gebhart/patrepeval huggingface dataset:
Array MAPPIT: High-Throughput Interactome Analysis in Mammalian Cells (2009)

Physical interactions between proteins play a key role in probably every cellular process. Efforts to chart the protein interaction networks are ongoing in a number of model organisms using a diversity of approaches. The resulting genome-wide interaction maps will provide a scaffold for further detailed functional analysis. We developed MAPPIT, a mammalian two-hybrid approach that allows identification and analysis of mammalian protein-protein interactions in their native environment. Here, we introduce an efficient MAPPIT assay that permits high-throughput screening of arrayed collections of proteins and complements a previously published cDNA library screening approach. We validated both methods in screens for interaction partners of the Cullin-based E3 ubiquitin ligase subunits SKP1 and Elongin C. In addition to a number of known interactors, novel SKP1 and Elongin C binding proteins were identified. The array assay is an important addition to the MAPPIT suite of technologies that is expected to significantly increase its utility as a toolbox to screen for novel interactors of proteins or small molecules.
Asynchronous N-Layered Division Multiplexing (N-LDM) (2016)

Layered Division Multiplexing (LDM) is a novel non-orthogonal multiplexing access (NOMA) technique, based on power allocation techniques, which has been recently included in the ATSC 3.0 Digital Television Terrestrial (DTT) standard. In the recent literature, the LDM capabilities have been studied just for the two layered case, mainly when one of the layers is targeting mobile/indoor services and the other one high throughput programs. The main objective of this paper is to extend the study of multilayer LDM potential applications to communication paradigms not analyzed so far. First of all, a study of the A-layered theoretical capacity is presented, and after that, new application scenarios that will take advantage of this case will be presented. Finally, several practical simulations to confirm the aforementioned theoretical results will be discussed.
Supplementary Figure 4 from Aging of Preleukemic Thymocytes Drives CpG Island Hypermethylation in T-cell Acute Lymphoblastic Leukemia (2023)

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On the Design of Optimal Sub-Pixel Motion Compensation Interpolation Filters for Video Compression (2015)

In this paper, the design of optimal temporal prediction for video coding is addressed as a quantization design problem. In the proposed framework, a codebook consisting of a set of interpolation filters is optimized to achieve rate-distortion optimality. The optimization process jointly affects two aspects of motion compensation to achieve rate distortion optimality: 1) The size of the codebook or motion vector (MV) resolution and 2) The filter coefficients for each sub-sample interpolation filter. Note that filter coefficients dictate the behavior of the interpolation filter in terms of signal-noise shaping.
Explicit multicast routing algorithms for constrained traffic engineering (2003)

This paper presents a new traffic engineering technique for dynamic constrained multicast routing, where the routing request of traffic arrives one-by-one. The objective we adopted is to minimize the maximum of link utilization. Although this traffic engineering is useful to relax the most heavily congested link in the Internet backbone, the total network resources, i.e. sum of link bandwidth consumed, could be wasted when the acquired path is larger (in terms of number of hops) than the conventional shortest path. Accordingly we find a multicast tree for routing request that satisfies the hop-count constraint. We formulate this problem as a mixed-integer programming problem and propose a new heuristic algorithm to find a multicast tree for multicast routing request. The presented heuristic algorithm uses the link-state information, i.e. link utilization, for multicast tree selection and is amenable to distributed implementation. The extensive simulation results show that the proposed traffic engineering technique and heuristic algorithm efficiently minimize the maximum of link utilization better than the shortest path.
Preliminary Formation of Deep Trench Capacitors (1990)

A Tegal 700 plasma etcher was used to etch trenches in (100) p-type silicon wafers using a SF6102 plasma. Silicon etch rates of approximately 1.17 microns/minute and a Si:Si02 selectivity ratio of 22.0 were obtained. Scanning Electron Micrographs show the etch was isotropic in nature with an aspect ratio of approximately 2:1.
When Outcomes Diverge: Age and Cardiovascular Risk as Determinants of Mortality and ICU Admission in COVID-19 (2023)

Background: Hospital mortality and admission to the Intensive Care Unit (ICU) are markers of disease severity in COVID-19 patients. Cardiovascular co-morbidities are one of the Academic Editor: Atsushi Tanaka Received: 17 June 2022 Accepted: 12 July 2022 Published: 15 July 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). main determinants of negative outcomes. In this study we investigated the impact of cardiovascular co-morbidities on mortality and admission to the ICU in first-wave COVID-19 patients. Methods: Amulticenter, retrospective, cohort study. A total of 1077 patients were analyzed for mortality and ICU admission. Cardiovascular risk factors were explored as determinants of the outcomes after correction for other confounders. Results: In the multivariable model, after correction for age, only a history of heart failure remained independently associated (p = 0.0013) with mortality (hazard ratio 2.22, 95% confidence interval 1.37 to 3.62). Age showed a mortality risk increase of 8% per year (hazard ratio 1.08, 95% confidence interval 1.05 to 1.10, p = 0.001). The transition from ward to the ICU had, as a single determinant, the age, but in a reversed fashion (hazard ratio 0.96, 95% confidence interval 0.94 to 0.98, p = 0.0002). Conclusions: Once adjusted for the main determinant of mortality (age) heart failure only remained independently associated with mortality. Admission to the ICU was less likely for elderly patients. This may reflect the catastrophic impact of the first wave of COVID-19 pandemic in terms of ICU bed availability in Lombardy, leading to a selection process for ICU admission.
An Extensive Simplex Method Mapping the Global Feasibility (2002)

