gebhart/patrepeval huggingface dataset:
Study on a New Preparation of D-Glucose Rich Fractions from Various Lignocelluloses through a Two-step Extraction with Sulfuric Acid (2009)

Preparing D-glucose with comparatively high yield and purity from many kinds of lignocelluloses through a basically unified method is an important technology because almost all of the yeasts show limitative use of carbon sources in ethanol fermentation. Although cellulase is of great interest in the production of D-glucose, the enzyme degradation demands a pre-treatment for loosening the hard structure of lignocelluloses. A typical acid hydrolysis of lignocelluloses digesting directly to monosaccharides is also used; however, the hydrolysate contains not only a mixture of pentose and hexose but also some chemicals inhibiting the growth of yeast. Therefore, representative samples of hardwood (Japanese oak), softwood (Japanese cedar) and annual plants (sugar cane bagasse) were examined in order to look for a convenient method of collecting oligosaccharides from these biomasses employing the concept that high-molecular-weight molecules with hard structure are gradually loosened and then degraded into low-molecular-weight molecules with strong alkaline or strong acid under mild conditions. Potassium hydroxide was suitable for the annual plant but insufficient for wood in the segregation of hemicellulose and cellulose. Concentrations of sulfuric acid for extracting selectively the majority of hemicelluloses from annual plants and wood were 42.5 and 44% (v/v), respectively. Lignocellulose (100 mg) was treated with the concentrated sulfuric acid (10 mL) at 20°C for 5 h under 120 rpm shaking condition. A treatment with 55% (v/v) sulfuric acid of the residual material under the same conditions was appropriate for preparation of oligosaccharides composed chiefly of D-glucose.
Evaluation of PCR-Generated Chimeras, Mutations, and Heteroduplexes with 16S rRNA Gene-Based Cloning (2001)

To evaluate PCR-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16S ribosomal DNA (rDNA)-based cloning approach, a model community of four species was constructed from alpha, beta, and gamma subdivisions of the division Proteobacteria as well as gram-positive bacterium, all of which could be distinguished by HhaI restriction digestion patterns. The overall PCR artifacts were significantly different among the three Taq DNA polymerases examined: 20% for Z-Taq, with the highest processitivity; 15% for LA-Taq, with the highest fidelity and intermediate processitivity; and 7% for the conventionally used DNA polymerase, AmpliTaq. In contrast to the theoretical prediction, the frequency of chimeras for both Z-Taq (8.7%) and LA-Taq (6.2%) was higher than that for AmpliTaq (2.5%). The frequencies of chimeras and of heteroduplexes for Z-Taq were almost three times higher than those of AmpliTaq. The total PCR artifacts increased as PCR cycles and template concentrations increased and decreased as elongation time increased. Generally the frequency of chimeras was lower than that of mutations but higher than that of heteroduplexes. The total PCR artifacts as well as the frequency of heteroduplexes increased as the species diversity increased. PCR artifacts were significantly reduced by using AmpliTaq and fewer PCR cycles (fewer than 20 cycles), and the heteroduplexes could be effectively removed from PCR products prior to cloning by polyacrylamide gel purification or T7 endonuclease I digestion. Based upon these results, an optimal approach is proposed to minimize PCR artifacts in 16S rDNA-based microbial community studies.
Gaussian Free-Energy Dependence of Electron-Transfer Rates in Iridium Complexes (1990)

The kinetics of photoinduced electron-transfer (ET) reactions have been measured in a series of synthetic donor-acceptor complexes. The electron donors are singlet or triplet excited iridium(I) dimers (Ir(2)), and the acceptors are N-alkylpyridinium groups covalently bound to phosphinite ligands on the Ir(2) core. Rate constants for excited-state ET range from 3.5 x 10(6) to 1.1 x 10(11) per second, and thermal back ET (pyridinium radical to Ir(2)(+)) rates vary from 2.0 x 10(10) to 6.7 x 10(7) per second. The variation of these rates with driving force is in remarkably good agreement with the Marcus theory prediction of a Gaussian free-energy dependence.
Engineering RNA–Protein Complexes with Different Shapes for Imaging and Therapeutic Applications (2014)

