gebhart/patrepeval huggingface dataset:
Abstract 1555: Pan-cancer patterns of synthetic lethality: statistical modeling of gene dependency profiles (2017)

Abstract We present a methodology to fit statistical models of cell-viability profiles from RNAi-gene knockdowns. This method allows us to classify genes according to the degree of skewness in their viability distributions. The set of genes with the highest degree of skewness is highly enriched with many known oncogenes and tumor suppressors. We characterize many of these genes, compare them against the results of large sequencing efforts, and use them as inputs to a matrix-decomposition procedure that identifies the most salient cell viabilities shared by different cancer types. We catalog these pan-cancer patterns of synthetic lethality and characterize them by the genomic, transcriptional, and phenotypic features. This analysis provides a rich catalog of the most salient Achilles’ Heels of Pan-Cancer that can be helpful to identify new therapeutic strategies across cancers. Citation Format: Huwate Yeerna, Ramya Rangan, Andrew Aguirre, William Kim, Francisca Vazquez, Barbara Weir, Mahmoud Ghandi, Aviad Tsherniak, Jesse Boehm, William Hahn, Jill Mesirov, Pablo Tamayo. Pan-cancer patterns of synthetic lethality: statistical modeling of gene dependency profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1555. doi:10.1158/1538-7445.AM2017-1555
Simian virus 40-specific proteins in the membranes of simian virus 40-transformed hamster and mouse cells. (1977)

Membranes of simian virus 40-transformed hamster lymphocytes and phagocytes, as well as of transformed mouse fibroblasts, contain two classes of antigenic virus-specific protein. The isoelectric points of these proteins, as defined by isoelectric focusing/immune electrophoresis are at pH 4.5 and 4.7. The molecular weights of the pI 4.5 and pI 4.7 components, determined by isoelectric focusing/dodecyl sulfate polyacrylamide electrophoresis, lie near 58,000 and 90,000-110,000, respectively. The pI 4.5 and pI 4.7 proteins are tentatively identified with the surface (transplantation) and U antigens, respectively.
Laser-tweezer-controlled solid immersion lens for high-resolution imaging in microfluidic and biological samples (2004)

A novel technique is presented which integrates the capacity of a laser tweezer to optically trap and manipulate objects in three-dimensions with the resolution-enhanced imaging capabilities of a solid immersion lens (SIL). Up to now, solid immersion lens imaging systems have relied upon cantilever-mounted SILs that are difficult to integrate into microfluidic systems and require an extra alignment step with external optics. As an alternative to the current state-of-art, we introduce a device that consists of a free-floating SIL and a laser optical tweezer. In our design, the optical tweezer, created by focusing a laser beam through high numerical aperture microscope objective, acts in a two-fold manner: both as a trapping beam for the positioning and alignment of the SIL and as an near-field scanning beam to image the sample through the SIL. Combining the alignment, positioning, and imaging functions into a single device allows for the direct integration of a high resolution imaging system into microfluidic and biological environments.
Evaluation of voltage source IGBT converters for three-phase induction motor drives (2011)

Modern induction machine (IM) drives are subject to a variety of system perturbations, i.e., weak grid conditions and the resulting DC-link voltage fluctuations, that could possibly compromise machine performance characteristics such as speed, torque, and load current. This paper investigates such circumstances, specifically the influence of DC-link variations on the IM drive under different control and modulation strategies and addresses the timely issues of power loss calculation methods in the most common voltage source three-phase PWM converters (VSC) with active front-end unit (AFE). The AFE converts the AC line input into a controlled DC-link voltage, which is then used as input into a three-phase IM drive, based on an IGBT voltage source inverter (VSI). It should be noted that within this work an AFE is used to control the DC link voltage, ultimately mimicking weak grid conditions. The AFE of the IM drive adopts the hysteresis-based modulation technique and the VSI is controlled by space vector PWM-based methods. The IM drive will be evaluated using different control strategies and verified based on the test-bed using a control system rapid prototyping environment such as dSPACE.
High resolution transmission electron microscopy of CdTe–HgTe superlattice cross sections (2020)

