gebhart/patrepeval huggingface dataset:
Quantitative biomolecular imaging by dynamic nanomechanical mapping (2014)

The ability to 'see' down to nanoscale has always been one of the most challenging obstacles for researchers to address fundamental questions. For many years, researchers have been developing scanning probe microscopy techniques to improve imaging capability at nanoscale. Among them, atomic force microscopy (AFM) has received considerable attention, which allows probing topography of biological species at real space under physiological environment. Importantly, force measurements in AFM enable researchers to reveal not only the topography but also the relevant physical-chemical properties. AFM-based dynamic nanomechanical mapping (DNM) provides insights into the functions of biological systems by the interpretation of 'force', which are inaccessible by most of the other analytic techniques. This review is aiming to shed light on these recently developed AFM-based DNM techniques for biomolecular imaging, and discuss the relative applications in biological research from the nanomechanical point of view.
Two neural pathways for Fourier and non-Fourier motion (2002)

Humans can perceive non-Fourier visual motion, i.e., motion that contains no coherent structure in the distribution of stimulus energy in the spatiotemporal frequency domain. The question that still remains unanswered is whether this non-Fourier motion is analyzed by a separate neural pathway or whether there is a unique pathway that is responsible for both Fourier and non-Fourier motion analysis. We present experimental evidence that strongly supports the separate-pathway hypothesis, and we suggest a possible computational model that can account for the data.
RNAi-mediated downregulation of MMP-2 activates the extrinsic apoptotic pathway in human glioma xenograft cells (2009)

Malignant gliomas are characterized by invasive and infiltrative behavior that generally involves the destruction of normal brain tissue. Strategies to treat infiltrating gliomas, such as chemotherapy and gene therapy, have remained largely unsuccessful. The infiltrative nature of gliomas can be attributed largely to proteases, which include serine, metallo- and cysteine- proteases. Our previous work and that of others strongly suggest a relationship between the expression of uPAR, MMP-9, and MMP-2; this relationship is generally indicative of the infiltrative phenotype of gliomas. In the present study, we have demonstrated that the RNAi-mediated downregulation of MMP-2 induces apoptosis in the 4910 human glioma xenograft cell line. Using Western blot analysis, we observed that caspase-8 levels increased in MMP-2-downregulated cells whereas TRADD and TRAF-2 levels decreased. Further, NIK levels increased in MMP-2-downregulated cells. To determine the nuclear localization of AIF and IkappaBalpha, we analyzed the levels of AIF, IkappaBalpha and pIkappaBalpha in the cytosolic and nuclear fractions of MMP-2-downregulated cells. Western blot analysis revealed that MMP-2 downregulation resulted in the translocation of AIF to the nucleus and also inhibited the nuclear localization of pIkappaBalpha. To confirm the involvement of AIF, we performed FACS analysis to determine the integrity of the mitochondrial membrane using the MitoPT method. FACS analysis showed that the downregulation of MMP-2 caused a collapse in the mitochondrial cell membrane. Immunolocalization of AIF revealed that in MMP-2-downregulated cells, AIF translocates to the nucleus, thereby enabling the induction of apoptosis. RT-PCR analysis revealed that caspase-8 was overexpressed 57-fold, whereas p73 was downregulated 28-fold. Evidence of apoptosis was determined by TUNEL assay and visualization of nuclear fragmentation by DAPI staining. In summary, it is evident from our results that MMP-2 downregulation induces caspase-8 and AIF-mediated apoptosis and, as such, shows potential for glioma therapy.
Oxime Decorated Cavitands Functionalized through Solvent-Assisted Grinding (2010)

In order to assemble supramolecular capsules, there is a need for reliable and effective synthetic methods for decorating cavitand-based host structures with appropriate functional groups. The synthesis of four different cavitands of significantly different depth and interior volume functionalized with four aldoxime groups capable of forming homomeric or heteromeric capsules through hydrogen bonding is reported. The final step in each synthesis, the aldehyde to oxime transformation, has been achieved in excellent yields through 'solvent assisted grinding'.
Freezing and Lyophilizing Alters the Structure of Bentonite Gels (1962)