Understanding the global feasibility of engineering decision-making problems is fundamental to the synthesis of rational engineering decisions. An Extensive Simplex Method is presented to solve the global feasibility for a linear decision model relating multiple decision variables to multiple performance measures, and constrained by corresponding limits. The developed algorithm effectively traverses all extreme points in the feasible space and establishes the graph structure reflecting the active constraints and their connectivity. The algorithm demarcates basic and nonbasic variables at each extreme point, which is exploited to traverse the active constraints and merge the degenerate extreme points. Finally, a random model generator is presented with the capability to control the matrix sparseness and the model degeneracy for an arbitrary number of decision variables and performance measures. The results indicate that all these model properties are significant factors affect the total number of extreme points, their connected graph, and the global feasibility.
New method to measure coronary velocity and coronary flow reserve (2011)

Coronary flow reserve (CFR) is an important index of coronary microcirculatory function. The objective of this study was to validate the reproducibility and accuracy of intravascular conductance catheter-based method for measurements of baseline and hyperemic coronary flow velocity (and hence CFR). The absolute coronary blood velocity was determined by measuring the time of transit of a saline injection between two pairs of electrodes (known distance) on a conductance catheter during a routine saline injection without the need for reference flow. In vitro validation was made in the velocity range of 5 to 70 cm/s in reference to the volume collection method. In 10 swine, velocity measurements were compared with those from a flow probe in coronary arteries at different CFR attained by microsphere embolization. In vitro, the mean difference between the proposed method and volume collection was 0.7 ± 1.34 cm/s for steady flow and -0.77 ± 2.22 cm/s for pulsatile flow. The mean difference between duplicate measurements was 0 ± 1.4 cm/s. In in vivo experiments, the flow (product of velocity and lumen cross-sectional area that is also measured by the conductance catheter) was determined in both normal and stenotic vessels and the mean difference between the proposed method and flow probe was -1 ± 12 ml/min (flow ranged from 10 to 130 ml/min). For CFR, the mean difference between the two methods was 0.06 ± 0.28 (range of 1 to 3). Our results demonstrate the reproducibility and accuracy of velocity and CFR measurements with a conductance catheter by use of a standard saline injection. The ability of the combined measurement of coronary lumen area (as previously validated) and current velocity and CFR measurements provides an integrative diagnostic tool for interventional cardiology.
Prostate expression of endothelins and their receptors in rat growth (2008)

Endothelins (ETs) have been shown to have mitogenic effects on prostate cells in vitro. To study a relationship between ETs and prostate growth, we investigated expression of ET-1 and ET-3 and their receptors ETA and ETB in the dorsolateral (DLP) and ventral (VP) prostate lobes of rats aged 3 weeks, 3 months, and 22 months. The weight ratio of each lobe to the body was not different at 3 weeks but increased more in the DLP than in the VP at 3 months; the ratio did not change at 22 months. The density of the major receptor ETA, measured by radio-labelled ET-1 binding to prostate membrane particulates, was highest at 3 weeks in both prostate lobes and decreased thereafter. mRNA expression levels of ETA, ETB, ET-1, and ET-3 in the DLP and ETA in the VP, as assessed by relative multiplex reverse transcription-polymerase chain reaction, were highest at 3 weeks, and no significant change was seen in mRNA expression of ET-converting enzyme-1. The highest expression of ETA and the ligands at 3 weeks, followed by dramatic growth at 3 months in the DLP, suggests a role of ETA-mediated signal transduction in prostate growth of rats and possibly of humans.
SPIM (Stanford Pipelined Iterative Multiplier): A Pipelined 64 X 64 Bit Iterative Multiplier (1988)

