gebhart/patrepeval huggingface dataset:
Multicenter comparison of outcomes for clinical and pathologic T3a renal cell carcinoma. (2020)

758 Background: The identification of venous thrombus in patients with renal cell carcinoma (RCC) is particularly challenging, with a substantial number upstaged to pathologic T3a following intervention. We compared survival outcomes between patients with initial cT3a status versus those upstaged to pT3a. Methods: This is a retrospective, multicenter analysis of patients with cT3a or pT3a RCC who underwent operative management. Primary outcome was recurrence-free survival (RFS). Secondary outcomes were overall survival (OS) and cancer-specific survival (CSS). Cox regression multivariable analysis (MVA) was utilized for primary outcome. Kaplan-Meier analyses (KMA) were conducted to describe RFS, OS, and CSS with log-rank test comparing clinical and upstaged pathologic T3a groups. Results: 770 patients were analyzed (cT3a 184, pT3a 586, median follow-up 28 months). Average pathologic tumor size was smaller in pT3a (7.2 cm vs 8.7 cm, p &lt; 0.01), with no significant differences in clinical variables. A similar proportion underwent radical nephrectomy (vs. partial) (89.7% cT3a and 85.0% pT3a, p = 0.11) with no significant different in positive margin rate (3.8% cT3a, 4.8% pT3a, p = 0.23). However, a higher proportion of patients with cT3a disease were pathologically node positive (19.0% vs. 10.8%, p &lt; 0.01) and demonstrated a higher rate of recurrence (cT3a 51.1% vs. pT3a 34.1%, p &lt; 0.01) despite shorter mean follow-up (cT3a 33.0 vs. pT3a 50.7 mo, p &lt; 0.01). MVA for RFS revealed cT3a staging (pT3a referent, HR 1.72, p &lt; 0.01), positive margins (HR 2.85, p &lt; 0.01), and clear cell histology (HR 1.68, p &lt; 0.01) to be independently associated with higher recurrence rate, while partial nephrectomy (radical referent, HR 0.259, p &lt; 0.01) was associated with a decreased rate. KMA revealed 5-year RFS of 34.4% and 60.6% for cT3a and pT3a respectively (p &lt; 0.01). KMA for secondary outcomes revealed 5-year OS rates of 56.7% and 62.0% (p = 0.02) and 5-year CSS of 74.4% and 67.7% for cT3a and pT3a respectively (p = 0.01). Conclusions: Patients with cT3a RCC have poorer oncologic outcomes than those with upstaged pT3a RCC. Suspected venous involvement on pre-operative imaging may indicate more aggressive or advanced disease than that found during surgery.
The ATLAS Simulation Infrastructure (2010)

52 páginas, 10 figuras, 18 tablas.-- This article is distributed under the terms of the Creative&#13;\nCommons Attribution Noncommercial License.-- et al. (The ATLAS Collaboration).
Estimation of scattered particle exposure in ion beam aperture array lithography (2006)

In ion beam proximity lithography, ions that are incident on the nominally opaque regions of a stencil mask can scatter into the open windows and escape, exposing a wide area of the substrate. Since these ions can lose much of their initial energy in the mask, the scattered particle exposure is concentrated near the resist surface. The resulting loss of contrast can be mitigated to some extent by using aperture array lithography (AAL) where a mask of reduced density minimizes the number of windows from which a scattered ion can escape. Even so, the problem worsens as the pitch of an array, printed by multiple, offset exposures of the AAL mask, shrinks below about 250nm. The only solution is to increase the mask thickness, hence the window aspect ratio, to reduce the escape angles of the scattered particles. In this article, the authors characterize an effective background dose η in the first 75nm of poly(methylmethacrylate) resist for 30keV He+ ion exposures of 0.6μm thick masks with 45, 80, and 110nm circular windows on 150, 300, and 400nm pitches, respectively. They project that η would be (6.8±0.8)%(σ) of the primary ion dose for the printing of dense arrays, with period equal to twice the window diameter, over this range of feature sizes.
<title>Environmental and substrate material factors' effect on metal lithography corrosion</title> (1997)

