gebhart/patrepeval huggingface dataset:
beta-Catenin associates with the actin-bundling protein fascin in a noncadherin complex. (1996)

Catenins were first characterized as linking the cytoplasmic domains of cadherin cell-cell adhesion molecules to the cortical actin cytoskeleton. In addition to their essential role in modulating cadherin adhesivity, catenins have more recently been indicated to participate in cell and developmental signaling pathways. beta-Catenin, for example, associates directly with at least two receptor tyrosine kinases and transduces developmental signals within the Wnt pathway. Catenins also complex with the tumor suppressor protein adenomatous polyposis coli (APC), which appears to have a role in regulating cell proliferation. We have used the yeast two-hybrid method to reveal that fascin, a bundler of actin filaments, binds to beta-catenin's central Armadillo repeat domain. Western blotting of immunoprecipitates from cell line and mouse and rat brain extracts indicate that this interaction exists in vivo. Fascin and beta-catenin's association was further substantiated in vitro using purified proteins isolated from recombinant bacterial and baculoviral sources. Immunoprecipitation analysis indicates that fascin additionally binds to plakoglobin, which is highly homologous to beta-catenin but not to p120cas, a newly described catenin which contains a more divergent Armadillo-repeat domain. Immunoprecipitation, in vitro competition, and domain-mapping experiments demonstrate that fascin and E-cadherin utilize a similar binding site within beta-catenin, such that they form mutually exclusive complexes with beta-catenin. Immunofluorescence microscopy reveals that fascin and beta-catenin colocalize at cell-cell borders and dynamic cell leading edges of epithelial and endothelial cells. In addition to cell-cell borders, cadherins were unexpectedly observed to colocalize with fascin and beta-catenin at cell leading edges. It is conceivable that beta-catenin participates in modulating cytoskeletal dynamics in association with the microfilament-bundling protein fascin, perhaps in a coordinate manner with its functions in cadherin and APC complexes.
Flat channel-passband-wavelength multiplexing and demultiplexing devices by multiple-Rowland-circle design (1997)

A new robust optical design for widening the channel passband of wavelength demultiplexers is presented. Instead of a traditional one-Rowland-circle design, a multi-Rowland-circle structure is proposed to tailor the focused image formed by the grating. The properties of channel passband can be controlled by adjusting the positions of the circles. Nearly perfect flat-channel passband was achieved by our simulation.
The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin. (1995)

The macrocyclic polyketides rapamycin and FK506 are potent immunosuppressants that prevent T-cell proliferation through specific binding to intracellular protein receptors (immunophilins). The cloning and specific alteration of the biosynthetic genes for these polyketides might allow the biosynthesis of clinically valuable analogues. We report here that three clustered polyketide synthase genes responsible for rapamycin biosynthesis in Streptomyces hygroscopicus together encode 14 homologous sets of enzyme activities (modules), each catalyzing a specific round of chain elongation. An adjacent gene encodes a pipecolate-incorporating enzyme, which completes the macrocycle. The total of 70 constituent active sites makes this the most complex multienzyme system identified so far. The DNA region sequenced (107.3 kbp) contains 24 additional open reading frames, some of which code for proteins governing other key steps in rapamycin biosynthesis.
Morphological study of biodegradable PEO/PLA block copolymers (1987)

A series of PEO/PLA copolymers, covering a wide range of compositions and segmental lengths, was synthesized, and their morphology was investigated by means of DSC and IR studies. For matrices comprising PEO chains with molecular weights below 3400, no soft-segment crystallinity was detected. When long hard segments were present, essentially monophasic, semicrystalline polymers were obtained, with PLA blocks melting around 130 degrees C. Polymers containing longer soft segments (PEO 6000) exhibited a two-phase matrix, with both components being able to crystallize. The relative degree of crystallinity of PEO and PLA blocks was also determined. The thermal history of the sample strongly affected the morphology of the matrix, especially when both blocks were long enough to crystallize. To further explore these polymers, solvent cast films were prepared and their morphology assessed. Casting from acetone, which is an excellent solvent for PLA, resulted in hard blocks exhibiting lower degrees of crystallinity, while methanol had a similar effect on PEO soft segments.
CRYPTOCOCCAL INFECTION AND TH1-TH2 CYTOKINE BALANCE (2002)

