gebhart/patrepeval huggingface dataset:
Safety and tolerance of recombinant interferon alfa-2a (roferon®-A) in Cancer Patients (1986)

Recombinant interferon alfa-2a (Roferon-A, Hoffmann-La Roche Inc., Nutley, NJ) has been evaluated in clinical trials of more than 1300 patients with a broad spectrum of oncologic disease. Patients with either solid tumors or hematologic malignancies were treated with daily or three-times-weekly intramuscular injections for induction periods ranging from 8 to 16 weeks. Doses ranged from 1 X 10(6) units to 124 X 10(6) units per injection. When administered in low daily doses (approximately 3 X 10(6) units), Roferon-A was well tolerated, and dose attenuation was rarely required. Change to three-times-weekly treatment regimen at the same dose was usually sufficient to control toxicity when it occurred in this group of low-dose patients. Those patients receiving higher doses frequently required dose attenuation to 50% of the starting dose to improve clinical tolerance. Virtually all patients treated with Roferon-A experienced some degree of acute toxicity manifested as fever, chills, myalgia, and/or headache. These reactions usually occurred with initial dosing and frequently improved spontaneously with continued administration of the drug. Acetaminophen pretreatment was generally useful in ameliorating these symptoms. Common adverse experiences occurring after repeated dosing included fatigue, anorexia, and weight loss. Serious adverse reactions including cardiovascular and neurologic toxicity have occurred infrequently, primarily at higher doses. Hematologic toxicity and elevations in liver function parameters were also observed, but rarely required dose attenuation. Adverse effects were usually reversible after dose reduction or discontinuation of therapy. Approximately 27% of all patients developed antibodies to rHuIFN-alpha 2A during treatment. No adverse clinical sequelae have been associated with antibody development to date.
ETS1 regulates the expression of ATXN2 (2012)

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant disorder caused by the expansion of a CAG tract in the ATXN2 gene. The SCA2 phenotype is characterized by cerebellar ataxia, neuropathy and slow saccades. SCA2 foreshortens life span and is currently without symptomatic or disease-modifying treatments. Identifying function-specific therapeutics for SCA2 is problematic due to the limited knowledge of ATXN2 function. As SCA2 is likely caused by a gain-of-toxic or gain-of-normal function like other polyglutamine disorders, targeting ATXN2 expression may represent a valid therapeutic approach. This study characterized aspects of ATXN2 expression control using an ATXN2 promoter-luciferase (luc) reporter construct. We verified the fidelity of construct expression by generating transgenic mice expressing the reporter construct. High reporter expression was seen in the cerebellum and olfactory bulb in vivo but there was relatively low expression in other tissues, similar to the expression of endogenous ataxin-2. We verified the second of two possible start codons as the functional start codon in ATXN2. By evaluating deletions in the ATXN2 promoter, we identified an E-twenty six (ETS)-binding site required for ATXN2 expression. We verified that endogenous ETS1 interacted with the ATXN2 promoter by an electromobility supershift assay and chromatin immunoprecipitation polymerase chain reaction. ETS1 overexpression increased ATXN2-luc (ATXN2-luciferase) as well as endogenous ATXN2 expression. Deletion of the putative ETS1-binding site abrogated the effects on the expression of ATXN2-luc. A dominant negative ETS1 and an ETS1 short-hairpin RNA both reduced ATXN2-luc expression. Our study broadens the understanding on the transcriptional control of ATXN2 and reveals specific regulatory features of the ATXN2 promoter that can be exploited therapeutically.
Survey of MicroRNA expression in pediatric brain tumors (2010)

MicroRNAs are differentially expressed between pediatric CNS neoplasms and normal tissue suggesting that they may play a significant role in oncogenesis. A greater understanding of aberrant miRNA expression in pediatric brain tumors may aid in the development of novel therapies. The characterization of tumor-specific miRNA signatures may aid in the discovery of biomarkers with diagnostic or prognostic utility.
Disruption of BSEP Function in HepaRG Cells Alters Bile Acid Disposition and Is a Susceptive Factor to Drug-Induced Cholestatic Injury (2016)