During quick-freezing with liquid nitrogen all but two molecular layers of water moved from between the crystals of saturated bentonite gels. The water molecules appear to have migrated to ice crystals forming near the clay crystals. Lyophilizing removed the ice crystals and further reduced interlayer water. Both quick-freezing and lyophilizing altered the original gel structure.
Demonstrating the<i>In Situ</i>Biodegradation Potential of Phenol Using Bio‐Sep<sup>®</sup>Bio‐Traps<sup>®</sup>and Stable Isotope Probing (2013)

Abstract The effect of phenol concentration on phenol biodegradation at an industrial site in the south of Wales, United Kingdom, was investigated using standard Bio‐Sep ® Bio‐Traps ® and Bio‐Traps ® coupled with stable isotope probing (SIP). Unlike many 13 C‐amendments used in SIP studies (such as hydrocarbons) that physically and reversibly adsorb to the activated carbon component of the Bio‐Sep ® beads, phenol is known to irreversibly chemisorb to activated carbon. Bio‐Traps ® were deployed for 32 days in nine site groundwater monitoring wells representing a wide range of phenol concentrations. Bio‐Traps ® amended with 13 C‐phenol were deployed together with non‐amended Bio‐Traps® in three wells. Quantitative polymerase chain reaction (qPCR) analysis of Bio‐Traps ® post‐deployment indicated an inhibitory effect of increasing phenol concentration on both total eubacteria and aerobic phenol‐utilizing bacteria as represented by the concentration of phenol hydroxylase gene. Despite the chemisorption of phenol to the Bio‐Sep ® beads, activated carbon stable isotope analysis showed incorporation of 13 C into biomass and dissolved inorganic carbon (DIC) in each SIP Bio‐Trap ® indicating that chemisorbed amendments are bioavailable. However, there was a clear effect of phenol concentration on 13 C incorporation in both biomass and DIC confirming phenol inhibition. These results suggest that physical reductions of the phenol concentrations in some areas of the plume will be required before biodegradation of phenol can proceed at a reasonable rate. © 2013 Wiley Periodicals, Inc.
Evidence for excessive Th2 CD4+ subset activity in vivo. (1993)

Although distinct Th1 and Th2 CD4+ subsets are apparent in in vitro studies, controversy exists over whether these subsets occur functionally in vivo. We describe a patient whose presenting laboratory features of elevated IgG4 and IgE and eosinophilia suggested high levels of IL-4 and IL-5 and in vivo expansion of the CD4+ Th2 subset. Anti-CD3-activated patient PBL induced heightened levels of IgG4 and IgE from normal B cells, indicating that the patient's abnormal Ig isotypes were T cell driven. Stimulated PBL from the patient secreted more IL-4, compared with control PBL, but similar levels of IFN-gamma. Semiquantitative reverse polymerase chain reaction demonstrated that activated PBL from the patient produced higher IL-4 and IL-5, lower IL-2, and similar IFN-gamma mRNA levels, compared with controls. FACS analysis showed that the patient expressed an expanded population of CD4+Leu-8+CD45RA- cells, the memory-effector population, and RNA in situ hybridization confirmed that the CD4+Leu-8+CD45RA- population of the patient was enriched for IL-4-transcribing cells. Moreover, IL-4-transcribing cells outnumbered IFN-gamma-transcribing cells by 2:1 in the memory-effector CD4 population, confirming that Th2 cells exist in vivo within the expanded CD4+Leu-8+CD45RA- population. Taken together, these results provide evidence that Th2 cells exist in vivo and they suggest that the expanded Th2 population produces excessive cytokines that may contribute to the sinopulmonary pathology of the patient.
Inhibition of mineralocorticoid receptor is a renoprotective effect of the 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitor pitavastatin (2010)

The beneficial effects of pitavastatin are likely attributable, at least in part, to attenuation of the mineralocorticoid receptor-dependent inflammatory mediator, matrix protein, and cathepsin expressions induced by AT1R-mediated NADPH oxidase activation in the kidneys of a salt-induced hypertensive Dahl salt-sensitive rat model.
Substructure in the Radiation Survival Response at Low Dose in Cells of Human Tumor Cell Lines (1996)

