gebhart/patrepeval huggingface dataset:
Polygenic risk, susceptibility genes, and breast cancer over the life course (2020)

ABSTRACT Polygenic risk scores (PRS) for breast cancer have potential to improve risk prediction, but there is limited information on their clinical applicability. We set out to study how PRS could help in clinical decision making. Among 99,969 women in the FinnGen study with 6,879 breast cancer cases, the PRS was associated not only with breast cancer incidence but also with a range of breast cancer-related endpoints. Women with a breast cancer PRS above the 90 th percentile had both higher breast cancer mortality (HR 2.40, 95%CI 1.82-3.17) and higher risk for non-localized disease at diagnosis (HR 2.94, 95%CI 2.63-3.28), compared to those with PRS &lt;80 th percentile. The PRS modified the breast cancer risk of two high-impact frameshift risk variants. Women with the c.1592delT variant in PALB2 (242-fold enrichment in Finland, 263 carriers) and an average PRS (20-80 th percentile) had a lifetime risk of breast cancer at 58% (95%CI 50-66%), which increased to 85% (70-100%) with a high PRS (&gt;90 th percentile), and decreased to 27% (15-39%) with a low PRS (&lt;20 th percentile). Similarly, for c.1100delC in CHEK2 (3.7-fold enrichment; 1,543 carriers), the respective lifetime risks were 27% (95%CI 25-30%), 59% (52-67%), and 18% (13-22%). Among breast cancer cases, a PRS &gt;90 th percentile was associated with risk of contralateral breast cancer with HR 1.66 (95%CI 1.24-2.22). Finally, the PRS significantly refined the risk assessment of women with first-degree relatives diagnosed with breast cancer, i.e. the combination of high PRS (&gt;90 th percentile) and a positive family-history was associated with a 2.33-fold elevated risk (95%CI 1.57-3.46) compared to a positive family history alone. These findings demonstrate opportunities for a comprehensive way of assessing genetic risk in the general population, in breast cancer patients, and in unaffected family members.
Yb(OTf)3-Catalyzed Oxymercuration of Homoallylic Alcohol-Derived Hemiacetals and Hemiketals (2000)

1,3-Diol synthons, protected as acetonides or benzylidene acetals, may be synthesized efficiently from homoallylic alcohols and acetone or benzaldehyde by oxymercuration of the derived hemiketals and hemiacetals with HgClOAc. The use of catalytic amounts of Yb(OTf)(3) is crucial to the success of the reaction, which was determined to be reversible.
ChemInform Abstract: Altering the Stereochemistry of Allylation Reactions of Cyclic α‐ Sulfinyl Radicals: Effects of Solvents and Lewis Acids. (1994)

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.
Synthesis and Preliminary in Vitro Biological Evaluation of 4-[(4-Hydroxyphenyl)sulfanyl]but-3-en-2-one, a 4-Mercaptophenol Derivative Designed As a Novel Bifunctional Antimelanoma Agent (2009)

We report the synthesis and preliminary in vitro biological evaluations of 4-[(4-hydroxyphenyl)sulfanyl]but-3-en-2-one, a compound designed as a potential bifunctional antimelanoma agent, bearing both a tyrosinase-activatable phenolic moiety and a GSH-reactive alpha,beta-unsaturated carbonyl group. Both the E (1) and Z (2) isomers of the synthesized compound proved to be very good substrates of mushroom tyrosinase, reacted quickly with GSH at physiological pH, and showed a significant cytotoxic activity against B16F1 murine melanoma cells.
Imaging via inversion of ellipsoidal projections of solutions to the linear acoustic wave equation (medical ultrasound) (1989)