High resolution transmission electron microscopy was used for CdTe-HgTe superlattice observation. Defects, such as stacking faults, impurity segregation and dislocations were observed. The polarity of the CdTe substrates was determined by electron diffraction. Thus a (111) A face, Cd face, was shown to lie at the epitaxy interface. Knowing the polarity of the crystals relative to the interface it is possible to determine the atom types at dislocation cores.
RFID Authentication, Efficient Proactive Information Security within Computational Security (2009)

We consider repeated communication sessions between a RFID Tag (e.g., Radio Frequency Identification, RFID Tag) and a RFID Verifier. A proactive information theoretic security scheme is proposed. The scheme is based on the assumption that the information exchanged during at least one of every n successive communication sessions is not exposed to an adversary. The Tag and the Verifier maintain a vector of n entries that is repeatedly refreshed by pairwise xoring entries, with a new vector of n entries that is randomly chosen by the Tag and sent to the Verifier as a part of each communication session. The general case in which the adversary does not listen in k &gt; 0 sessions among any n successive communication sessions is also considered. A lower bound of n(k+1) for the number of random numbers used during any n successive communication sessions is proven. In other words, we prove that an algorithm must use at least n(k+1) new random numbers during any n successive communication sessions. Then a randomized scheme that uses only O(n log n) new random numbers is presented. A computational secure scheme which is based on the information theoretic secure scheme is used to ensure that even in the case that the adversary listens in all the information exchanges, the communication between the Tag and the Verifier is secure.
TIE-2 expressing monocytes in human cancers (2017)

Tumor-associated macrophages (TAM) are well known as a key player in the tumor microenvironment, which support cancer progression. More recently, a lineage of monocytes characterized by the expression of the TIE-2/Tek angiopoietin receptor identified a subset of circulating and tumor-associated monocytes endowed with proangiogenic activity. TIE-2 expressing monocytes (TEM) were found both in humans and mice. Here, we review the phenotypes and functions of TEM reported so far in human cancer and their potential use as markers of cancer progression and metastasis. Finally, we discuss the therapeutic approaches currently used or proposed to target TEM.
Distributed Light Sensing with Convex Potential Fibers (2010)

We report on a photoconductive fiber that supports decaying and convex electrical potential profiles capable of localizing a point of illumination, and propose a scheme to perform distributed optical sensing.
HYDROCORTISONE AND INHIBITORS OF PROSTAGLANDIN SYNTHESIS POTENTIATION OF ALLOGRAFT SURVIVAL IN MlCE (1981)

We studied the effects on survival of allogeneic skin grafts after treatment with hydrocortisone and/or inhibitors of prostaglandin synthesis: indomethacin and flufenamate. We found a marked synergistic effect of combined treatment with hydrocortisone and indomethacin or flufenamate. Neither hydrocortisone nor indomethacin or flufenamate, when given alone in relatively small doses, caused delayed graft rejection. However, when small doses of hydrocortisone were used in combination with flufenamate or indomethacin, the median survival time (MST) of allogeneic grafts was prolonged from 11.4 days to 20.9 and 23.8 days, respectively. Moreover, the increase in graft survival was comparable to that obtained by treatment with relatively high doses of azathioprine alone or combined with hydrocortisone. The finding of synergism between low doses of prostaglandin synthesis inhibitors and glucocorticoids in delaying graft rejection suggests that such treatment might provide a relatively safer means of achieving clinical immunosuppression than the high doses of steroids and azathioprine currently in use.
Experimental Investigation of the Mechanical Behavior of Aluminum Adhesive Joints under Mixed-Mode Loading Conditions (2018)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;In recent years, structural adhesives have rapidly become the preferred alternative to resistance spot welding in fabricating stronger, lighter aluminum connections. Connections inevitably undergo and must withstand complex quasi-static and/or dynamic loads during their service life. Therefore, understanding how loading conditions affect the mechanical behavior of adhesive joints is vital to their design and the advancement of structural safety. Quasi-static and dynamic tests are performed to analyze both the strength and failure modes of aluminum 6062 substrates bonded by an adhesive (Darbond EP-1506) for an array of loading directions. An Arcan test device, which enables application of mixed-mode loads ranging from pure peel (mode I) to pure shear (mode II) to the adhesive layer, is employed in quasi-static testing. A self-designed medium-speed test machine is utilized to perform dynamic testing. To avoid severe system oscillations exhibited in force measurements during dynamic testing, the Arcan test device is replaced by a set of integrated fixtures to improve stiffness and reduce fixture weight. To induce manifold mechanical responses in the adherend and adhesive materials, the specimens are subjected to a mixture of transverse and shear forces. Experimental results demonstrate that the fracture displacement increases with an increase in testing angle of the applied force, indicating that ductile fracture predominates brittle fracture and governs failure when shear loading is significant in mixed loading scenarios, especially for dynamic tests. Furthermore, dynamic strengthening is observed in samples subjected to peel loading, but is undiscovered in samples tested under mixed loading conditions, where interfacial failure is more likely to occur compared to cohesive failure. This observation reveals that the cohesive zone is reinforced by the strain rate effect, whereas the interface between the adhesive and adherend does not experience this phenomenon.&lt;/div&gt;&lt;/div&gt;
High Peak Power Operation of a 1- μ m GaAs-Based Optically Pumped Semiconductor Laser (2011)