In the present study, we characterized in vitro biosynthesis and disposition of bile acids (BAs) as well as hepatic transporter expression followed by ABCB11 (BSEP) gene knockout in HepaRG cells (HepaRG-KO cells). BSEP KO in HepaRG cells led to time-dependent BA accumulation, resulting in reduced biosynthesis of BAs and altered BA disposition. In HepaRG-KO cells, the expression of NTCP, OATP1B1, OATP2B1, BCRP, P-gp, and MRP2 were reduced, whereas MRP3 and OCT1 were up-regulated. As a result, BSEP KO altered the disposition of BAs and subsequently underwent adaptive regulations of BA synthesis and homeostasis to enable healthy growth of the cells. Although BSEP inhibitors caused no or slight increase of BAs in HepaRG wild type cells (HepaRG-WT cells), excessive intracellular accumulation of BAs was observed in HepaRG-KO cells exposed to bosentan and troglitazone, but not dipyridamole. LDH release in the medium was remarkably increased in HepaRG-KO cultures exposed to troglitazone (50 μM), suggesting drug-induced cellular injury. The results revealed that functional impairment of BSEP predisposes the cells to altered BA disposition and is a susceptive factor to drug-induced cholestatic injury. In total, BSEP inhibition might trigger the processes but is not a sole determinant of cholestatic cellular injury. As intracellular BA accumulation is determined by BSEP function and the subsequent adaptive gene regulation, assessment of intracellular BA accumulation in HepaRG-KO cells could be a useful approach to evaluate drug-induced liver injury (DILI) potentials of drugs that could disrupt other BA homeostasis pathways beyond BSEP inhibition.
Automatic netlist extraction for measurement-based characterization of off-chip interconnect (1996)

An approach is presented for modeling board level, package-level, and MCM substrate-level interconnect circuitry based an measured time domain refectometry data. The time-domain scattering parameters of a multiport system are used to extract a SPICE netlist which uses standard elements to match the behavior of the device up to a user-specified cutoff frequency. Linear or nonlinear circuits may be connected to the model ports, and the entire circuit simulated in a standard circuit simulator. Two-port and four-port example microstrip circuits are characterized, and the simulation results are compared with measured data. Delay, reflection transmission, and crosstalk are accurately modeled in each case.
Phase Transitions in Ionic Gels (1980)

The polymer network of a gel, under certain conditions, undergoes a discrete transition in equilibrium volume with changes in solvent composition or temperature. This Letter demonstrates that ionization of the gel network plays an essential role in the phase transition. The volume collapse is also observed when the $p\mathrm{H}$ within the gel is varied.
Factor H facilitates the clearance of GBM bound iC3b by controlling C3 activation in fluid phase (2009)

Dense deposit disease (DDD) is strongly associated with the uncontrolled activation of the complement alternative pathway. Factor H (CFH)-deficient (Cfh(-/-)) mice spontaneously develop C3 deposition along the glomerular basement membrane (GBM) with subsequent development of glomerulonephritis with features of DDD, a lesion dependent on C3 activation. In order to understand the role of CFH in preventing renal damage associated with the dysregulation of the alternative pathway we administered purified mouse CFH (mCFH) to Cfh(-/-) mice. 24h following the administration of mCFH we observed an increase in plasma C3 levels with presence of intact C3 in circulation showing that mCFH restored control of C3 activation in fluid phase. mCFH resulted in the reduction of iC3b deposition along the GBM. The exogenous mCFH was readily detectable in plasma but critically not in association with C3 along the GBM. Thus, the reduction in GBM C3 was dependent on the ability of mCFH to regulate C3 activation in plasma. Western blot analysis of glomeruli from Cfh(-/-) mice demonstrated the presence of iC3b. Our data show that the C3 along the GBM in Cfh(-/-) mice is the C3 fragment iC3b and that this is derived from plasma C3 activation. The implication is that successful therapy of DDD is likely to be achieved by therapies that inhibit C3 turnover in plasma.
Construction of Polymeric δ-Graph:  A Doubly Fused Tricyclic Topology (2005)

