gebhart/patrepeval huggingface dataset:
Data from Pharmacologic Abrogation of the Mitotic Spindle Checkpoint by an Indolocarbazole Discovered by Cellular Screening Efficiently Kills Cancer Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;The mitotic spindle checkpoint represents a signal transduction pathway that prevents the onset of anaphase until all chromosomes are properly aligned on a metaphase plate. Partial inactivation of this checkpoint allows premature separation of sister chromatids and results in aneuploidy, which might contribute to tumorigenesis. Unlike other cell cycle checkpoints, the spindle checkpoint is essential for cell viability, giving rise to the idea that the spindle checkpoint itself might represent a valuable target for anticancer therapy. We used a cell-based screen and identified the indolocarbazole compound Gö6976 as a pharmacologic inhibitor of the spindle checkpoint. Gö6976 potently overrides a spindle checkpoint–mediated mitotic arrest by abrogating the phosphorylation and kinetochore localization of several spindle checkpoint proteins. We identified the Aurora-A and Aurora-B kinases, which have been previously implicated in proper mitotic progression and spindle checkpoint function, as targets for Gö6976. Accordingly, Gö6976 treatment causes severe mitotic abnormalities and chromosome alignment defects, which are not properly detected by the drug-inactivated spindle checkpoint. This results in an aberrant progression of mitosis, leading to apoptosis in various human cancer cell lines, including spindle checkpoint–compromised cancer cells. Thus, our work describes a novel and promising strategy for anticancer treatment that targets the mitotic spindle checkpoint. [Cancer Res 2009;69(9):3874–83]&lt;/p&gt;&lt;/div&gt;
Receiver Initiated MAC Design for Ad Hoc Networks Based on Multiuser Detection (2008)

Recent technological developments in code division multiple access (CDMA) with multiuser detection (MUD) make multiple packets reception a more appropriate model for the physical layer of future wireless networks. To take advantage of the new features, a shift of responsibility from transmitters to
Outcomes following redo sternotomy for aortic surgery (2012)

Proximal thoracic aortic reconstruction performed with or without hypothermic circulatory arrest (HCA) is an effective surgical strategy for aortic pathology. In this study, the clinical outcomes of patients undergoing reoperative proximal thoracic aortic surgery were evaluated. A retrospective review was performed for reoperative proximal aortic surgery from 2004 to date. Patient data were abstracted from the society of thoracic surgeons (STS) institutional database and patient charts. Univariate analysis was conducted on the HCA group in order to determine the impact of variables on in-hospital mortality. Kaplan-Meier survival estimates were calculated for long-term survival analysis. One hundred and twenty-two patients were included in the analysis. Twenty-seven (22.1%) were female, and the mean age was 53.8 years. Seventy-seven (63.1%) patients had an aortic root replacement, and 93 (76.2%) patients underwent aortic arch replacement. Circulatory arrest was performed in 92 (75.4%) patients. Operative mortality occurred in 14 patients (11.5%). Complications included re-exploration for haemorrhage (nine patients, 7.4%), stroke (four, 3.3%), renal failure (13, 10.7%) and major adverse events (18, 14.8%). Univariate and multivariate analyses of HCA patients showed cardiopulmonary bypass (CPB) time, preoperative renal failure and prior coronary revascularization as independent predictors of mortality. Reoperative proximal aortic surgery can be performed with acceptable morbidity and mortality. These data also suggest that HCA represents a safe operative strategy for this patient population.
Physicochemical, Mechanical, and Biological Properties of Bone Cements Prepared with Functionalized Methacrylates (2004)

