gebhart/patrepeval huggingface dataset:
Identification of Targetable FGFR Gene Fusions in Diverse Cancers (2013)

Through a prospective clinical sequencing program for advanced cancers, four index cases were identified which harbor gene rearrangements of FGFR2, including patients with cholangiocarcinoma, breast cancer, and prostate cancer. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, we identified additional FGFR fusions with intact kinase domains in lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins induced cell proliferation. Two bladder cancer cell lines that harbor FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Because of the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts, which incorporate transcriptome analysis for gene fusions, are poised to identify rare, targetable FGFR fusions across diverse cancer types.
Non-cryopreserved peripheral blood progenitor cells collected by a single very large-volume leukapheresis: A simplified and effective procedure for support of high-dose chemotherapy (2000)

High-dose chemotherapy with autologous peripheral blood progenitor cell (PBPC) support has become a widely used treatment strategy. In order to simplify the procedure, a single very large-volume leukapheresis programme combined with short-term refrigerated storage of the PBPC was developed. Seventy-two patients suffering from various relatively chemosensitive malignancies received high-dose chemotherapy, consisting of agents with short in vivo half-lives and 24 to 48 hours later, the refrigerated PBPC were reinfused. A single very large-volume apheresis was sufficient to obtain at least 2 x 10(6)/kg CD34+ cells in 58 patients (81%), and 63% had at least 2.5 x 10(6) CD34+ cells/kg. Only two patients (3%) were transplanted with less than 1 x 10(6) CD34+ cells/kg. In three patients (4%) leukapheresis was repeated because of insufficient number of PBPC. The median CD34+ cell count was 3 x 10(6)/kg. A median of 38.5 L blood (range, 21 to 59) was processed, which accounted for a median of 9 x patient's total blood volume. Very large-volume leukapharesis was well tolerated with symptomatic hypocalcemia being the most common (18%) side-effect. The median time to neutrophils >1.5 x 10(9)/L, and to self-supporting platelet count >25 x 10(9)/L, was 10 and 12 days after reinfusion of PBPC graft, respectively. There were no treatment-related deaths. Our results indicate that this simplified approach of PBPC transplantation can be associated with prompt hematologic recovery in most patients and that it can be useful in settings where facilities are limited or for certain diseases where conditioning regimens with short half-life are appropriate. J. Clin. Apheresis, 15:236-241, 2000.
A Comparison of Equation-Based and AIMD Congestion Control (2000)

This paper considers AIMD-based (Additive-Increase Multiplicative-Decrease) congestion control mechanisms that are TCP-compatible (i.e., that compete reasonably fairly with TCP), but that reduce their sending rate less sharply than does TCP in response to a single packet drop. The paper then briefly compares these smoother AIMD-based congestion control mechanisms with TFRC (TCP-Friendly Rate Control), which makes use of equation-based congestion control.
Collagen Phagocytosis by Fibroblasts Is Regulated by Decorin (2005)

Decorin is a small, leucine-rich proteoglycan that binds to collagen and regulates fibrillogenesis. We hypothesized that decorin binding to collagen inhibits phagocytosis of collagen fibrils. To determine the effects of decorin on collagen degradation, we analyzed phagocytosis of collagen and collagen/decorin-coated fluorescent beads by Rat-2 and gingival fibroblasts. Collagen beads bound to gingival cells by alpha2beta1 integrins. Binding and internalization of decorin/collagen-coated beads decreased dose-dependently with increasing decorin concentration (p < 0.001). Inhibition of binding was sustained over 5 h (p < 0.001) and was attributed to interactions between decorin and collagen and not to decorin-collagen receptor interactions. Both the non-glycosylated decorin core protein and the thermally denatured decorin significantly inhibited collagen bead binding (approximately 50 and 89%, respectively; p < 0.05). Mimetic peptides corresponding to leucine-rich repeats 1-3, encompassed by a collagen-binding approximately 11-kDa cyanogen bromide fragment of decorin and leucine-rich repeats 4 and 5, previously shown to bind to collagen, were tested for their ability to inhibit collagen bead binding. Although the synthetic peptide 3 alone exhibited saturable binding to collagen, neither peptides 3 nor 1 and 2 markedly inhibited phagocytosis. Leucine-rich repeat 3 bound to a triple helical peptide containing the alpha2 integrin-binding site of collagen. When collagen beads were co-incubated with peptides 3 and 4, inhibition of collagen phagocytosis (55%) was equivalent to intact native/recombinant core protein. Thus a novel collagen binding domain in decorin acts cooperatively with leucine-rich repeat 4 to mask the alpha2beta1 integrin-binding site on collagen, an important sequence for the phagocytosis of collagen fibrils.
Mechanistic basis for the recognition of laminin-511 by α6β1 integrin (2017)