A doubly fused tricyclic polymer architecture, corresponding to a δ-graph, has been constructed effectively through metathesis polymer cyclization (MPC) of an 8-shaped dicyclic polymer precursor having two allyl groups placed at opposite positions of the two rings of the 8-shaped structure. The 8-shaped polymer precursor has been obtained through the covalent conversion of an electrostatic self-assembly (composed of two units of the linear poly(tetrahydrofuran)s, poly(THF)s, having pyrrolidinium salt end groups and having a pendant allyl group at the middle of the chain, carrying a tetrafunctional carboxylate counteranion) by the heating treatment under appropriate dilution to cause the ring-opening reaction of pyrrolidinium salt groups by carboxylate anions.
JARID1B promotes metastasis and epithelial-mesenchymal transition via PTEN/AKT signaling in hepatocellular carcinoma cells (2015)

JARID1B is a member of the family of JmjC domain-containing proteins that removes methyl residues from methylated lysine 4 on histone H3 lysine 4 (H3K4). JARID1B has been proposed as an oncogene in many types of tumors; however, its role and underlying mechanisms in hepatocellular carcinoma (HCC) remain unknown. Here we show that JARID1B is elevated in HCC and its expression level is positively correlated with metastasis. In addition Kaplan-Meier survival analysis showed that high expression of JARID1B was associated with decreased overall survival of HCC patients. Overexpression of JARID1B in HCC cells increased proliferation, epithelial-mesenchymal transition, migration and invasion in vitro, and enhanced tumorigenic and metastatic capacities in vivo. In contrast, silencing JARID1B in aggressive and invasive HCC cells inhibited these processes. Mechanistically, we found JARID1B exerts its function through modulation of H3K4me3 at the PTEN gene promoter, which was associated with inactive PTEN transcription. PTEN overexpression blocked JARID1B-driven proliferation, EMT, and metastasis. Our results, for the first time, portray a pivotal role of JARID1B in stimulating metastatic behaviors of HCC cells. Targeting JARID1B may thus be a useful strategy to impede HCC cell invasion and metastasis.
A Rice WRKY Gene Encodes a Transcriptional Repressor of the Gibberellin Signaling Pathway in Aleurone Cells (2004)

The molecular mechanism by which GA regulates plant growth and development has been a subject of active research. Analyses of the rice (Oryza sativa) genomic sequences identified 77 WRKY genes, among which OsWRKY71 is highly expressed in aleurone cells. Transient expression of OsWRKY71 by particle bombardment specifically represses GA-induced Amy32b alpha-amylase promoter but not abscisic acid-induced HVA22 or HVA1 promoter activity in aleurone cells. Moreover, OsWRKY71 blocks the activation of the Amy32b promoter by the GA-inducible transcriptional activator OsGAMYB. Consistent with its role as a transcriptional repressor, OsWRKY71 is localized to nuclei of aleurone cells and binds specifically to functionally defined TGAC-containing W boxes of the Amy32b promoter in vitro. Mutation of the two W boxes prevents the binding of OsWRKY71 to the mutated promoter, and releases the suppression of the OsGAMYB-activated Amy32b expression by OsWRKY71, suggesting that OsWRKY71 blocks GA signaling by functionally interfering with OsGAMYB. Exogenous GA treatment decreases the steady-state mRNA level of OsWRKY71 and destabilizes the GFP:OsWRKY71 fusion protein. These findings suggest that OsWRKY71 encodes a transcriptional repressor of GA signaling in aleurone cells.
BID Binds to Replication Protein A and Stimulates ATR Function following Replicative Stress (2011)

Proapoptotic BH3-interacting death domain agonist (BID) regulates apoptosis and the DNA damage response. Following replicative stress, BID associates with proteins of the DNA damage sensor complex, including replication protein A (RPA), ataxia telangiectasia and Rad3 related (ATR), and ATR-interacting protein (ATRIP), and facilitates an efficient DNA damage response. We have found that BID stimulates the association of RPA with components of the DNA damage sensor complex through interaction with the basic cleft of the N-terminal domain of the RPA70 subunit. Disruption of the BID-RPA interaction impairs the association of ATR-ATRIP with chromatin as well as ATR function, as measured by CHK1 activation and recovery of DNA replication following hydroxyurea (HU). We further demonstrate that the association of BID with RPA stimulates the association of ATR-ATRIP to the DNA damage sensor complex. We propose a model in which BID associates with RPA and stimulates the recruitment and/or stabilization of ATR-ATRIP to the DNA damage sensor complex.
A novel 2‐decenoic acid thioester ameliorates corticosterone‐induced depression‐ and anxiety‐like behaviors and normalizes reduced hippocampal signal transduction in treated mice (2015)