Cytokines have been recognized as key factors in determining host resistance to infectious pathogens. In particular, Th1-Th2 cytokine balance in hosts is profoundly associated with the outcome of infection caused by intracellular microbes. In a murine model of pulmonary and disseminated infection with Cryptococcus neoformans, an opportunistic fungal pathogen that frequently leads to fatal meningoencephalitis in severely immunocompromised hosts, expression of cytokine mRNA in the lungs from infected animals revealed Th2-dominant profiles, while administration of IL-12, which rescued mice from fatal infection, converted such balance toward Th1-dominant states in a drastic fashion. Thus, commitment of Th phenotypes critically determines host sensitivity to cryptococcal infection. In this review, we described how Th1-Th2 cytokine balance influences host protective responses to C. neoformans, and we identify the host and pathogen factors that regulate such balance.
Comparing Autonomous Underwater Vehicle (AUV) and Vessel-based Tracking Performance for Locating Acoustically Tagged Fish (2014)

Autonomous underwater vehicles (AUV’s) are increasingly used to collect physical, chemical, and biological information in the marine environment. Recent efforts include merging AUV technology with acoustic telemetry to provide information on the distribution and movements of marine fish. We compared surface vessel and AUV tracking capabilities under rigorous conditions in coastal waters near Juneau, Alaska. Tracking surveys were conducted with a REMUS 100 AUV equipped with an integrated acoustic receiver and hydrophone. The AUV was programmed to navigate along predetermined routes to detect both reference transmitters at 20–500 m depths and tagged fish and crabs in situ. Comparable boat surveys were also conducted. Transmitter depth had a major impact on tracking performance. The AUV was equally effective or better than the boat at detecting reference transmitters in shallow water, and significantly better for transmitters at deeper depths. Similar results were observed for tagged animals. Red king crab, Paralithodes camtschaticus, at moderate depths were recorded by both tracking methods, while only the AUV detected Sablefish, Anoplopoma fimbria, at depths exceeding 500 m. Strong currents and deep depths caused problems with AUV navigation, position estimation, and operational performance, but reflect problems encountered by other AUV applications that will likely diminish with future advances, enhanced methods, and increased use.
SQL-like big data environments: Case study in clinical trial analytics (2015)

Big Data deals with enormous volumes of complex and exponentially growing data sets from multiple sources. With rapid growth in technology, we are now able to generate immense amount of data in almost any field imaginable including physical, biological and biomedical sciences. With the diversity and amount of data in health care industry there is an increasing need to evaluate the components in big data frameworks and gauge their adaptability to analytics techniques. However, a key step in adapting big data tools is the portability of relational databases to big data environment. Since SQL is considered to be the de-facto language for interactive queries, in this paper, we evaluate the performance of SQL-like big data solutions for the portability of existing relational databases. Our work focuses on benchmarking multiple SQL-like big data technologies over Hadoop based distributed file system (HDFS) for Study Data Tabulation Model (SDTM) used in clinical trial databases for improving the efficiency of research in clinical trials. We use publically available clinical trial data (from National Institute on Drug Abuse (NIDA)), which follows SDTM, as a test bed to measure key parameters like usability, adaptability, modularity, robustness and efficiency of these solutions. With the intention to demonstrate how current clinical trial functionality can be replicated on a big data backend with high SQL-like functionality, we evaluate several types of ad-hoc SQL queries.
On the role of Cro in λ prophage induction (2005)

The lysogenic state of bacteriophage lambda is exceptionally stable yet the prophage is readily induced in response to DNA damage. This delicate epigenetic switch is believed to be regulated by two proteins; the lysogenic maintenance promoting protein CI and the early lytic protein Cro. First, we confirm, in the native configuration, the previous observation that the DNA loop mediated by oligomerization of CI bound to two distinct operator regions (O(L) and O(R)), increases repression of the early lytic promoters and is important for stable maintenance of lysogeny. Second, we show that the presence of the cro gene might be unimportant for the lysogenic to lytic switch during induction of the lambda prophage. We revisit the idea that Cro's primary role in induction is instead to mediate weak repression of the early lytic promoters.
Factors Influencing Lactose Crystallization (1974)