Bone cements prepared with methyl methacrylate (MMA) as a base monomer and either methacrylic acid (MAA) or diethyl amino ethyl methacrylate (DEAEMA) as comonomers were characterized in terms of curing behavior, mechanical properties, and their in vitro biocompatibility. The curing time and setting temperature were found to be composition dependent while the residual monomer was not greatly affected by the presence of either acidic or alkaline comonomers in the bone cements. For samples with MAA comonomer, a faster curing time and higher setting temperature were observed when compared to the cement with DEAEMA comonomer. In terms of mechanical properties, the highest compressive strength was exhibited by formulations containing MAA, while the highest impact strength was shown by the formulations prepared with DEAEMA. There were no differences observed between the two formulations for tensile, shear, and bending strength values. Similarly, fatigue crack propagation studies did not reveal differences with the addition of either DEAEMA or MAA. No differences were observed in the initial number of attached primary rat femur osteoblasts on the different bone cements and positive controls. However, after 48 h there was a reduced proliferation in the cells grown on bone cements containing MAA.
Medial-Axis-Based Cartograms (2005)

Cartographers and geographers were making cartograms for centuries before digital computers and displays became available. In data visualization, an area cartogram distorts a map by resizing its regions according to some external geography-related parameter, such as population or epidemiological data. Cartograms are difficult to draw by hand because it's difficult to simultaneously optimize shape and area error while preserving the original map's topology. Automated methods for drawing cartograms have therefore received considerable interest. A method for generating cartograms that combines iterative relocation of a map's vertices with medial-axis-based transformations retains the input map's topology.
Design of a Wheelchair Robot for Active Postural Support (2018)

This paper describes the design and control architecture of a novel Wheelchair-mounted Robot for Active Postural Support (WRAPS). The WRAPS is a robotic exoskeleton that allows limited degrees-of-freedom (DOFs) of the trunk relative to the pelvis. There are three DOFs in the sagittal plane of the human body and one in lateral bending. The work is motivated by the needs of individuals with impaired trunk motor control, who currently rely on the use of passive and predominantly static supports to maintain a static posture. These devices can be overly restrictive and inhibit the user in their activities of daily living (ADLs). The WRAPS is capable of supporting a human user within their active range of torso motion. It has the potential to assist users in their ADLs while encouraging a dynamic range of healthy postures.
Stoichiometric Engineering of Chalcogenide Semiconductor Alloys for Nanophotonic Applications (2019)

A variety of alternative plasmonic and dielectric material platforms-among them nitrides, semiconductors, and conductive oxides-have come to prominence in recent years as means to address the shortcomings of noble metals (including Joule losses, cost, and passive character) in certain nanophotonic and optical-frequency metamaterial applications. Here, it is shown that chalcogenide semiconductor alloys offer a uniquely broad pallet of optical properties, complementary to those of existing material platforms, which can be controlled by stoichiometric design. Using combinatorial high-throughput techniques, the extraordinary epsilon-near-zero, plasmonic, and low/high-index characteristics of Bi:Sb:Te alloys are explored. Depending upon composition they can, for example, have plasmonic figures of merit higher than conductive oxides and nitrides across the entire UV-NIR range, and higher than gold below 550 nm; present dielectric figures of merit better than conductive oxides at near-infrared telecommunications wavelengths; and exhibit record-breaking refractive indices as low as 0.7 and as high as 11.5.
End-to-End Speech Separation with Unfolded Iterative Phase Reconstruction (2018)

This paper proposes an end-to-end approach for single-channel speaker-independent multi-speaker speech separation, where time-frequency (T-F) masking, the short-time Fourier transform (STFT), and its inverse are represented as layers within a deep network.Previous approaches, rather than computing a loss on the reconstructed signal, used a surrogate loss based on the target STFT magnitudes.This ignores reconstruction error introduced by phase inconsistency.In our approach, the loss function is directly defined on the reconstructed signals, which are optimized for best separation.In addition, we train through unfolded iterations of a phase reconstruction algorithm, represented as a series of STFT and inverse STFT layers.While mask values are typically limited to lie between zero and one for approaches using the mixture phase for reconstruction, this limitation is less relevant if the estimated magnitudes are to be used together with phase reconstruction.We thus propose several novel activation functions for the output layer of the T-F masking, to allow mask values beyond one.On the publiclyavailable wsj0-2mix dataset, our approach achieves state-ofthe-art 12.6 dB scale-invariant signal-to-distortion ratio (SI-SDR) and 13.1 dB SDR, revealing new possibilities for deep learning based phase reconstruction and representing a fundamental progress towards solving the notoriously-hard cocktail party problem.
Integrated Limb Mechanism Robot ASTERISK (2006)

