gebhart/patrepeval huggingface dataset:
A TRIBUTE TO A LIVING LEGEND (Special Issue in Honor of the 70th Birthday of Dr. Atta-ur-Rahman.) (2012)

History rarely witnesses the emergence of personalities whose monumental achievements change the course of science and technology in a country. Prof. Atta-ur-Rahman FRS, is one of such outstanding personalities whose contributions are multi-dimensional. For over half a century, he advanced our understanding of natural products and bioorganic chemistry, and inspired several generations of young scientists to choose these branches of chemical science as their future endeavors. From a humble beginning of independent research in an institution of a developing country, he advanced to capture the attention of the world’s natural product and medicinal chemistry communities with his seminal discoveries and his excellent leadership. He mentored a large number of young scholars from all over the world. Thus his enthusiasm for research and learning has spread globally. His research journey began with the development of synthetic approaches to complex anti-tumor alkaloids. He discovered over a thousand natural products, many of which proved to be novel with exciting biological properties. Around 850 publications, 25 international patents and over 114 books, published by major international publishers, are evidence to his enormous contributions in the field of natural products. The contributions of Prof. Atta-ur-Rahman go beyond his achievements in the field of chemical sciences. His leadership as the Federal Minister for Science and Technology, Information Technology and Higher Education of Pakistan, during 2000-2008 has completely changed the landscape of higher education in Pakistan. This included a significant increase in the number of universities from 57 to 137, tripling of the students’ enrolment from 257,000 to 810,000, increasing the national research output from 600 publications annually to 5,000 publications annually and raising university standards so much so that several universities in Pakistan are now ranked among the top 400 in the world. His work has received universal recognition and for this, he was honored with numerous awards and honorary doctorate degrees by many universities including the University of Cambridge. He is also the only scientist from the Islamic world to have been elected as a Fellow of the Royal Society (London) in recognition of research work carried out within an Islamic country in the 350 years old history of the Royal Society. Prof. Rahman is the first scientist from the Muslim world to have won the prestigious UNESCO Science Prize (1999) in the 35 year-old history of the Prize. He was elected Honorary Life Fellow of Kings College, Cambridge University, UK in 2007. Prof. Atta-ur-Rahman was conferred the TWAS (The Academy of sciences for Developing World) Prize for Institution Building in Durban, South Africa in 2009 in recognition of his contributions for bringing about revolutionary changes in the higher education sector in Pakistan. The Austrian government also honoured him with its highest civil award (“Grosse Goldene Ehrenzeischen am Bande
Axial flow blood pumps. (2003)

Each year, thousands of cardiac patients await healthy donor hearts for transplantation. Due to the current shortage of donor hearts (approximately 2300 per year), these patients often require supplemental circulatory support until a transplant becomes available. This supplemental support is often provided by a mechanical heart pump or left ventricular assist device (LVAD). This article explores one type of LVAD, specifically the design and development of axial flow ventricular assist devices (VAD). We discuss the design details, and experimental or clinical experience with the following axial flow support systems: Hemopump, MicroMed DeBakey VAD, Jarvik 2000, HeartMate II, Streamliner, Impella, Berlin INCOR I, Valvo pump, and IVAP. All of these devices demonstrate promise in providing bridge-to-transplant and ultimately destination therapy for adult cardiac failure patients.
The Pfam protein families database: towards a more sustainable future (2015)

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.
The Potential for Speech Intelligibility Improvement Using the Ideal Binary Mask and the Ideal Wiener Filter in Single Channel Noise Reduction Systems: Application to Auditory Prostheses (2012)

Whereas state-of-the-art single-channel noise reduction algorithms for auditory prostheses demonstrate an appreciable suppression of the noise and improved speech quality, they are unable, thus far, to improve the intelligibility of noise-degraded speech signals. Alternative approaches to speech enhancement using a binary time-frequency mask have demonstrated substantial intelligibility improvements in low signal-to-noise-ratio (SNR) conditions under ideal settings, making this a promising research direction for auditory prostheses. These approaches exploit the sparsity and disjoint-ness of speech spectra in their short-time-frequency representation to preserve only the target-dominant time-frequency regions in the processed output. State-of-the-art noise reduction algorithms in contrast are soft-decision approaches which weight each time-frequency region in proportion to the prevailing SNR. However, the potential for intelligibility improvement using these approaches has not been examined systematically vis-à-vis the binary mask alternative. This contribution compares the performance of an ideal soft-decision system, exemplified by the ideal Wiener filter (IWF), and the ideal binary mask (IBM) for single-channel speech enhancement for auditory prostheses. To obtain results relevant to this application area, a (relatively) low spectral resolution, modelled using the Bark-spectrum scale, is used for both the IWF and the IBM. This spectral resolution is comparable to that being used in commercial hearing instruments. The comparison is in terms of potential for intelligibility improvement and resulting signal quality. Intelligibility tests carried out under various noise conditions and SNRs show that the IWF leads to higher intelligibility scores than the IBM in low SNR conditions. Under non-ideal parameter estimates, it is demonstrated that the IWF approach is also much less sensitive to estimation errors. Quality-wise, a preference for the IWF exists. This was evaluated using a two-stage, pair-wise preference-rating test.
PGE2-Driven Expression of c-Myc and OncomiR-17-92 Contributes to Apoptosis Resistance in NSCLC (2014)