Abstract : A 64 by 64 bit iterating multiplier, SPIM (Stanford Pipelined Iterative Multiplier) is presented. The pipelined array consists of a small tree of 4:2 adders. The 4:2 tree is better suited than a Wallace tree for a VLSI implementation because it is a more regular structure. A 4:2 carry save accumulator at the bottom of the array is used to iteratively accumulate partial products, allowing a partial array to be used, which reduces area. SPIM was fabricated in a 1.6 micron CMOS process. It has a core size of 3.8 X 6.5mm and contains 41 thousand transistors. The on chip clock generator runs at an internal clock frequency of 85MHz. The latency for a 64 X 64 bit fractional multiply is under 120ns, with a pipeline rate of one multiply every 47ns.
A new silver–silver-bonded dimer complex: solid-state structure of bis[μ-2H-1,3-benzoxazine-2,4(3H)-dionato]disilver(I) (2006)

The first structure of a silver complex of an aromatic cyclic amide has been determined. The complex is a centrosymmetric dimer, [Ag(C8H4NO3)2], with the same eight-membered ring construction as silver carboxyl­ates, including a significantly short Ag—Ag bond [2.8042 (12) Å].
Suppressing phase disproportionation in quasi-2D perovskite light-emitting diodes (2023)

Electroluminescence efficiencies and stabilities of quasi-two-dimensional halide perovskites are restricted by the formation of multiple-quantum-well structures with broad and uncontrollable phase distributions. Here, we report a ligand design strategy to substantially suppress diffusion-limited phase disproportionation, thereby enabling better phase control. We demonstrate that extending the π-conjugation length and increasing the cross-sectional area of the ligand enables perovskite thin films with dramatically suppressed ion transport, narrowed phase distributions, reduced defect densities, and enhanced radiative recombination efficiencies. Consequently, we achieved efficient and stable deep-red light-emitting diodes with a peak external quantum efficiency of 26.3% (average 22.9% among 70 devices and cross-checked) and a half-life of ~220 and 2.8 h under a constant current density of 0.1 and 12 mA/cm<sup>2</sup>, respectively. Our devices also exhibit wide wavelength tunability and improved spectral and phase stability compared with existing perovskite light-emitting diodes. These discoveries provide critical insights into the molecular design and crystallization kinetics of low-dimensional perovskite semiconductors for light-emitting devices.
Pretreatment serum squamous cell carcinoma antigen: a newly identified prognostic factor in early-stage cervical carcinoma. (1996)

The determination of pretreatment serum SCC-ag level provides a new prognostic factor in early-stage disease, particularly in patients with small tumor size. In future trials to assess the value of new treatment strategies, pretreatment serum SCC-ag levels can be used to help identify patients with a poor prognosis.
GAN based Single Image Super-Resolution via Spatially Adaptive De-normalization (2021)

Despite recent advances in technologies on single image super-resolution using deep neural networks, the key question still remains how to recover finer textures and edges. To solve this super-resolution problem, many recent researches have been using conditional generative adversarial network. However, restoring high resolution images using conditional generative adversarial network is disadvantageous in expressing fine textures and edges because there occurs the loss of spatial and high frequency informations. In this paper, informations on images in different scales are added hierarchically by using a spatially adaptive de-normalization method. This method can restore fine textures and edges of an image by inserting different scale informations for each layers in pyramid structure. In experimental results, the efficiency of the proposed method is proved by showing better performance to restore textures and edges in high quality, comparing with other state-of-the art techniques.
In Vitro Epithelial Organoid Generation Induced by Substrate Nanotopography (2015)

The extracellular matrix (ECM) exhibits tissue-specific topography and composition and plays a crucial role in initiating the biochemical and biomechanical signaling required for organizing cells into distinct tissues during development. How single cells assemble into structures featuring specific shapes in response to external cues is poorly understood. We examined the effect of substrate nanotopography on the morphogenesis of several types of epithelial cells and found that in response to the topography, Calu-3 and MDCK-II cells formed organoids that closely resemble their morphology in vivo. This finding represents the first demonstration that substrate nanotopography, one of the first physical cues detected by cells, can by itself induce epithelial tissue-like organization. Our results provide insights, in terms of a new aspect of ECM topography, into the design of future tissue-engineering systems and the study of mechanosignaling in the epithelium during normal development and tumor progression.
Demonstration of Distance Emulation for an Orbital-Angular-Momentum Beam (2015)

We design and experimentally demonstrate a free-space distance emulator for propagating OAM beams over long distances in a lab environment. The performance of the system is assessed by measuring spot radius and radius of curvature of propagated beams.
Cobalt(II) Chloride Hexahydrate-Diisopropylamine Catalyzed Mild and Chemoselective Reduction of Carboxylic Esters with Sodium Borohydride (2009)

The cobalt-catalyzed reduction of unsaturated α-cyano carboxylic esters using sodium borohydride (NaBH4) leads to the corresponding saturated cyano alcohols in high yields. In particular, the new catalytic system cobalt(II) chloride-diisopropylamine in combination with NaBH4 showed excellent activity in the chemoselective reduction of a variety of carboxylic esters to their corresponding alcohols in good to excellent yields under mild conditions.
Preparation of high T c Tl-Ba-Ca-Cu-O thin films by pulsed laser evaporation and Tl2O3 vapor processing (1989)

