gebhart/patrepeval huggingface dataset:
Abstract 4178: Global assessment of the protein tyrosine phosphatome in cancer (2014)

Abstract Receptor tyrosine kinases and non-receptor tyrosine kinases are an important class of molecules controlling a large number of processes from growth to metabolic regulation. These tyrosine kinases have been well studied and scrutinized for their role in these normal processes as well as abnormal processes, such as cancer. Parallel to these kinases are more that 100 tyrosine phosphatases, which also fall into either receptor or non receptor classifications. While some of these phosphatases antagonize the tyrosine kinases others including many of the receptor bound phosphatases are critical in their own right in signaling processes such as pro survival, proliferation, etc. Although tyrosine kinases have been well studied, the study of tyrosine phosphatases has lagged. Numerous tyrosine phosphatases have been identified that are misregulated and important for cancer growth including PTPRD in breast cancer, and PTPRZ1 in small cell lung cancer as well as many others. However there has been no comprehensive study of all PTPs or the protein tyrosine phosphatome (PTPome), to identify which have a role in cancer. We as a cancer community are fortunate to have access to such a wide array of data types from a number of data sources such as TCGA, where we can determine if the PTPs are mis regulated in more than 20 types of cancers. We used TCGA data for all tumor types and subsetted the data to analyze the PTPome for all data types including expression, methylation, copy number and sequence data where available. Thus far we have identified known PTPs involved in a number of cancers, including PTPRD and PTPRZ1, but have also identified a number of PTPs altered in cancers that were less characterized such as the alteration of PTPRD in melanoma which is predominantly by mutations with much fewer deletions. While many of these mutations are missense and are difficult to characterize there are also a number of non-sense mutations, which would severely alter function as well as a number of splice site mutation of which some severely alter function and others are likely to alter function. The identification of this PTP is but one example to demonstrate the richness of this dataset. This analysis has been extremely useful to identify the PTPs that are altered in cancer and these results will be useful to many in the research community that are interested in PTP involvement in cancer but will also be of even greater use to those researchers who have not appreciated the vast importance of these under studied proteins. Citation Format: Nicholas Tonks, Robert Lucito. Global assessment of the protein tyrosine phosphatome in cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4178. doi:10.1158/1538-7445.AM2014-4178
Mechanically Tunable Single-Walled Carbon Nanotube Films as a Universal Material for Transparent and Stretchable Electronics (2019)

Soft, flexible, and stretchable electronic devices provide novel integration opportunities for wearable and implantable technologies. Despite the existing efforts to endow electronics with the capability of large deformation, the main technological challenge is still in the absence of suitable materials for the manufacturing of stretchable electronic circuits and devices with active (sensitive) and passive (stable) components. Here, we present a universal material, based on single-walled carbon nanotube (SWCNT) films deposited on a polydimethylsiloxane (PDMS) substrate, which can act as a material being both sensitive and insensitive to strain. The diverse performance of SWCNT/PDMS structures was achieved by two simple dry-transfer fabrication approaches: SWCNT film deposition onto the as-prepared PDMS and on the prestretched PDMS surface. The correlation between applied strain, microstructural evolution, and electro-optical properties is discussed on the basis of both experimental and computational results. The SWCNT/PDMS material with the mechanically tunable performance has a small relative resistance change from 0.05 to 0.07, while being stretched from 10 to 40% (stable electrode applications). A high sensitivity of 20.1 of the SWCNT/PDMS structures at a 100% strain was achieved (strain sensing applications). Our SWCNT/PDMS structures have superior transparency and conductivity compared to the ones reported previously, including the SWCNT/PDMS structures, obtained by wet processes.
Utilization and outcomes of aortic valve replacements (from the United States readmissions database) (2022)

More studies are needed to understand the timing, indications and utilization of AVR in this population.
Methods of Studying Retinal Vessels in Health and Diseases (2023)