Abstract Aberrant expression of microRNAs (miRNA) with oncogenic capacities (oncomiRs) has been described for several different malignancies. The first identified oncomiR, miR-17-92, is frequently overexpressed in a variety of cancers and its targets include the tumor suppressor PTEN. The transcription factor c-Myc (MYC) plays a central role in proliferative control and is rapidly upregulated upon mitogenic stimulation. Expression of c-Myc is frequently deregulated in tumors, facilitating proliferation and inhibiting terminal differentiation. The c-Myc–regulated network comprises a large number of transcripts, including those encoding miRNAs. Here, prostaglandin E2 (PGE2) exposure rapidly upregulates the expression of the MYC gene followed by the elevation of miR-17-92 levels, which in turn suppresses PTEN expression, thus enhancing apoptosis resistance in non–small cell lung cancer (NSCLC) cells. Knockdown of MYC expression or the miR-17-92 cluster effectively reverses this outcome. Similarly, miR-17-92 levels are significantly elevated in NSCLC cells ectopically expressing COX-2. Importantly, circulating miR-17-92 was elevated in the blood of patients with lung cancer as compared with subjects at risk for developing lung cancer. Furthermore, in patients treated with celecoxib, miR-17-92 levels were significantly reduced. These data demonstrate that PGE2, abundantly produced by NSCLC and inflammatory cells in the tumor microenvironment, is able to stimulate cell proliferation and promote resistance to pharmacologically induced apoptosis in a c-Myc and miR-17-92–dependent manner. Implications: This study describes a novel mechanism, involving c-Myc and miR-17-92, which integrates cell proliferation and apoptosis resistance. Mol Cancer Res; 12(5); 765–74. ©2014 AACR.
How much off-the-shelf knowledge is transferable from natural images to pathology images? (2020)

Deep learning has achieved a great success in natural image classification. To overcome data-scarcity in computational pathology, recent studies exploit transfer learning to reuse knowledge gained from natural images in pathology image analysis, aiming to build effective pathology image diagnosis models. Since transferability of knowledge heavily depends on the similarity of the original and target tasks, significant differences in image content and statistics between pathology images and natural images raise the questions: how much knowledge is transferable? Is the transferred information equally contributed by pre-trained layers? If not, is there a sweet spot in transfer learning that balances transferred model's complexity and performance? To answer these questions, this paper proposes a framework to quantify knowledge gain by a particular layer, conducts an empirical investigation in pathology image centered transfer learning, and reports some interesting observations. Particularly, compared to the performance baseline obtained by a random-weight model, though transferability of off-the-shelf representations from deep layers heavily depend on specific pathology image sets, the general representation generated by early layers does convey transferred knowledge in various image classification applications. The trade-off between transferable performance and transferred model's complexity observed in this study encourages further investigation of specific metric and tools to quantify effectiveness of transfer learning in future.
Holdup counters for the Plutonium Fuel Production Facility--PFPF (1990)

A neutron coincidence counting system has been developed for assaying plutonium holdup in glove boxes at the automated mixed-oxide fuel fabrication facility, PFPF, in Japan. The time-correlated neutron emission rate arising from the spontaneous fission decay of plutonium isotopes is measured and converted to grams of plutonium contained in the glove box. Each detection system consists of a pair of polyethylene slabs containing {sup 3}He proportional counters and associated electronics. These slabs are placed on either side of the glove box that is to be measured for plutonium holdup. The detectors are moved by a portable lifter to map out the coincidence response from the entire glove box. Results of a design optimization study that considered detector efficiency, as well as overall size and weight and how these parameters interface with the procedure of mapping the glove box, are presented. The use of Los Alamos transport code, MCNP, in the detector design optimization and in aid of calibration is also discussed. 2 refs., 8 figs., 1 tab.
Phosphorylation, Subcellular Localization, and Membrane Orientation of the Alzheimer's Disease-associated Presenilins (1997)