The Integrated Limb Mechanism (ILM) concept deals with a dual arm-leg integrating the leg for locomotion and the arm for manipulation, while it enables a robot, for example, to operate flexibly in different work and situations, dual use requires that components are compact and mobile. Integrated software controlling the leg and arm is also required for implementing the actual robot. The ILM robot ASTEIRSK has six limbs arranged radially around the center to enable locomotion and manipulation capabilities omnidirectionally. ASTERISK features upper and lower symmetrical body and workability. We propose a design for the ILM and develop a small robot I/O controlling robot motion and monitoring sensors. In multimodal performance, ASTERISK uses omnidirectional drive control to walk hexapodally alternating tripod gait and creeping for restricted mobility. The new transportation way of hexapod walking style on a grid ceiling is proposed. Experiments deal with the detection of heat sources using infrared sensors and remote control to handle an object using two arms.
RTS,S: Toward a first landmark on the Malaria Vaccine Technology Roadmap (2015)

The Malaria Vaccine Technology Roadmap calls for a 2015 landmark goal of a first-generation malaria vaccine that has protective efficacy against severe disease and death, lasting longer than one year. This review focuses on product development efforts over the last five years of RTS,S, a pre-erythrocytic, recombinant subunit, adjuvanted, candidate malaria vaccine designed with this goal of a first-generation malaria vaccine in mind. RTS,S recently completed a successful pivotal Phase III safety, efficacy and immunogenicity study. Although vaccine efficacy was found to be modest, a substantial number of cases of clinical malaria were averted over a 3-4 years period, particularly in settings of significant disease burden. European regulators have subsequently adopted a positive opinion under the Article 58 procedure for an indication of active immunization of children aged 6 weeks up to 17 months against malaria caused by Plasmodium falciparum and against hepatitis B. Further evaluations of the benefit, risk, feasibility and cost-effectiveness of RTS,S are now anticipated through policy and financing reviews at the global and national levels.
Desiccation cracks provide evidence of lake drying on Mars, Sutton Island member, Murray formation, Gale crater: REPLY (2018)

We thank Pratt (2018) for his Comment on our paper (Stein et al., 2018) concerning the formation of a polygonal network of sandstone cracks in mudstone slabs in the Sutton Island member of the Murray formation investigated by the Curiosity rover in Gale Crater, Mars. Pratt proposes an additional potential formation mechanism for the generation and filling of the cracks not explicitly addressed by us, which is that they are dewatering features resulting from the liquefaction and injection of sediment into fissures due to seismic shock.
APPROPRIATENESS OF EUCALYPTUS CAMAL / DULENSIS, CASUARINA EQUISETIFOLIA AND OLEA EUROPAEA TREES IN SHELTERBELT OF AL-ASHRAF NAJAF CITY (2015)

The research has conducted on shelterbelt of Al-Ashraf Najaf city to explore suitability of four Eucalyptus camaldulensis Dehnh. Forms and two other tree species; Casuarina equisetifolia and Olea europaea to the local dominant sever conditions. Development in growth was studied through the interval of five years. Growth parameters included height, DBH stem diameter, main stem height, crown diameter, and stem girth were investigated. Distance from water supply was inspected, too. Results showed superiority of E. camaldulensis upon other species. Investigations showed weakness in growth of C. equisetifolia where most of trees could not resist because of their position in opposite to sandy wind stream that deposited sand on plants. So survival percentage was lower than that of the two other species. O. europaea trees did not show a rate of growth required for such purpose but it might be beneficial for an economic objectives through olive fruit production. Forms of E. camaldulensis revealed lesser relative differences in growth parameters than observed before five years. Form no. II possessed distinctive tree height and stem diameter, while form III gave smallest growth traits. Other form parameters did not different significantly. The most effective factor was the distance from water source where far trees (300 m) had smaller growth traits than those located at 200 m and 100 m distances, that’s might because inefficiency of the used drip irrigation system.
CCDC 709757: Experimental Crystal Structure Determination (2009)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Network intrusion visualization with NIVA, an intrusion detection visual analyzer with haptic integration (2003)