Tl-Ba-Ca-Cu-O superconducting thin films with zero-resistance temperatures up to 115 K have been prepared using a Tl2 O3 vapor process on Ba-Ca-Cu-O precursor thin films. The Ba-Ca-Cu-O thin films were made by laser deposition on Y-stabilized ZrO2 substrates. This technique minimizes problems caused by the toxicity of Tl2 O3, and its subsequent decomposition to the volatile and toxic Tl2 O upon heating. Therefore, it may have practical application in the fabrication of high Tc Tl-Ba-Ca-Cu-O superconducting thin-film devices.
Timing Analysis of a Microprocessor PLL Using High Quantum Efficiency Superconducting Single Photon Detector (SSPD) (2004)

Abstract This paper describes the analysis of a Phase-Locked Loop (PLL) internal phase detection circuit built in IBM’s 0.13 µm Silicon On Insulator (SOI) CMOS technology by using the Picosecond Imaging Circuit Analysis (PICA) [1,2] tool equipped with the high quantum efficiency Superconducting Single-Photon Detector (SSPD) [3,4]. Signals corresponding to the internal nodes of the PLL are for the first time measured and compared to circuit simulations in order to characterize the behavior of the different components of the circuit.
The State of the ML-universe (2020)

In the last few years, artificial intelligence (AI) and machine learning (ML) have become ubiquitous terms. These powerful techniques have escaped obscurity in academic communities with the recent onslaught of AI & ML tools, frameworks, and libraries that make these techniques accessible to a wider audience of developers. As a result, applying AI & ML to solve existing and emergent problems is an increasingly popular practice. However, little is known about this domain from the software engineering perspective. Many AI & ML tools and applications are open source, hosted on platforms such as GitHub that provide rich tools for large-scale distributed software development. Despite widespread use and popularity, these repositories have never been examined as a community to identify unique properties, development patterns, and trends.
Crosswell Electromagnetic Tomography in Saudi Arabia - From Field Surveys to Resistivity Mapping (2008)

A series of crosswell Electromagnetic surveys were made at the super giant Ghawar oil field in Saudi Arabia as part of an ongoing project to apply deep EM technology to map oil and water saturated regions within the field. The technology applies the principle electromagnetic induction and tomographic imaging to obtain the interwell resistivity distribution. The surveys which utilized existing wells and one newly drilled well were able to successfully collect data at well spacings of more than 800m. Recovered images were consistent with logs and often revealed an interwell resistivity section much different than the interpolated logs suggest.
<title>Optical up-conversion for passive millimeter-wave imaging</title> (1997)

Passive imaging at millimeter wavelengths is a constant struggle for increased sensitivity and angular resolution. Aperture synthesis is a particularly attractive technique for attacking these problems since it offers a high resolution from a given total antennas area and greater flexibility in the positioning of the antenna elements. This in turn can lead to a greater total collecting area and hence greater sensitivity than might be achievable with a single scanned antenna and with the additional benefit of electronic scanning. The high loss of millimeter-wave transmission lines means that received signals must be frequency translated to a more suitable frequency prior to transport to correlators. Although down conversion enables transmission by coaxial cables, up conversion onto optical carriers enables very low-loss optical fibers to be used for transmission and electronically programmable delay lines. In this paper we describe proof-of-principle experiments that demonstrate the application of optical up-conversion in aperture synthesis and also the direct formation of an image on a conventional optical camera from millimeter-wave signals modulated onto an optical carrier.
Immunocytochemical demonstration of dopamine-beta-hydroxylase and cytochrome B561 on the axonal reticulum in bovine sympathetic neurons. (1992)

In sympathetic neurons the axonal reticulum can be considered an extension of the secretory pole of the Golgi apparatus. If this tubular system indeed represents the neurosecretory apparatus, it would likely contain on its membranes the enzymes involved in catecholamine synthesis. To test this hypothesis, we investigated the distribution of dopamine-beta-hydroxylase and cytochrome b561 in bovine splenic nerve and nerve terminals in the vas deferens with an immunogold procedure after glycolmethacrylate embedding. Counterstaining with phosphotungstic acid at low pH selectively revealed the axonal reticulum elements. With antibodies against both enzymes, gold labeling was observed over the large dense-cored vesicles, the Golgi-associated axonal reticulum, the reticulum within axons, and the tubular complex at the nerve terminal. From our results it can be concluded that in sympathetic neurons the axonal reticulum represents a tubular neurosecretory system, extending from the Golgi apparatus in the cell soma to the nerve terminal. This concept emphasizes the local production of neurosecretory vesicles and may be of importance in the interpretation of neuronal transmission in normal and diseased states.