The role of various factors in lactose crystallization was determined by measuring weight gains of lactose crystals during 20 h storage in lactose solutions (30 g a-hydrate/lO0 ml water) containing various additives. Supersaturation was not varied and crystal growth was not diffusion-controlled under the test cortditions. Washing the crystals with distilled water speeded subsequent growth in pure solutions. In edible and fermentation grades of lactose, impurities accelerated growth initially and then slowed it abruptly. In "demineralized wheys also, growth was accelerated but continued fast in subsequent tests. Acceleration of growth by alcohol supports the step theory rather than supersaturation. High acidity (pH < 1) greatly accelerated crystallization, with sulfuric acid especially effective approaching the crystallization rate of sucrose. Acetic and lactic acids, however, were inhibitory. fi-Lactose, glucose, and maltose accelerated crystal growth rather than being inhibitory as suggested in the literature.
Influence of Ca2+ on the structure of reptilase-derived and thrombin-derived fibrin gels (1986)

The effects of Ca2+ ion on the structure of thrombin-derived and reptilase-derived fibrin gels formed at various ionic strengths were studied turbidimetrically. For both enzymes clotting times were shorter, final gel turbidities were higher and fibre mass/length ratios were increased as the ionic strength was lowered. The addition of 5 mM-Ca2+ augmented each of these effects for any given ionic strength. In the thrombin system, Ca2+ increased the final gel turbidity from 0.04 to 0.26 A632.8 at ionic strength 0.15. Under identical conditions in the reptilase system, the final gel turbidity increased from 0.03 A632.8 in the absence of Ca2+ to 0.345 A632.8 in the presence of 5 mM-Ca2+. In the thrombin system, fibre mass/length ratios increased from 0.4 X 10(12) to 6.9 X 10(12) Da/cm in the absence of Ca2+, and from 4.4 X 10(12) to 7.9 X 10(12) Da/cm in the presence of Ca2+, as the ionic strengths were decreased from 0.15 to 0.08 and to 0.11 respectively. In the reptilase system, the mass/length ratios increased from 0.9 X 10(12) to 5.8 X 10(12) Da/cm in the absence of Ca2+, and from 4.8 X 10(12) to 8.7 X 10(12) Da/cm in the presence of Ca2+, as the ionic strengths were decreased from 0.15 to 0.08 and to 0.10 respectively. At ionic strengths below 0.10, the presence of 5 mM-Ca2+ caused precipitation and macroscopic aggregation of fibrinogen upon the addition of either enzyme. In the presence of 5 mM-Ca2+, the fibres composing thrombin-induced and reptilase-induced gels were virtually identical.
Quartz crystal microbalance with dissipation monitoring: enabling real-time characterization of biological materials and their interactions. (2008)

In recent years, there has been a rapid growth in the number of scientific reports in which the quartz crystal microbalance (QCM) technique has played a key role in elucidating various aspects of biological materials and their interactions. This article illustrates some key advances in the development of a special variation of this technique called quartz crystal microbalance with dissipation monitoring (QCM-D). The main feature and advantage of QCM-D, compared with the conventional QCM, is that it in addition to measuring changes in resonant frequency (Deltaf), a simultaneous parameter related to the energy loss or dissipation (DeltaD) of the system is also measured. Deltaf essentially measures changes in the mass attached to the sensor surface, while DeltaD measures properties related to the viscoelastic properties of the adlayer. Thus, QCM-D measures two totally independent properties of the adlayer. The focus of this review is an overview of the QCM-D technology and highlights of recent applications. Specifically, recent applications dealing with DNA, proteins, lipids, and cells will be detailed. This is not intended as a comprehensive review of all possible applications of the QCM-D technology, but rather a glimpse into a few highlighted application areas in the biomolecular field that were published in 2007.
Transmission confocal laser scanning microscopy with a virtual pinhole based on nonlinear detection (2003)