Laminins regulate diverse cellular functions through interaction with integrins. Two regions of laminins-three laminin globular domains of the α chain (LG1-3) and the carboxyl-terminal tail of the γ chain (γ-tail)-are required for integrin binding, but it remains unclear how the γ-tail contributes to the binding. We determined the crystal structure of the integrin binding fragment of laminin-511, showing that the γ-tail extends to the bottom face of LG1-3. Electron microscopic imaging combined with biochemical analyses showed that integrin binds to the bottom face of LG1-3 with the γ1-tail apposed to the metal ion-dependent adhesion site (MIDAS) of integrin β1. These findings are consistent with a model in which the γ-tail coordinates the metal ion in the MIDAS through its Glu residue.
Interaction factors of multi-layered magnetic thin film system (1990)

Magnetostatic interaction factors of coupled magnetic thin films are proposed to assist the analysis of the electric and magnetic properties of such systems. The factors, f/sub y/ and f/sub z/, which are diagonal elements of an interaction tensor, are proportional to the interaction energies due to the magnetization in y and z directions. Three-dimensional mathematical expressions of these factors are developed. The interaction energy of the system in each film can be determined numerically using these factors. As a result, the magnetoresistive character of the system can be obtained numerically. The interaction factor decreases rapidly as the distance is increased, with the rate of decrease being faster for thinner films. The numerical solution of the output character of a coupled thin-film read head agrees with previous experimental findings.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nanopores Suggest a Negligible Influence of CpG Methylation on Nucleosome Packaging and Stability (2014)

Nucleosomes are the fundamental repeating units of chromatin, and dynamic regulation of their positioning along DNA governs gene accessibility in eukaryotes. Although epigenetic factors have been shown to influence nucleosome structure and dynamics, the impact of DNA methylation on nucleosome packaging remains controversial. Further, all measurements to date have been carried out under zero-force conditions. In this paper, we present the first automated force measurements that probe the impact of CpG DNA methylation on nucleosome stability. In solid-state nanopore force spectroscopy, a nucleosomal DNA tail is captured into a pore and pulled on with a time-varying electrophoretic force until unraveling is detected. This is automatically repeated for hundreds of nucleosomes, yielding statistics of nucleosome lifetime vs electrophoretic force. The force geometry, which is similar to displacement forces exerted by DNA polymerases and helicases, reveals that nucleosome stability is sensitive to DNA sequence yet insensitive to CpG methylation. Our label-free method provides high-throughput data that favorably compares with other force spectroscopy experiments and is suitable for studying a variety of DNA-protein complexes.
Weak light performance and spectral response of different solar cell types (2005)

ABSTRACT: A large number of possible PV-powered products should be able to operate under indoor lighting conditions. In order to make good product designs of indoor operated PV-devices (ipv), a more extended dataset of PV characteristics than just standard test condition (STC) parameters is required. Within the SYN-Energy project framework, which aims to improve design methods for PV-powered consumer devices, this paper presents results of IV-curves measured for solar cells of different technologies at irradiance levels between 1…1000W/m2. The resulting European cell efficiencies are calculated. In addition, measurements of the spectral responses at different bias light intensities and spectra were performed. By adopting the measurement findings to indoor irradiation scenarios, we outline the impact on ipv energy yields regarding spectral response and the efficiency decrease towards low light levels. This is performed by applying a simplified daylight factor approach to the measured characteristics of commercial available PV at lower/indoor light levels and implementing solar cells spectral response using de-rating factors.
The Quest for High‐Performance Host Materials for Electrophosphorescent Blue Dopants (2007)