The explosive growth of malicious activities on worldwide communication networks, such as the Internet, has highlighted the need for efficient intrusion detection systems. The efficiency of traditional intrusion detection systems is limited by their inability to effectively relay relevant information due to their lack of interactive/immersive technologies. We explore several network visualization techniques geared towards intrusion detection on small and large-scale networks. We also examine the use of haptics in network intrusion visualization. By incorporating concepts from electromagnetics, fluid dynamics, and gravitational theory, we show that haptic technologies can provide another dimension of information critical to the efficient visualization of network intrusion data. Furthermore, we explore the applicability of these visualization techniques in conjunction with commercial network intrusion detectors. Finally, we present a network intrusion visualization application with haptic integration, NIVA which allows the analyst to interactively investigate as well as efficiently detect structured attacks across time and space using advanced interactive three-dimensional displays.
Abstract LB-145: Folliculin interacts with p0071 (Plakophilin-4) and deficiency is associated with disordered RhoA signalling, epithelial polarization and cytokinesis (2012)

Abstract Inherited mutations in the folliculin gene (FLCN) cause the Birt-Hogg-Dubé syndrome of familial hair follicle tumours (fibrofolliculomas), lung cysts and kidney tumours. Though folliculin has features of a tumour suppressor, the precise function of the FLCN gene product is not well characterised. We identified plakophilin-4 (PKP4, p0071) as a potential novel folliculin interacting protein by yeast-2-hybrid analysis. We confirmed the interaction of folliculin with p0071 by co-immunoprecipitation studies and, in view of previous studies linking p0071 to regulation of rho-signalling, cytokinesis and intercellular junction formation, we investigated the effect of cell folliculin status on p0071-related functions. Folliculin and p0071 partially colocalised at cell junctions and in mitotic cells, at the midbody during cytokinesis. Previously, p0071 has been reported to regulate RhoA signalling during cytokinesis and we found that folliculin deficiency was associated with increased expression and activity of RhoA and evidence of disordered cytokinesis. Treatment of folliculin deficient cells with a downstream inhibitor of RhoA signalling (the ROCK inhibitor Y-27632) reversed the increased cell migration phenotype observed in folliculin deficient cells. Deficiency of folliculin and of p0071 resulted in tight junction defects and mislocalisation of E-cadherin in IMCD-3 renal tubular cells. These findings suggest that aspects of folliculin tumour suppressor function are linked to interaction with p0071 and regulation of RhoA signalling. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-145. doi:1538-7445.AM2012-LB-145
Synthesis and Characterization of Biocompatible Sulfoxide-Containing Molecular Bottlebrushes (2022)

Macromolecular bottlebrushes (MBs) are emerging as an attractive polymer architecture for biomedical applications. Herein, synthesis and characterization of sulfoxide-containing water-soluble MBs with poly(2-(methylsulfinyl)ethyl acrylate) (PMSEA) side chains with varying grafting densities are reported. Highly hydrophilic PMSEA side chains were prepared by grafting-from poly(2-bromoisobutyryloxyethyl methacrylate) (PBiBEM) using photoATRP with either CuBr2/TPMA (tris(2-pyridylmethyl)amine), CuBr2/TPMA*3 (tris([(4-methoxy-2,5-dimethyl)-2-pyridyl]methyl)amine), or CuBr2/Me6TREN (tris(2-dimethylaminoethyl)amine), which were photochemically reduced to the appropriate amount of activators CuBr/ligand to start atom transfer radical polymerization (ATRP). Kinetic experiments showed that the polymerization was the fastest using CuBr2/Me6TREN at 6-fold excess of ligand to Cu. Additionally, the increase of ligand concentration resulted in a faster reaction with CuBr2/Me6TREN. A series of PMSEA MBs with grafting densities of 30%, 50%, and 100% was synthesized. The PMSEA MBs exhibited tunable hydrodynamic lubrication properties and low cytotoxicity against different types of cells. PMSEA MBs reveal rheological properties characteristic for nonentangled polymer melts. Densely grafted PMSEA MBs showed a nonlinear relationship between the coefficient of friction and the applied force.
Abstract 30: ApoE and ApoCIII Interact to Modulate the Metabolism of HDL ApoA-I in Humans (2016)