Molecular machines composed of RNA–protein (RNP) complexes may expand the fields of molecular robotics, nanomedicine, and synthetic biology. However, constructing and directly visualizing a functional RNP nanostructure to detect and control living cell function remains a challenge. Here we show that RNP nanostructures with modular functions can be designed and visualized at single-RNP resolution in real time. The RNP structural images collected in solution through high-speed atomic force microscopy showed that a single RNP interaction induces a conformational change in the RNA scaffold, which supports the nanostructure formation designed. The specific RNP interaction also improved RNA nanostructure stability in a serum-containing buffer. We developed and visualized functional RNPs (e.g., to detect human cancer cells or knockdown target genes) by attaching a protein or RNA module to the same RNA scaffold of an optimal size. The synthetic RNP architecture may provide alternative materials to detect and control functions in target mammalian cells.
Prediction of Collision Cross-Section Values for Small Molecules: Application to Pesticide Residue Analysis (2017)

The use of collision cross-section (CCS) values obtained by ion mobility high-resolution mass spectrometry has added a third dimension (alongside retention time and exact mass) to aid in the identification of compounds. However, its utility is limited by the number of experimental CCS values currently available. This work demonstrates the potential of artificial neural networks (ANNs) for the prediction of CCS values of pesticides. The predictor, based on eight software-chosen molecular descriptors, was optimized using CCS values of 205 small molecules and validated using a set of 131 pesticides. The relative error was within 6% for 95% of all CCS values for protonated molecules, resulting in a median relative error less than 2%. In order to demonstrate the potential of CCS prediction, the strategy was applied to spinach samples. It notably improved the confidence in the tentative identification of suspect and nontarget pesticides.
Improved motion estimation by spatial transformations and overlap (2002)

We propose a new motion model that applies overlapped motion compensation to a motion field generated by spatial transformations based motion estimation. This overlapped spatial transformations (OST) model successfully addresses the inability of the conventional block-matching technique to compensate for complex motion and inside-block motion field discontinuities. For the best performance the overlap technique must be used in both the motion estimation and compensation processes. Simulation results show that, for the tested image sequences, the quality of the motion compensated predicted images, measured in PSNR to the original images, on the average, is increased by 1.5 dB over overlapped and non-overlapped block-matching motion estimation, for the same generated motion vectors overhead. Combining low prediction error and smooth predicted images this model is suitable for very low bit rate video coding.
The future of immune checkpoint therapy (2015)

Immune checkpoint therapy, which targets regulatory pathways in T cells to enhance antitumor immune responses, has led to important clinical advances and provided a new weapon against cancer. This therapy has elicited durable clinical responses and, in a fraction of patients, long-term remissions where patients exhibit no clinical signs of cancer for many years. The way forward for this class of novel agents lies in our ability to understand human immune responses in the tumor microenvironment. This will provide valuable information regarding the dynamic nature of the immune response and regulation of additional pathways that will need to be targeted through combination therapies to provide survival benefit for greater numbers of patients.
Heterocyclic compounds XII. Quinazoline derivatives as potential antifertility agents (1979)

Abstract Several quinazoline derivatives incorporating a trans ‐stillbene moiety were synthesized as potential post‐coital antifertility agents. Some of these compunds showed low level activity in rats.
Secure program execution via dynamic information flow tracking (2004)

We present a simple architectural mechanism called dynamic information flow tracking that can significantly improve the security of computing systems with negligible performance overhead. Dynamic information flow tracking protects programs against malicious software attacks by identifying spurious information flows from untrusted I/O and restricting the usage of the spurious information.Every security attack to take control of a program needs to transfer the program's control to malevolent code. In our approach, the operating system identifies a set of input channels as spurious, and the processor tracks all information flows from those inputs. A broad range of attacks are effectively defeated by checking the use of the spurious values as instructions and pointers.Our protection is transparent to users or application programmers; the executables can be used without any modification. Also, our scheme only incurs, on average, a memory overhead of 1.4% and a performance overhead of 1.1%.
Cytochrome o (bo) is a proton pump in Paracoccus denitrificans and Escherichia coli (1989)