Presenilins 1 and 2 are unglycosylated proteins with apparent molecular mass of 45 and 50 kDa, respectively, in transfected COS-1 and Chinese hamster ovary cells. They colocalize with proteins from the endoplasmic reticulum and the Golgi apparatus in transfected and untransfected cells. In COS-1 cells low amounts of intact endogeneous presenilin 1 migrating at 45 kDa are detected together with relative larger amounts of presenilin 1 fragments migrating between 18 and 30 kDa. The presenilins have a strong tendency to form aggregates (mass of 100-250 kDa) in SDS-polyacrylamide gel electrophoresis, which can be partially resolved when denatured by SDS at 37 degrees C instead of 95 degrees C. Sulfation, glycosaminoglycan modification, or acylation of the presenilins was not observed, but both proteins are posttranslationally phosphorylated on serine residues. The mutations Ala-246 --> Glu or Cys-410 --> Tyr that cause Alzheimer's disease do not interfere with the biosynthesis or phosphorylation of presenilin 1. Finally, using low concentrations of digitonin to selectively permeabilize the cell membrane but not the endoplasmic reticulum membrane, it is demonstrated that the two major hydrophilic domains of presenilin 1 are oriented to the cytoplasm. The current investigation documents the posttranslational modifications and subcellular localization of the presenilins and indicates that postulated interactions with amyloid precursor protein metabolism should occur in the early compartments of the biosynthetic pathway.
Maximum energy traveltimes calculated in the seismic frequency band (1996)

Abstract Prestack Kirchhoff migration using first-arrival traveltimes has been shown to produce poor images in areas of complex structure. To avoid this problem, I propose a new method for calculating traveltimes that estimates the traveltime of the maximum energy arrival, rather than the first arrival. This method estimates a traveltime that is valid in the seismic frequency band, not the usual high-frequency approximation. Instead of solving the eikonal equation for the traveltime, I solve the Helmholtz equation to estimate the wavefield for a few frequencies. I then perform a parametric fit to the wavefield to estimate a traveltime, amplitude, and phase. The images created by using these parameters in a Kirchhoff imaging algorithm are comparable in quality to those created using full-wavefield, finite-difference, shot-profile migration.
Des outils chimiques et biologiques pour améliorer le diagnostic d’impact in situ des produits phytosanitaires (2020)

National audience
A 2.5-GHz Receiver Front-End With <formula formulatype="inline"> <tex Notation="TeX">$Q$</tex></formula>-Boosted Post-LNA <formula formulatype="inline"> <tex Notation="TeX">$N$</tex></formula>-Path Filtering in 40-nm CMOS (2014)

This paper presents the analysis, design, and measurements of a 2.5-GHz receiver front-end in a 40-nm CMOS technology. The front-end utilizes RLC-resonator quality factor (Q) boosting and four-phase N-path filtering to improve the blocker filtering capabilities of the low-noise amplifier (LNA). Systematic analysis is performed in order to obtain a thorough design approach. Particular attention is paid to the passive mixer switches in the RLC case, for which we show that minimum switch resistance does not provide best noise figure (NF), nor best relative blocker attenuation. Moreover, the N-path filter extends the stable operating region of a Q-boosted LNA, and adding a noisy Q-boosting circuit can actually improve the receiver NF in practical realizations. The experimental CMOS front-end is flip-chip packaged, and a parasitic-aware input matching method for the electrostatic-discharge-protected LNA is proposed, analyzed, and verified. In nominal operation, the programmable front-end achieves a measured gain of 39 dB, an NF of 3.5 dB, and an out-of-band input-referred third order intercept point of > 0 dBm, while consuming 48 mA from a 1.1-V supply.
Retinal toxicity in a multinational inception cohort of patients with systemic lupus on hydroxychloroquine (2022)

This is the first assessment of HCQ and retinal disease in incident SLE. We did not see any cases of retinopathy within the first 4 years of HCQ. Cumulative HCQ may be associated with increased risk. Ophthalmology monitoring (and formal assessment of cases of potential toxicity, by a retinal specialist) remains important, especially in patients on HCQ for 10+ years, those needing higher doses and those of older age at SLE diagnosis.
Separation for boundary to CSG conversion (1993)

important applications of b-rep -CSG conversion arise in solid modeling, image processing, and c,lsewhere. In addition, the problem is of considerable theoretical interest. One of the most difficult steps in performing b-rep ~CSG conversion for a curved solid object consists of determining o set of half-spaces that is sufficient for a CSG representation of the solid. This usually requires the construction of additional half-spaces whose boundaries do not contribute to the boundary of the solid. Such half-spaces are called separating half-spaces because their purpose is to separate certain subsets inside the solid from those outside of the solid, Construction of separating half-spaces is specific to a particular geometric domain, but several generic approaches are possible. We use the information present in the boundary of the solid being converted to study the constraints on the degree of separating half-spaces, and show that a suff]cicnt set of linear separating half-spaces exists for any solid whose boundary contains only planar edges. A compl[,te construction is given for solids whose faces lie in convex surfaces. Separation for more L,cneral solids, whose b-rep includes othm surfaces and nonplanar edges, is alsa discussed, but this general problem remains poorly understood. We apply the boundary-based separation to solids hounded by genera] quadric surfaces, Specifically, we prove that a sufficient set of linear separating half-spaces exists for any such solid and consider the required constructions in several common situations. The presented results allowed a successful implementation of an experimental b-rep + CSW conversion system that converts natural quadric b-reps in ]>:lras(J]ldTMt(} ~~clcnt C'SG representations in PADL-2 Categ[jric,s and Subject Ilescriptors
A Wide Bandwidth and Wide Beamwidth CDMA/GSM Base Station Antenna Array With Low Backlobe Radiation (2005)