Monitoring techniques were used to analyze metal lithography corrosion on post-metal etch processes and after solvent processing. Liquid ion chromatography (LIC) techniques were used to monitor the chlorine ion concentration on the wafers following plasma metal etch processing, and energy dispersive x-ray spectroscopy (EDS) techniques were used to monitor the level of fluorine ions which prevented native oxide growth that protects the metallization from solvent damage. Characterizations were run to identify the significant integrated circuit process factors and environmental conditions that increased the corrosion occurrence or severity above the baseline level. Monitoring of the environmental corrosion risk was done with LIC and air quality monitors. Wafer processing and substrate factors significant to corrosion occurrence were: (1) underlying oxide type, (2) photoresist type, (3) pattern density of the metal geometries, (4) metal etch wafer position, (5) connection to substrate by vias/contacts, (6) humidity, (7) backside condition of the wafer, (8) overetch step chlorine flow, and (9) metal thickness, in increasing significance. Significant reduction in measured corrosive ion levels and observed corrosion defects was obtained with modified processing schemes.
Theory of lateral field electro-absorption modulation in quantum dot heterostructures (2023)

Electro-absorption modulators operate based on the quantum-confined Stark effect (QCSE). In quantum well and existing quantum dot (QD) structures, the use of top and bottom contacts allows application of an electric field along the growth direction. In this work, we theoretically analyse the QCSE in QD structures, investigating whether a lateral field orientation provides an appreciable QCSE sufficient to implement lateral QD-EAMs suitable for integration in photonic integrated circuits. We focus on InAs/GaAs QD structures close to 1300 nm, showing how the dot dimensions and built-in piezoelectric potential impact the calculated absorption spectrum as a function of applied lateral field.
Directed evolution: From a staphylococcal lipase to a phospholipase (2000)

The lipase of Staphylococcus aureus (SAL) is able to degrade lipids and p-nitrophenylesters but is not active on phospholipid substrates. Interestingly, the homologous lipase from Staphylococcus hyicus is highly active on phospholipids. In order to investigate the molecular basis for this difference in substrate specificity, phospholipase activity was introduced into SAL by directed evolution strategy. In this approach, sequential rounds of error-prone PCR were performed in combination with a screening of the resulting mutant libraries. The screening was based on a high-throughput plate assay and a subsequent chromogenic assay in 96-well plate format to accurately determine the enzymatic activities in cell lysates of a selected number of clones. After 4 rounds of error-prone PCR, two products were obtained, displaying a 7.8- and 9.2-fold increase in absolute phospholipase activity and a 5.9- and 6.9-fold increase in phospholipase/ lipase activity ratio. A final round of DNA shuffling with these two products and wildtype (WT)-SAL was performed to combine beneficial mutations and to eliminate neutral or deleterious mutations. This procedure yielded a best variant containing 6 amino acid mutations displaying a 11.6-fold increase in absolute phospholipase activity and a 11.5-fold increase in phospholipase/lipase ratio as compared to the starting point. The character of the mutations and their possible effects on substrate specificity are discussed.
Detecting Bone Lesions in X-Ray Under Diverse Acquisition Conditions (2022)

The diagnosis of primary bone tumors is challenging, as the initial complaints are often non-specific. Early detection of bone cancer is crucial for a favorable prognosis. Incidentally, lesions may be found on radiographs obtained for other reasons. However, these early indications are often missed. In this work, we propose an automatic algorithm to detect bone lesions in conventional radiographs to facilitate early diagnosis. Detecting lesions in such radiographs is challenging: first, the prevalence of bone cancer is very low; any method must show high precision to avoid a prohibitive number of false alarms. Second, radiographs taken in health maintenance organizations (HMOs) or emergency departments (EDs) suffer from inherent diversity due to different X-ray machines, technicians and imaging protocols. This diversity poses a major challenge to any automatic analysis method. We propose to train an off-the-shelf object detection algorithm to detect lesions in radiographs. The novelty of our approach stems from a dedicated preprocessing stage that directly addresses the diversity of the data. The preprocessing consists of self-supervised region-of-interest detection using vision transformer (ViT), and a foreground-based histogram equalization for contrast enhancement to relevant regions only. We evaluate our method via a retrospective study that analyzes bone tumors on radiographs acquired from January 2003 to December 2018 under diverse acquisition protocols. Our method obtains 82.43% sensitivity at 1.5% false-positive rate and surpasses existing preprocessing methods. For lesion detection, our method achieves 82.5% accuracy and an IoU of 0.69. The proposed preprocessing method enables to effectively cope with the inherent diversity of radiographs acquired in HMOs and EDs.
Test of lepton flavor universality using B0→D*−τ+ντ decays with hadronic τ channels (2023)

