gebhart/patrepeval huggingface dataset:
Relationships between Signaling Pathway Usage and Sensitivity to a Pathway Inhibitor: Examination of Trametinib Responses in Cultured Breast Cancer Lines (2014)

Cellular signaling pathways involving mTOR, PI3K and ERK have dominated recent studies of breast cancer biology, and inhibitors of these pathways have formed a focus of numerous clinical trials. We have chosen trametinib, a drug targeting MEK in the ERK pathway, to address two questions. Firstly, does inhibition of a signaling pathway, as measured by protein phosphorylation, predict the antiproliferative activity of trametinib? Secondly, do inhibitors of the mTOR and PI3K pathways synergize with trametinib in their effects on cell proliferation? A panel of 30 human breast cancer cell lines was chosen to include lines that could be classified according to whether they were ER and PR positive, HER2 over-expressing, and "triple negative". Everolimus (targeting mTOR), NVP-BEZ235 and GSK2126458 (both targeting PI3K/mTOR) were chosen for combination experiments. Inhibition of cell proliferation was measured by IC50 values and pathway utilization was measured by phosphorylation of signaling kinases. Overall, no correlation was found between trametinib IC50 values and inhibition of ERK signaling. Inhibition of ERK phosphorylation was observed at trametinib concentrations not affecting proliferation, and sensitivity of cell proliferation to trametinib was found in cell lines with low ERK phosphorylation. Evidence was found for synergy between trametinib and either everolimus, NVP-BEZ235 or GSK2126458, but this was cell line specific. The results have implications for the clinical application of PI3K/mTOR and MEK inhibitors.
Hybrid method for enhanced detection of coherent signals using circular antenna arrays (2015)

This paper proposes a modified hybrid method that combines Received Signal Strength (RSS) and Direction of Arrival (DOA) estimation based on MUSIC (Multiple Signal Classification) using circular antenna array. Simulation results are carried out to verify the improved performance obtained using the proposed hybrid method. This takes the form of successful detection of coherent signals at a higher accuracy and lower Root Mean Square Error (RMSE) in comparison with conventional method.
The robotic touch : how robots change architecture : Gramazio & Kohler, research ETH Zurich 2005-2013 (2014)

The synthesis of data and material, which failed to develop in the early digital age, is being realised in today's architecture. This becomes apparent in various medial, spatial and structural manifestations; where data and material can no longer be interpreted as parallel features but rather as being innate expressions of architecture, that have become essential to construction in a new digital age. Closely related to this development is the increasing use of robots in the building process; enabling the fundamental integration of data and material, programming and construction, where processes are developed based on fixed rules, analysed, and then translated to practical construction. Using robots in architecture has not to date been comprehensively researched; The Robotic Touch examines the the theory and practice robot-based building processes and the specific implications of using robots, within architectural design, looking to the future of this innovative and cutting-edge technology.
Mapping multiple components of malaria risk for improved targeting of elimination interventions (2017)

There is a long history of considering the constituent components of malaria risk and the malaria transmission cycle via the use of mathematical models, yet strategic planning in endemic countries tends not to take full advantage of available disease intelligence to tailor interventions. National malaria programmes typically make operational decisions about where to implement vector control and surveillance activities based upon simple categorizations of annual parasite incidence. With technological advances, an enormous opportunity exists to better target specific malaria interventions to the places where they will have greatest impact by mapping and evaluating metrics related to a variety of risk components, each of which describes a different facet of the transmission cycle. Here, these components and their implications for operational decision-making are reviewed. For each component, related mappable malaria metrics are also described which may be measured and evaluated by malaria programmes seeking to better understand the determinants of malaria risk. Implementing tailored programmes based on knowledge of the heterogeneous distribution of the drivers of malaria transmission rather than only consideration of traditional metrics such as case incidence has the potential to result in substantial improvements in decision-making. As programmes improve their ability to prioritize their available tools to the places where evidence suggests they will be most effective, elimination aspirations may become increasingly feasible.
Down-regulation of p-coumaroyl quinate/shikimate 3′-hydroxylase (C3′H) and cinnamate 4-hydroxylase (C4H) genes in the lignin biosynthetic pathway of Eucalyptus urophylla × E. grandis leads to improved sugar release (2015)