Damsgaard, C., Lauridsen, H. Deep vascular imaging in the eye with flow-enhanced ultrasound. Journal of Visualized Experiments. (176), e62986 (2021). Macouzet-Romero, F. J., Ochoa-Máynez, G. A., Pérez-García, O., Pérez-Aragón, B. J., Lima-Gómez, V. Evaluation of capillary and other vessel contribution to macular perfusion density measured with optical coherence tomography angiography. Journal of Visualized Experiments. (180), e63033 (2022). Subirada, P. V. et al. Quantification of vascular parameters in whole mount retinas of mice with non-proliferative and proliferative retinopathies. Journal of Visualized Experiments. (181), e63126 (2022). Vaglienti, M. V., Subirada, P. V., Barcelona, P. F., Bonacci, G., Sanchez, M. C. Quantification of reactive oxygen species using 2',7'-dichlorofluorescein diacetate probe and flow-cytometry in Müller glial cells. Journal of Visualized Experiments. (183), e63337 (2022). Tomaszewsk, R., Rajpurohit, P., Cheng, M., Tawfik, A. Isolation of primary mouse retinal pigmented epithelium cells. Journal of Visualized Experiments. (189), e63543 (2022). Elmasry, K., Moustafa, M., Al-Shabrawey, M. Retinal explant of the adult mouse retina as an ex vivo model for studying retinal neurovascular diseases. Journal of Visualized Experiments. (190), e63966 (2022).
Comparative Anti-glycation and α-Glucosidase Inhibitory Studies of Metabolite, 9β,12β-Dihydroxy-9β,10α-pregna-4,6-diene-3,20-dione with Dydrogesterone (2013)

AZIZUDDIN*, SAIMA RASHEED, SUAD NAHEED AND MUHAMMAD IQBAL CHOUDHARY Department of Chemistry, Federal Urdu University of Arts, Science & Technology, Gulshan-e-Iqbal Campus, Karachi-75300, Pakistan. H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan. Department of Biotechnology, Jinnah University for Women, 5-C, Nazimabad, Karachi-74600, Pakistan. azizpobox1@yahoo.com
Progression following chemotherapy is a novel predictor of poor outcome following pulmonary metastasectomy in sarcoma patients (2010)

Blackmon, Shanda H. MD, MPH, FACS; Stephens, Elizabeth H. MD, PhD; Correa, Arlene M. PhD; Roth, Jack A. MD; Hofstetter, Wayne MD; Benjamin, Robert MD; Mehran, Reza MD; Swisher, Stephen G. MD; Walsh, Garrett L. MD; Vaporciyan, Ara A. MD, FACS Author Information
Design and Synthesis of Amphiphilic Xanthone-Based, Membrane-Targeting Antimicrobials with Improved Membrane Selectivity (2013)

This work describes how to tune the amphiphilic conformation of α-mangostin, a natural compound that contains a hydrophobic xanthone scaffold, to improve its antimicrobial activity and selectivity for Gram-positive bacteria. A series of xanthone derivatives was obtained by cationic modification of the free C3 and C6 hydroxyl groups of α-mangostin with amine groups of different pKa values. Modified structures using moieties with high pKa values, such as AM-0016 (3b), exhibited potent antimicrobial properties against Gram-positive bacteria. Compound 3b also killed bacteria rapidly without inducing drug resistance and was nontoxic when applied topically. Biophysical studies and molecular dynamics simulations revealed that 3b targets the bacterial inner membrane, forming an amphiphilic conformation at the hydrophobic-water interface. In contrast, moieties with low pKa values reduced the antimicrobial activity of the parent compound when conjugated to the xanthone scaffold. This strategy provides a new way to improve "hits" for the development of membrane-active antibiotics that target drug-resistant pathogens.
Development of Alpine Skis Using FE Simulations (2016)