Spheroplasts from aerobically grown wild-type Paracoccus denitrificans cells respire with succinate despite specific inhibition of the cytochrome bc1 complex by myxothiazol. Coupled to this activity, which involves only b-type cytochromes, there is translocation of 1.5-1.9 h+/e- across the cytoplasmic membrane. Similar H+ translocation ratios are observed during oxidation of ubiquinol in spheroplasts from aerobically grown mutants of Paracoccus lacking cytochrome c oxidase, or deficient in cytochrome c, as well as in a strain of E. coli from which cytochrome d was deleted. These observations show that the cytochrome o complex is a proton pump much like cytochrome aa3 to which it is structurally related.
Immunosuppression in experimental cryptococcosis in rats. Induction of afferent T suppressor cells to a non-related antigen (1987)

To demonstrate the nature of the suppressor cells elicited in rats infected with Cryptococcus neoformans and immunized with human serum albumin (HSA), spleen mononuclear (SpM) cells were fractionated through a nylon wool column. The adherent and non-adherent populations were collected and transferred to syngeneic rats. In all cases, the non-adherent or T-enriched cells adoptively transferred suppression to HSA, however, the suppressive effects of the non-adherent cells were never as great as those of the unpassed population of SpM cells. The fractions adherent to nylon wool also diminished the delayed-type hypersensitivity response to HSA although this was not significant, but glass-adherent cells did exhibit significant suppressor activity. Immunized, non-infected rats were used as donor controls. Furthermore, we showed that the T-enriched-cells are sensitive to treatment with low doses of cyclophosphamide and that they bind HSA. These data indicate that immune suppression of the induction of the delayed-type hypersensitivity response to HSA in cryptococcosis can occur as a result of infection with C. neoformans, and that at least one mechanism involved is the induction of adherent and non-adherent suppressor cells. Characterization of the non-adherent cells indicates that they are Ts1 cells.
Hepatic Blood Perfusion Estimated by Dynamic Contrast-Enhanced Computed Tomography in Pigs (2012)

Using the DCE-CT slope method, HA perfusion estimates were accurate at low and normal flow rates, whereas PV perfusion estimates were inaccurate and imprecise. At high flow rate, both HA perfusion estimates were significantly biased.
First-line therapy with gemcitabine and paclitaxel in locally, recurrent or metastatic breast cancer: A phase II study (2005)

GT exhibited encouraging activity and tolerable toxicity as first-line therapy in metastatic breast cancer. Phase III trials for further evaluation are ongoing.
In Vivo Characterization of the Pharmacodynamics of Flucytosine in a Neutropenic Murine Disseminated Candidiasis Model (2000)

In vivo pharmacodynamic parameters have been characterized for a variety of antibacterial agents. These parameters have been studied in correlation with in vivo outcomes in order to determine (i) which dosing parameter is predictive of outcome and (ii) the magnitude of that parameter associated with efficacy. Very little is known of the pharmacodynamics of antifungal agents. We used a neutropenic murine model of disseminated candidiasis to correlate the pharmacodynamic parameters (percentage of time above the MIC, area under the concentration-time curve [AUC]/MIC and peak level/MIC) for flucytosine (5-FC) in vivo with efficacy as measured by organism number in homogenized kidney cultures after 24 h of therapy. The pharmacokinetics of 5-FC in infected mice were linear. Serum half-lives ranged from 0.36 to 0.43 h. Infection was achieved by intravenous inoculation of 10(6) CFU of yeast cells per ml via the lateral tail vein of neutropenic mice. Groups of mice were treated with fourfold escalating total doses of 5-FC ranging from 1.56 to 400 mg/kg of body weight/day divided into one, two, four, or eight doses over 24 h. Increasing doses produced minimal concentration-dependent killing ranging from 0 to 0.9 log(10) CFU/kidneys. 5-FC did, however, produce a dose-dependent suppression of growth after levels in serum had fallen below the MIC. The fungistatic dose increased from 6 to 8 mg/kg with dosing every 3 and 6 h to 70 mg/kg at with dosing every 24 h. Nonlinear regression analysis was used to determine which pharmacodynamic parameter best correlated with efficacy. Time above the MIC was the parameter best predictive of outcome, while AUC/MIC was only slightly less predictive (time above MIC, R(2) = 85%; AUC/MIC, R(2) = 77%; peak level/MIC, R(2) = 53%). Maximal efficacy was observed when levels exceeded the MIC for only 20 to 25% of the dosing interval. If one considers drug kinetics in humans, these results suggest reevaluation of current dosing regimens.
Increased anxiety behaviors in autoimmune mice. (1996)