The branching fraction $\mathcal{B}({B}^{0}\ensuremath{\rightarrow}{D}^{*\ensuremath{-}}{\ensuremath{\tau}}^{+}{\ensuremath{\nu}}_{\ensuremath{\tau}})$ is measured relative to that of the normalization mode ${B}^{0}\ensuremath{\rightarrow}{D}^{*\ensuremath{-}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}$ using hadronic ${\ensuremath{\tau}}^{+}\ensuremath{\rightarrow}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}({\ensuremath{\pi}}^{0}){\overline{\ensuremath{\nu}}}_{\ensuremath{\tau}}$ decays in proton-proton collision data at a center-of-mass energy of 13 TeV collected by the LHCb experiment, corresponding to an integrated luminosity of $2\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$. The measured ratio is $\mathcal{B}({B}^{0}\ensuremath{\rightarrow}{D}^{*\ensuremath{-}}{\ensuremath{\tau}}^{+}{\ensuremath{\nu}}_{\ensuremath{\tau}})/\mathcal{B}({B}^{0}\ensuremath{\rightarrow}{D}^{*\ensuremath{-}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}{\ensuremath{\pi}}^{+})=1.70\ifmmode\pm\else\textpm\fi{}0.1{0}_{\ensuremath{-}0.10}^{+0.11}$, where the first uncertainty is statistical and the second is related to systematic effects. Using established branching fractions for the ${B}^{0}\ensuremath{\rightarrow}{D}^{*\ensuremath{-}}{\ensuremath{\pi}}^{+}{\ensuremath{\pi}}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}$ and ${B}^{0}\ensuremath{\rightarrow}{D}^{*\ensuremath{-}}{\ensuremath{\mu}}^{+}{\ensuremath{\nu}}_{\ensuremath{\mu}}$ modes, the lepton universality test $\mathcal{R}({D}^{*\ensuremath{-}})\ensuremath{\equiv}\mathcal{B}({B}^{0}\ensuremath{\rightarrow}{D}^{*\ensuremath{-}}{\ensuremath{\tau}}^{+}{\ensuremath{\nu}}_{\ensuremath{\tau}})/\mathcal{B}({B}^{0}\ensuremath{\rightarrow}{D}^{*\ensuremath{-}}{\ensuremath{\mu}}^{+}{\ensuremath{\nu}}_{\ensuremath{\mu}})$ is calculated, $\mathcal{R}({D}^{*\ensuremath{-}})=0.247\ifmmode\pm\else\textpm\fi{}0.015\ifmmode\pm\else\textpm\fi{}0.015\ifmmode\pm\else\textpm\fi{}0.012$, where the third uncertainty is due to the uncertainties on the external branching fractions. This result is consistent with the Standard Model prediction and with previous measurements.
Heterogeneous biomedical database integration using a hybrid strategy: a p53 cancer research database. (2007)

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.).
Useful Database of Effective Gettering Sites for Metal Impurities in Si Wafers with First Principles Calculation (2015)

Fe, Ni, and Cu atoms diffuse very quickly in Si and are the main targets for metal gettering. W, Hf, and Mo atoms, for example, which diffuse very slowly in Si have also recently become gettering targets in addition to these metals. Therefore, proximity gettering techniques by using ion implantation are also being considered. Not only implanted elements but intrinsic point defects exist and form several complexes after the heat-treatment for Si crystal recovery. This research systematically investigated the binding energy of twelve important metals (Ti, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Hf, Ta, and W) with dopants (B, C, P, As, and F) and their complexes with intrinsic point defects (vacancies (Vs) and self-interstitials (Is)) by using first principles calculation. The database should be useful in designing effective gettering sites for metal impurities partially covering proximity gettering in LSI manufacturing processes.
Evaluating FPGAs for floating-point performance (2008)