The ski manufacturing industry is characterized by short product life cycles and high innovation pressure in order to meet customer's expectations of progressive improvements of skis. To reduce development time a FE model was developed and validated to simulate the influence of changes of the ski construction on its bending and torsional stiffness. Moreover, the study aimed to evaluate the feasibility of a novel ski sandwich construction with a load dependent bending stiffness. Therefore, the FE model was used to define required strain-stiffening of a single construction layer material to reach a perceptible change of the overall ski's bending stiffness. Two existing skis with identical geometry but distinctive differences of their torsional and bending stiffness were modelled using ANSYS Workbench. The sandwich construction was modelled by 18 solid bodies with bonded contacts: core, sidewalls, edges, upper and lower face with 13 layers including 3 additional resin interlayers. Orthotropic linear elastic material properties were taken from data sheets of suppliers and from material tests of the manufacturer. Sweep meshing was used to create an all-hex mesh of solid elements. Static structural simulations of a 3-point bending test and a torsion test were run in accordance to existing laboratory tests to validate the model. For both skis, the FE model showed good agreement with the experimental data for ski A and B. The simulated overall bending stiffness (center spring constant) was, respectively 2.8% and 3.2% higher compared to the experiments. The elastic curves revealed the model as slightly too stiff at the afterbody and too soft at the forebody. The simulated torsional stiffness (torsional spring constant) was, respectively 2.1% and 4.2% lower than found in the experiments. In the development process, for example, the model was then used to quantify the influence of edge profile heights on the ski's overall bending stiffness (3% per 0.1 mm edge height). The application of strain-stiffening materials to realize a load depending ski stiffness turned as not feasible due to too small strains within the ski structure. A realistic representation of the different construction layers of an alpine ski is still challenging, especially due to the heterogeneity of the fibre compound layers and the resin distribution. Using bulk properties of the upper and lower face of the sandwich construction is not an alternative. To virtually test the influence of new materials and layups every single layer has to be represented. Using two skis for validation and additional resin interlayers for calibration appeared appropriate in order to achieve adequate model results.
Polyphosphazene Polymer (2019)

Abstract Polyphosphazenes are a unique class of inorganic–organic hybrid polymers with a backbone composed of alternating phosphorus and nitrogen atoms. The ease with which the precursor prepolymer poly(dichlorophosphazene) can be modified has resulted in a versatile polymer system. The labile nature of the P−Cl bonds has allowed the substitution of chlorine atoms with groups like alkoxy‐, aryloxy, alkyl ether, fluoroalkoxy, amino acid/peptide esters, drug molecules, transition metal groups, and many more. Careful selection of the side groups offers efficient control of material properties such as bioactivity, crystallinity, solubility, and surface characteristics. Hence, these properties have led to the use of this exceptional class of polymers in a broad range of applications such as biomaterials for regenerative engineering and drug delivery, elastomers, solid membranes for gas/liquid separation, optical materials, flame retardants, and electrolytes for energy storage cells. This article gives an overview of the synthetic routes of polyphosphazene polymers and their composition–structure–properties relationships and highlights their applications in various fields.
Accelerating molecular discovery through data and physical sciences: Applications to peptide-membrane interactions (2018)

Simulation and data analysis have evolved into powerful methods for discovering and understanding molecular modes of action and designing new compounds to exploit these modes. The combination provides a strong impetus to create and exploit new tools and techniques at the interfaces between physics, biology, and data science as a pathway to new scientific insight and accelerated discovery. In this context, we explore the rational design of novel antimicrobial peptides (short protein sequences exhibiting broad activity against multiple species of bacteria). We show how datasets can be harvested to reveal features which inform new design concepts. We introduce new analysis and visualization tools: a graphical representation of the k-mer spectrum as a fundamental property encoded in antimicrobial peptide databases and a data-driven representation to illustrate membrane binding and permeation of helical peptides.
Hodgkin disease: clinical utility of CT in initial staging and treatment. (1988)