Abstract We report a systematic comparison study of 3,5‐di( N ‐carbazolyl)tetraphenylsilane (SimCP) and N , N ′‐dicarbazolyl‐3,5‐benzene (mCP), which are used as the host materials for phosphorescent blue dopants in organic light‐emitting diodes (OLEDs). On the basis of photoexcitation emission spectroscopy, thermal stability analysis, photoelectron analysis, charge transport measurements, and molecular dynamics (MD) simulations, we conclude that the non‐π‐conjugated meta‐substituted triphenylsilyl moiety of SimCP exerts a unique hindering effect on the molecular packing characteristics in the condensed phase. The chemical origin of the superior performance of SimCP over mCP is revealed, and is expected to be helpful for the molecular design of effective host materials for enhancing the performance of blue phosphorescent OLEDs.
Transdermal Permeability of N-Acetyl-D-Glucosamine (2007)

Transdermal permeation of N-acetyl-D-glucosamine (NAG), a metabolite of glucosamine was examined. Glucosamine salts are nutraceuticals used in the oral treatment of osteoarthritis. Sparse information is available regarding glucosamine and NAG transdermal or percutaneous transport and absorption. Permeability of NAG in various enhancer suspensions was evaluated by using shed snakeskin as a model membrane via Franz-type cell diffusion studies. Negligible permeability was observed for NAG in neat solutions of known membrane permeation enhancers ethanol, oleic acid, isopropyl myristate, and isopropyl palmitate, as well as from saturated solutions of NAG in water or phosphate buffer. Permeability measurements obtained from saturated solutions of NAG in DMSO and phosphate buffer solutions containing ethanol at 2%, 5%, 10%, 25%, and 50% demonstrated excellent permeation. Permeability coefficients of the phosphate buffer/ethanol solutions at 5%, 10%, and 25% were about threefold larger in value as those for saturated DMSO solution, whereas the 2% and 50% solution values were lower.
An Autonomous Mobile Robotic System for Surveillance of Indoor Environments (2010)

The development of intelligent surveillance systems is an active research area. In this context, mobile and multi-functional robots are generally adopted as means to reduce the environment structuring and the number of devices needed to cover a given area. Nevertheless, the number of different sensors mounted on the robot, and the number of complex tasks related to exploration, monitoring, and surveillance make the design of the overall system extremely challenging. In this paper, we present our autonomous mobile robot for surveillance of indoor environments. We propose a system able to handle autonomously general-purpose tasks and complex surveillance issues simultaneously. It is shown that the proposed robotic surveillance scheme successfully addresses a number of basic problems related to environment mapping, localization and autonomous navigation, as well as surveillance tasks, like scene processing to detect abandoned or removed objects and people detection and following. The feasibility of the approach is demonstrated through experimental tests using a multisensor platform equipped with a monocular camera, a laser scanner, and an RFID device. Real world applications of the proposed system include surveillance of wide areas (e.g. airports and museums) and buildings, and monitoring of safety equipment.
A map of human cancer signaling (2007)

We conducted a comprehensive analysis of a manually curated human signaling network containing 1634 nodes and 5089 signaling regulatory relations by integrating cancer-associated genetically and epigenetically altered genes. We find that cancer mutated genes are enriched in positive signaling regulatory loops, whereas the cancer-associated methylated genes are enriched in negative signaling regulatory loops. We further characterized an overall picture of the cancer-signaling architectural and functional organization. From the network, we extracted an oncogene-signaling map, which contains 326 nodes, 892 links and the interconnections of mutated and methylated genes. The map can be decomposed into 12 topological regions or oncogene-signaling blocks, including a few 'oncogene-signaling-dependent blocks' in which frequently used oncogene-signaling events are enriched. One such block, in which the genes are highly mutated and methylated, appears in most tumors and thus plays a central role in cancer signaling. Functional collaborations between two oncogene-signaling-dependent blocks occur in most tumors, although breast and lung tumors exhibit more complex collaborative patterns between multiple blocks than other cancer types. Benchmarking two data sets derived from systematic screening of mutations in tumors further reinforced our findings that, although the mutations are tremendously diverse and complex at the gene level, clear patterns of oncogene-signaling collaborations emerge recurrently at the network level. Finally, the mutated genes in the network could be used to discover novel cancer-associated genes and biomarkers.
Neural stem cells: involvement in adult neurogenesis and CNS repair (2008)

