a mouse gene encoding a 65-kDa protein (FKBP65) that shares homology with members of the FK506-binding protein (FKBP) class of immunophilins. Predicted amino acid sequence shows that this protein shares significant homology with FKBP12 (46%), FKBP13 (43%), FKBP25 (35%), and FKBP52 (26%). FKBP65 contains four predicted peptidylprolyl cistrans-isomerase (PPIase) signature domains, and, although similar in size, is distinct from FKBP52 (also identified as FKBP59, hsp56, or HBI), which contains three FKBP12-like PPIase domains. With N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as the substrate, recombinant FKBP65 is shown to accelerate the isomerization of the prolyl peptide bond with a catalytic efficiency similar to other family members. This isomerization activity is inhibited by FK506 and rapamycin, but is not sensitive to Cyclosporin A. Based on Northern blot analysis, FKBP65 mRNA transcripts are present in lung, spleen, heart, brain, and testis. A polyclonal antibody, raised against a COOH-terminal peptide (amino acid residues 566-581), was used to immunoprecipitate FKBP65 from NIH3T3 cells and demonstrate that FKBP65 is a glycoprotein. In addition, [32P]orthophosphate labeling experiments show that FKBP65 is also a phosphoprotein. These results suggest that FKBP65 is a new FKBP family member.
Temporally resolved catecholamine spikes correspond to single vesicle release from individual chromaffin cells. (1991)

Secretion of catecholamines from single bovine chromaffin cells in culture was elicited by brief pressure ejections from a micropipette containing nicotine, carbamoylcholine, or potassium ions or by mechanical stimulation. Release was monitored electrochemically with a carbon-fiber microelectrode placed adjacent to the cell. Cyclic voltammetry was used to identify secreted species, whereas constant potential amperometry was used for improved temporal resolution (millisecond range) of catecholamine detection. During secretion, brief current spikes were observed, which were shown to be due to detection of catecholamines by electrooxidation. The spikes have the physical characteristics of multimolecular packets of catecholamines released at random times and locations from the surface of the single cell. The half-width of the spikes was found to increase with an increase in cell-electrode spacing. The properties of the catecholamine spikes correlate well with expectations based on secretion from individual storage vesicles. Spikes do not occur in the absence of Ca2+ in the buffer, and the majority of spikes are found to be distributed between 0.2 and 2 picocoulombs, corresponding to 1-10 attomoles of catecholamine detected. The frequency of the spikes increases with the intensity of the stimulus, but the average quantity of catecholamine in each spike is independent of the stimulus. Thus, these measurements represent time-resolved observation of quantal secretion of catecholamines and provide direct evidence for the exocytotic hypothesis.
Escherichia coli mutants with altered control of alcohol dehydrogenase and nitrate reductase (1980)

Mutants of Escherichia coli which overproduce alcohol dehydrogenase were obtained by selection for the ability to use ethanol as an acetate source in a strain auxotrophic for acetate. A mutant having a 20-fold overproduction of alcohol dehydrogenase was able to use ethanol only to fulfill its acetate requirement, whereas two mutants with a 60-fold overproduction were able to use ethanol as a sole carbon source. The latter two mutants produced only 25% of the wild-type level of nitrate reductase, when grown under anaerobic conditions. Alcohol dehydrogenase production was largely unaffected by catabolite repression but was repressed by nitrate under both aerobic and anaerobic conditions. The genetic locus responsible for alcohol dehydrogenase overproduction was located at min 27 on the E. coli genetic map; the gene order, as determined by transduction, was trp tonB adh chlC hemA. The possible relationship of alcohol dehydrogenase to anaerobic redox systems such as formate-nitrate reductase is discussed.
A tissue-specific enhancer confers Pit-1-dependent morphogen inducibility and autoregulation on the pit-1 gene. (1993)

Pit-1 is a tissue-specific POU domain factor obligatory for the appearance of three cell phenotypes in the anterior pituitary gland. Expression of the pit-1 gene requires the actions of a cell-specific 390-bp enhancer, located 10 kb 5' of the pit-1 transcription initiation site, within sequence that proves essential for effective pituitary targeting of transgene expression during murine development. The enhancer requires the concerted actions of a cell-specific cis-active element, Pit-1 autoregulatory sites, and atypical morphogen response elements. Pituitary ontogeny in the Pit-1-defective Snell dwarf mouse reveals that pit-1 autoregulation is not required for initial activation or continued expression during critical phases of Pit-1 target gene activation but, subsequently, is necessary for maintenance of pit-1 gene expression following birth. A potent 1,25-dihydroxyvitamin D3-responsive enhancer element defines a physiological site in which a single nucleotide alteration in the sequence of core binding motifs modulates the spacing rules for nuclear receptor response elements. Unexpectedly, the major retinoic acid response element is absolutely dependent on Pit-1 for retinoic acid receptor function. On this DNA element, Pit-1 appears to function as a coregulator of the retinoic acid receptor, suggesting an intriguing linkage between a cell-specific transcription factor and the actions of morphogen receptors that is likely to be prototypic of mechanisms by which other cell-specific transcription factors might confer morphogen receptor responsivity during mammalian organogenesis.