One hundred seven consecutive new cases of Hodgkin disease were evaluated with chest radiography and computed tomography (CT) for initial staging. The data were evaluated with regard to five popular treatment protocols for Hodgkin disease. Thoracic CT scans were normal in 30 of 31 patients who had normal radiographs. In the remaining 76 patients, CT demonstrated 194 new sites of disease and disproved 25 suspected sites of disease. The use of CT scans changed the staging of disease in 20 patients, 16 of whom had extranodal extension. The effect of using CT findings on treatment depended on whether radiation therapy was used, and, if so, which treatment protocol was followed. The use of CT findings would have changed the treatment in 6.5%-62.7% of new cases of Hodgkin disease. The authors recommend that CT scans be obtained in all patients with Hodgkin disease, especially those with abnormal chest radiographs.
SARS-CoV-2 variants of concern Alpha, Beta, Gamma and Delta have extended ACE2 receptor host-ranges (2021)

Abstract Following the emergence of SARS-CoV-2 in China in late 2019 a number of variants have emerged, with two of these – Alpha and Delta – subsequently growing to global prevalence. One characteristic of these variants are changes within the Spike protein, in particular the receptor binding domain (RBD). From a public health perspective these changes have important implications for increased transmissibility and immune escape; however, their presence could also modify the intrinsic host-range of the virus. Using viral pseudotyping we examined whether the variants of concern (VOCs) Alpha, Beta, Gamma and Delta have differing host ACE2 receptor usage patterns, focusing on a range of relevant mammalian ACE2 proteins. All four VOCs were able to overcome a previous restriction for mouse ACE2, with demonstrable differences also seen for individual VOCs with rat, ferret or civet ACE2 receptors, changes which we subsequently attribute to N501Y and E484K substitutions within the Spike RBD.
Mature bone marrow erythroid burst-forming units do not require T cells for induction of erythropoietin-dependent differentiation. (1980)

Cell-cell interactions between mature T cells and peripheral blood null cells induce erythropoietin-stimulated differentiation of peripheral blood-derived erythroid progenitors. By the use of complement-fixing cytolytic murine hybridoma and antibody uniquely reactive with mature T lymphocytes, this dependence of immature peripheral blood erythroid burst-forming unit (BFU-E) differentiation upon mature T cells or a T cell conditioned medium is confirmed. By using the same antibody, it is demonstrated that the differentiation of mature bone marrow BFU-E does not require either mature T cells or lymphocyte mitogenic factor. These findings do not preclude the presence in the bone marrow of other cells, perhaps even immature T cells, that influence erythropoietin-dependent erythroid differentiation of mature marrow BFU-E.
On the Development of a New Master Device Used for Medical Tasks (2018)

This paper discusses the design of a new spherical parallel manipulator (SPM), which is used as a master device for medical tasks. This device is obtained by changing the kinematics of a classic SPM to eliminate the singularity from the device's useful workspace. The kinematic models of the new device are studied. The geometric parameters of the new device are optimized to eliminate the singularity. A prototype of the new master device is presented. Experiments are carried out using the device which allowed the control of a surgical robot.
Applications of the Acousto-Optic Effect on Glass Integrated Optic Devices (2006)

We present in this paper a study of acousto-optic interactions with guided waves on glass substrate. A beam of elastic of waves in the Megahertz range, generated with a PZT ceramic, crosses a waveguide realised by ion-exchange in a glass substrate. Elastic waves modify locally the refractive index of glass. We make use of this effect to propose novel integrated sensors like a polarization analyzer sensor and to improve devices like optical modulators and displacement sensors
Enhancing application performance using heterogeneous memory architectures on a many-core platform (2016)