A wide bandwidth and wide beamwidth L-probe-fed patch antenna array with a novel design of grounded structure is proposed and tested. The antenna is made of stacked patches supported by plastic screws. The patches are proximity fed via L-shaped probe. By cutting slots in two vertical side walls of a box-shaped grounded structure, an impedance bandwidth larger than 20% (SWR<1.5), an H-plane beamwidth over 90/spl deg/, and much reduction in backlobe radiation can be obtained. Details of the proposed antenna, simulation, and experimental results are presented and discussed.
Integration of ethical training into undergraduate senior design projects on wireless communications (2015)

Wireless communications engineers may face complex ethical dilemmas while designing products for consumers. At Florida International University's Electrical and Computer Engineering Department, we place great importance on training our students to address such ethical dilemmas, in alignment with ABET requirements. To this end, an ethical training framework is integrated into our two-semester senior design project course. In addition to the codes of ethics, our students use "The Theory Model" to make decisions based on ethical theories. For the solution of ethical dilemmas by means of ethical theories, they apply a modified version of the line drawing method. In this article we briefly explain the theories and methods that our students consider when facing ethical dilemmas. Then we present excerpts from four past senior design projects related to wireless communications. We also summarize the methodology the students use for identifying the best option to address ethical dilemmas.
Ferromagnetic resonance study of exchange coupled (Ga,Mn)As/GaAs/(Ga,Mn)As heterostructures (2007)

36th International School on the Physics of Semiconducting Compounds, Jaszowiec, POLAND, JUN 09-15, 2007
Current and Future Challenges of Software Engineering for Services and Applications (2016)

ICT (Information and Communication Technology) and, in particular, software is more and more pervasive and it cannot be considered anymore as a minor element of a complex systems. In domains like cloud, big data, IoT (Internet of Things), CPS (Cyber-Physical Systems) it is the core element. We need to consolidate the software engineering discipline, which, despite the impressive achievements in the area of software technology, is probably one of the youngest scientific and technological disciplines with about 60 years of history. This paper summarizes the challenges that the Software Engineering for Services and Applications (SE4SA) cluster is considering as relevant.
Improved platelet compatiblity of water vapour glow discharge treated non‐woven poly(ethylene terephthalate) leukocyte‐reduction filters for different types of platelet concentrates (2001)

Non-woven poly[ethylene terephthalate] (NW-PET) filter fabric, usually used for leucocyte removal of red cells, was modified by water vapour glow discharge (WVGD) treatment to improve platelet compatibility. Modified filter material was evaluated with different kinds of platelet concentrates (PCs). In addition, modified filter materials were gamma-sterilized and tested after different time intervals at different storage conditions. Modification of the filter material resulted in an improved platelet recovery after filtration of PC from 57 to about 80%. No significant difference in platelet recovery was observed when filtering either freshly prepared (79 +/- 3.5%, mean +/- SD), overnight-stored single BC-PC (78 +/- 3.3%), overnight-stored single PRP-PC (75 +/- 8.8%) or overnight-stored pooled BC-PC (79 +/- 8.9%). However, freshly prepared pooled BC-PC gave a significantly higher platelet recovery (84 +/- 3.5%). Leukocyte depletion did not differ significantly between the different types of PC. gamma-Sterilization and subsequent storage of the modified filter material for 5, 14 and 26 weeks at 20 degrees C or 37 degrees C had no significant influence on the filtration results of overnight-stored pooled BC-PC. The results of the present study show that WVGD-treated NW-PET is platelet compatible and can be used for leucocyte removal from preferably BC-PC. It can be gamma-sterilized and stored for at least 6 months prior to filtration without affecting the platelet recovery and leucocyte removal.
An Introduction to Numerical Analysis (1990)

Error: Its Sources, Propagation, and Analysis. Rootfinding for Nonlinear Equations. Interpolation Theory. Approximation of Functions. Numerical Integration. Numerical Methods for Ordinary Differential Equations. Linear Algebra. Numerical Solution of Systems of Linear Equations. The Matrix Eigenvalue Problem. Appendix. Answers to Selected Problems. Index.