gebhart/patrepeval huggingface dataset:
Characterization techniques of ion bombardment damage on electronic devices during plasma processing—plasma process-induced damage (2021)

Abstract Plasma processing plays an important role in manufacturing leading-edge electronic devices such as ULSI circuits. Reactive ion etching achieves fine patterns with anisotropic features in metal-oxide-semiconductor field-effect transistors (MOSFETs). In contrast, it has been pointed out over the last four decades that plasma processes not only modify the surface morphology of materials but also degrade the performance and reliability of MOSFETs as a result of defect generation in materials such as crystalline Si substrate and dielectric films. This negative aspect of plasma processing is defined as plasma (process)-induced damage (PID) which is categorized mainly into three mechanisms, i.e. physical, electrical, and photon-irradiation interactions. This article briefly discusses the modeling of PID and provides historical overviews of the characterization techniques of PID, in particular, by the physical interactions, i.e. ion bombardment damage.
Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma (2011)

Squamous cell carcinomas (SCCs) are one of the most frequent forms of human malignancy, but, other than TP53 mutations, few causative somatic aberrations have been identified. We identified NOTCH1 or NOTCH2 mutations in ~75% of cutaneous SCCs and in a lesser fraction of lung SCCs, defining a spectrum for the most prevalent tumor suppressor specific to these epithelial malignancies. Notch receptors normally transduce signals in response to ligands on neighboring cells, regulating metazoan lineage selection and developmental patterning. Our findings therefore illustrate a central role for disruption of microenvironmental communication in cancer progression. NOTCH aberrations include frameshift and nonsense mutations leading to receptor truncations as well as point substitutions in key functional domains that abrogate signaling in cell-based assays. Oncogenic gain-of-function mutations in NOTCH1 commonly occur in human T-cell lymphoblastic leukemia/lymphoma and B-cell chronic lymphocytic leukemia. The bifunctional role of Notch in human cancer thus emphasizes the context dependency of signaling outcomes and suggests that targeted inhibition of the Notch pathway may induce squamous epithelial malignancies.
Numerical comparison of X-ray differential phase contrast and attenuation contrast (2012)

We present a numerical tool to compare directly the contrast-to-noise-ratio (CNR) of the attenuation- and differential phase-contrast signals available from grating-based X-ray imaging for single radiographs. The attenuation projection is differentiated to bring it into a modality comparable to the differential phase projection using a Gaussian derivative filter. A Relative Contrast Gain (RCG) is then defined as the ratio of the CNR of image values in a region of interest (ROI) in the differential phase projection to the CNR of image values in the same ROI in the differential attenuation projection. We apply the method on experimental data of human breast tissue acquired using a grating interferometer to compare the two contrast modes for two regions of interest differing in the type of tissue. Our results indicate that the proposed method can be used as a local estimate of the spatial distribution of the ratio δ/β, i.e., real and imaginary part of the complex refractive index, across a sample.
SuppTable3 from Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer (2023)

&lt;p&gt;Supplementary Table 3 lists all CNAs&lt;/p&gt;
LOCALIZATION OF ACTION OF THE IS50-ENCODED TRANSPOSASE PROTEIN (1986)

The movement of the bacterial insertion sequence IS50 and of composite elements containing direct terminal repeats of IS50 involves the two ends of IS50, designated O (outside) and I (inside), which are weakly matched in DNA sequence, and an IS50 encoded protein, transposase, which recognizes the O and I ends and acts preferentially in cis. Previous data had suggested that, initially, transposase interacts preferentially with the O end sequence and then, in a second step, with either an O or an I end. To better understand the cis action of transposase and how IS50 ends are selected, we generated a series of composite transposons which contain direct repeats of IS50 elements. In each transposon, one IS50 element encoded transposase (tnp+), and the other contained a null (tnp-) allele. In each of the five sets of composite transposons studied, the transposon for which the tnp+ IS50 element contained its O end was more active than a complementary transposon for which the tnp- IS50 element contained its O end. This pattern of O end use suggests models in which the cis action of transposase and its choice of ends is determined by protein tracking along DNA molecules.
Changes in cytokine production and T cell subpopulations in experimentally induced zinc-deficient humans (1997)