The 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> generation Intel® Xeon Phi processor (codenamed Knights Landing) is Intel's first self-booting Xeon Phi processor that is aimed at the HPC market. Like its predecessor, KNL is a many-core, highly threaded processor featuring an innovative on-die mesh interconnect and an on-package high bandwidth memory MCDRAM in addition to DRAM DDR-2400, which makes it possible for many HPC applications to achieve much higher performance by leveraging heterogeneous memory configuration. In this paper, we look at the programming challenges for software developers to create and manipulate data using different memory modes and a heap management API to satisfy the ever-increasing demand for high bandwidth and low latency. We start with a functional KNL architecture introduction with an emphasis on the memory subsystem and memory usage model, followed by the utility tools required to run the applications under various scenarios. We then present a profiler-based heterogeneous memory optimization framework for all memory-bandwidth-intensive applications. The new memory object features in Intel® VTune™ Amplifier will be introduced and discussed. Finally, we show how to leverage different kinds of memory by using a user extensible memory heap management API also known as memkind API. Throughout our discussions, we will use a classic streaming application in quantitative finance, the Black-Scholes benchmark. We show how to highlight the memory bottleneck using the new memory profiling features in the Intel VTune Amplifier and how to achieve high bandwidth by removing the bottleneck and by allocating memory threads between different types of memory. In the end, we show the peak performance we can achieve on KNL by using a combination of MCDRAM and DDR.
Thermally activated dissipation in Bi/sub 2. 2/Sr/sub 2/Ca/sub 0. 8/Cu/sub 2/O/sub 8+//sub delta/ (1988)

A new dissipation behavior is reported in superconducting Bi/sub 2.2/Sr/sub 2/Ca/sub 0.8/Cu/sub 2/O/sub 8+//sub delta/ for all temperatures below T/sub c/ and all magnetic fields exceeding H/sub c//sub 1/. The current-independent electrical resistivity is thermally activated and can be described by an Arrhenius law with a single prefactor and a magnetic-field- and orientation-dependent activation energy U/sub 0/(H,phi). This behavior is markedly different from past observations and will be discussed in terms of flux creep and flux flow. This thermally activated behavior implies a finite resistance at all temperatures and all fields exceeding H/sub c//sub 1/ determined by the activation energy as the only parameter.
Physiological and oenological traits of different<i>Dekkera/Brettanomyces bruxellensis</i>strains under wine-model conditions (2008)

Contamination of wine by Dekkera/Brettanomyces bruxellensis is mostly due to the production of off-flavours identified as vinyl- and especially ethyl-phenols, but these yeasts can also produce several other spoiling metabolites, such as acetic acid and biogenic amines. Little information is available about the correlation between growth, viability and off-flavour and biogenic amine production. In the present work, five strains of Dekkera bruxellensis isolated from wine were analysed over 3 months in wine-like environment for growth, cell survival, carbon source utilization and production of volatile phenols and biogenic amines. Our data indicate that the wine spoilage potential of D. bruxellensis is strain dependent, being strictly associated with the ability to grow under oenological conditions. 4-Ethyl-phenol and 4-ethyl-guaiacol production ranged between 0 and 2.7 and 2 mg L(-1), respectively, depending on the growth conditions. Putrescine, cadaverine and spermidine were the biogenic amines found.
Green Recovery of Rare Earths from Waste Cathode Ray Tube Phosphors: Oxidative Leaching and Kinetic Aspects (2016)

In this work, we developed a green and efficient process for the recovery of rare earths from waste cathode ray tube phosphors. The mixture of hydrochloric acid and hydrogen peroxide was identified as the most suitable leaching agent due to the synergistic effect. The effects of various parameters on leaching process were explored, and the optimal conditions with stirring speed 600 rpm, temperature 313 K, 1 M of H2O2, 4 M of HCl, and leaching time of 90 min were determined. Furthermore, a possible reaction mechanism was proposed, and the kinetics for the leaching process was investigated in detail. The leaching process was found to follow a shirking-core model, with the chemical reaction as the rate-controlling step. The apparent activation energy of the reaction was calculated as 52.3 kJ/mol, and the reaction orders for H2O2 and HCl were established as 0.82 and 2.13, respectively. The kinetic equation was established. Moreover, the optimal leaching conditions were applied to the waste phosphors, and the oxalate precipitation process was employed, achieving the recovery rate of rare earths >99.5%. After calcining, a well crystallized (Y0.95Eu0.05)2O3 product with a purity of 99% was obtained with an average diameter of 5 μm.