Recent advances in stem cell research, including the selective expansion of neural stem cells (NSCs) in vitro , the induction of particular neural cells from embryonic stem cells in vitro , the identification of NSCs or NSC-like cells in the adult brain and the detection of neurogenesis in the adult brain (adult neurogenesis), have laid the groundwork for the development of novel therapies aimed at inducing regeneration in the damaged central nervous system (CNS). There are two major strategies for inducing regeneration in the damaged CNS: (i) activation of the endogenous regenerative capacity and (ii) cell transplantation therapy. In this review, we summarize the recent findings from our group and others on NSCs, with respect to their role in insult-induced neurogenesis (activation of adult NSCs, proliferation of transit-amplifying cells, migration of neuroblasts and survival and maturation of the newborn neurons), and implications for therapeutic interventions, together with tactics for using cell transplantation therapy to treat the damaged CNS.
Preparation, characterization and degradation characteristics of polyanhydrides containing poly(ethylene glycol) (1999)

Poly(ethylene glycol) (PEG) segments were introduced into a polyanhydride main chain by copolymerization of terminal-carboxylated poly(ethylene glycol) with diacidic monomers (sebacic acid and trimellitylimidoglycine). IR and 1H NMR spectroscopy confirmed the copolymer structures. DSC analysis showed that these polyanhydrides have low Tg and low crystallinity. In vitro degradation tests indicated that introducing PEG segments accelerated the degradation rate of these polymers and the degradation duration could be manipulated from 3 days to 3 weeks. The pH of the environment caused by the polymer degradation was lower than 5.0; therefore, the polyanhydrides could be used as components of a newly designed pulsed-release device for peptide and protein delivery. © 1999 Society of Chemical Industry
Expression of animal virus genomes (1971)

The world of animal viruses appears to offer
an unfathomable diversity of specimens but, as
the molecular biology of the replication of many
viruses has been studied, a pattern of behavior
has emerged. The viruses can be divided into
classes, each of which has its own method of
transmitting its genetic information from one
generation to the next and its own style of expressing
its genetic information. Although in
some cases the data are still fragmentary it is
possible to outline the behavior of these systems
and to place them in a formal scheme. In this
paper I will present such a scheme and I will
discuss in some detail the behavior of three viral
systems which have been investigated in my
laboratory. Furthermore, I will discuss some of
the implications of the existence of these viral
systems in the context of the behavior of normal
cells.
Endothelial Dysfunction in Cardiovascular Diseases: The Role of Oxidant Stress (2000)

Accumulating evidence suggests that oxidant stress alters many functions of the endothelium, including modulation of vasomotor tone. Inactivation of nitric oxide (NO(.)) by superoxide and other reactive oxygen species (ROS) seems to occur in conditions such as hypertension, hypercholesterolemia, diabetes, and cigarette smoking. Loss of NO(.) associated with these traditional risk factors may in part explain why they predispose to atherosclerosis. Among many enzymatic systems that are capable of producing ROS, xanthine oxidase, NADH/NADPH oxidase, and uncoupled endothelial nitric oxide synthase have been extensively studied in vascular cells. As the role of these various enzyme sources of ROS become clear, it will perhaps be possible to use more specific therapies to prevent their production and ultimately correct endothelial dysfunction.
In your pocket: smartcards (1997)