In earlier studies using asynchronously growing Chinese hamster cells, we observed substructure in the survival response at low doses. The substructure appeared to result from subpopulations of cells having different, cell cycle phase-dependent radiosensitivity. We have now applied the same flow cytometry and cell sorting technique to accurately measure the responses of cells of eight different asynchronously growing human tumor cell lines, representing a wide range in radiosensitivity. When the data were fitted with a linear-quadratic (LQ) function, most of these lines showed substructure similar to that observed in Chinese hamster cells, with the result that values of alpha and beta were dependent on the dose range used for fitting. Values of alpha describing the low-dose response were typically smaller (by as much as 2.2 times) than the alpha describing the high-dose response, while values of beta were larger at low doses. Values of alpha/beta from our measurements are in reasonable agreement with other values published recently if we fit the data for the high-dose range (excluding, for example, 0-4 Gy), which corresponds to a conventional survival response measurement. However, the values of alpha/beta describing the low-dose range were, on average, 2.8-fold smaller. The results show that the usual laboratory measurement of cell survival over 2 or 3 logs of cell killing, if fitted with a single LQ function, will yield alpha and beta values which may give a rather poor description of cell inactivation at low dose in asynchronous cells, no matter how carefully those measurements are done, unless the low-dose range is fitted separately. The contribution of killing represented by the beta coefficient at low doses was found to be surprisingly large, accounting for 40-70% of cell inactivation at 2 Gy in these cell lines. A two-population LQ model provides excellent fits to the data for most of the cell lines though, as one might expect with a five-parameter model, the best-fitting value of the various parameters is far from unique, and the values are probably not reliable indicators of the size and radiosensitivity of the different cell subpopulations. At very low dose, below 0.5-1 Gy, another order of substructure is observed: the hypersensitive response; this is described in the accompanying paper (Wouters et al., Radiat. Res. 146, 399-413, 1996).
Assessing branching structure for biomass and wood quality estimation using terrestrial laser scanning point clouds (2018)

Terrestrial laser scanning (TLS) accompanied by quantitative tree-modeling algorithms can potentially acquire branching data non-destructively from a forest environment and aid the development and calibration of allometric crown biomass and wood quality equations for species and geographical regions with inadequate models. However, TLS’s coverage in capturing individual branches still lacks evaluation. We acquired TLS data from 158 Scots pine (Pinus sylvestris L.) trees and investigated the performance of a quantitative branch detection and modeling approach for extracting key branching parameters, namely the number of branches, branch diameter (bd) and branch insertion angle (bα) in various crown sections. We used manual point cloud measurements as references. The accuracy of quantitative branch detections decreased significantly above the live crown base height, principally due to the increasing scanner distance as opposed to occlusion effects caused by the foliage. bd was generally underestimated, when comparing to the manual reference, while bα was estimated accurately: tree-specific biases were 0.89 cm and 1.98°, respectively. Our results indicate that full branching structure remains challenging to capture by TLS alone. Nevertheless, the retrievable branching parameters are potential inputs into allometric biomass and wood quality equations.
Data associated with 'On-chip preparation of nanoscale contrast agents toward high-resolution ultrasound imaging' (2016)

This data set supports images and graphs in a the manuscript listed above. In brief: a new microfluidic method for the generation of sub-micron sized lipid stabilised particles containing perfluorocarbon (PFC). The nanoparticles are produced in a unique atomisation-like flow regime at high production rates, in excess of 106 particles / s and at high concentration, typically > 1011 particles / mL. The average particle diameter appears to be around 100-200 nm. These particles, suspected of being a mix of liquid and gaseous C4F10 due to Laplace pressure, then phase convert into nanometer sized bubbles on the application of US. In vitro ultrasound characterisation from these nanoparticle populations showed strong backscattering compared to aqueous filled liposomes of a similar size. The nanoparticles were stable upon injection and gave excellent contrast enhancement when used for in vivo imaging, compared to microbubbles with an equivalent shell composition.
Polyriboinosinic:polyribocytidylic acid enhances rabbit slow-wave sleep (1988)