We have utilized an experimental model of human zinc deficiency for study of cytokines production by TH1 and TH2 cells. Additionally, we determined ratios of CD4+ to CD8+ and CD4+ CD45RA+ to CD4+CD45RO+ cells and percentages of CD73+ T cytolytic cells in the CD8+ subset. The data were collected during baseline, at the end of the zinc-restricted period, and following zinc repletion. Our results showed that functions of TH1 cells, as evidenced by production of interferon-gamma, interleukin-2 (IL-2), and tumor necrosis factor-alpha, were decreased, whereas functions of TH2 cells (production of IL-4, IL-6, and IL-10) were unaffected by zinc deficiency. Thus an imbalance between TH1 and TH2 cells resulted because of zinc deficiency in humans. Our studies also showed that zinc may be required for regeneration of new CD4+ T lymphocytes and maintenance of T cytolytic cells. We conclude that an imbalance between TH1 and TH2 cells, decreased recruitment of T naive cells, and decreased percentage of T cytolytic cells may account for decreased cell-mediated immune functions in zinc-deficient subjects.
Understanding and predicting the orientation of heteroleptic and homoleptic phosphors in organic light-emitting materials (2016)

Non-isotropic transition dipole orientation can enhance the efficiency of organic light-emitting diodes. Therefore, we analyzed the underlying mechanism by combining the use of different deposition techniques as well as iridium-complexes with special physical properties.
Spatial shrinkage/expansion patterns between breast density measured in two MRI scans evaluated by non-rigid registration (2011)

Breast MRI acquires many images from the breast, and computer-aided algorithms and display tools are often used to assist the radiologist's interpretation. Women with lifetime risk greater than 20% of developing breast cancer are recommended to receive annual screening MRI, but the current breast MRI computer-aided-diagnosis systems do not provide the necessary function for comparison of images acquired at different times. The purpose of this work was to develop registration methods for evaluating the spatial change pattern of fibroglandular tissue between two breast MRI scans of the same woman taken at different times. The registration method is based on rigid alignment followed by a non-rigid Demons algorithm. The method was tested on three different subjects who had different degrees of changes in the fibroglandular tissue, including two patients who showed different spatial shrinkage patterns after receiving neoadjuvant chemotherapy before surgery, and one control case from a normal volunteer. Based on the transformation matrix, the collapse of multiple voxels on the baseline images to one voxel on the follow-up images is used to calculate the shrinkage factor. Conversely, based on the reverse transformation matrix the expansion factor can be calculated. The shrinkage/expansion factor, the deformation magnitude and direction, as well as the Jacobian determinate at each location can be displayed in a 3D rendering view to show the spatial changes between two MRI scans. These different parameters show consistent results and can be used for quantitative evaluation of the spatial change patterns. The presented registration method can be further developed into a clinical tool for evaluating therapy-induced changes and for early diagnosis of breast cancer in screening MRI.
Content Caching and User Scheduling in Heterogeneous Wireless Networks (2016)

To facilitate content delivery to mobile users, we propose a content caching and distribution framework for the heterogeneous OFDM networks, where a library of files available at the macro base station (MBS) can be distributively cached in multiple serving nodes (SNs). SNs are capable of both receiving unstored files from MBS and transmitting files to the associated users. For a given group of file downloading requests, the user scheduling scheme is jointly designed with the content caching scheme so that the number of served users is maximized for a given amount of spectrum and time. First, the corresponding downlink throughput maximization problem is shown to be NP-hard. Then, for the system with one MBS and one SN, the design of the joint user scheduling and caching scheme is transformed into a binary linear programming problem. For the system with one MBS and two SNs, the joint scheduling and caching (JSC) algorithm has been proposed to tap on the potential of the coded multicasting scheme between MBS and SNs. The proposed algorithm can be extended to networks with arbitrary number of SNs. Simulation results demonstrate that the JSC algorithm provides a significant sum throughput gain.
Accepted from open call - Forward high-speed wireless packet data service in is-2000 - 1xev-dv (2003)

This article describes enhancements to the physical layer design of single-carrier (1×) cdma2000/sup /spl reg// wireless networks introduced by Revision C of the IS-2000 standard (commonly referred to as 1×EV-DV). These improvements are mainly for the support of high-speed wireless packet data service on the forward (base station to mobile station) link. A new shared channel, the forward packet data channel, F-PDCH, is introduced to significantly increase spectral efficiency. This is accomplished through smart, channel-dependent scheduling of base station, BS, resources by taking advantage of the delay-tolerant nature of data traffic. This shared channel utilizes fast link adaptation through adaptive modulation and coding supported by the feedback of channel quality information. A form of hybrid ARQ type II technique commonly referred to as asynchronous adaptive incremental redundancy compensates for frame error events due to imperfect link adaptation. The impact of the new channel on voice capacity of the system is designed to be minimal because the F-PDCH utilizes resources that are not consumed by real-time users.
Low-Cost Inkjet Printing Technology for the Rapid Prototyping of Transducers (2017)

