gebhart/patrepeval huggingface dataset:
Photoactivated Spatiotemporally-Responsive Nanosensors of in Vivo Protease Activity (2015)

Proteases play diverse and important roles in physiology and disease, including influencing critical processes in development, immune responses, and malignancies. Both the abundance and activity of these enzymes are tightly regulated and highly contextual; thus, in order to elucidate their specific impact on disease progression, better tools are needed to precisely monitor in situ protease activity. Current strategies for detecting protease activity are focused on functionalizing synthetic peptide substrates with reporters that emit detection signals following peptide cleavage. However, these activity-based probes lack the capacity to be turned on at sites of interest and, therefore, are subject to off-target activation. Here we report a strategy that uses light to precisely control both the location and time of activity-based sensing. We develop photocaged activity-based sensors by conjugating photolabile molecules directly onto peptide substrates, thereby blocking protease cleavage by steric hindrance. At sites of disease, exposure to ultraviolet light unveils the nanosensors to allow proteases to cleave and release a reporter fragment that can be detected remotely. We apply this spatiotemporally controlled system to probe secreted protease activity in vitro and tumor protease activity in vivo. In vitro, we demonstrate the ability to dynamically and spatially measure metalloproteinase activity in a 3D model of colorectal cancer. In vivo, veiled nanosensors are selectively activated at the primary tumor site in colorectal cancer xenografts to capture the tumor microenvironment-enriched protease activity. The ability to remotely control activity-based sensors may offer a valuable complement to existing tools for measuring biological activity.
Phase contrast and surface energy hysteresis in tapping mode scanning force microsopy (1999)

Phase imaging is one of the most attractive features of tapping mode scanning force microscopy operation. In this paper we analyse the relationship between phase contrast imaging and the energy loss due to tip–sample interaction forces. An analytical relationship is obtained between the phase shift and the energy loss. Experiments performed on graphite are in agreement with the analytical expression. Copyright © 1999 John Wiley & Sons, Ltd.
Minimal-Risk Scoring Matrices for Sequence Analysis (1999)

We introduce a minimal-risk method for estimating the frequencies of amino acids at conserved positions in a protein family. Our method, called minimal-risk estimation, finds the optimal weighting between a set of observed amino acid counts and a set of pseudofrequencies, which represent prior information about the frequencies. We compute the optimal weighting by minimizing the expected distance between the estimated frequencies and the true population frequencies, measured by either a squared-error or a relative-entropy metric. Our method accounts for the source of the pseudofrequencies, which arise either from the background distribution of amino acids or from applying a substitution matrix to the observed data. Our frequency estimates therefore depend on the size and composition of the observed data as well as the source of the pseudofrequencies. We convert our frequency estimates into minimal-risk scoring matrices for sequence analysis. A large-scale cross-validation study, involving 48 variants of seven methods, shows that the best performing method is minimal-risk estimation using the squared-error metric. Our method is implemented in the package EMATRIX, which is available on the Internet at http://motif.stanford.edu/ematrix.
The Design, Fabrication and Characterization Of A Novel Miniature Silicon Microphone Diaphragm (2009)

A novel miniature silicon microphone diaphragm is described that is highly robust when subjected to stresses that may arise during the fabrication process. The novel diaphragm is composed of a reinforced plate supported on carefully designed hinges. The overall dimension of the polysilicon diaphragm is 1mm by 1mm by 40 microns. The measured response of the diaphragm closely resembles that of an ideal rigid plate over a frequency range extending well beyond the audible range. This approach leads to a structure that is remarkably robust and tolerant of the stresses that have plagued efforts to fabricate miniature microphones [1]. Potential applications include advanced consumer products such as cell phones, portable digital devices, and camcorders.
2 kW CW ytterbium fiber laser with record diffraction-limited brightness (2006)

2 kW CW output power at 1075 nm from a highly efficient all-fiber-format ytterbium fiber laser with M/sup 2/<1.2 was demonstrated. As a result, a record diffraction-limited brightness (W/(M/sup 2/*M/sup 2/)) of 1400 W is achieved.
Wireless Hydrotherapy Smart-Suit Network for Posture Monitoring (2007)

A wireless smart-suit network for monitoring body kinetics, heart and respiratory rate during hidrocinesiotherapy sessions is presented. Sensing modules composed by 3-axis accelerometers, 3-axis magnetometers and interface electronics are used to monitor the body kinetics. Heart rate is measured using an ear clip infrared sensor and respiratory frequency is measured with inductance plethysmography. The sensor network is integrated in a swimming suit and data is transmitted in real time to a base station using a 2.4 GHz RF transceiver. Measurements of the rotation of shoulders, hips and spine are performed with a resolution of less than 2 degrees. A new MAC protocol for wireless sensing and actuation, LPRT protocol, implemented in MICAz motes is used. Some of the characteristics of the proposed protocol are low power consumption, real-time support and loss intolerant traffic. The protocol uses contention-free operation and retransmission scheme and is very flexible and has high throughput efficiency.
Cancer chemotherapy handbook (1980)

Contains information on the biotechnology agents for cancer treatment and support. Additional individual drug monographs have been added to include many non-standard experimental therapies. The use of new recombinant proteins is also emphasized.
Hypoxia-Induced Down-regulation of BRCA1 Expression by E2Fs (2005)

Decreased BRCA1 expression in the absence of genetic mutation is observed frequently in sporadic cancers of the breast and other sites, although little is known regarding the mechanisms by which the expression of this gene can be repressed. Here, we show that activating and repressive E2Fs simultaneously bind the BRCA1 promoter at two adjacent E2F sites in vivo, and that hypoxia induces a dynamic redistribution of promoter occupancy by these factors resulting in the transcriptional repression of BRCA1 expression. Functionally, we show that hypoxia is associated with impaired homologous recombination, whereas the nonhomologous end-joining (NHEJ) repair pathway is unaffected under these conditions. Repression of BRCA1 expression by hypoxia represents an intriguing mechanism of functional BRCA1 inactivation in the absence of genetic mutation. We propose that hypoxia-induced decreases in BRCA1 expression and consequent suppression of homologous recombination may lead to genetic instability by shifting the balance between the high-fidelity homologous recombination pathway and the error-prone NHEJ pathway of DNA repair. Furthermore, these findings provide a novel link between E2Fs and the transcriptional response to hypoxia and provide insight into the mechanisms by which the tumor microenvironment can contribute to genetic instability in cancer.
Construction of Chiral Tri‐ and Tetra‐Arylmethanes Bearing Quaternary Carbon Centers: Copper‐Catalyzed Enantioselective Propargylation of Indoles with Propargylic Esters (2016)

Copper-catalyzed enantioselective propargylation of indoles with propargylic esters and sequential Huisgen cycloaddition with azides lead to the construction of chiral triarylmethanes, bearing a quaternary carbon center, with high to excellent enantioselectivities. The result described herein can be used in the enantioselective preparation of a tetraarylmethane.
Inhibition of Lipid Peroxidation Restores Impaired Vascular Endothelial Growth Factor Expression and Stimulates Wound Healing and Angiogenesis in the Genetically Diabetic Mouse (2001)

Impaired wound healing is a well-documented phenomenon in experimental and clinical diabetes. Experimental evidence suggests that a defect in vascular endothelial growth factor (VEGF) regulation might be associated with wound-healing disorders. We studied the involvement of lipid peroxidation in the pathogenesis of altered VEGF expression in diabetes-related healing deficit by using an incisional skin-wound model produced on the back of female diabetic C57BL/KsJ db+/ db+ mice and their normal (db+/+m) littermates. Animals were then randomized to the following treatment: raxofelast (15 mg.kg(-1).day(-1) i.p.), an inhibitor of lipid peroxidation, or its vehicle (DMSO/NaCl 0.9%, 1:1 vol: vol). The animals were killed on different days (3, 6, and 12 days after skin injury), and the wounded skin tissues were used for histological evaluation, for analysis of conjugated dienes (CDs), as an index of lipid peroxidation and wound breaking strength. Furthermore, we studied the time course of VEGF mRNA expression throughout the skin-repair process (3, 6, and 12 days after skin injury), by means of reverse transcriptase-polymerase chain reaction, as well as the mature protein in the wounds. Diabetic mice showed impaired wound healing with delayed angiogenesis, low breaking strength, and increased wound CD content when compared with their normal littermates. In healthy control mice, a strong induction of VEGF mRNA was found between day 3 and day 6 after injury, while no significant VEGF mRNA expression was observed at day 12 after injury. In contrast, VEGF mRNA levels, after an initial increase (day 3), were significantly lower in diabetic mice than in normal littermates, and light induction of VEGF mRNA expression was also present at day 12 after injury. Similarly, the wound content of the angiogenic factor was markedly changed in diabetic mice. Administration of raxofelast did not modify the process of wound repair in normal mice, but significantly improved the impaired wound healing in diabetic mice through the stimulation of angiogenesis, re-epithelization, and synthesis and maturation of extracellular matrix. Moreover, raxofelast treatment significantly reduced wound CD levels and increased the breaking strength of the wound. Lastly, the inhibition of lipid peroxidation restored the defect in VEGF expression during the process of skin repair in diabetic mice and normalized the VEGF wound content. The current study provides evidence that lipid peroxidation inhibition restores wound healing to nearly normal levels in experimental diabetes-impaired wounds and normalizes the defect in VEGF regulation associated with diabetes-induced skin-repair disorders.
Comparison of methods for measuring kerogen pyrolysis rates and fitting kinetic parameters (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComparison of methods for measuring kerogen pyrolysis rates and fitting kinetic parametersAlan K. Burnham, Robert L. Braun, Hugh R. Gregg, and Alain M. SamounCite this: Energy Fuels 1987, 1, 6, 452–458Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://pubs.acs.org/doi/10.1021/ef00006a001https://doi.org/10.1021/ef00006a001research-articleACS PublicationsRequest reuse permissionsArticle Views849Altmetric-Citations226LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effects of Slime Produced by Clinical Isolates of Coagulase-Negative Staphylococci on Activities of Various Antimicrobial Agents (1998)

A novel in vitro semiquantitative method was developed to investigate the influence of staphylococcal slime on the activities of 22 antimicrobial agents. Pefloxacin, teicoplanin, and vancomycin demonstrated remarkable decreases in efficacy: 30, 52, and 63%, respectively. The activity of rifampin was not significantly reduced (0.99%), whereas all other agents tested were modestly affected (<15% decrease). These data could be influential in the treatment of implant-associated infections caused by slime-producing staphylococci.
[Maintenance treatment of Crohn's disease using orally administered mesalazine (Pentasa). A controlled multicenter study. The Study Groups on the Treatment of Inflammatory Digestive Disorders]. (1993)

Pentasa (2 g/day for 2 years) is a safe and effective maintenance treatment for Crohn's disease when given within 3 months of achieving remission.
Structure of Cellulases and Their Applications (1997)

(1997). Structure of Cellulases and Their Applications. Biotechnology and Genetic Engineering Reviews: Vol. 14, No. 1, pp. 365-414.
Synthesis of a Fourfold Enlarged Porphyrin with an Extremely Large, Diamagnetic Ring‐Current Effect (1986)

The [26]porphyrin 1·2 CF3COO⊖ exhibits remarkable properties. It is formed formally by insertion of four vinyl units into the porphyrin ring. The difference between the δ values of the inner and outer protons of 1·2CF3COO⊖ is extremely large (25.3 ppm)! For comparison, the value for [18]annulenes is 12.1 Noteworthy is also the extremely large ε value of over 900 000 as well as the biomimetic synthesis of the molecule from a monopyrrole.
Surface acoustic wave (SAW) directed droplet flow in microfluidics for PDMS devices (2009)

We direct the motion of droplets in microfluidic channels using a surface acoustic wave device. This method allows individual drops to be directed along separate microchannel paths at high volume flow rates, which is useful for droplet sorting.
Genetic Analysis of Viruses Associated with Emergence of Rift Valley Fever in Saudi Arabia and Yemen, 2000-01 (2002)