ApoE has potential roles in HDL metabolism by promoting enlargement and clearance, and apoCIII could delay apoE-mediated clearance by the liver as it does for VLDL metabolism. To determine whether apoE and apoCIII modulate the kinetics of apoA-I HDL, we compared the metabolism of apoA-I in HDL subspecies that have apoE, apoCIII, both, or neither. We recruited 10 participants (4M, 6F) with low HDL-C (range 24-54 mg/dl) and BMI between 25-35 kg/m 2 . They were given an IV bolus of d3-leucine and blood collected up to 46hr. HDL was isolated from plasma by anti-apoA-I immunoaffinity chromatography, separated by sequential anti-apoE and anti-apoCIII chromatography, and size-separated using NDPAGE into alpha-1, alpha-2, alpha-3, and prebeta-1 HDL. ApoA-I was purified from HDL subspecies on SDS-PAGE, and pool size of apoA-I was determined from the protein bands, adjusted to plasma total apoA-I. D3-leucine enrichment was measured by GC-MS. We used SAAM-II modeling software to compute apoA-I fractional catabolic rates (FCR) and fluxes for each HDL subspecies using a published multicompartmental model. The main findings from our preliminary model investigation are: - The liver secretes a range of HDL sizes for each of these HDL subspecies. About 2-6% of plasma HDL apoA-I is associated with apoE and/or apoCIII. Regardless of size, apoE- and apoCIII-containing HDL are detectable in the circulation slightly earlier after tracer administration than HDL containing neither apoE nor apoCIII. - HDL that contains apoE but not apoCIII is especially active in size conversions, such as generating prebeta-1 HDL. Prebeta-1 HDL types are not a universal precursor of larger size HDL. - HDL that contains apoE but not apoCIII has about a 4-fold increased FCR (range 1.3-8.8) across all sizes of HDL compared to other HDL subspecies, consistent with the role of apoE as a liver receptor ligand. When coexisting with apoE, apoCIII abolished the apoE-accelerated clearance, making the FCR similar to that of HDL that does not have apoE. But, when apoCIII is present on HDL that does not have apoE, there is no reduction in clearance compared to HDL containing neither apolipoprotein. In conclusion, these results suggest that apoE accelerates the metabolism of HDL apoA-I, whereas apoCIII impedes this process.
Reducing motion artifact in sequential-scan dual-energy CT imaging by incorporating deformable registration within joint statistical image reconstruction (2021)

Dual-energy computed tomography (DECT) has been widely used to reconstruct basis components. In previous studies, ou DECT algorithm has shown high accuracy in stopping power ratio (SPR) estimation of fixed objects for proton radiotherapy planning. However, patient movement between sequential data acquisitions may lead to severe motion artifacts in the component images. In order to reduce or eliminate the motion artifacts in clinical applications, we combine a deformable registration method with an accurate joint statistical iterative reconstruction algorithm, dual-energy alternating minimization (DEAM). Image registration is a process of geometrically aligning two or more images. We implement a multi-modality symmetric deformable registration method based on Advanced Normalization Tools (ANTs) to automatically align the scans we acquire for the same patient. The precalculated registration mapping and its inverse are then embedded into each iteration of the DEAM algorithm. The performance of warped DEAM is quantitatively assessed. Theoretically, the performance of warped DEAM on moved patients should be comparable to the performance of the original DEAM algorithm on fixed objects. The warped DEAM algorithm reduces motion artifacts while preserving the accuracy of the iterative joint statistical CT reconstruction algorithm, which enables us to reconstruct accurate results from sequentially scanned dual-energy patient data.