Backscattered energy from a medium with nearly constant velocity measured by an omnidirectional source-sensor comes from spherical shells centered at the source-sensor location. If source and sensor locations differ, the energy comes from ellipsoidal shells. To image the scattering potential or reflectivity of the medium, backscattered energy must be projected onto ellipsoids with a weighting factor dependent on the eccentricity of the ellipsoid. Eccentricity is the ratio of the separation of source and sensor to the path length from source to scatterer to sensor. Because path length changes with time, this weighting factor is, in general, time-dependent. It is consistent only if the source and sensor location are the same, in which case its value is unity. To estimate scattering potential or reflectivity at a given site, the backscattered signal which could have arisen from that site as measured by a given source-sensor pair is weighted by that pair's time-dependent ellipsoidal factor, then the weighted backscattered signals are averaged over all available source-sensor pairs.
Towards Understanding the Performance of P4 Programmable Hardware (2019)

P4 programmable data planes are becoming more popular due to the flexibility they provide in describing the packet processing pipeline. P4 successfully abstracts the processing pipeline of data planes using a limited set of constructs. The performance variation as a function of the configured P4 pipeline is an important aspect that should be studied. Analyzing the impact of different P4 constructs on packet latency helps in understanding the overall performance of P4 programmable devices. In this paper, we analyze the impact of a basic set of P4 constructs on packet processing latency to derive the influential parameters. We use the derived results to propose a method for estimating the packet latency of P4-based network functions implemented using the surveyed P4 constructs. Finally, we validate the accuracy of the proposed method by applying it to realistic network functions.
Structure and Electrochemical Properties of a Mechanochemically Processed Silicon and Oxide-Based Nanoscale Composite as an Active Material for Lithium-Ion Batteries (2017)

Si is essential as an active material in Li-ion batteries because it provides both high charge and optimal cycling characteristics. A composite of Si particles, Cu particles, and pure H 2 O was realized to serve as an anode active material and optimize the charge–discharge characteristics of Li-ion batteries. The composite was produced by grinding using a planetary ball mill machine, which allowed for homogenous dispersion of nanoscale Cu 3 Si as Si–Cu alloy grains and nanoscale Si grains in each poly-Si particle produced. Furthermore, some Si particles were oxidized by H 2 O, and oxidized Si was distributed throughout the composite, mainly as silicon monoxide. As a result, each Si particle included silicon monoxide and conductive Cu 3 Si materials, allowing for effective optimization of the recharging and charge-discharge characteristics. Thus, a new and simple process was realized for synthesizing a Si active material composited with silicon oxides, including silicon monoxide. This Si-rich conductive material is suitable as an anode for Li-ion batteries with high charge and optimized cycling properties.
Monomeric C‐reactive protein via endothelial CD31 for neurovascular inflammation in an ApoE genotype‐dependent pattern: A risk factor for Alzheimer’s disease? (2021)

In chronic peripheral inflammation, endothelia in brain capillary beds could play a role for the apolipoprotein E4 (ApoE4)-mediated risk for Alzheimer's disease (AD) risk. Using human brain tissues, here we demonstrate that the interactions of endothelial CD31 with monomeric C-reactive protein (mCRP) versus ApoE were linked with shortened neurovasculature for AD pathology and cognition. Using ApoE knock-in mice, we discovered that intraperitoneal injection of mCRP, via binding to CD31 on endothelial surface and increased CD31 phosphorylation (pCD31), leading to cerebrovascular damage and the extravasation of T lymphocytes into the ApoE4 brain. While mCRP was bound to endothelial CD31 in a dose- and time-dependent manner, knockdown of CD31 significantly decreased mCRP binding and altered the expressions of vascular-inflammatory factors including vWF, NF-κB and p-eNOS. RNAseq revealed endothelial pathways related to oxidative phosphorylation and AD pathogenesis were enhanced, but endothelial pathways involving in epigenetics and vasculogenesis were inhibited in ApoE4. This is the first report providing some evidence on the ApoE4-mCRP-CD31 pathway for the cross talk between peripheral inflammation and cerebrovasculature leading to AD risk.
Thermal stability of organic thin-film transistors with self-assembled monolayer dielectrics (2010)