The first confirmed Rift Valley fever outbreak outside Africa was reported in September 2000, in the Arabian Peninsula. As of February 2001, a total of 884 hospitalized patients were identified in Saudi Arabia, with 124 deaths. In Yemen, 1,087 cases were estimated to have occurred, with 121 deaths. Laboratory diagnosis of Rift Valley fever virus (RVFV) infections included virus genetic detection and characterization of clinical specimens by reverse transcription-polymerase chain reaction, in addition to serologic tests and virus isolation. Genetic analysis of selected regions of virus S, M, and L RNA genome segments indicated little genetic variation among the viruses associated with disease. The Saudi Arabia and Yemen viruses were almost identical to those associated with earlier RVF epidemics in East Africa. Analysis of S, M, and L RNA genome segment sequence differences showed similar phylogenetic relationships among these viruses, indicating that genetic reassortment did not play an important role in the emergence of this virus in the Arabian Peninsula. These results are consistent with the recent introduction of RVFV into the Arabian Peninsula from East Africa.
Quasicontinuous wavelength tuning in super-structure-grating (SSG) DBR lasers (1996)

The paper describes the design of a super-structure-grating distributed Bragg reflector (SSG-DBR) laser for broad quasicontinuous wavelength tuning with stable single-mode operation. The phase distributions and the effective coupling coefficients of SSG's are optimized to obtain both broad tuning range and high mode selectivity. A computer-aided simulation of wavelength tuning, where the effects of the waveguide loss increase and inhomogeneous gain spectrum are included, provides an optimum cavity structure and indicates the possibility of more than 70 mm quasicontinuous tuning in a 1.55 /spl mu/m InGaAsP-InP SSG-DBR laser. Experimental results for 34 nm quasicontinuous tuning with a properly designed device are also presented.
Mosaicing a Wide Geometric Field of View for Effective Interaction in Augmented Reality (2007)

In this paper, we have addressed the usability issue of augmented reality systems. In order to overcome the lack of view into the interaction space in nominal AR systems, we proposed to create and use a mosaiced image as a cost effective and practical solution. One of the obvious problem is that even if the view span is increased by the mosaicing, because of the fixed and limited resolution/size of the display(either HMD or upright display), the content must be viewed in smaller scale. Yang et al. has found out that increasing the geometric field of view can be tolerated to some degree without much degradation in task performance [3]. In our pilot experiment, a comparison of our mosaiced AR display to the nominal set up improved task performance when the task involved manipulation of many tangible props in a relatively wide area. Our future work is to conduct a more formal usability study and address other AR usability issues.
The Chlorination of Pyrroles. Part II (1971)

We report the chlorination of pyrryl-2-glyoxylic acid and derivatives and hence a synthesis of O,O′-dimethylpyoluteorin and 5-dechloro-O,O′-dimethylpyoluteorin. The different behavior of these compounds on demethylation is described and explained.
Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from Aspergillus awamori var. X100 to 2.4-.ANG. resolution (1993)

The three-dimensional structure of the complex of 1-deoxynojirimycin with glucoamylase II-(471) from Aspergillus awamori var. X100 has been determined to 2.4-A resolution. The model includes residues corresponding to residues 1-471 of glucoamylase I from Aspergillus niger, two molecules of bound 1-deoxynojirimycin and 605 sites for water molecules. The crystallographic R factor from refinement is 0.119, and the root-mean-squared deviation in bond distances is 0.012 A. The inhibitor complex confirms the location of the active site in the packing void of the alpha/alpha-barrel as proposed by Aleshin et al. [Aleshin, A., Golubev, A., Firsov, L., & Honzatko, R. B. (1992) J. Biol. Chem. 267, 19291-19298]. One inhibitor molecule is associated with strong electron density and represents the principal site of interaction of 1-deoxynojirimycin with the enzyme. The other 1-deoxynojirimycin molecule is associated with weak electron density and therefore, probably represents a binding site of low affinity. Interactions of 1-deoxynojirimycin with the enzyme at its principal site involve Arg 45, Asp 55, Arg 305, and carbonyl 177. In addition, a water molecule (water 500) hydrogen bonds to Glu 400 and the 6-hydroxyl of 1-deoxynojirimycin and is at an approximate distance of 3.3 A from the "anomeric" carbon of the inhibitor. The structural arrangement of functional groups near the inhibitor molecule suggests that Glu 179 is a catalytic acid, Glu 400 a catalytic base, and water 500 the attacking nucleophile in the hydrolysis of maltooligosaccharides. The relevance of the X-ray work to proposed mechanisms of enzymatic hydrolysis of oligosaccharides is discussed.
Orthotopic transplantation of v-src–expressing glioma cell lines into immunocompetent mice: establishment of a new transplantable in vivo model for malignant glioma (2007)