Lowering lignin content rather than altering sinapyl alcohol/coniferyl alcohol/4-coumaryl alcohol ratios was found to have the largest impact on reducing recalcitrance of the transgenic eucalyptus variants. The development of lower recalcitrance trees opens up the possibility of using alternative pretreatment strategies in biomass conversion processes that can reduce processing costs.
Mirikizumab Regulates Genes Involved in Ulcerative Colitis Disease Activity and Anti-TNF Resistance: Results From a Phase 2 Study (2023)

This is the first large-scale gene expression study of inflamed mucosa from patients with UC treated with anti-IL23p19 therapy. These results provide molecular evidence for mucosal healing from an extensive survey of changes in transcripts that improve our understanding of the molecular effects of IL-23p19 inhibition in UC.
Additional file 5: of QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles (2015)

Supporting evidence for applicability of QQ-SNV for SNV calling on Illumina NGS sequencing data of any read length. (PDF 32 kb)
Capacitance and Inductance Sensor Circuits for Detecting the Lengths of Open- and Short-Circuited Wires (2009)

The length of an open- or short-circuited wire is linearly proportional to the capacitance or inductance of the wire, respectively. Several types of simple and inexpensive circuits are introduced to measure these values. Open-circuited (capacitance) measurements are very effective. Short-circuited (inductance) measurements are more difficult, and not all of the circuits worked well. A 555 timer circuit was found to have the best overall performance to locate the ends of both open- and short-circuited wires. The capacitance and inductance values of various types of aircraft wires were measured and verified with analytical equations.
Policy decisions on endocrine disruptors should be based on science across disciplines: a response to Dietrich et al. (2013)

A. C. Gore, J. Balthazart, D. Bikle, D. O. Carpenter, D. Crews, P. Czernichow, E. Diamanti-Kandarakis, R. M. Dores, D. Grattan, P. R. Hof, A. N. Hollenberg, C. Lange, A. V. Lee, J. E. Levine, R. P. Millar, R. J. Nelson, M. Porta, M. Poth, D. M. Power, G. S. Prins, E. C. Ridgway, E. F. Rissman, J. A. Romijn, P. E. Sawchenko, P. D. Sly, O. Soder, H. S. Taylor, M. Tena-Sempere, H. Vaudry, K. Wallen, Z. Wang, L. Wartofsky, and C. S. Watson
Architecture of a stream processing system (2014)

After discussing how SPAs are developed, visualized, and debugged in Chapters 3 to 5, this chapter will focus primarily on describing the architectural underpinnings of a conceptual SPS application runtime environment.
Paper-Based, Multi-Fueled Enzymatic Fuel Cell with Passive Microfluidic Flow (2014)

Enzymatic fuel cell (EFC) technology offers several advantages over the conventional electrochemical power sources: higher energy density, low-cost, environmentally-friendly and renewable biocatalysts, room temperature and pH neutral operating environment, and fuel flexibility via a variety of renewable fuels ( e.g. sugars and alcohols). The development of a flexible, paper-based system can significantly increase the utility of the device. The developed system was based on microfluidic passive evaporative pump action provided by the paper and ensured continuous delivery of fuel to the electrodes. The multi-enzymatic anode, consisting of several oxidative enzymes, was capable of simultaneously or separately converting glucose and/or ethanol fuels to electrical energy. Coupled with an air-breathing enzymatic cathode the complete cell produced 800 µW /cm 2 at 0.3V. Employing our previously developed carbon nanotube (CNT) based ink we developed a series of enzymatic anodes: with immobilized glucose dehydrogenase (GDH); with immobilized alcohol dehydrogenase (ADH); and with co-immobilized GDH and ADH enzymes. Additionally, in order to investigate multi-oxidation of a single fuel (ethanol) anodes were developed with co-immobilized ADH and aldehyde dehydrogenase (AlDH). Half-cell experiments were performed on the various enzymatic anodes to determine limits of performance as well as stability and compatibility with non-complementary fuels. Results are depicted in Figure 1. Bilirubin oxidase (BOx) air-breathing cathode was also developed, characterized and optimized for best performance. The composite cathode consisted of three layers: Toray paper (TP) current collector layer; Teflon-treated carbon black (XC-35) gas diffusional layer, and high conductivity CNT paper catalytic layer. All three layers were fused together in a hydraulic press at 500 psi. BOx was tethered to the surface of the catalytic layer through the use of bi-functional chemical linker (1-Pyrenebutanoic acid, succinimidyl ester, PBSE), which forms peptide bonds with the enzyme through the succinimidyl moiety and π-π stacks on CNTs through the pyrene moiety. Such approach resulted in increased stability of the enzyme at the electrode surface when compared to physical adsorption deposition method. Once the individual components of the fuel cell were developed and optimized, the complete EFC was constructed and tested. The GDH-based and ADH/AlDH-based systems were analyzed in respective fuels. The experimental power curve for the GDH EFC is illustrated in Figure 2. Finally, in order to demonstrate actual application, three paper-based EFCs were connecter in series and immersed in Gatorade ® (fuel). This system was then employed to power a digital clock continuously for several days (Figure 3). References: Y. Ulyanova., US Air Force SBIR Phase I Award, Contract # FA8650-12-M-5165, 2012. Y. Ulyanova., US Air Force SBIR Phase II Award, Contract # FA8650-13-C-5071, 2013-2015.
Thermal inhibition and control of second harmonic generation in periodically poled LiNbO<inf>3</inf> crystals (2006)