We have investigated the annealing effects on 2 V-operation pentacene organic thin-film transistors (TFTs) with self-assembled monolayer-based gate dielectrics. When pentacene TFTs without passivation layers are annealed at 100 °C, the pentacene crystal structure changes to the bulk phase, resulting in an irreversible degradation of electronic performances. This degradation is suppressed by a 2.5-μm-thick passivation layer. The mobility of the encapsulated TFTs decreases by only 12% upon annealing at 140 °C. We have also investigated the bias-stress effect and found the drain current of low-voltage pentacene TFTs annealed at 70 °C decreases by 1% during continuous bias stress for 1 h.
A bistable liquid-crystal display mode based on electrically driven smectic A layer reorientation (2007)

We describe a device geometry using interdigital electrodes that enables the electrically driven reorientation of smectic A layers from a homeotropic state (dark between crossed polarizers) to a planar state (bright between crossed polarizers) and back again. The resulting electro-optic effect is strongly bistable and gives high contrast ratio and fast response, rendering it a potential candidate for flexible-display applications.
Towards sub-nanometer real-space observation of spin and orbital magnetism at the Fe/MgO interface (2017)

While the performance of magnetic tunnel junctions based on metal/oxide interfaces is determined by hybridization, charge transfer, and magnetic properties at the interface, there are currently only limited experimental techniques with sufficient spatial resolution to directly observe these effects simultaneously in real-space. In this letter, we demonstrate an experimental method based on Electron Magnetic Circular Dichroism (EMCD) that will allow researchers to simultaneously map magnetic transitions and valency in real-space over interfacial cross-sections with sub-nanometer spatial resolution. We apply this method to an Fe/MgO bilayer system, observing a significant enhancement in the orbital to spin moment ratio that is strongly localized to the interfacial region. Through the use of first-principles calculations, multivariate statistical analysis, and Electron Energy-Loss Spectroscopy (EELS), we explore the extent to which this enhancement can be attributed to emergent magnetism due to structural confinement at the interface. We conclude that this method has the potential to directly visualize spin and orbital moments at buried interfaces in magnetic systems with unprecedented spatial resolution.
Theory of aberration fields for general optical systems with freeform surfaces (2014)

This paper utilizes the framework of nodal aberration theory to describe the aberration field behavior that emerges in optical systems with freeform optical surfaces, particularly φ-polynomial surfaces, including Zernike polynomial surfaces, that lie anywhere in the optical system. If the freeform surface is located at the stop or pupil, the net aberration contribution of the freeform surface is field constant. As the freeform optical surface is displaced longitudinally away from the stop or pupil of the optical system, the net aberration contribution becomes field dependent. It is demonstrated that there are no new aberration types when describing the aberration fields that arise with the introduction of freeform optical surfaces. Significantly it is shown that the aberration fields that emerge with the inclusion of freeform surfaces in an optical system are exactly those that have been described by nodal aberration theory for tilted and decentered optical systems. The key contribution here lies in establishing the field dependence and nodal behavior of each freeform term that is essential knowledge for effective application to optical system design. With this development, the nodes that are distributed throughout the field of view for each aberration type can be anticipated and targeted during optimization for the correction or control of the aberrations in an optical system with freeform surfaces. This work does not place any symmetry constraints on the optical system, which could be packaged in a fully three dimensional geometry, without fold mirrors.
An epidermal growth factor‐ricin a chain (EGF‐RTA)‐resistant mutant and an epidermal growth factor‐Pseudomonas endotoxin (EGF‐PE)‐resistant mutant have distinct phenotypes (1989)