The high rate of engraftment, the similarity to the high-grade malignant glioma of origin, and the rapid, locally invasive growth of these tumors should make this murine model useful in testing novel therapies for human malignant gliomas.
Chemical design of radiolabeled antibody fragments for low renal radioactivity levels. (1999)

The renal uptake of radiolabeled antibody fragments presents a problem in targeted imaging and therapy. We hypothesized that the renal radioactivity levels of radiolabeled antibody fragments could be reduced if radiolabeled compounds of urinary excretion were released from glomerularly filtered antibody fragments before they were incorporated into renal cells by the action of brush border enzymes, present on the lumen of renal tubules. 3'-[131I]Iodohippuryl N(epsilon)-maleoyl-L-lysine ([131I]HML) was conjugated with a thiolated Fab fragment because the glycyl-lysine sequence in HML is a substrate for a brush border enzyme and metaiodohippuric acid is released by cleavage of the linkage. Fab fragments were also radiolabeled by direct radioiodination (125I-Fab) or by conjugation with meta-[125I]-iodohippuric acid via an amide bond [N-(5-maleimidopentyl) 3'-iodohippuric acid amide ([125I]MPH-Fab)] or an ester bond [maleimidoethy 3'-iodohippurate ([125I]MIH-Fab)] by procedures similar to those used for [131I]HML-Fab. In biodistribution experiments in mice, [131I]HML-Fab demonstrated markedly low renal radioactivity levels with kidney:blood ratios of radioactivity of 1 from 10 min to 1 h due to rapid release of meta-[131I]iodohippuric acid. [125]MIH-Fab and 1251-Fab reached their peak ratios of 3.8 and 7.3 at 1 h, respectively, and [125I]MPH-Fab showed the maximum ratio of 16.8 at 6 h. In subcellular distribution studies, both [125I]MIH-Fab and 125I-Fab showed migration of radioactivity from the membrane to the lysosomal fraction of the renal cells from 10 to 30 min postinjection, whereas the majority of the radioactivity was detected only in the membrane fraction after administration of [131I]HML-Fab at both time points. In nude mice, [131I]HML-Fab showed one-quarter of the renal radioactivity of simultaneously administered 125I-Fab without impairing the target radioactivity levels 3 h after injection. These findings indicated that HML is a useful reagent for targeted imaging and therapy using antibody fragments as vehicles. These findings also suggested that the radiochemical design of radiolabeled antibody fragments that liberate radiometabolites of urinary excretion from antibody fragments by the action of brush border enzymes may constitute a new strategy for reducing the renal radioactivity levels of antibody fragments.
Novel Methods of Insulin Delivery: An Update (1998)

Conventional insulin therapies involve multiple daily subcutaneous injections. However, the resultant disposition of insulin and blood glucose differs considerably from that following the physiological secretion of pancreatic insulin. A variety of alternative routes/methods have been investigated to improve systemic insulin delivery. Peroral and nasal insulin administration have demonstrated good potential for the treatment of diabetes. Facilitated transdermal delivery has also enjoyed success in promoting the systemic delivery of insulin. In addition, pulmonary, buccal, and ocular insulin administration have been shown to decrease serum glucose concentrations. Other methods that have been investigated for their potential in systemic insulin delivery include rectal, vaginal, and uterine routes.