Computational study of nanosecond pulse laser radiation in periodically poled LiNbO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> crystals reveals the complex spatio-temporal evolution of the 1.064 μm fundamental harmonic and second harmonic energy fields with associated temperature fields, leading to the thermal dephasing and inhibition of second harmonic generation.
IMG-10. MAGNETIC RESONANCE FUNCTIONAL IMAGING BIOMARKER FOR DISTINGUISHING HIGH GRADE FROM LOW GRADE PEDIATRIC BRAIN TUMORS (2023)

Abstract This study aims to show that the ratio between perfusion MRI (RCBV) and diffusion MRI (ADC - apparent diffusion coefficient) is more effective in distinguishing low-grade from high-grade pediatric brain tumors than either parameter (RCBV or ADC) alone. After IRB approval was obtained, an initial pilot prospective study was performed that included 38 patients (newborn - 18 years) (22 females and 16 males). All MRI exams were performed on a 1.5 T or 3.0 T scanner. Surgically resected tumors were classified as low grade (WHO I, II) or high grade (WHO III, IV). ROIs were selected using tumor boundaries delineated on the FLAIR sequence, excluding perilesional edema. Both standardized and normalized perfusion RCBV (sRCBV, nRCBV) as well as diffusion (ADC) mean values were acquired. Then sRCBV/ADC ratios were calculated. Statistical analysis included the Wilcoxon-Mann-Whitney t-test using an alpha=0.05 as the level of significance. The results of this preliminary study revealed that the sRCBV/ADC ratio calculations were more effective at separating high grade from low grade tumors than were RCBV or ADC values alone. As a result of this original pilot study, the calculated sRCBV/ADC ratio has occasionally been used as a clinical tool at our institution. In order to validate the results from this original pilot study, we have collected additional retrospective data to increase sample size. We plan to share the results of this additional data in order to validate that the sRCBV/ADC ratio is an easy-to-use imaging biomarker that can effectively separate high grade from low grade pediatric brain tumors. This information is useful for patient care in that it can potentially help predict prognosis which is essential for parental counseling, and potentially reduce the need for invasive tests and biopsies.
APC I1307K polymorphism as a predictive factor for colorectal neoplasia recurrence. (2013)