H2Oe12 is a mutant HeLa cell line selected for resistance to the toxicity of a chimeric protein conjugate composed of epidermal growth factor (EGF) and the toxic A chain of ricin (RTA). ET-28 is a mutant KB cell line selected for resistance to the toxicity of a chimeric protein conjugate composed of EGF and Pseudomonas exotoxin (PE). In this report we describe the presence or absence, in these mutants, of cross-resistance to the two toxic conjugates and the effects of ammonium chloride, leupeptin, and adenovirus cotreatments on toxin efficacies. ET-28 cells, the EGF-PE-resistant cells, are resistant to both EGF-PE and EGF-RTA. In contrast, H2Oe12 cells, the EGF-RTA-resistant cells, are as sensitive to EGF-PE toxicity as are their parent HeLa cells. Ammonium chloride cotreatment substantially reduces the resistance of H2Oe12 cells to EGF-RTA but has little or no effect on the resistance of ET-28 cells to either EGF-RTA or EGF-PE. Leupeptin has no effect on the toxicity of either chimeric conjugate on any of the four cell lines, effect on the toxicity of either chimeric conjugate on any of the four cell lines, despite its demonstrated ability to inhibit cellular degradation of EGF. In contrast, adenovirus cotreatment enhances the toxicity of EGF-RTA and EGF-PE on all cells tested, and completely nullifies the relative resistance of H2Oe12 and ET-28 cells to these toxic conjugates. H2Oe12 and ET-28 cells appear to be altered in distinct, possibly endosomal, functions.
Exact Minimization of Energy Functional for NR Method With Line-Search Technique (2009)

The line-search technique was usually introduced to the Newton-Raphson (NR) method in order to improve the convergence characteristic of nonlinear magnetic field analysis with the toughness magnetic nonlinearlity. In this paper, we proposed the NR method combined with the optimal step size using exact functional minimization in every nonlinear iteration. The convergence process and computation time were investigated, and compared with the conventional line-search technique using the approximate functional minimization.
Immunoconjugates and new molecular targets in hairy cell leukemia (2012)

Abstract Hairy cell leukemia (HCL) is a B-cell malignancy that in its classic form is exquisitely sensitive to single-agent purine analog therapy, but that is associated in many patients with late relapse and eventual purine analog resistance. Minimal residual disease, which is present in most patients achieving complete remission with purine analogs, retains Ags that are ideal for targeted therapy. Rituximab, which targets CD20, is active as a single agent, particularly if combined with purine analogs. Recombinant immunotoxins targeting either CD25 or CD22 and containing truncated Pseudomonas exotoxin have achieved major responses in relapsed/refractory HCL. Moxetumomab pasudotox in phase 1 testing achieved responses in 86% of such patients (complete in 46%) without dose limiting toxicity and often without MRD. Soluble CD22 has been used for improved detection and monitoring of HCL, particularly the poor-prognosis variant that lacks CD25. Ig rearrangements unique for each HCL patient have been cloned, sequenced, and followed by real-time quantitative PCR using sequence-specific reagents. Analysis of these rearrangements has identified an unmutated IGVH4-34–expressing poor-prognosis variant with immunophenotypic characteristics of either classic or variant HCL. The BRAF V600E mutation, reported in 50% of melanomas, is present in &gt; 85% of HCL cases that are both classic and express rearrangements other than IGVH4-34, making HCL a potential target for specific inhibitors of BRAF V600E. Additional targets are being defined in both classic and variant HCL, which should improve both detection and therapy.
Reductions of soliton interactions and timing jitters by chirped fiber Bragg grating filters (1997)

This letter numerically investigates a comparison between soliton interaction and timing jitter effects using transmission fiber that contains: (1) the zigzag-sliding-frequency Fabry-Perot filters (ZSF FPFs) alone and (2) both the ZSF FPFs and chirped fiber Bragg grating filters (CFBGFs). We have found that the latter scheme is more effective for reducing the soliton interactions and noise-induced timing jitters, because the CFBGFs introduce a large positive second-order dispersion and plays the dual role of a filter and a dispersion compensation fiber.
Ionic Liquids: Perspectives for Organic and Catalytic Reactions (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Predicted microscopic cortical brain images for optimal craniotomy positioning and visualisation (2020)