We present a transmission-mode confocal laser scanning microscope system based on the use of second-harmonic generation (SHG) for signal detection. Our method exploits the quadratic intensity dependence of SHG to preferentially reveal unscattered signal light and reject out-of-focus scattered background. The SHG crystal acts as a virtual pinhole that remains self-aligned without the need for descanning.
Effect and Content of Arginine Vasopressin in Normal and Obstructed Rat Urinary Bladder: An in Vivo and in Vitro Investigation (1993)

The present investigation was performed to evaluate the possible role of arginine vasopressin (AVP) in detrusor instability in the obstructed rat urinary bladder. The effect of AVP on normal and obstructed rat detrusor smooth muscle was tested in vivo and in vitro. Arginine vasopressin given as a closed intraarterial injection to the bladder transiently decreased micturition volume and increased micturition frequency during cystometry in control rats. In rats with infravesical outlet obstruction the effect of AVP on cystometrical parameters was negligible. In accordance with this finding, the efficacy of AVP in contracting detrusor muscle in vitro was much lower for obstructed bladders than for controls. The EC50 values were, however, similar. Arginine vasopressin added to the bath had no effect on nerve-mediated contractile responses. Obstruction led to a transient decrease in immunoreactive AVP concentration, but the total amount of AVP per bladder increased significantly after 6 weeks of obstruction as a consequence of the 14-fold increase in bladder weight. The decreased excitatory effect of AVP in obstructed bladder makes a role for this peptide in the development of detrusor instability less likely.
Modern physical organic chemistry (2006)

1: Introduction to Structure and Models of Bonding 2: Strain and Stability 3: Solutions and Noncovalent Binding Forces 4: Molecular Recognition and Supramolecular Chemistry 5: Acid-Base Chemistry 6: Stereochemistry 7: Energy Surfaces and Kinetic Analyses 8: Experiments Related to Thermodynamics and Kinetics 9: Catalysis 10: Organic Reaction Mechanisms Part 1: Reactions Involving Additions and/or Eliminations 11: Organic Reaction Mechanisms Part II: Substitutions at Aliphatic Centers and Thermal Isomerizations/Rearrangements 12: Organotransition Metal Reaction Mechanisms and Catalysis 13. Organic Polymer and Materials Chemistry 14. Advanced Concepts in Electronic Structure Theory 15: Thermal Pericyclic Reactions 16: Photochemistry 17: Electronic Organic Materials
Calpain inhibition protects against Taxol-induced sensory neuropathy (2003)

Taxol is a highly effective anticancer agent that causes peripheral neuropathy as its major toxic side effect. The neuropathy is characterized by degeneration of sensory axons that may be severe enough to be dose limiting. Axonal degeneration involves the activation of the calcium-activated proteases calpains, and here we tested whether systemic inhibition of calpains with the peptide alpha-ketoamide calpain inhibitor AK295 can reduce the clinical and pathological effects of Taxol in a rodent model of Taxol neuropathy. In mice with Taxol neuropathy, AK295 reduced the degree of axonal degeneration in sensory nerve roots, and improved clinical measures of neuropathy, including behavioural and electrophysiological function. These findings were consistent for both 3- and 6-week models of neuropathy. In vitro, Taxol caused activation of both calpains and caspases in PC12 cells. AK295 inhibited the activation of calpains but did not interfere with the antimitotic effects of Taxol on microtubules, nor did it inhibit caspase-mediated cell death. These data implicate calpains in the pathogenesis of Taxol neuropathy, and demonstrate that AK295 can prevent axonal degeneration and clinical neuropathy in mice. In addition, AK295 did not interfere with the primary antineoplastic effects of Taxol on microtubules and cell death, suggesting that systemic calpain inhibition may be a good strategy for preventing neuropathy in patients being treated with Taxol.
A new pulsed electric field therapy for melanoma disrupts the tumor's blood supply and causes complete remission without recurrence (2009)