1526 Background: The use of surveillance colonoscopy to detect disease recurrence after initial colorectal neoplasia resection has increased significantly in the past decade. Currently, predictive factors at index colonoscopy include only histo-pathologic characteristics such as adenoma number, size, type and dysplasia. The goal of the current study is to identify additional factors (i.e., genetic markers) that increase the risk of subsequent lesions and may optimize the use of surveillance colonoscopies. Methods: A prospective analysis of 383 consecutive Israeli subjects with an initial neoplastic finding in screening colonoscopy. The participants were followed over a period of 10 years, and underwent up to five surveillance colonoscopies. Clinical data regarding potential risk factors for colorectal cancer as well as blood samples were collected. Genetic polymorphisms were detected using real-time PCR from DNA extracted from peripheral mononuclear cells. Results: The overall prevalence of recurrent Colorectal carcinoma and adenoma was 9.4% (36/383) and 69% (268/383) respectively, with a median of 4.8 years from index colonoscopy. In a univariate analysis, subjects with recurrent lesions had significantly higher number of adenomas at index colonoscopy (3.9 Vs 1.1, p=0.001), increased rate of high grade dysplasia (65.8% Vs 50%, p=0.018), and a non-significant trend for larger adenomas and villous histology. The APC I1307K gene variant was detected in 11.8% of subjects with recurrent lesions compared to 3.8% of subjects with normal follow-up colonoscopies (p=0.03). In a multivariate logistic regression (adjusted to age, sex, family history of CR neoplasia, time to recurrence and number of colonoscopies performed), the I1307K variant and the presence of dysplasia were the only significant predictive factors for recurrent neoplasia with an OR of 3.27 (1-11.02, p=0.05) and 1.72 (1.02-2.89, p=0.04) respectively. Conclusions: The APC I1307K gene variant is an important predictive factor for recurrent colorectal neoplasia after a positive index colonoscopy and should be considered as part of the criteria for high risk subjects among Israeli Jews.
Human Action Recognition Bases on Local Action Attributes (2015)

Human action recognition received many interest in the computer vision community. Most of the existing methods focus on either construct robust descriptor from the temporal domain, or computational method to exploit the discriminative power of the descriptor. In this paper we explore the idea of using local action attributes to form an action descriptor, where an action is no longer characterized with the motion changes in the temporal domain but the local semantic description of the action. We propose an novel framework where introduces local action attributes to represent an action for the final human action categorization. The local action attributes are defined for each body part which are independent from the global action. The resulting attribute descriptor is used to jointly model human action to achieve robust performance. In addition, we conduct some study on the impact of using body local and global low-level feature for the aforementioned attributes. Experiments on the KTH dataset and the MV-TJU dataset show that our local action attribute based descriptor improve action recognition performance.
Photoresponse of YBCO microthermometers below the transition temperature (1994)

YBCO microthermometers to be used in composite bolometers are working either on the resistive transition or on the critical current transition, as shown earlier. YBCO microbridges obtained by different techniques and processes, of thicknesses varying from 30 nm to 200 nm, and of widths between 10 micrometers and 30 micrometers have been thus qualified. Results are in good accordance with those predicted by the simplified thermal model. A noise measurement has been made on the voltage fluctuations using a conventional current bias. The previously published results have been greatly improved in terms of sensitivity and detectivity, using either a constant current or a constant voltage DC bias.
Fusogenic Liposome can be Used as an Effective Vaccine Carrier for Peptide Vaccination to Induce Cytotoxic T Lymphocyte (CTL) Response (2005)

We reported previously that fusogenic liposome (FL) introduced antigen protein encapsulated in the liposome directly into the cytoplasm of the antigen presenting cells, and that it induced immune responses. In the present study, we encapsulated TAX38-46, an HTLV-I derived protein and an antigen peptide model, into FL. The ability to induce effective cytotoxic T lymphocytes (CTL) responses in immunized mice was evaluated. Results showed FL could induce CTL response effectively and suggested that FL is a potential peptide vaccine carrier.
Characterization of two influenza A viruses from a pilot whale (1986)

Influenza A viruses of the H13N2 and H13N9 subtypes were isolated from the lung and hilar node of a pilot whale. Serological, molecular, and biological analyses indicate that the whale isolates are closely related to the H13 influenza viruses from gulls.
China's Isolation (1997)

Abstract This chapter examines the international relations of China during the 1950s and 1960s. At the end of 1961, the principal international worry of the Chinese leadership was the worsening dispute with Soviet Union Premier Nikita Khrushchev. The tension between the two communist superpowers continued despite the signing of an agreement at the eighty-one-party meeting in 1960. This conflict was a major influence in China's rejection of tentative olive branches offered by the U.S. government, and this hostility in turn served to increase China's isolation.
Recursive Designs and Feedback Passivation (1997)