We report room-temperature high-peak-power operation of an optically pumped semiconductor laser based on the InGaAs/GaAs material system. We present the design of the semiconductor structure and optimization strategies to extract the maximum pulsed peak power. The gain structure was pumped by a 775-nm Alexandrite laser with a pulsewidth adjustable from 400 ns to 1 μs and a repetition rate of 3 Hz. A new record peak power of 400 W at a wavelength of 1020 nm was obtained with a Gaussian-shaped submicrosecond pulse. An optical-to-optical efficiency of 28% is demonstrated at maximum power. The key parameters limiting the output power are discussed.
Cooperative multi-user MIMO based on limited feedback in downlink OFDM systems (2008)

Multi-cellular radio systems are often limited due to the presence of cochannel interference. Physical layer concepts as e.g. interference rejection combining, optimize the receiver side and thus strengthen the signal while combating the interference at the terminal side only. It is well known that joint transceiver optimization, i.e. coordinated joint transmission from several base stations, yields large capacity improvement for downlink transmission. However, the performance highly depends on the available channel knowledge. We focus on how to realize a decentralized and limited cooperative downlink transmission in a multi-cellular network. This yields the crucial question: Is an efficient cooperative transmission possible by using simple channel quality identifiers, or is channel state information at the transmitter mandatory? Further, we use minimum mean square error equalization at the terminal side to combat residual cochannel interference. For baseline we apply receiver optimization only and compare these results with those obtained from cooperative transmission. We demonstrate potential capacity gains in a cellular orthogonal frequency division multiplexing system and their scaling with the number of cooperating antenna arrays.
Smoking does not contribute to duodenal ulcer relapse after Helicobacter pylori eradication. (1992)

Cigarette smoking is believed to be one of the major factors influencing duodenal ulcer (DU) recurrence. However, the influence of cigarette smoking on DU recurrence after the eradication of Helicobacter pylori has not been separately addressed. The aim of this study was to investigate DU relapse rate in smokers and nonsmokers, both with confirmed eradication of H. pylori. Patients with H. pylori eradication, demonstrated at endoscopy 4 wk post-treatment, were included in the study. Smoking history was obtained with a standard questionnaire, and patients were followed endoscopically, both yearly and at symptomatic recurrence, to detect anatomical DU recurrence. Of the 197 (121M:76F) patients enrolled in the study and followed for 1-6 yr, 80 (41%) were smokers, smoking 5-40 cigarettes/day. The 117 (59%) nonsmokers included 31 (26%) patients who had ceased smoking 4-20 yr ago. Another seven (9%) smokers ceased smoking during the follow-up period. In the 197 patients with eradicated H. pylori and cured DU, there has been no recurrence of ulcer, regardless of smoking status. We conclude that in patients with DU in whom H. pylori infection is eradicated, ulcer disease does not recur, as observed for up to 6 yr. Furthermore, cigarette smoking is not a risk factor for DU recurrence, provided H. pylori is eradicated.
Emulsifying effects of block copolymers in incompatible polymer blends (1988)