The human autoimmune disorder systemic lupus erythematosus (SLE) is often accompanied by psychiatric manifestations including anxiety. In this study, the performance of SLE-prone NZB x NZW F1 (B/W) hybrid mice was compared with nonautoimmune NZW control mice on 3 anxiety tasks: the elevated plus maze, the open-field drink test, and the novel-object task. B/W mice displayed decreased activity as well as an anxiety profile in all 3 tasks, which was characterized by avoidance of open and exposed places even when the motivation to explore these areas was high. Cytokines are overexpressed in autoimmune disease, and NZW controls injected with the cytokine interferon-alpha displayed an anxiety profile in the plus maze. Thus, cytokines may play a role in the genesis of the behavioral manifestations of autoimmune disease.
The Electronic Spectroscopy of Dyes (1968)

Modern theories of the light‐absorption process and their application to dye molecules are reviewed. The factors governing the intensity and the wavelength of the absorption and the emission of light by dyes are discussed, together with the various fates of electronic‐excitation energy. The spectroscopic consequences of ordered dye aggregation are examined.
MHC‐peptide‐specific antibodies reveal inefficient presentation of an HLA‐A*0201‐restricted, Melan‐A‐derived peptide after active intracellular processing (2007)

MHC-peptide-specific Fab antibodies binding to HLA-A*0201 complexes presenting the wild-type EAAGIGILTV (EAA) or analogue Melan-A 10-mer ELAGIGILTV (ELA) peptide were generated to study efficacy of peptide processing and presentation. None of the selected Fab antibodies detected the naturally processed EAA/HLA-A*0201 complex on melanoma tumor cells, confirming the known low peptide number on the cell surface. To study the effect of peptide presentation and processing in more detail, genes coding for the A27L-mutated Melan-A protein or the processed ELA peptide were introduced into HLA-A*0201(+) B cells by infection with the respective recombinant vaccinia virus construct producing equimolar amounts of GFP-ubiquitin directly linked to the fragment of interest. Correlating GFP expression to actual numbers of peptide presented, 1100-2600 [corrected] ELA peptides had to be synthesized to be presented by a single MHC class I antigen-peptide complex. This number increased 10- to 20-fold when ELA peptide presentation from the A27L-mutated full length Melan-A protein was studied, since 16000-52000 [corrected] GFP molecules needed to be synthesized for the detection of one ELA peptide. Our results indicate that peptide processing rather than presentation is the rate-limiting step in our experimental setting and is much more ineffective for Melan-A than has been previously shown for other MHC class I-restricted epitopes.
Interactive Effects of Albumin and Phosphate Ions on the Corrosion of CoCrMo Implant Alloy (2007)

The corrosion behavior of CoCrMo alloy in simulated body fluids has been analyzed by electrochemical techniques and surface analysis. Interaction of albumin and phosphates present in the body fluids on the passive film of the alloy was also investigated. Electrochemical techniques such as potentiodynamic and potentiostatic polarization and electrochemical impedance spectroscopy were employed. Further, ex situ X-ray photoelectron spectroscopy and Auger electron spectroscopy analysis of the passive films were carried out. The study reveals that phosphates and proteins present in simulated body fluid play a significant role in the electrochemical properties of the metal/oxide/electrolyte interface. Surface analysis showed that both species competitively adsorb on the alloy surface. For a given passive potential, the impedance behavior of passive CoCrMo was found to depend on the way passive conditions were established. A simple model has been developed assuming a multilayer structure of the surface including an outer layer where albumin and phosphate ions adsorb, the passive film (inner layer), and the metal. This model is consistent with the obtained electrochemical and surface analysis results.
The Cross-Talk Between Gut Microbiota and Lungs in Common Lung Diseases (2020)