The problem of feedback stabilization is reformulated as feedback passivation so that the construction of a stabilizing feedback is translated into the construction of a passivating output. This construction is restricted by two geometric requirements of passivity: a relative degree one and a minimum phase property. We show how backstepping and forwarding, the two building blocks of recursive Lyapunov designs, compelement each other by each removing one of the two obstacles to feedback passivation.
Cytomimetic Biomaterials: Fabrication, Characterization, and Applications (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Concise Enantioselective Synthesis of (+)-L-733,060 and (+)-T-2328 via Sequential Proline Catalysis (2016)

A new, sequential proline-catalyzed approach to the synthesis of (+)-L-733,060 and (+)-T-2328 in high optical purity (93% ee) is described starting from phenyl <i>N</i>-Boc imine. The strategy involves proline-catalyzed Mannich reaction of an arylimine with acetaldehyde followed by α-aminoxylation/Wittig olefination in a sequential fashion as the key steps.
[The cystic fibrosis gene, its product CFTR protein and its mutations]. (1993)

Cystic fibrosis (CF) is a fatal genetic disease primarily affecting Caucasians. Its etiology is complex, but it is chiefly a disease of electrolyte transport characterized by defects in fluid secretion by several epithelia. In this review are analyzed the data obtained since the cloning of the CF gene and the characterization of its product, the CF transmembrane conductance regulator (CFTR) protein, which has been shown to act like a cAMP-regulated chloride channel. This protein is a member of a family of ATP-binding proteins that are membrane-spanning, are found in a number of prokaryotic and eucaryotic cells, and have two ATP-binding domains. Unique to this family of proteins, the CFTR possesses an additional highly charged domain (the R domain). The majority of CF chromosomes (70%) have a single Phenylalanine codon deletion at position 508 of the protein (delta F508). A large number of other rare mutations (more than 230) have also been identified. This rapid accumulation of data is essential to genetic diagnosis and will aid in understanding the structure and function of the protein.
Manipulating Nanoscale Features on the Surface of Dye‐Loaded Microbubbles to Increase Their Ultrasound‐Modulated Fluorescence Output (2014)

The nanoscale surface features of lipid-coated microbubbles can dramatically affect how the lipids interact with one another as the microbubble diameter expands and contracts under the influence of ultrasound. During microbubble manufacturing, the different lipid shell species naturally partition forming concentrated lipid islands. In this study the dynamics of how these nanoscale islands accommodate the expansion of the microbubbles are monitored by measuring the fluorescence intensity changes that occur as self-quenching lipophilic dye molecules embedded in the lipid layer change their distance from one another. It was found that when the dye molecules were concentrated in islands, less than 5% of the microbubbles displayed measurable fluorescence intensity modulation indicating the islands were not able to expand sufficiently for the dye molecules to separate from one another. When the microbubbles were heated and cooled rapidly through the lipid transition temperature the islands were melted creating an even distribution of dye about the surface. This resulted in over 50% of the microbubbles displaying the fluorescence-modulated signal indicating that the dye molecules could now separate sufficiently to change their self-quenching efficiency. The separation of the surface lipids in these different formations has significant implications for microbubble development as ultrasound and optical contrast agents.
Synthesis of a biotin functionalized pyrrole and its electropolymerization: toward a versatile avidin biosensor (1998)

The synthesis of a biotinylated pyrrole and its copolymerization with pyrrole for the purpose of constructing an electronic conducting polymer (ECP) avidin sensor is reported, using fluorescence detection to determine the efficiency of the sensing process.
Isotope-specific detection of low density materials with mono-energetic (gamma)-rays (2009)

The first demonstration of isotope-specific detection of a low-Z, low density object, shielded by a high-Z and high density material using mono-energetic gamma-rays is reported. Isotope-specific detection of LiH shielded by Pb and Al is accomplished using the nuclear resonance fluorescence line of {sup 7}Li at 0.478 MeV. Resonant photons are produced via laser-based Compton scattering. The detection techniques are general and the confidence level obtained is shown to be superior to that yielded by conventional x-ray/{gamma}-ray techniques in these situations.