We characterized mice administered corticosterone (CORT) at a dose of 20 mg/kg for 3 weeks to determine their suitability as a model of mood disorders and found that the time immobilized in the tail suspension test was longer and the time spent in the open arms of the elevated plus-maze test was shorter than those of the vehicle-treated group, findings demonstrating that chronic CORT induced both depression-like and anxiety-like behaviors. Furthermore, the levels of phosphorylated extracellular signal-regulated kinase (pERK) 1/2 in the hippocampus and cerebral cortex were reduced in the CORT-treated group. Using this model, we investigated the protective effect of the ester, thioester, and amide compounds of 2-decenoic acid derivatives (termed compounds A, B, and C, respectively). The potency of the protective activity against the CORT-induced depression-like or anxiety-like behaviors and the reduction in pERK1/2 level were found to be in the following order: compound B > compound C > compound A. Therefore, we further investigated the therapeutic activity of only compound B, and its effect on depression-like behavior was observed after oral administration for 1 or 2 weeks, and its effect on anxiety-like behavior was observed after oral administration for 3 weeks. The ratios of phosphorylated ERK1/2, Akt, and cAMP-response element-binding protein to their respective nonphosphorylated forms were smaller in the CORT-treated group than in the vehicle-treated group; however, subsequent treatment with compound B at either 0.3 or 1.5 mg/kg significantly ameliorated this reduction. Compound B appeared to elicit intracellular signaling, similar to that elicited by brain-derived neurotrophic factor, and its mode of action was shown to be novel and different from that of fluvoxamine, a currently prescribed drug for mood disorders.
An asynchronous on-chip network router with quality-of-service (QoS) support (2004)

This paper presents an asynchronous on-chip network router with quality-of-service (QoS) support. The router uses a virtual channel architecture with a priority-based scheduler to differentiate between multiple connections with various QoS requirements sharing the same physical channel. A gate-level prototype of the router has been built and its functionality and performance evaluated. The simulations show that the router is capable of offering a high-level of QoS within the capacity limitations of the network.
The Locations of Collagens with Different Thermal Stabilities in Fibrils of Bovine Reticular Dermis (1988)

The techniques of differential scanning calorimetry and electron microscopy were combined to locate collagens with different thermal stabilities in bovine dermis. When calfskin was heated at 1.25 degrees C/min, denatured cores developed in the fibrils at 65 degrees C, leaving native-banded sheaths. Coincident with the initiation of shrinkage and loss of molecular orientation at 68 degrees C, the sheaths of the fibrils began to be denatured at distributed sites along the fibrils. At 80 degrees C the collagen lost its organized fibrillar structure. When thermally labile crosslinks had been stabilized by reduction with borohydride, an endotherm lying above 66 degrees C was suppressed, with proportional lowering of the total enthalpy change, and a fibrous texture revealing a helical subfibrillar structure remained. The three populations of collagen are located in the same fibrils. One, located in the cores of the fibrils, is half denatured at 68 degrees C. Another, established by crosslinks, is competent to sustain the regular appearance of fibrils even after 56% of the collagen in them has been denatured. This population is located as sheaths at the peripheries of the collagen fibrils. A third, denaturing below 59 degrees C, is codistributed with one or both of the two others.
Tuning acetylated chromatin with HAT inhibitors: A novel tool for therapy (2010)

Epigenetics, the heritable changes that do not involve DNA sequences, give dynamic propulsion to a static genome and modulate genome accessibility by acting through multiple layers of regulation, ultimately ending with a variable organization of chromatin. The main player in chromatin reprograming is the nucleosome, which modifies its association to DNA depending on a variety of post-translational modifications (PTMs) on histone tails. PTMs act directly on higher order chromatin structures and affect the degree of DNA wrap around the histone octamer and the interaction and/or sequential recruitment of chromatin-associated proteins and transcription factors at defined regions. Recently genomic approaches revealed a far more complex epigenome involving key proteins of cell signaling.
Inhibition of mTORC1/2 Overcomes Resistance to MAPK Pathway Inhibitors Mediated by PGC1α and Oxidative Phosphorylation in Melanoma (2014)