Emerging findings indicate there is a vital cross-talk between gut microbiota and the lungs, which is known as gut-lung axis. The gut disturbances in lung diseases including allergy, asthma, chronic obstructive pulmonary disease, cystic fibrosis and lung cancer were observed by extensive studies. Investigating how gut microbiota impact other distant organs is of great interest in recent years. Although it has not been fully understood whether the disturbance is the cause or effect of lung diseases, alterations in the gut microbial species and metabolites have been linked to changes in immune responses and inflammation as well as the disease development in the lungs. In this article, we systemically review the role and mechanisms underlying the changes in the constituent of gut microbiota and metabolites in lung diseases. In particular, the roles of gut-lung axis in mediating immune responses and reshaping inflammation are highlighted. Furthermore, we discuss the potential of strategies to manipulate the gut microbiota and metabolites as the therapeutic approach for lung diseases.
Aqueous Synthesis of Zinc Blende CdTe/CdS Magic-Core/Thick-Shell Tetrahedral-Shaped Nanocrystals with Emission Tunable to Near-Infrared (2010)

We demonstrate the synthesis of near-IR-emitting zinc blende CdTe/CdS tetrahedral-shaped nanocrystals with a magic-sized (approximately 0.8 nm radius) CdTe core and a thick CdS shell (up to 5 nm). These high-quality water-soluble nanocrystals were obtained by a simple but reliable aqueous method at low temperature. During the growth of the shell over the magic core, the core/shell nanocrystals change from type I to type II, as revealed by their enormous photoluminescence (PL) emission peak shift (from 480 to 820 nm) and significant increase in PL lifetime (from approximately 1 to approximately 245 ns). These thick-shell nanocrystals have a high PL quantum yield, high photostability, compact size (hydrodynamic diameter less than 11.0 nm), and reduced blinking behavior. The magic-core/thick-shell nanocrystals may represent an important step toward the synthesis and application of next-generation colloidal nanocrystals from solar cell conversion to intracellular imaging.
Monoclonal Antibody Prophylaxis Against thein VivoToxicity of Ricin in Mice (1993)

A BALB/c murine IgG1 monoclonal antibody, designated BG11-G2, specific for ricin was generated. BG11-G2 antibody did not bind to either purified ricin chain A or chain B, but recognized an antigenic determinant whose conformation requires the combination of the two chains in the formation of the native ricin molecule. It did not react with the protein synthesis inhibitor, T-2 mycotoxin, or with the sodium channel blockers, saxitoxin and tetrodotoxin. As little as 0.78 micrograms/ml of BG11-G2 IgG1 anti-ricin monoclonal antibody completely protected against the in vitro toxicity of ricin as determined by [3H]leucine uptake in EL-4 cell assays. Passive intraperitoneal infusion of purified BG11-G2 antibody into BALB/c mice one day prior to a lethal challenge with ricin considerably delayed the onset of toxicity and death. Better protection was obtained with BG11-G2 infused before and after ricin challenge.
Resources for the design of CRISPR gene editing experiments (2015)

CRISPR-based approaches have quickly become a favored method to perturb genes to uncover their functions. Here, we review the key considerations in the design of genome editing experiments, and survey the tools and resources currently available to assist users of this technology.
Application of an approximate time delay to a Posicast control system† (1971)

The performance of a method of producing relatively long time delays, using truncated Fourier series expansion, applied to a Posicast control system was investigated. The controlled system had a long natural period and was lightly damped. Both the Posicast control and the system were simulated on an analogue computer. The response of the system to step inputs with Posicast showed dramatic improvement over the uncompensated system. The overall system approached the theoretical response of an ideal Posicast system. A series of runs was made with successively cruder approximations of the delay function. Response was not seriously degraded until the frequency of the truncated terms became comparable to the upper 3 dB frequency of the controlled system. Other waveforms were tested, including sine, square, sawtooth and quasi-random signals. In all cases, the performance of the system was well behaved. The approximate method of delay, therefore, offers a means of implementing Posicast control with systems requiring relatively long delays of continuously variable inputs.
Collagenase Inhibitors: Their Design and Potential Therapeutic Use (1987)

Click to increase image sizeClick to decrease image sizeKey Words: : Collagenasemammalianinhibitorthiolhydroxamatemodelpeptidetherapeutic uses