Drowsiness and fever are common symptoms of many viral diseases. It has been postulated that double-stranded RNA (dsRNA) produced during viral replication may cause these symptoms by direct toxic effects or by inducing interferon (IFN) or other cytokine production. Polyriboinosinic:polyribocytidylic acid (poly I:C), a pyrogenic and IFN-inducing synthetic dsRNA, and polyriboadenylic:polyribouridylic acid (poly A:U), a less effective pyrogen and IFN-inducing substance, were used as models of viral dsRNA to further characterize the physiological response to dsRNA. Poly I:C was injected either intravenously or intracerebroventricularly into rabbits, and electroencephalograph, body movement, and brain temperature were monitored over the next 6 h; blood samples were taken 24 h postinjection. Poly I:C increased slow-wave sleep duration, suppressed rapid-eye-movement sleep, and induced fever but failed to raise plasma Cu. Dose-dependent responses occurred after intravenous or intracerebroventricular injections; minimal effective doses were 0.3 micrograms/kg (iv) and 1.0 ng (icv). Poly A:U failed to alter the sleep or temperature parameters measured. Responses elicited by poly I:C were distinct from those elicited by bacterial products, e.g., endotoxin enhances plasma Cu levels, thus implying different mechanisms. We conclude that poly I:C enhances slow-wave sleep and body temperature without provoking the acute-phase rise in plasma Cu. These effects may be initiated through an IFN-mediated process.
Adaptive finite element strategies for shell structures (1992)

The present paper extends existing finite element adaptive refinement (AR) techniques to shell structures, which have heretofore been neglected in the AR literature. Specific challenges in applying AR to shell structures include: (1) physical discontinuities (e.g., stiffener intersections); (2) boundary layers; (3) sensitivity to geometric imperfections; (4) the sensitivity of most shell elements to mesh distortion, constraint definition and/or thinness; and (5) intrinsic geometric nonlinearity. All of these challenges but (5) are addressed here.
Heparin-affinity patterns and composition of extracellular superoxide dismutase in human plasma and tissues (1993)

The tetrameric extracellular superoxide dismutase (EC-SOD) in human tissues and plasma has previously been found to be heterogenous with regard to heparin affinity and could be divided into at least three classes: A, lacking heparin affinity; B, with weak affinity; and C, with strong affinity. Using rigorous extraction conditions and an extensive set of anti-proteolytic agents, tissue EC-SOD is now shown to be almost exclusively of native homotetrameric C-class. Plasma EC-SOD on the other hand is shown to be mainly composed of a complex mixture of heterotetramers with modifications probably residing in the C-terminal heparin-binding domain. Proteolytic truncations appear to be a major cause of this heterogeneity. The findings suggest that, since 99% of the EC-SOD in the human body exists in the extravascular space of tissue, EC-SOD is primarily synthesized in tissues and secreted as homotetrameric native EC-SOD C. This tissue EC-SOD C should exist almost completely sequestered by heparin sulphate proteoglycans. C-terminal modifications subsequently occurring in the EC-SOD C would weaken the binding to heparan sulphate proteoglycan, facilitate entrance to the vasculature through capillaries and lymph flow, and finally result in the heterogeneous plasma EC-SOD pattern. With the new extraction and analysis procedure, the tissue content of EC-SOD is found to be higher than previously reported. It is found, for example, when compared with Mn-SOD, to be higher in umbilical cord and uterus, about equal in placenta and testis and as high as that of CuZn-SOD in umbilical cord. The findings suggest that the protection level against superoxide radicals provided by EC-SOD in the tissue interstitial space, given the small distribution volume, is not much less prominent than that bestowed on the intracellular space by CuZn-SOD and Mn-SOD.
Overview of the TREC-2005 Enterprise Track (2005)

The goal of the enterprise track is to conduct experiments with enterprise data — intranet pages, email archives, document repositories — that reflect the experiences of users in real organisations, such that for example, an email ranking technique that is effective here would be a good choice for deployment in a real multi-user email search application. This involves both understanding user needs in enterprise search and development of appropriate IR techniques.
LC-MS-(TOF) Analysis Method for Benzodiazepines in Urine Samples from Alleged Drug-Facilitated Sexual Assault Victims (2006)