The worldwide boom in smartcard deployment is accelerating their evolution. What can be found in a typical wallet?, In all likelihood, bills and coins, a variety of credit cards, a driver's license, a transit pass, a voter registration card, a library card, a video rental card, insurance cards, frequent flyer and car rental cards, a telephone charge card. By the end of the century, all of these documents might be replaced by just two or three smartcards. Because they can store and protect relatively large amounts of data, smartcards are being used in a number of ways around the world, replacing a wallet's contents bit by bit. Stored value cards were in place last year (1996) in Atlanta, Ga., at Olympic venues, standing in for coins and bills. A health card identifying the holder's insurance provider and account number has been issued to every citizen of Germany, and plans are in place to add such medical information as the name of the holder's doctor, blood type, allergic reactions, medications, next of kin, and instructions in case of emergency. Smart social security cards in Spain interface with a kiosk system that can provide updated information on benefits and eligibility, as well as pertinent job opportunities. Today, most smartcards handle a single application, but will realize their true value when a single card can address multiple applications.
cAMP and cGMP Play an Essential Role in Galvanotaxis of Cell Fragments (2015)

Cell fragments devoid of the nucleus and major organelles are found in physiology and pathology, for example platelets derived from megakaryocytes, and cell fragments from white blood cells and glioma cells. Platelets exhibit active chemotaxis. Fragments from white blood cells display chemotaxis, phagocytosis, and bactericidal functions. Signaling mechanisms underlying migration of cell fragments are poorly understood. Here we used fish keratocyte fragments and demonstrated striking differences in signal transduction in migration of cell fragments and parental cells in a weak electric field. cAMP or cGMP agonists completely abolished directional migration of fragments, but had no effect on parental cells. The inhibition effects were prevented by pre-incubating with cAMP and cGMP antagonists. Blocking cAMP and cGMP downstream signaling by inhibition of PKA and PKG also recovered fragment galvanotaxis. Both perturbations confirmed that the inhibitory effect was mediated by cAMP or cGMP signaling. Inhibition of cathode signaling with PI3K inhibitor LY294002 also prevented the effects of cAMP or cGMP agonists. Our results suggest that cAMP and cGMP are essential for galvanotaxis of cell fragments, in contrast to the signaling mechanisms in parental cells.
Reflow Mechanisms of Contact Vias in VLSI Processing (1986)

During glass reflow of contact vias in VLSI processing, occurrences of a sidewall overhang (i.e., bulging and, as a result, formation of a reentrant angle at the base of a via) and, in extreme cases, closure of vias were observed when a low temperature flowing borophosphosilicate glass was used with closely spaced vias. A detailed consideration of the forces and mechanisms involved in reflow indicates that neither the chemical nature of the glass nor the specific processing parameters of reflow are factors in altering this phenomenon. Consideration of an idealized geometry shows that a sidewall overhang within vias will occur after reflow if the glass thickness is more than a critical fraction of the spacing between vias; this critical fraction is calculated to occur near a value of 0.4. At all glass thicknesses, a certain amount of overhang will develop at an intermediate stage of reflow, but then this overhang disappears for a subcritical glass thickness or grows for a supercritical glass thickness. In extreme cases, a large overhang can lead to spreading at the glass‐substrate interface, which contributes to closure of vias.
Phase II Proof-of-Concept Study of Pazopanib Monotherapy in Treatment-Naive Patients With Stage I/II Resectable Non–Small-Cell Lung Cancer (2010)

Short-duration pazopanib was generally well tolerated and demonstrated single-agent activity in patients with early-stage NSCLC. Several target genes were dysregulated after pazopanib treatment, validating target-specific response and indicating a persistent pazopanib effect on lung cancer tissue. Further clinical evaluation of pazopanib in NSCLC is planned.
The Separation of the Enantiomers of a Variety of Non-Steroidal Anti-Inflammatory Drugs Nsaids) as Their Anilide Derivatives Using a Chiral Stationary Phase (1990)

Abstract Widespread demand for accurate determinations of the enantiomenc purity of pharmaceutical used in synthetic and pharmacological research has increased the need for reliable and efficacious methods for separating the stereoisomers of a variety of biologically active compounds. Here we present a procedure for the separation of the enantiomers of a number of non-steroidal anti-inflammatory drugs (NSAIDs), as their anilide derivatives, by HPLC using chiral stationary phases. The chromatographic conditions the chiral stationary phase, and the choice of the derivitizing amine can be altered to accomodate various requirements.