We have discovered a new, ultrafast therapy for treating skin cancer that is extremely effective with a total electric field exposure time of only 180 microsec. The application of 300 high-voltage (40 kV/cm), ultrashort (300 nsec) electrical pulses to murine melanomas in vivo triggers both necrosis and apoptosis, resulting in complete tumor remission within an average of 47 days in the 17 animals treated. None of these melanomas recurred during a 4-month period after the initial melanoma had disappeared. These pulses generate small, long-lasting, rectifying nanopores in the plasma membrane of exposed cells, resulting in increased membrane permeability to small molecules and ions, as well as an increase in intracellular Ca(2+), DNA fragmentation, disruption of the tumor's blood supply and the initiation of apoptosis. Apoptosis was indicated by a 3-fold increase in Bad labeling and a 72% decrease in Bcl-2 labeling. In addition, microvessel density within the treated tumors fell by 93%. This new therapy utilizing nanosecond pulsed electric fields has the advantages of highly localized targeting of tumor cells and a total exposure time of only 180 microsec. These pulses penetrate into the interior of every tumor cell and initiate DNA fragmentation and apoptosis while at the same time reducing blood flow to the tumor. This new physical tumor therapy is drug free, highly localized, uses low energy, has no significant side effects and results in very little scarring.
Phase II study of pentostatin in advanced T‐cell lymphoid malignancies (2004)

At these doses, pentostatin was reasonably well tolerated and is an effective drug for the treatment of T-cell lymphomas.
Effects of annealing and isothermal crystallization upon crystalline forms of poly(vinylidene fluoride) (1975)

Abstract Poly(vinylidene fluoride) exists in three crystalline forms. Optimum conditions for preparing form III were established by infrared spectroscopy, differential scanning calorimetry, and x‐ray diffraction measurements. Form III is easily obtained by annealing mats of solution‐grown crystals of form II at 175–185°C and is also preferentially formed by isothermal crystallization from the melt between 165 and 175°C. Below 165° crystallization of form II is favored. The melting point of form III is higher than that of form II.
Nuclear protein isoforms: Implications for cancer diagnosis and therapy (2010)

Post-translational modifications (PTMs) of nuclear proteins play essential roles in the regulation of gene transcription and signal transduction pathways. Numerous studies have demonstrated a correlation between specific nuclear protein isoforms and cellular malignant process. This communication reviews the impact of major PTM events such as phosphorylation, acetylation, methylation, ubiquitination, and sumoylation on several important nuclear proteins including p53, histones, proliferating cellular nuclear antigen (PCNA), and retinoblastoma protein (Rb) in the process. In addition, the implications of the PTMs as cancer biomarkers and therapeutic targets are considered.
The Fuzzy Math of Solid Tumor Stem Cells: A Perspective (2007)

Apparently effective therapeutic agents very often fail to cure cancer patients. It is therefore attractive to wonder whether a specific resistant cell subset should be recognized and separately targeted. In solid tumors, such as carcinomas, a minor population of "cancer stem cells" has been proposed and sought experimentally in human tumors and isolated cell populations. It is often overlooked that the rationale and supportive data are essentially numerical and can be evaluated as such. A reevaluation of the published studies and related claims within awarded U.S. patents suggests that the mathematical support for the concept of therapeutically useful stem cells is weak and may even invalidate the foundations of these publications and patent claims. Mathematical arguments should be used more consistently, because they can serve as a guide for interpreting studies into cancer stem cells of solid tumors.
Applications for microfluidic components (2002)

Microfluidics is a new field of application for moving, storing, and managing very small quantities of fluids. The major end users for microfluidic components are existing and newly created companies that compete in the health care market. Specific applications include in-vitro diagnostics, analytical equipment, pharmaceutical drug delivery, and clinical chemistry. Other users include customers that manufacture analytical equipment for food and drinks testing, and the life sciences scientific community. The single largest existing market is in ink-jet printer heads. Dominated by global giants like H-P, IBM, and Canon, the micro-machining of ink-jet nozzles and printheads is a key technology for business success in consumer and commercial printing. The demand for these tiny pumps, valves, and chambers in the health care applications is driven by three factors: the need for cost and time efficiency in managed health care; the shift toward point-of-care testing; and the human genome project. The article discusses the design and applications of microfluidic components.