Abstract We discuss some theoretical aspects of interfacial and emulsifying activity of block copolymers A‐B in incompatible blends of homopolymers A and B. We predict the reduction in interfacial tension due to equilibrium adsorption of copolymers at the interface. It is shown that for an appropriate choice of block copolymer composition and molecular weight a very low interfacial tension can be achieved. This suggests a possible existence of a thermodynamically controlled stable droplet phase in which minority homopolymer particles protected by an interfacial film are suspended in a majority homopolymer matrix. The size distribution of the droplets depends on the rigidity and spontaneous radius of curvature of the interfacial film which, as we show, can be controlled by molecular parameters of copolymers.
Prediction of Fatigue Strength of Motorcycle Exhaust System Considering Vibrating and Thermal Stresses (2015)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;A method applicable in the design stage to predict fatigue strength of a motorcycle exhaust system was developed. In this prediction method, a vibrating stress, thermal stresses, stresses resulting from the assembling of the exhaust system components and a deterioration of fatigue strength of materials originated from high temperature were simultaneously taken into account. For the prediction of the vibrating stress, flexible multibody dynamics was applied to get modeling accuracy for vibration characteristics of the entire motorcycle and the exciting force delivered from engine vibrations. The thermal conduction analysis and the thermal deformation analysis based on finite element method (FEM) were applied for the prediction of thermal stresses in the exhaust system components. The temperature distribution on the surfaces of the exhaust system components is required for calculations of the thermal stresses. The heat transfer analysis, which was composed by combing a one-dimensional (1D) engine cycle simulation and an air flow simulation around the vehicle by 3D-CFD, was used for the estimation of temperature distributions. To validate the developed method, the correlations between the simulations and the actual measurements were analyzed for the vibrating stress, the temperature distribution, the thermal stresses and the fatigue safety factor. High correlations were yielded between them proving the validity of the new method.&lt;/div&gt;&lt;/div&gt;
Low phase noise optical burst transmitter for TIme and Spectral optical Aggregation solution (2017)

Sub-Lambda Photonically Switched Network (SLPSN) solutions are able to improve the use of capacity in data networks while limiting the growth of energy consumption. Recently, we have proposed the TIme and Spectral optical Aggregation (TISA) concept in order to respond to operator's needs of flexibility in the allocation of network resources. Additionally, the TISA solution makes a better use of already deployed network resources. In TISA, each source sends data in the form of bursts that only occupies a spectral sub-band, thus offering purely optical aggregation and disaggregation in both time and spectral domains with the finest possible granularity. Wavelength-based routing is then performed passively in the network. A fast tunable laser with low phase noise is necessary to implement the TISA transmitter but, current existing commercial lasers can't meet these two specifications. In this paper we present a transmitter solution fulfilling the switching time and low phase noise requirements. We give experimental results of a CO-MB-OFDM transmitter realized by combining optical gates and low phase noise lasers and report its performance in a back-to-back configuration.
Responders to low-dose ATG induce CD4+ T cell exhaustion in type 1 diabetes (2023)

BACKGROUNDLow-dose anti-thymocyte globulin (ATG) transiently preserves C-peptide and lowers HbA1c in individuals with recent-onset type 1 diabetes (T1D); however, the mechanisms of action and features of the response remain unclear. Here, we characterized the post hoc immunological outcomes of ATG administration and their potential use as biomarkers of metabolic response to therapy (i.e., improved preservation of endogenous insulin production).METHODSWe assessed gene and protein expression, targeted gene methylation, and cytokine concentrations in peripheral blood following treatment with ATG (n = 29), ATG plus granulocyte colony-stimulating factor (ATG/G-CSF, n = 28), or placebo (n = 31).RESULTSTreatment with low-dose ATG preserved regulatory T cells (Tregs), as measured by stable methylation of FOXP3 Treg-specific demethylation region (TSDR) and increased proportions of CD4+FOXP3+ Tregs (P < 0.001) identified by flow cytometry. While treatment effects were consistent across participants, not all maintained C-peptide. Responders exhibited a transient rise in IL-6, IP-10, and TNF-α (P < 0.05 for all) 2 weeks after treatment and a durable CD4+ exhaustion phenotype (increased PD-1+KLRG1+CD57- on CD4+ T cells [P = 0.011] and PD1+CD4+ Temra MFI [P < 0.001] at 12 weeks, following ATG and ATG/G-CSF, respectively). ATG nonresponders displayed higher proportions of senescent T cells (at baseline and after treatment) and increased methylation of EOMES (i.e., less expression of this exhaustion marker).CONCLUSIONAltogether in these exploratory analyses, Th1 inflammation-associated serum and CD4+ exhaustion transcript and cellular phenotyping profiles may be useful for identifying signatures of clinical response to ATG in T1D.TRIAL REGISTRATIONClinicalTrials.gov NCT02215200.FUNDINGThe Leona M. and Harry B. Helmsley Charitable Trust (2019PG-T1D011), the NIH (R01 DK106191 Supplement, K08 DK128628), NIH TrialNet (U01 DK085461), and the NIH NIAID (P01 AI042288).
Perturbed mitochondria–ER contacts in live neurons that model the amyloid pathology of Alzheimer's disease (2019)

