gebhart/patrepeval huggingface dataset:
Targeting a ribonucleoprotein complex containing the caprin-1 protein and the c-Myc mRNA suppresses tumor growth in mice: an identification of a novel oncotarget (2014)

Tylophorine compounds have been the focus of drug development for decades. Tylophorine derivatives exhibit anti-cancer activities but their cellular targets remain unknown. We used a biotinylated tylophorine derivative to probe for the interacting cellular target(s) of tylophorine. Tylophorine directly binds to caprin-1 and consequently enhances the recruitment of G3BP1, c-Myc mRNA, and cyclin D2 mRNA to form a ribonucleoprotein complex. Subsequently, this tylophorine targeted ribonucleoprotein complex is sequestered to the polysomal fractions and the protein expressions of the associated mRNA-transcripts are repressed. Caprin-1 depleted carcinoma cells become more resistant to tylophorine, associated with decreased formation of the ribonucleoprotein complex targeted by tylophorine. Consequently, tylophorine downregulates c-Myc and cyclins D1/D2, causing hypophosphorylation of Rb and suppression of both processing-body formation and the Warburg effect. Gene expression profiling and gain-of-c-Myc-function experiments also revealed that the downregulated c-Myc contributes to the anti-oncogenic effects of tylophorine compounds. Furthermore, the potent tylophorine derivative dibenzoquinoline-33b elicited a similar effect, as c-Myc protein levels were also decreased in xenograft tumors treated with dibenzoquinoline-33b. Thus, tylophorine compounds exert anti-cancer activity predominantly by targeting and sequestering the caprin-1 protein and c-Myc mRNA associated ribonucleoprotein complex.
A Rotating Annular Die to Control the Biaxial Orientation in Melt Processed Thermotropic Liquid Crystalline Cellulose Derivatives (1986)

Article A Rotating Annular Die to Control the Biaxial Orientation in Melt Processed Thermotropic Liquid Crystalline Cellulose Derivatives was published on December 1, 1986 in the journal Journal of Polymer Engineering (volume 6, issue 1-4).
Fine-Grained Control-Flow Integrity for Kernel Software (2016)

Modern systems assume that privileged software always behaves as expected, however, such assumptions may not hold given the prevalence of kernel vulnerabilities. One idea is to employ defenses to restrict how adversaries may exploit such vulnerabilities, such as Control-Flow Integrity (CFI), which restricts execution to a Control-Flow Graph (CFG). However, proposed applications of CFI enforcement to kernel software are too coarse-grained to restrict the adversary effectively and either fail to enforce CFI comprehensively or are very expensive. We present a mostly-automated approach for retrofitting kernel software that leverages features of such software to enable comprehensive, efficient, fine-grained CFI enforcement. We achieve this goal by leveraging two insights. We first leverage the conservative function pointer usage patterns found in the kernel source code to develop a method to compute fine-grained CFGs for kernel software. Second, we identify two opportunities for removing CFI instrumentation relative to prior optimization techniques: reusing existing kernel instrumentation and creating direct transfers, where possible. Using these insights, we show how to choose optimized defenses for kernels to handle system events, enabling comprehensive and efficient CFI enforcement. We evaluate the effectiveness of the proposed fine-grained CFI instrumentation by applying the retrofitting approach comprehensively to FreeBSD, the MINIX microkernel system, and MINIX's user-space servers, and applying this approach partly to the BitVisor hypervisor. We show that our approach eliminates over 70% of the indirect targets relative to the best current, fine-grained CFI techniques, while our optimizations reduce the instrumentation necessary to enforce coarse-grained CFI. The performance improvement due to our optimizations ranges from 51%/25% for MINIX to 12%/17% for FreeBSD for the average/maximum microbenchmark overhead. The evaluation shows that fine-grained CFI instrumentation can be computed for kernel software in practice and can be enforced more efficiently than coarse-grained CFI instrumentation.
Exhaled breath condensate: methodological recommendations and unresolved questions (2005)