In recent years there has been an increase in the number of reports in the U.S. of the use of drugs to commit sexual assault. In 1994, a nationwide urine testing program was developed to assess the incidence of the use of drugs to facilitate sexual assault and provide information for use in the investigation of these crimes. Urine samples were collected from victims of suspected drug-induced sexual assault by law enforcement agencies, emergency rooms, and rape crisis centers. The most implicated drug class was benzodiazepines, either alone or in combination with alcohol. In this report, a procedure was developed for the screening of 22 benzodiazepines in human urine by liquid chromatography-time of flight-mass spectrometry [LC-MS-(TOF)]. The limit of quantitation for all benzodiazepines ranged from 2 to 10 ng/mL, and the limit of detection was 0.5 to 3.0 ng/mL. These results suggest that the method sensitivity is suitable to screen for all 22 benzodiazepines in human urine at low levels. The method was used to analyze samples previously reported to have screened positive for benzodiazepines by immunoassay at 50 ng/mL cut off but failed to confirm by a gas chromatography-MS method. The results of reanalysis of these samples using this LC-MS method are reported.
A comprehensive examination of breast cancer risk loci in African American women (2014)

Genome-wide association studies have identified 73 breast cancer risk variants mainly in European populations. Given considerable differences in linkage disequilibrium structure between populations of European and African ancestry, the known risk variants may not be informative for risk in African ancestry populations. In a previous fine-mapping investigation of 19 breast cancer loci, we were able to identify SNPs in four regions that better captured risk associations in African American women. In this study of breast cancer in African American women (3016 cases, 2745 controls), we tested an additional 54 novel breast cancer risk variants. Thirty-eight variants (70%) were found to have an association with breast cancer in the same direction as previously reported, with eight (15%) replicating at P < 0.05. Through fine-mapping, in three regions (1q32, 3p24, 10q25), we identified variants that better captured associations with overall breast cancer or estrogen receptor positive disease. We also observed suggestive associations with variants (at P < 5 × 10(-6)) in three separate regions (6q25, 14q13, 22q12) that may represent novel risk variants. Directional consistency of association observed for ∼65-70% of currently known genetic variants for breast cancer in women of African ancestry implies a shared functional common variant at most loci. To validate and enhance the spectrum of alleles that define associations at the known breast cancer risk loci, as well as genome-wide, will require even larger collaborative efforts in women of African ancestry.
Quantification of juvenile hormone III in the sedgeCyperus iria L.: comparison of HPLC and radioimmunoassay (2000)

Juvenile hormone III (JH III), a sesquiterpenoid involved in the regulation of insect development and reproduction, appears to be ubiquitous in insects and has also been isolated from some species of sedge. The quantification of JH III extracted from the sedge Cyperus iria by HPLC and by radioimmunoassay (RIA) has been compared. The RIA, developed originally to determine insect haemolymph titres, was optimized for the analysis of plant tissues. The antiserum 31867 displayed minimal cross-reactivity with precursors of JH III from the insect biosynthetic pathway or with extracts from related plant species. Analysis of standards and plant extracts by HPLC and RIA confirmed that there was no significant difference between the ability of these two techniques to quantify JH III (paired t-test). Therefore, RIA was subsequently used to determine the distribution of JH III in mature plants of C. iria. Substantial concentrations were detected in the above-ground plant tissues (0.2–1.2 µg/g fresh weight), but the majority of JH III was found in the roots (43.5 µg/g fresh weight). Copyright © 2000 John Wiley & Sons, Ltd.
What Happens When the Research Ends? Factors Related to the Sustainability of a Technology-Infused Mathematics Curriculum (2011)

this study examines factors related to the sustainability of simcalc mathworlds (scmW), a technology-infused mathematics curriculum. We surveyed middle school teachers one year after their participation in a randomized trial where they were introduced to scmW curriculum, to identify factors related to their continued use of the materials in ways congruent with the developers’ intent. Fifty-two percent of teachers surveyed sustained their use of the scmW curriculum. Factors related to sustained use included student ses, preintervention student mathematics ability, teachers’ perceived coherence and perceived utility of the intervention, and the active nature of the scmW professional development.
ChemInform Abstract: Vicarious Nucleophilic Substitution of Hydrogen in Aldehydes and Knoevenagel Reaction of Iminium Salts with α‐Halocarbanions. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.