During a craniotomy, the skull is opened to allow surgeons to have access to the brain and perform the procedure. The position and size of this opening are chosen in a way to avoid critical structures, such as vessels, and facilitate the access to tumors. Planning the operation is done based on pre-operative images and does not account for intra-operative surgical events. We present a novel image-guided neurosurgical system to optimize the craniotomy opening. Using physics-based modeling we define a cortical deformation map that estimates the displacement field at candidate craniotomy locations. This deformation map is coupled with an image analogy algorithm that produces realistic synthetic images that can be used to predict both the geometry and the appearance of the brain surface before opening the skull. These images account for cortical vessel deformations that may occur after opening the skull and is rendered in a way that increases the surgeon's understanding and assimilation. Our method was tested retrospectively on patients data showing good results and demonstrating the feasibility of practical use of our system.
CORR Insights®: No Infection Reduction Using Chlorhexidine Wipes in Total Joint Arthroplasty (2013)

Where Are We Now? Periprosthetic joint infection (PJI) remains among the most vexing challenges in total joint arthroplasty. Prevention of this complication is desirable, given the morbidity, mortality, and overall costs associated with its treatment. However, considerable controversies remain about which approaches may help us achieve this important goal. There are numerous proposed interventions to reduce PJI, such as patient screening for Staphylococcus aureus, various skin preparation techniques, the use of dilute betadine lavage, and antibiotic loaded cement. All of these interventions are associated with some monetary cost, as well as physician and/or patient time and effort. Additionally, it is unclear what effect patient-related factors such as obesity, diabetes, nutritional status, or even genetics contribute to the frequency of this complication. It remains uncertain whether these factors are more or less important than specific strategies for prevention. Where Do We Need to Go? In the study by Farber et al., the authors examined the efficacy of chlorhexidine wipes, administered by a nurse in the holding area approximately 1 hour preoperatively in a large, retrospective study of 3715 patients. The authors compared the risk of PJI at 1 year between 1891 patients who received the wipes and 1824 patients who did not, as they underwent surgery prior to initiation of the protocol. The authors concluded that chlorhexidine wipes did not reduce the risk of PJI. The authors noted in their discussion that although the study was large, they may still have been underpowered to identify a difference in the risk of PJI, given both the number of patients available for the study and the low rate of infection prior to initiating the chlorhexidine protocol. How Do We Get There? This study highlights many of the challenges involved in determining the best strategies for reducing the risk of PJI, including the need to study large patient populations. Ideally, these studies should be randomized controlled trials, which are both expensive and difficult to administer if for no other reason than patients in the US healthcare system are oftentimes hesitant to participate in these kinds of trials. Organizations such as the Musculoskeletal Infection Society and other specialty societies may be well-positioned to help direct and organize future studies that help us to determine the optimal approaches for reducing the prevalence of PJI. Finally, future studies that help us determine which patient-related factors are most strongly associated with PJI are needed. The goal would be to disseminate and use those practice-based interventions that work (such as preincisional antibiotics or the use of skin clippers as opposed to razors), and to better understand in the future which patient-related factors can be modified (such as glycemic control or nutritional status) to reduce the risk of PJI.
3D heterogeneous opto-electronic integration technology for system-on-silicon (SOS) (2009)

We proposed 3D heterogeneous opto-electronic integration technology for system-on-silicon (SOS). In order to realize 3D opto-electronic integrated system-on-silicon (SOS), we developed novel heterogeneous integration technology of LSI, MEMS and optoelectronic devices by implementing 3D heterogeneous opto-electronic multi-chip module composed with LSI, passives, MEMS and optoelectronic devices. The electrical interposer mounted with amplitude shift keying (ASK) LSI, LC filter and pressure-sensing MEMS chips and the optical interposer embedded with vertical-cavity surface-emitting laser (VCSEL) and photodiode (PD) chips are precisely bonded to form 3D opto-electronic multi-chip module. Opto-electronic devices are electrically connected via through-silicon vias (TSVs) which were formed into the interposers. Micro-fluidic channels are formed into the interposer by wafer direct bonding technique. 3D heterogeneous opto-electronic multi-chip module is successfully implemented for the first time.