Field programmable gate arrays (FPGAs) have been available for more than 25 years. Initially they were used to simplify embedded processing circuits and then expanded into simulating application specific integrated circuit (ASIC) designs. In the past few years they have grown in density and speed to replace ASICs in some applications and to assist microprocessors as attached accelerators. This paper will calculate the floating-point peak performance for three types of FPGAs using 64-bit, 32-bit, and 24-bit word lengths and compare this with a reference quad-core microprocessor. These calculations are further refined to estimate the actual performance of these FPGAs at floating-point calculations and compared with the microprocessor at its optimal design point and also away from this design point. Lastly, the paper explores the nature of floating-point calculations and looks at examples where the same algorithmic accuracy can be achieved with non-floating-point calculations.
Strong location dependent surface enhanced Raman scattering on individual gold semishell and nanobowl particles (2010)

We demonstrate strong spatial localization of SERS on single symmetry-reduced gold semishell and nanobowl particles. A ∼30 nm carbon nanoparticle acts as a Raman reporter and is placed on different locations on a single semishell or nanobowl by e-beam induced deposition method, and remarkably different SERS intensities are observed.
CD38 as a pan-hematologic target for chimeric antigen receptor T cells (2023)

Many hematologic malignancies are not curable with chemotherapy and require novel therapeutic approaches. Chimeric antigen receptor (CAR) T-cell therapy is 1 such approach that involves the transfer of T cells engineered to express CARs for a specific cell-surface antigen. CD38 is a validated tumor antigen in multiple myeloma (MM) and T-cell acute lymphoblastic leukemia (T-ALL) and is also overexpressed in acute myeloid leukemia (AML). Here, we developed human CD38-redirected T cells (CART-38) as a unified approach to treat 3 different hematologic malignancies that occur across the pediatric-to-adult age spectrum. Importantly, CD38 expression on activated T cells did not impair CART-38 cells expansion or in vitro function. In xenografted mice, CART-38 mediated the rejection of AML, T-ALL, and MM cell lines and primary samples and prolonged survival. In a xenograft model of normal human hematopoiesis, CART-38 resulted in the expected reduction of hematopoietic progenitors, which warrants caution and careful monitoring of this potential toxicity when translating this new immunotherapy into the clinic. Deploying CART-38 against multiple CD38-expressing malignancies is significant because it expands the potential for this novel therapy to affect diverse patient populations.
ChemInform Abstract: A General Method for Controlling Glycosylation Stereochemistry in the Synthesis of 2′‐Deoxyribose Nucleosides. (1991)

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.
Radical cations of ethylene oxide and other oxiranes prepared by exposure to ionizing radiation. An electron spin resonance study (1986)

Exposure of dilute solutions of tetramethyl oxirane in trichlorofluoromethane to 60C γ-rays at 77 K gave a species identified as the ring-opened radical cation, [graphic omitted]. Its e.s.r. spectrum comprised 13 lines with A(1H)= 15.1 G. This species had an intense violet colour, and there was no evidence for the cyclic cation. Similarly, the cations of cyclopentene oxide and cyclohexene oxide gave red–violet colours and complex e.s.r. spectra which were interpreted in terms of the oxirane ring opening to give 6- and 7-membered cyclic cations only.Both the 2,3-cis-dimethyl and the monomethyl derivatives on exposure at 4 K gave poorly defined e.s.r. spectra and no coloration. On warming to ca. 30 K the spectra became better defined and at 77 K intense red colours appeared together with new e.s.r. features which could be analysed in terms of the open-ring structures.Oxirane itself gave a spectrum with splitting due to four equivalent protons, together with small extra splittings probably due to coupling to a chlorine nucleus. The proton coupling of ca. 16 G is close to that for the two α-protons of the open-chain radical (Ċtext-decoration:overlineHtext-decoration:overlineMtext-decoration:overlineetext-decoration:overlineOĊHMe)+, which strongly supports an open structure. However, there was no visible absorption band under all conditions in CFCl3. In marked contrast, a very similar e.s.r. spectrum of five lines was obtained from solutions in SF6 at 77 K, but these solutions had an intense orange–red coloration. These results are tentatively interpreted in terms of a cyclic cation for oxirange in CFCl3, but an ‘open’ cation in SF6, both having very similar proton hyperfine coupling constants. Similarly, the acquisition of colour and change in the e.s.r. spectrum of the monomethyl and dimethyl derivatives is explained in terms of ring-opening in the 40–70 K region for solutions in CFCl3.
The Continuous Combinatorial Auction Architecture (2014)