The use of fixed fibroblasts from familial and sporadic Alzheimer's disease patients has previously indicated an upregulation of mitochondria-ER contacts (MERCs) as a hallmark of Alzheimer's disease. Despite its potential significance, the relevance of these results is limited because they were not extended to live neurons. Here we performed a dynamic <i>in vivo</i> analysis of MERCs in hippocampal neurons from McGill-R-Thy1-APP transgenic rats, a model of Alzheimer's disease-like amyloid pathology. Live FRET imaging of neurons from transgenic rats revealed perturbed 'lipid-MERCs' (gap width <10 nm), while 'Ca<sup>2+</sup>-MERCs' (10-20 nm gap width) were unchanged. <i>In situ</i> TEM showed no significant differences in the lipid-MERCs:total MERCs or lipid-MERCs:mitochondria ratios; however, the average length of lipid-MERCs was significantly decreased in neurons from transgenic rats as compared to controls. In accordance with FRET results, untargeted lipidomics showed significant decreases in levels of 12 lipids and bioenergetic analysis revealed respiratory dysfunction of mitochondria from transgenic rats. Thus, our results reveal changes in MERC structures coupled with impaired mitochondrial functions in Alzheimer's disease-related neurons.This article has an associated First Person interview with the first author of the paper.
Heterobimetallic copper(i) complexes bearing both 1,1′-bis(diphenylphosphino)ferrocene and functionalized 3-(2′-pyridyl)-1,2,4-triazole (2019)

Copper(<sc>i</sc>) 1,1′-bis(diphenylphosphino)ferrocene complexes are well regulated by functional 3-(2′-pyridyl)-1,2,4-triazole exhibiting mono-anionic η<sup>2</sup>(N1,N2) and neutral η<sup>2</sup>(N1,N2) and η<sup>2</sup>(N1,N4) chelating modes.
Protein Prenylation in Trypanosomatids (2001)

The trypanosomatids include a number of parasites that cause widespread disease in man and domestic livestock in most tropical parts of the world. Organisms that cause devastating diseases include Trypanosoma brucei (T. brucei), Trypanosoma cruzi (T. cruzi), and various leishmania species, including Leishmania mexicana amazonensis (L. amazonensis) and Leishmania braziliensis (L. braziliensis).
Dispersion characteristics of wide slotlines on thin dielectric substrates in a two dimensional phased array environment (1990)

Constant width slot antennas(CWSA) and various types of tappered slot antennas(TSA) have attractive features like ease of construction, compatibility with MIC/MMIC technologies, Wider bandwidth,… for focal plane and phased array applications. Radiation and input circuit characteristics of a single isolated TSA/CWSA element has been investigated by several workers, but there are relatively few published works dealing with its behaviour in an array. The reports reflecting recent progresses in TSA array or subarray technology, for example, very interesting review of current art presented in(1) have based their studies on single element characteristics. Interaction between neighboring elements especially when the spacing between them is less than half a wavelength, has significant effects on element characteristics and the array as a whole. Important parameters such as pattern shape, beamwidth, bandwidth, S.L.L, directivity, and gain are quite sensitive to small variations in propagation constant along the antenna (2),(3). Consequently the knowledge of this parameter or equivalently the guided wavelength as a function of frequency and the other physical parameters of a uniform(CWSA) or nonuniform(TSA) structure in an array configuration is crucial for theoretical prediction of the system performances. For this purpose, mutual effects which are not fully understood yet should be taken into account properly.