Recently, there has been an upsurge in efforts dedicated to developing low-cost flexible electronics by exploiting innovative materials and direct printing technologies. This interest is motivated by the need for low-cost mass-production, shapeable, and disposable devices, and the rapid prototyping of electronics and sensors. This review, following a short overview of main printing processes, reports examples of the development of flexible transducers through low-cost inkjet printing technology.
Renewable and cooling aware workload management for sustainable data centers (2012)

Recently, the demand for data center computing has surged, increasing the total energy footprint of data centers worldwide. Data centers typically comprise three subsystems: IT equipment provides services to customers; power infrastructure supports the IT and cooling equipment; and the cooling infrastructure removes heat generated by these subsystems. This work presents a novel approach to model the energy flows in a data center and optimize its operation. Traditionally, supply-side constraints such as energy or cooling availability were treated independently from IT workload management. This work reduces electricity cost and environmental impact using a holistic approach that integrates renewable supply, dynamic pricing, and cooling supply including chiller and outside air cooling, with IT workload planning to improve the overall sustainability of data center operations. Specifically, we first predict renewable energy as well as IT demand. Then we use these predictions to generate an IT workload management plan that schedules IT workload and allocates IT resources within a data center according to time varying power supply and cooling efficiency. We have implemented and evaluated our approach using traces from real data centers and production systems. The results demonstrate that our approach can reduce both the recurring power costs and the use of non-renewable energy by as much as 60% compared to existing techniques, while still meeting the Service Level Agreements.
An efficient fashion-driven learning approach to model user preferences in on-line shopping scenarios (2010)

In this work we tackle the problem of search personalization for on-line soft goods shopping. By learning what the user likes and what the user does not like, better search rankings and therefore a better overall shopping experience can be obtained. The first contribution of the work is in terms of feature selection: given the specific nature of the domain, we combine the traditional visual and text feature into a fashion-driven low dimensional space, compact yet very discriminative. On the learning stage, we describe a two step hybrid learning algorithm, that combines a discriminative model learned off-line over historical data, with an extremely efficient generative model, updated on-line according to the user behavior. Qualitative and quantitative analyses show promising results.
Plasma biomarkers associated with adverse outcomes in patients with calcific aortic stenosis (2021)

Plasma biomarkers are strongly associated with the risk of adverse outcomes in patients with AS. Biomarkers of inflammation and calcification were most strongly related to prognosis.
Layered, Tunable Graphene Oxide Heterostructures for Wearable Electrocardiogram Sensors. (2021)

Nanoscale engineered materials combined with wireless technologies within Internet of Things (IoT) can deliver new level of health diagnostics. A reduced graphene oxide-nylon composite material is developed and tested, demonstrating its usefulness as a materials for sensors in a wearable, long term electrocardiogram (ECG) monitoring. The heterostructure is analyzed structurally, chemically and electrically by scanning electron microscope (SEM), atomic force microscopy (AFM), Fourier Transform Infrared (FTIR) spectroscopy, and resistivity analysis. Analysis finds interesting tunability of electrical and optical properties, while live ECG data demonstrate its signal transduction capability and suitability as an ECG sensor.
Electronic Matrix Isolation Spectroscopic Studies of the Group IIA Metal—Water Photochemistry (1984)

This paper reports the results of an investigation of the electronic structures of the Group IIA metal atom hydration reaction intermediates (M. . . OH2 adducts) and their subsequent photolysis products (HMOH and MOH). For the adduct, the metal—water interaction is sufficiently strong so as to perturb significantly the electronic structure of the metal atom, which results in a unique band structure for the adduct that is red-shifted from the metal atomic resonance transition. Selective photolysis studies are conducted to assist in deconvoluting the complex band structure of the adduct. Molecular orbital theory is invoked to interpret the nature of the ground and excited states of the adduct. Molecular orbital and electronic state-to-state correlation arguments are presented to rationalize the chemical reaction dynamics of the adduct along ground and excited state potential energy surfaces.
ChemInform Abstract: A Novel Synthetic Route to Morpholin‐2,3‐diones from 2‐Amino Alcohols. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Rapid and precise genome engineering in a naturally short-lived vertebrate (2022)

Abstract The African turquoise killifish is a powerful vertebrate system to study complex phenotypes at scale, including aging and age-related disease. Here we develop a rapid and precise CRISPR/Cas9-mediated knock-in approach in the killifish. We show its efficient application to precisely insert fluorescent reporters of different sizes at various genomic loci, to drive cell-type- and tissue-specific expression. This knock-in method should allow the establishment of humanized disease models and the development of cell-type-specific molecular probes for studying complex vertebrate biology.
Learning to predict part mobility from a single static snapshot (2017)

We introduce a method for learning a model for the mobility of parts in 3D objects. Our method allows not only to understand the dynamic functionalities of one or more parts in a 3D object, but also to apply the mobility functions to static 3D models. Specifically, the learned part mobility model can predict mobilities for parts of a 3D object given in the form of a single static snapshot reflecting the spatial configuration of the object parts in 3D space, and transfer the mobility from relevant units in the training data. The training data consists of a set of mobility units of different motion types. Each unit is composed of a pair of 3D object parts (one moving and one reference part), along with usage examples consisting of a few snapshots capturing different motion states of the unit. Taking advantage of a linearity characteristic exhibited by most part motions in everyday objects, and utilizing a set of part-relation descriptors, we define a mapping from static snapshots to dynamic units. This mapping employs a motion-dependent snapshot-to-unit distance obtained via metric learning. We show that our learning scheme leads to accurate motion prediction from single static snapshots and allows proper motion transfer. We also demonstrate other applications such as motion-driven object detection and motion hierarchy construction.
Targeted variant detection using unaligned RNA-Seq reads (2019)

Mutations identified in acute myeloid leukemia patients are useful for prognosis and for selecting targeted therapies. Detection of such mutations using next-generation sequencing data requires a computationally intensive read mapping step followed by several variant calling methods. Targeted mutation identification drastically shifts the usual tradeoff between accuracy and performance by concentrating all computations over a small portion of sequence space. Here, we present <i>km</i>, an efficient approach leveraging k-mer decomposition of reads to identify targeted mutations. Our approach is versatile, as it can detect single-base mutations, several types of insertions and deletions, as well as fusions. We used two independent cohorts (The Cancer Genome Atlas and Leucegene) to show that mutation detection by <i>km</i> is fast, accurate, and mainly limited by sequencing depth. Therefore, <i>km</i> allows the establishment of fast diagnostics from next-generation sequencing data and could be suitable for clinical applications.
Cellular and viral determinants that regulate HIV-1 infection in macrophages (1994)

Macrophages in brain, lung, and lymphatics constitute a major HIV reservoir during subclinical infection and disease. During HIV transmission macrophages are seemingly one of the first cells infected, being as efficient as T cells in supporting productive viral replication. Macrophages control a myriad of cell-mediated immune responses that regulate the levels of infection and lead to viral persistence. HIV determinants control viral entry and productive replication and, taken together with cellular differentiation factors, decide the outcome of virus-macrophage interactions. Most important, many clinical manifestations of HIV infection such as encephalitis, myelopathy, pneumonitis, and lymphadenopathy are closely linked to viral replication. Indeed, tissue pathology often correlates with viral gene expression in tissue macrophages. Taken together, these observations provide strong support for a central role of macrophages in progressive HIV infection and its clinical manifestations.
Optical Waves Transmission Raised by Localized Surface Plasmons (2007)

A corrugated metal thin film can enhance the emission of light-emitting devices by the assistance of radiative surface plasmons. But, away from the resonant frequency, the metal thin film has a shielding effect on transmission. We replace the corrugated thin film by a discontinuous metal nanostructure, the isolated metal nanohemispheres can induce localized surface plasmons. The angular dependence and two different wavelengths are studied. The reflection on dielectric layers may be reduced and the transmission could be raised by the localized surface plasmons even the resonance condition is not fulfilled. The scattered E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> component is sensitive to the tilt angle, it might be useful to some novel applications.
Multi-modal Probabilistic Prediction of Interactive Behavior via an\n Interpretable Model (2019)

For autonomous agents to successfully operate in real world, the ability to\nanticipate future motions of surrounding entities in the scene can greatly\nenhance their safety levels since potentially dangerous situations could be\navoided in advance. While impressive results have been shown on predicting each\nagent's behavior independently, we argue that it is not valid to consider road\nentities individually since transitions of vehicle states are highly coupled.\nMoreover, as the predicted horizon becomes longer, modeling prediction\nuncertainties and multi-modal distributions over future sequences will turn\ninto a more challenging task. In this paper, we address this challenge by\npresenting a multi-modal probabilistic prediction approach. The proposed method\nis based on a generative model and is capable of jointly predicting sequential\nmotions of each pair of interacting agents. Most importantly, our model is\ninterpretable, which can explain the underneath logic as well as obtain more\nreliability to use in real applications. A complicate real-world roundabout\nscenario is utilized to implement and examine the proposed method.\n