Metabolic heterogeneity is a key factor in cancer pathogenesis. We found that a subset of BRAF- and NRAS-mutant human melanomas resistant to the MEK inhibitor selumetinib displayed increased oxidative phosphorylation (OxPhos) mediated by the transcriptional coactivator PGC1α. Notably, all selumetinib-resistant cells with elevated OxPhos could be resensitized by cotreatment with the mTORC1/2 inhibitor AZD8055, whereas this combination was ineffective in resistant cell lines with low OxPhos. In both BRAF- and NRAS-mutant melanoma cells, MEK inhibition increased MITF expression, which in turn elevated levels of PGC1α. In contrast, mTORC1/2 inhibition triggered cytoplasmic localization of MITF, decreasing PGC1α expression and inhibiting OxPhos. Analysis of tumor biopsies from patients with BRAF-mutant melanoma progressing on BRAF inhibitor ± MEK inhibitor revealed that PGC1α levels were elevated in approximately half of the resistant tumors. Overall, our findings highlight the significance of OxPhos in melanoma and suggest that combined targeting of the MAPK and mTORC pathways may offer an effective therapeutic strategy to treat melanomas with this metabolic phenotype.
The Amulet environment: new models for effective user interface software development (1997)

The Amulet user interface development environment makes it easier for programmers to create highly interactive, graphical user interface software for Unix, Windows and the Macintosh. Amulet uses new models for objects, constraints, animation, input, output, commands, and undo. The object system is a prototype instance model in which there is no distinction between classes and instances or between methods and data. The constraint system allows any value of any object to be computed by arbitrary code and supports multiple constraint solvers. Animations can be attached to existing objects with a single line of code. Input from the user is handled by "interactor" objects which support reuse of behavior objects. The output model provides a declarative definition of the graphics and supports automatic refresh. Command objects encapsulate all of the information needed about operations, including support for various ways to undo them. A key feature of the Amulet design is that all graphical objects and behaviors of those objects are explicitly represented at run time, so the system can provide a number of high level built-in functions, including automatic display and editing of objects, and external analysis and control of interfaces. Amulet integrates these capabilities in a flexible and effective manner.
Nonlinear Fano-Resonant Dielectric Metasurfaces (2015)

Strong nonlinear light-matter interaction is highly sought-after for a variety of applications including lasing and all-optical light modulation. Recently, resonant plasmonic structures have been considered promising candidates for enhancing nonlinear optical processes due to their ability to greatly enhance the optical near-field; however, their small mode volumes prevent the inherently large nonlinear susceptibility of the metal from being efficiently exploited. Here, we present an alternative approach that utilizes a Fano-resonant silicon metasurface. The metasurface results in strong near-field enhancement within the volume of the silicon resonator while minimizing two photon absorption. We measure a third harmonic generation enhancement factor of 1.5 × 10(5) with respect to an unpatterned silicon film and an absolute conversion efficiency of 1.2 × 10(-6) with a peak pump intensity of 3.2 GW cm(-2). The enhanced nonlinearity, combined with a sharp linear transmittance spectrum, results in transmission modulation with a modulation depth of 36%. The modulation mechanism is studied by pump-probe experiments.
Drug-to-Genome-to-Drug, Step 2: Reversing Selectivity in a Series of Antiplasmodial Compounds (2011)

In a recent paper, we have described the discovery of antimalarial compounds derived from tadalafil, using a drug-to-genome-to-drug approach ( J. Med. Chem. 2011 , 54 ( 9 ), pp 3222 - 3240 ). We have shown that these derivatives inhibit the phosphodiesterase activity of Plasmodium falciparum and the parasite growth in culture. In this paper, we describe the optimization of these compounds. A direct consequence of our approach based on gene orthology is the lack of selectivity of the compounds over the original activity on the human target. We demonstrate here that it is possible to take advantage of subtle differences in SAR between HsPDE5 inhibition and antiplasmodial activity to improve significantly the selectivity. In particular, the replacement of the piperonyl group in compound 2 by a dimethoxyphenyl group was the best way to optimize selectivity. This observation is consistent with the differences between human and plasmodial sequences in the Q2 pocket receiving this group.