The paper reports the architecture of a continuous combinatorial auction. Preferences are based on sets of items and feasibility requires the nonintersection of sets. Countdown clocks replace eligibility and activity requirements typical of rounds-based auctions. Bids remain in the system to be combined with new bids to form winning collections. Increment requirements dictate improvements over appropriate collections of existing bids. The auction evolved from experimental methods and operates at high levels of efficiency. Field applications are reported and result in natural equilibration in a few hours as opposed to days or weeks required by round-based architectures.
Simulation of Slow Variable-Angle Spinning NMR Spectra. Application to13C Bonded to N (1996)

Simulations of NMR spectra for spin-12 nuclei in rigid solids spun at relatively slow speeds and at angles other than the magic angle are presented. Particular emphasis is on the case where13C is bonded to a quadrupolar nucleus such as14N. The feasibility of quantitatively extracting the chemical-shift tensor, bond lengths through the dipolar interaction, and the electric-field gradient of the neighboring nucleus from a single (1-D) spectrum is demonstrated. The sensitivity of the observed changes in the spectra to changes in the physical and experimental parameters is discussed and illustrated using nitrile13C spectra of solid CH3CN. Equations are derived to extend the theory beyond the adiabatic approximation.
A dual-voltage self-clamped IGBT for automotive ignition applications (2001)

Self-clamped inductive switching (SCIS) energy capability is a critical parameter of device performance for insulated gate bipolar transistors (IGBTs) used in automotive ignition applications. In this work, the authors propose a monolithic dual-voltage self-clamped IGBT to improve its SCIS energy capability. During an inductive turnoff process, the collector voltage of the proposed device is clamped first at a high level for a short period of time and then at a much lower level until the electromagnetic energy stored in the inductive coil is fully discharged. The concept has been verified and analyzed with extensive numerical device simulation. A monolithic prototype device based the concept has been designed and fabricated with a conventional eight-mask IGBT process. The preliminary experimental result is also reported.
ChemInform Abstract: A NEW METHOD FOR THE HYDROXYMETHYLATION OF CARBONYL COMPOUNDS (1984)

Abstract In Gegenwart von Sml, werden Oxoverbindungen (I) mit dem Chlormethyl‐benzyl‐ether (II) in die Alkohole (IV) übergeführt und dann hydrogenolytisch zu Diolen (V) gespalten.
Archive-Enabling Tagging Using Progressive Barcodes (2017)

We have previously described the Progressive Barcode, a high-density color barcode that changes over incrementally. This article expands on previously published work [S. J. Simske and A. M. Vans, &#x201C;Archive-enabling tagging using progressive barcodes,&#x201D; Proc. of Archiving (Los Angeles, CA, 2015), pp. 130&#x2010;135]. We describe how the progressive barcode works and its applicability to information workflows and archiving applications. In particular, we tie the progressive, or sequential, aspect of this approach to the temporal relationship of multiple items (including documents in a workflow, items in a supply chain, etc.) We present an inference model that allows for the possibility of the loss of tags (called knockout) that were originally created as part of a sequence of tags, usually in manufacturing or printing as examples. Taken together, the progressive barcode with the inference model is a self-contained mechanism for the support of workflows.
A 5 GHz Low Noise Amplifier with On-Chip Transformer-Balun (2006)

We present the design and implementation of a 5-6 GHz differential low noise amplifier (LNA) for WLAN applications. The LNA is fabricated in 0.25 mum SiGe BiCMOS process from STMicroelectronics. By using on-chip transformers a broadband impedance matching (3.5-11 GHz), conversion between single-end and differential signals and smaller chip size are achieved. The LNA exhibits a small signal gain of 14.25 dB and a noise figure of 4.1 dB. It draws 13.3 mA from 1.8 V power supply and exhibits and CP1 of -9 dBm. The chip size including pads is 0.68 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup>