gebhart/patrepeval huggingface dataset:
Characteristic C - V profile as a signature for electrostatic doping in FD-SOI (2020)

Metal-semiconductor-oxide-semiconductor (MSOS) structures form core parts of advanced FD-SOI devices. Extensive TCAD simulations of such MSOS structures show distinct C - V features, such as a characteristic capacitance hump, when contacted with extreme work function metals capable of supplying instant charge carriers in the lowly doped or undoped SOI layer. Such features are caused by volume inversion in the SOI layer, via electrostatic doping (ED), that becomes depleted for opposite biasing. The results show that the C - V analysis on relatively simple MSOS structures can be used to obtain the signature for ED in FD-SOI or alternative UTB devices.
Improvement of Isolated Myoclonus Phenotype in Myoclonus Dystonia after Pallidal Deep Brain Stimulation (2016)

This case series demonstrates that high frequency GPi-DBS is effective in treating isolated myoclonus in myoclonus-dystonia, regardless of the presence of SGCE mutation.
Trapping of the C5 Methylene Intermediate in Thymidylate Synthase (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTTrapping of the C5 Methylene Intermediate in Thymidylate SynthaseJ. E. Barrett, D. A. Maltby, D. V. Santi, and P. G. SchultzView Author Information Department of Chemistry, University of California at Berkeley, Berkeley, California 94720 Departments of Pharmaceutical Chemistry and Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143 Cite this: J. Am. Chem. Soc. 1998, 120, 2, 449–450Publication Date (Web):January 21, 1998Publication History Received12 September 1997Published online21 January 1998Published inissue 1 January 1998https://pubs.acs.org/doi/10.1021/ja973210thttps://doi.org/10.1021/ja973210trapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views295Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Carbene compounds,Monomers,Nutrition,Organic compounds,Peptides and proteins Get e-Alerts
Accelerated low-rank updates to tensor decompositions (2016)

Tensor analysis (through tensor decompositions) is increasingly becoming popular as a powerful technique for enabling comprehensive and complete analysis of real-world data. In many critical modern applications, large-scale tensor data arrives continuously (in streams) or changes dynamically over time. Tensor decompositions over static snapshots of tensor data become prohibitively expensive due to space and computational bottlenecks, and severely limit the use of tensor analysis in applications that require quick response. Effective and rapid streaming (or non-stationary) tensor decompositions are critical for enabling large-scale real-time analysis. We present new algorithms for streaming tensor decompositions that effectively use the low-rank structure of data updates to dynamically and rapidly perform tensor decompositions of continuously evolving data. Our contributions presented here are integral for enabling tensor decompositions to become a viable analysis tool for large-scale time-critical applications. Further, we present our newly-implemented parallelized versions of these algorithms, which will enable more effective deployment of these algorithms in real-world applications. We present the effectiveness of our approach in terms of faster execution of streaming tensor decompositions that directly translate to short response time during analysis.
Characterization and Control of Native Oxide on Silicon (1994)

Characterization and control methods of native oxide growth on silicon (Si) surfaces at room temperature and during temperature ramp-up are described. The X-ray photoelectron spectroscopy (XPS) data have sufficient resolution to discern the stepwise increase in the amount of native oxide on hydrofluoric acid (HF)-cleaned Si surfaces exposed to air at room temperature. The native oxide growth on HF-cleaned Si surfaces can be controlled by lowering oxygen or water concentration in the ambient of the process at room temperature and by passivating the Si surface for semiconductor processes at temperatures higher than 300° C. In situ control methods of native oxide growth result in low-resistance tungsten (W)/n + -Si contacts and very thin oxide films with high electrical insulating performance.
Investigation on the Self-discharge of the LiFePO<inf>4</inf>/C nanophosphate battery chemistry at different conditions (2014)

Lithium ion batteries with iron phosphate cathodes are gradually improving in their performance and gaining importance, and are more and more considered for new applications. Different aspects of this chemistry were studied in numerous publications; however, very little research was devoted to detailed empirical investigations in order to find out how self-discharge of this chemistry depends on different storing conditions. Precise knowledge about the level of the self-discharge of lithium ion battery cells is very important for improving the performance of the battery management system since it allows also for more precise determination of the actual battery SOC after prolonged storage. In this paper the self-discharge of the nanophosphate LiFePO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> /C is studied at different temperature, SOC conditions and at different SOH levels of the battery. Moreover, cell to cell differences in self-discharge caused by the manufacturing tolerances are investigated.
Burn Injury Reduces Neutrophil Directional Migration Speed in Microfluidic Devices (2010)

Thermal injury triggers a fulminant inflammatory cascade that heralds shock, end-organ failure, and ultimately sepsis and death. Emerging evidence points to a critical role for the innate immune system, and several studies had documented concurrent impairment in neutrophil chemotaxis with these post-burn inflammatory changes. While a few studies suggest that a link between neutrophil motility and patient mortality might exist, so far, cumbersome assays have prohibited exploration of the prognostic and diagnostic significance of chemotaxis after burn injury. To address this need, we developed a microfluidic device that is simple to operate and allows for precise and robust measurements of chemotaxis speed and persistence characteristics at single-cell resolution. Using this assay, we established a reference set of migration speed values for neutrophils from healthy subjects. Comparisons with samples from burn patients revealed impaired directional migration speed starting as early as 24 hours after burn injury, reaching a minimum at 72-120 hours, correlated to the size of the burn injury and potentially serving as an early indicator for concurrent infections. Further characterization of neutrophil chemotaxis using this new assay may have important diagnostic implications not only for burn patients but also for patients afflicted by other diseases that compromise neutrophil functions.
Quantitative Assessment of Classic Anteroinferior Bony Bankart Lesions by Radiography and Computed Tomography (2003)

These images gave decisive information as to whether an osseous glenoid defect required bone grafting to achieve stability after Bankart repair.
T/Key: Second-Factor Authentication From Secure Hash Chains (2017)

Time-based one-time password (TOTP) systems in use today require storing secrets on both the client and the server. As a result, an attack on the server can expose all second factors for all users in the system. We present T/Key, a time-based one-time password system that requires no secrets on the server. Our work modernizes the classic S/Key system and addresses the challenges in making such a system secure and practical. At the heart of our construction is a new lower bound analyzing the hardness of inverting hash chains composed of independent random functions, which formalizes the security of this widely used primitive. Additionally, we develop a near-optimal algorithm for quickly generating the required elements in a hash chain with little memory on the client. We report on our implementation of T/Key as an Android application. T/Key can be used as a replacement for current TOTP systems, and it remains secure in the event of a server-side compromise. The cost, as with S/Key, is that one-time passwords are longer than the standard six characters used in TOTP.
A coarse grain model for DNA (2007)

Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.
Cohort profile – MSK radiation workers: a feasibility study to establish a deceased worker sub-cohort as part of a multicenter medical radiation worker component in the million person study of low-dose radiation health effects (2019)

MSK has pioneered the use of novel radiation diagnostic and therapeutic approaches over time (including initial work with x-rays, radium, and radon), with workplace safety in mind, resulting in a variety of radiation worker exposure scenarios. The results of this feasibility sub-cohort of deceased radiation workers, and associated lessons learned may potentially be applied to an expanded multicenter study of about 170,000 medical radiation worker component of the MPS.
Diesel particulate matter2.5 promotes epithelial-mesenchymal transition of human retinal pigment epithelial cells via generation of reactive oxygen species (2020)

Although several studies have linked PM<sub>2.5</sub> (particulate matter with a diameter less than 2.5 μm) to ocular surface diseases such as keratitis and conjunctivitis, very few studies have previously addressed its effect on the retina. Therefore, the aim of this study was to evaluate the effect of PM<sub>2.5</sub> on epithelial-mesenchymal transition (EMT), a process involved in disorders of the retinal pigment epithelial (RPE) on APRE-19 cells. PM<sub>2.5</sub> changed the phenotype of RPE cells from epithelial to fibroblast-like mesenchymal, and increased cell migration. Exposure to PM<sub>2.5</sub> markedly increased the expression of mesenchymal markers, but reduced the levels of epithelial markers. Moreover, PM<sub>2.5</sub> promoted the phosphorylation of MAPKs and the expression of transforming growth factor-β (TGF-β)-mediated nuclear transcriptional factors. However, these PM<sub>2.5</sub>-mediated changes were completely reversed by LY2109761, a small molecule inhibitor of the TGF-β receptor type I/II kinases, and N-acetyl-L-cysteine (NAC), a reactive oxygen species (ROS) scavenger. Interestingly, NAC, but not LY2109761, effectively restored the PM<sub>2.5</sub>-induced mitochondrial defects, including increased ROS, decreased mitochondrial activity, and mitochondrial membrane potential disruption. Collectively, our findings indicate that the TGF-β/Smad/ERK/p38 MAPK signaling pathway is activated downstream of cellular ROS during PM<sub>2.5</sub>-induced EMT. The present study provides the first evidence that EMT of RPE may be one of the mechanisms of PM<sub>2.5</sub>-induced retinal dysfunction.
A Truncated Fourier Based Analytical Model for SRMs with Higher Number of Rotor Poles (2020)

Switched reluctance motors (SRM) have been seen as a potential candidate for automotive, aerospace as well as domestic applications and High-Rotor pole SRM (HR-SRM) present a significant advancement in this area. This machine configuration offers most of the the benefits offered by conventional SRMs and has shown significant benefits in efficiency and torque quality. However, HR-SRM has a narrower inductance profile with a lower saliency ratio as compared to a conventional SRM with an identical stator. This can make it inherently challenging to directly adopt mathematical models and sensorless control approaches currently in use. This paper presents a time-efficient analytical model for the characterization of a 6/10 SRM using an inductance model utilizing truncated Fourier series as well as multi-order polynomial curve-fitting algorithm. The inductance model is extended to accurately predict back-EMF and electromagnetic torque response towards obtaining a comprehensive model for every operating point of the machine during dynamic operation. The effectiveness of the proposed concept has analyzed for a prototype machine and verified using Finite Element Analysis (FEA).
Cooperating base station set selection and network reconfiguration in limited backhaul networks (2012)

Managing interference by Coordinated Multi-Point (CoMP) transmission/reception is an effective mechanism to achieve high data rates in future cellular networks, like Long Term Evolution (LTE)-Advanced. For CoMP, sets of Base Stations (BSs) have to be selected to jointly serve User Equipments (UEs). These sets are typically selected based on wireless characteristics only. However, using CoMP also poses strict capacity and latency requirements on the backhaul network, which are difficult to fulfill even with future optical technologies. Hence, these requirements additionally need to be taken into account when deciding which BSs jointly serve a given UE. We have developed a BSs selection heuristic for CoMP that takes into account both aspects: the wireless channels and the backhaul network status. This heuristic can also identify, for a particular wireless channel situation, which bottlenecks in the backhaul network make a desired BSs selection infeasible. We exploit this to dynamically adapt the backhaul network to the wireless requirements. We call this network reconfiguration. Our simulations show that the heuristic's solution quality is close to the optimum while execution time and memory consumption are reduced by multiple orders of magnitude compared to solving the problem via mathematical optimization. This allows real-world deployment of the heuristic. In addition, we simulate the network reconfiguration in a future backhaul network scenario based on Passive Optical Networks (PONs). The results illustrate how our approach helps to better exploit available backhaul resources.
Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA (2011)

Whole transcriptome sequencing by mRNA-Seq is now used extensively to perform global gene expression, mutation, allele-specific expression and other genome-wide analyses. mRNA-Seq even opens the gate for gene expression analysis of non-sequenced genomes. mRNA-Seq offers high sensitivity, a large dynamic range and allows measurement of transcript copy numbers in a sample. Illumina's genome analyzer performs sequencing of a large number (> 10(7)) of relatively short sequence reads (< 150 bp).The "paired end" approach, wherein a single long read is sequenced at both its ends, allows for tracking alternate splice junctions, insertions and deletions, and is useful for de novo transcriptome assembly. One of the major challenges faced by researchers is a limited amount of starting material. For example, in experiments where cells are harvested by laser micro-dissection, available starting total RNA may measure in nanograms. Preparation of mRNA-Seq libraries from such samples have been described(1, 2) but involves significant PCR amplification that may introduce bias. Other RNA-Seq library construction procedures with minimal PCR amplification have been published(3, 4) but require microgram amounts of starting total RNA. Here we describe a protocol for the Illumina Genome Analyzer II platform for mRNA-Seq sequencing for library preparation that avoids significant PCR amplification and requires only 10 nanograms of total RNA. While this protocol has been described previously and validated for single-end sequencing(5), where it was shown to produce directional libraries without introducing significant amplification bias, here we validate it further for use as a paired end protocol. We selectively amplify polyadenylated messenger RNAs from starting total RNA using the T7 based Eberwine linear amplification method, coined "T7LA" (T7 linear amplification). The amplified poly-A mRNAs are fragmented, reverse transcribed and adapter ligated to produce the final sequencing library. For both single read and paired end runs, sequences are mapped to the human transcriptome(6) and normalized so that data from multiple runs can be compared. We report the gene expression measurement in units of transcripts per million (TPM), which is a superior measure to RPKM when comparing samples(7).
Electronic States and Transport Phenomena of Pt Nanoparticle Catalysts Supported on Nb-Doped SnO2 for Polymer Electrolyte Fuel Cells (2019)

Semiconducting oxide nanoparticles are strongly influenced by surface-adsorbed molecules and tend to generate an insulating depletion layer. The interface between a noble metal and a semiconducting oxide constructs a Schottky barrier, interrupting the electron transport. In the case of a Pt catalyst supported on the semiconducting oxide Nb-doped SnO<sub>2</sub> with a fused-aggregate network structure (Pt/Nb-SnO<sub>2</sub>) for polymer electrolyte fuel cells, the electronic conductivity increased abruptly with increasing Pt loading, going from 10<sup>-4</sup> to 10<sup>-2</sup> S cm<sup>-1</sup>. The Pt X-ray photoemission spectroscopy (XPS) spectra at low Pt loading amount exhibited higher binding energy than that of pristine Pt metal. The peak shift for the Pt XPS spectra was larger than that of the Pt hard X-ray photoemission spectroscopy (HAXPES) spectra. For all of the spectra, the peaks approached the binding energy of pristine Pt metal with increasing Pt loading. The Sn XPS spectral peak proved the existence of Sn metal with increasing Pt loading, and the peak intensity was larger than that for HAXPES. These spectroscopic results, together with the scanning transmission electron microscopy with energy dispersive X-ray spectroscopy (STEM-EDX) spectra, proved that a PtSn alloy was deposited at the interface between Pt and Nb-SnO<sub>2</sub> as a result of the sintering procedure under dilute hydrogen atmosphere. Both Nb spectra indicated that the oxidation state of Nb was +5 and thus that the Nb cation acts as an n-type dopant of SnO<sub>2</sub>. We conclude that the PtSn alloy at the interface between Pt and Nb-SnO<sub>2</sub> relieved the effect of the Schottky barrier, enhanced the carrier donation from Pt to Nb-SnO<sub>2</sub>, and improved the electronic transport phenomena of Pt/Nb-SnO<sub>2</sub>.
Supplementary Figures S1-S5 from Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1 (2023)

&lt;p&gt;Overview of the screening strategy in haploid cells (S1); Correlation between ABCB1 and SMARCB1 mRNA expression levels across multiple human cancers represented in the TCGA database (S2); Correlation between SMARCB1 expression and doxorubicin resistance across multiple human cancers represented in the TCGA database (S3); SMARCB1 loss leads to ABCB1 upregulation, drug resistance and reduced Dox accumulation (S4); Hierarchical clustering reveals multiple classes of genes that are differentially expressed in WT Hap1 cells compared to Hap1 cells lacking SMARCB1 (S5).&lt;/p&gt;
Nanosurface design of dental implants for improved cell growth and function (2012)

A strategy was proposed for the topological design of dental implants based on an in vitro survey of optimized nanodot structures. An in vitro survey was performed using nanodot arrays with dot diameters ranging from 10 to 200 nm. MG63 osteoblasts were seeded on nanodot arrays and cultured for 3 days. Cell number, percentage undergoing apoptotic-like cell death, cell adhesion and cytoskeletal organization were evaluated. Nanodots with a diameter of approximately 50 nm enhanced cell number by 44%, minimized apoptotic-like cell death to 2.7%, promoted a 30% increase in microfilament bundles and maximized cell adhesion with a 73% increase in focal adhesions. An enhancement of about 50% in mineralization was observed, determined by von Kossa staining and by Alizarin Red S staining. Therefore, we provide a complete range of nanosurfaces for growing osteoblasts to discriminate their nanoscale environment. Nanodot arrays present an opportunity to positively and negatively modulate cell behavior and maturation. Our results suggest a topological approach which is beneficial for the design of dental implants.
Foreword (2016)

This article is reprinted from IEEE Journal of Solid-State Circuits, vol. 1, no. 1, p. 3, 1966. Here, presents the opening message from the 1996 International Solid-State Circuits Conference which discussed the creation of the IEEE Journal of Solid-State Circuits.
Proteolysis of Human Monocyte CD14 by Cysteine Proteinases (Gingipains) from Porphyromonas gingivalis Leading to Lipopolysaccharide Hyporesponsiveness (2000)

Cysteine proteinases (gingipains) elaborated from Porphyromonas gingivalis exhibit enzymatic activities against a broad range of host proteins and are considered key virulence factors in the onset and development of adult periodontitis and host defense evasion. In this study, we examined the ability of arginine-specific gingipains (high molecular mass Arg-specific gingipain (HRGP) and Arg-specific gingipain 2) and lysine-specific gingipain (KGP) to cleave monocyte CD14, the main receptor for bacterial cell surface components such as LPS. Binding of anti-CD14 mAb MY4 to human monocytes was almost completely abolished by 0.3 microM HRGP and KGP treatments for 15 min, and 1 microM RGP2 for 30 min. In contrast, the expressions of Toll-like receptor 4, and CD18, CD54, CD59, and HLA-A, -B, -C on monocytes were slightly increased and decreased, respectively, by 0. 3 microM HRGP and KGP. This down-regulation resulted from direct proteolysis, because 1) gingipains eliminated MY4 binding even to fixed monocytes, and 2) CD14 fragments were detected in the extracellular medium by immunoblot analysis. Human rCD14 was degraded by all three gingipains, which confirmed that CD14 was a substrate for gingipains. TNF-alpha production by monocytes after HRGP and KGP treatments was decreased at 1 ng/ml, but not at 20 microg/ml LPS, indicating that gingipains inhibited a CD14-dependent cell activation. These results suggest that gingipains preferentially cleave monocyte CD14, resulting in attenuation of the cellular recognition of bacteria, and as a consequence sustain chronic inflammation.