Collection of exhaled breath condensate (EBC) is a noninvasive method for obtaining samples from the lungs. EBC contains large number of mediators including adenosine, ammonia, hydrogen peroxide, isoprostanes, leukotrienes, nitrogen oxides, peptides and cytokines. Concentrations of these mediators are influenced by lung diseases and modulated by therapeutic interventions. Similarly EBC pH also changes in respiratory diseases. The aim of the American Thoracic Society/European Respiratory Society Task Force on EBC was to identify the important methodological issues surrounding EBC collection and assay, to provide recommendations for the measurements and to highlight areas where further research is required. Based on the currently available evidence and the consensus of the expert panel for EBC collection, the following general recommendations were put together for oral sample collection: collect during tidal breathing using a noseclip and a saliva trap; define cooling temperature and collection time (10 min is generally sufficient to obtain 1-2 mL of sample and well tolerated by patients); use inert material for condenser; do not use resistor and do not use filter between the subject and the condenser. These are only general recommendations and certain circumstances may dictate variation from them. Important areas for future research involve: ascertaining mechanisms and site of exhaled breath condensate particle formation; determination of dilution markers; improving reproducibility; employment of EBC in longitudinal studies; and determining the utility of exhaled breath condensate measures for the management of individual patients. These studies are required before recommending this technique for use in clinical practice.
Ultrasensitive Silicon Nanowire for Real-World Gas Sensing: Noninvasive Diagnosis of Cancer from Breath Volatolome (2014)

We report on an ultrasensitive, molecularly modified silicon nanowire field effect transistor that brings together the lock-and-key and cross-reactive sensing worlds for the diagnosis of (gastric) cancer from exhaled volatolome. The sensor is able to selectively detect volatile organic compounds (VOCs) that are linked with gastric cancer conditions in exhaled breath and to discriminate them from environmental VOCs that exist in exhaled breath samples but do not relate to the gastric cancer per se. Using breath samples collected from actual patients with gastric cancer and from volunteers who do not have cancer, blind analysis validated the ability of the reported sensor to discriminate between gastric cancer and control conditions with >85% accuracy, irrespective of important confounding factors such as tobacco consumption and gender. The reported sensing approach paves the way to use the power of silicon nanowires for simple, inexpensive, portable, and noninvasive diagnosis of cancer and other disease conditions.
Preservation and Library Management (1994)

Discusses the results of a questionnaire survey into preservation policies and practice in British libraries, focusing on responsibility for preservation, preservation policies, disaster control planning, staff training and user education, co‐operative initiatives, factors inhibiting preservation activity and spending on preservation. Findings indicate that preservation is considered most applicable to special collections and to rare or valuable items, and that funding is a major problem even in libraries with a strong commitment to preservation. Increased activity in areas such as disaster control planning indicate a greater awareness of preservation issues than in the past. Highlights the advantages of written preservation policies and the success of co‐operative initiatives such as Newsplan, suggesting that a national preservation policy would enable libraries to take a more rational approach to problems such as what to preserve and funding allocation, while helping to clarify their national heritage responsibilities.
Pulsed Doppler ultrasound system for the measurement of velocity distributions and flow disturbances in arterial prostheses (1989)

For the investigation of flow through prosthetic arteries a pulsed Doppler ultrasound system has been characterized. Preliminary in vitro experiments using this system are described; they verify its suitability for making velocity profile and flow disturbance measurements. The output from a frequency tracker is compared with spectral analysis of Doppler signals for both laminar and turbulent flow regimes and the root mean square fluctuations on the tracker output signal are used to identify transition from laminar to turbulent flow. In addition, the turbulent intensity of poststenotic flow is quantified at several axial locations and for different rates of flow. Finally, we present velocity profile measurements which were obtained using a deconvolution technique to account for the finite size of the sample volume.
Cross-linking of rabbit skeletal muscle troponin subunits: labeling of cysteine-98 of troponin C with 4-maleimidobenzophenone and analysis of products formed in the binary complex with troponin T and the ternary complex with troponins I and T (1988)

The sulfhydryl-specific, heterobifunctional, photoactivatable cross-linker 4-maleimidobenzophenone (BPMal) was used to study the interaction of rabbit skeletal muscle troponin subunits TnC, TnT, and TnI. TnC was labeled at Cys-98 by the maleimide moiety of BPMal and then mixed with either TnT alone or TnI plus TnT, in the presence of Ca2+. Upon photolysis, TnI and/or TnT formed covalent cross-links with TnC. The cross-linked TnC-TnT heterodimer obtained from the binary complex was digested into progressively smaller cross-linked peptides that were purified by HPLC and then characterized by amino acid analysis and sequencing. An initial cross-linked CNBr fraction contained the expected peptide CB9 (residues 84-135) of TnC, plus CNBr peptides spanning residues 152-230 of TnT. Results from a peptic digest of the CNBr cross-linked fraction permitted the identification of residues 159-197 as the most highly cross-linked region in TnT. A final subtilisin digest yielded a heterogeneous cross-linked fraction, which suggested that an especially high degree of cross-links was formed in the vicinity of residues 175-178 (Met-Lys-Lys-Lys) of TnT. Although this region of TnT had previously been implicated in binding, we show here for the first time that it is close to Cys-98 of TnC. In an analogous study on the binary complex of TnC and TnI [Leszyk, J., Collins, J. H., Leavis, P. C., & Tao, T. (1987) Biochemistry 26, 7042-7047], we previously showed that Cys-98 of TnC was cross-linked mainly to CN4, the "inhibitory region", of TnI.(ABSTRACT TRUNCATED AT 250 WORDS)
Bi-manual robotic paper manipulation based on real-time marker tracking and physical modelling (2011)

The ability to manipulate deformable objects, such as textiles or paper, is a major prerequisite to bringing the capabilities of articulated robot hands closer to the level of manual intelligence exhibited by humans. We concentrate on the manipulation of paper, which affords us a rich interaction domain and that has not yet been solved for anthropomorphic robot hands. A key ability needed for this is the robust tracking and modelling of paper under conditions of occlusion and strong deformation. We present a marker based framework that realizes these properties robustly and in real-time. We compare a purely mathematical representation of the paper manifold with a soft-body-physics model and demonstrate the use of our visual tracking method to facilitate the coordination of two anthropomorphic 20 DOF Shadow Dexterous Hands while they grasp a flat-lying piece of paper, using a combination of visually guided bulging and pinching.
Confined catalysis under two-dimensional materials (2017)

Confined microenvironments formed in heterogeneous catalysts have recently been recognized as equally important as catalytically active sites. Understanding the fundamentals of confined catalysis has become an important topic in heterogeneous catalysis. Well-defined 2D space between a catalyst surface and a 2D material overlayer provides an ideal microenvironment to explore the confined catalysis experimentally and theoretically. Using density functional theory calculations, we reveal that adsorption of atoms and molecules on a Pt(111) surface always has been weakened under monolayer graphene, which is attributed to the geometric constraint and confinement field in the 2D space between the graphene overlayer and the Pt(111) surface. A similar result has been found on Pt(110) and Pt(100) surfaces covered with graphene. The microenvironment created by coating a catalyst surface with 2D material overlayer can be used to modulate surface reactivity, which has been illustrated by optimizing oxygen reduction reaction activity on Pt(111) covered by various 2D materials. We demonstrate a concept of confined catalysis under 2D cover based on a weak van der Waals interaction between 2D material overlayers and underlying catalyst surfaces.
Rate of familial amyotrophic lateral sclerosis: a systematic review and meta-analysis (2010)

The rate of FALS among prospective population based registries is 5.1% (CI 4.1 to 6.1%), and not 10% as is often stated. Further detailed prospective population based studies of familial ALS are required to confirm this rate.
Audiovisual biofeedback improves the correlation between internal/external surrogate motion and lung tumor motion (2018)

Our results demonstrated that AV biofeedback improves the correlation of respiratory motion between surrogates and the tumor. This suggests a need for AV biofeedback for respiratory guidance utilizing respiratory surrogates during image-guided and MRI-guided radiotherapy in thoracic regions.
Structure of the Preamyloid Dimer of β-2-Microglobulin from Covalent Labeling and Mass Spectrometry (2010)

Beta-2-microglobulin (beta2m) self-associates into fibrillar amyloid deposits in the musculoskeletal system of patients undergoing hemodialysis treatment. Previous studies have shown that stoichiometric amounts of Cu(II) at near physiological conditions can cause beta2m to organize into native-like dimers prior to forming amyloid fibrils. Here, we report the results from selective covalent labeling reactions combined with mass spectrometry that provide insight into the amino acid residues that mediate dimer formation in the wild-type protein. Using three complementary covalent labeling reagents, we find that the dimer interface is formed by the antiparallel stacking of ABED beta-sheets from two beta2m monomers. In addition, our data clearly indicate that a dimer interface involving the interactions of D-D strands from separate protein units as seen in the recent crystal structures of two mutant beta2m oligomers is unlikely.
Central masking with bilateral cochlear implants (2013)

Across bilateral cochlear implants, contralateral threshold shift has been investigated as a function of electrode difference between the masking and probe electrodes. For contralateral electric masking, maximum threshold elevations occurred when the position of the masker and probe electrode was approximately place-matched across ears. The amount of masking diminished with increasing masker-probe electrode separation. Place-dependent masking occurred in both sequentially implanted ears, and was not affected by the masker intensity or the time delay from the masker onset. When compared to previous contralateral masking results in normal hearing, the similarities between place-dependent central masking patterns suggest comparable mechanisms of overlapping excitation in the central auditory nervous system.
ChemInform Abstract: 3‐V Full Cell Performance of Anode Framework TiNb<sub>2</sub>O<sub>7</sub>/Spinel LiNi<sub>0.5</sub>Mn<sub>1.5</sub>O<sub>4</sub>. (2011)

Abstract A carbon‐coated TiNb 2 O 7 anode and a LiNi 0.5 Mn 1.5 O 4 cathode are assembled into 3‐V full cell.
Characterization of five genes in the upper-pathway operon of TOL plasmid pWW0 from Pseudomonas putida and identification of the gene products (1989)

The upper operon of the TOL plasmid pWW0 of Pseudomonas putida encodes a set of enzymes which transform toluene and xylenes to benzoate and toluates. The genetic organization of the operon was characterized by cloning of the upper operon genes into an expression vector and identification of their products in Escherichia coli maxicells. This analysis showed that the upper operon contains at least five genes in the order of xylC-xylM-xylA-xylB-xylN. Between the promoter of the operon and xylC, there is a 1.7-kilobase-long space of DNA in which no gene function was identified. In contrast, most of the DNA between xylC and xylN consists of coding sequences. The xylC gene encodes the 57-kilodalton benzaldehyde dehydrogenase. The xylM and xylA genes encode 35- and 40-kilodalton polypeptides, respectively, which were shown by genetic complementation tests to be subunits of xylene oxygenase. The structural gene for benzyl alcohol dehydrogenase, xylB, encodes a 40-kilodalton polypeptide. The last gene of this operon is xylN, which synthesizes a 52-kilodalton polypeptide of unknown function.
Recovery of Minerals and Metals from Geothermal Fluids (2005)

Abstract not provided
Geometrically Accurate Topology-Correction of Cortical Surfaces Using Nonseparating Loops (2007)

In this paper, we focus on the retrospective topology correction of surfaces. We propose a technique to accurately correct the spherical topology of cortical surfaces. Specifically, we construct a mapping from the original surface onto the sphere to detect topological defects as minimal nonhomeomorphic regions. The topology of each defect is then corrected by opening and sealing the surface along a set of nonseparating loops that are selected in a Bayesian framework. The proposed method is a wholly self-contained topology correction algorithm, which determines geometrically accurate, topologically correct solutions based on the magnetic resonance imaging (MRI) intensity profile and the expected local curvature. Applied to real data, our method provides topological corrections similar to those made by a trained operator.
Living Ring-Opening Metathesis Polymerizations of 3,4-Disubstituted Cyclobutenes and Synthesis of Polybutadienes with Protic Functionalities (1996)

The compounds bis(phenylmethyl) cis-cyclobutene-3,4-dicarboxylate (1) and cis-3,4-bis(2-oxa-3-phenylpropyl)cyclobutene (2) were polymerized by ring-opening metathesis polymerizations using Mo(CHC(CH3)2R1)(NC6H3-2,6-diisopropyl)(OR2)2 (R1 = Ph, R2 = C(CH3)3, I; R1 = CH3, R2 = C(CF3)2CH3, II) as the initiator. For I as initiator, no chain termination or chain transfer processes were observed during the lifetime of the polymerization, showing that the polymerizations of 1 and 2 by I are living. Block copolymers containing 1 and 2 and diethyl cis-cyclobutene-3,4-dicarboxylate (5) were synthesized. The double bonds of the poly-2 and poly-3 ranged from 70% trans to 92% cis depending on the initiator and monomer used. Poly-1 and poly-2 were treated with iodotrimethylsilane and converted to the acid-functionalized and alcohol-functionalized poly-4 and poly-6, respectively. Block copolymers were treated with iodotrimethylsilane and converted to materials with blocks bearing protic functionalities and blocks bearing polar aprotic groups.
Effect of Oxygen Content on Defect Formation in Pure-Silica Core Fibers (1987)

There is slight lack of stoichiometry in pure silica glass, which varies according to the synthesis process. The lack of stoichiometry leads to defect formations: the 245 nm absorption band and drawing-induced E' centers are formed in oxygen-deficient silica, but peroxy radicals and drawing-induced 2 eV band are formed in oxygen-rich silica. The 245 nm band seems to be caused by the Si-Si bonding.
A Rising Titan:<i>TTN</i>Review and Mutation Update (2014)

The 364 exon TTN gene encodes titin (TTN), the largest known protein, which plays key structural, developmental, mechanical, and regulatory roles in cardiac and skeletal muscles. Prior to next-generation sequencing (NGS), routine analysis of the whole TTN gene was impossible due to its giant size and complexity. Thus, only a few TTN mutations had been reported and the general incidence and spectrum of titinopathies was significantly underestimated. In the last months, due to the widespread use of NGS, TTN is emerging as a major gene in human-inherited disease. So far, 127 TTN disease-causing mutations have been reported in patients with at least 10 different conditions, including isolated cardiomyopathies, purely skeletal muscle phenotypes, or infantile diseases affecting both types of striated muscles. However, the identification of TTN variants in virtually every individual from control populations, as well as the multiplicity of TTN isoforms and reference sequences used, stress the difficulties in assessing the relevance, inheritance, and correlation with the phenotype of TTN sequence changes. In this review, we provide the first comprehensive update of the TTN mutations reported and discuss their distribution, molecular mechanisms, associated phenotypes, transmission pattern, and phenotype-genotype correlations, alongside with their implications for basic research and for human health.
<i>SOX2</i> Expression Associates with Stem Cell State in Human Ovarian Carcinoma (2013)

The SRY-related HMG-box family of transcription factors member SOX2 regulates stemness and pluripotency in embryonic stem cells and plays important roles during early embryogenesis. More recently, SOX2 expression was documented in several tumor types including ovarian carcinoma, suggesting an involvement of SOX2 in regulation of cancer stem cells (CSC). Intriguingly, however, studies exploring the predictive value of SOX2 protein expression with respect to histopathologic and clinical parameters report contradictory results in individual tumors, indicating that SOX2 may play tumor-specific roles. In this report, we analyze the functional relevance of SOX2 expression in human ovarian carcinoma. We report that in human serous ovarian carcinoma (SOC) cells, SOX2 expression increases the expression of CSC markers, the potential to form tumor spheres, and the in vivo tumor-initiating capacity, while leaving cellular proliferation unaltered. Moreover, SOX2-expressing cells display enhanced apoptosis resistance in response to conventional chemotherapies and TRAIL. Hence, our data show that SOX2 associates with stem cell state in ovarian carcinoma and induction of SOX2 imposes CSC properties on SOC cells. We propose the existence of SOX2-expressing ovarian CSCs as a mechanism of tumor aggressiveness and therapy resistance in human SOC.
Second generation 50 K dual-mode sapphire oscillator (2006)

Low-temperature, high-precision sapphire resonators exhibit a turning point in mode frequency-temperature dependence at around 10 K. This, along with sapphire's extremely low dielectric losses at microwave frequencies, results in oscillator fractional frequency stabilities on the order of 10(-15). At higher temperatures the lack of a turning point makes single-mode oscillators very sensitive to temperature fluctuations. By exciting two quasi-orthogonal whispering gallery (WG) modes in a single sapphire resonator, a turning point in the frequency-temperature dependence can be found in the beat frequency between the two modes. A temperature control technique based on mode frequency temperature dependence has been used to maintain the sapphire at this turning point and the fractional frequency instability of the beat frequency has been measured to be at a level of 4.3 X 10(-14) over 1 s, dropping to 3.5 X 10(-14) over 4 s integration time.