gebhart/patrepeval huggingface dataset:
Transparent access to multiple bioinformatics information sources (2001)

This paper describes the Transparent Access to Multiple Bioinformatics Information Sources project, known as TAMBIS, in which a domain ontology for molecular biology and bioinformatics is used in a retrieval-based information integration system for biologists. The ontology, represented using a description logic and managed by a terminology server, is used both to drive a visual query interface and as a global schema against which complex intersource queries are expressed. These source-independent declarative queries are then rewritten into collections of ordered source-dependent queries for execution by a middleware layer. In bioinformatics, the majority of data sources are not databases but tools with limited accessible interfaces. The ontology helps manage the interoperation between these resources. The paper emphasizes the central role that is played by the ontology in the system. The project distinguishes itself from others in the following ways: the ontology, developed by a biologist, is substantial; the retrieval interface is sophisticated; the description logic is managed by a sophisticated terminology server. A full pilot application is available as a Java™ applet integrating five sources concerned with proteins. This pilot is currently undergoing field trials with working biologists and is being used to answer real questions in biology, one of which is used as a case study throughout the paper.
Enhancing human bodies with extra robotic arms and fingers: The Neural\n Resource Allocation Problem (2021)

The emergence of robot-based body augmentation promises exciting innovations\nthat will inform robotics, human-machine interaction, and wearable electronics.\nEven though augmentative devices like extra robotic arms and fingers in many\nways build on restorative technologies, they introduce unique challenges for\nbidirectional human-machine collaboration. Can humans adapt and learn to\noperate a new limb collaboratively with their biological limbs without\nsacrificing their physical abilities? To successfully achieve robotic body\naugmentation, we need to ensure that by giving a person an additional\n(artificial) limb, we are not in fact trading off an existing (biological) one.\nIn this manuscript, we introduce the "Neural Resource Allocation" problem,\nwhich distinguishes body augmentation from existing robotics paradigms such as\nteleoperation and prosthetics. We discuss how to allow the effective and\neffortless voluntary control of augmentative devices without compromising the\nvoluntary control of the biological body. In reviewing the relevant literature\non extra robotic fingers and limbs we critically assess the range of potential\nsolutions available for the "Neural Resource Allocation" problem. For this\npurpose, we combine multiple perspectives from engineering and neuroscience\nwith considerations from human-machine interaction, sensory-motor integration,\nethics and law. Altogether we aim to define common foundations and operating\nprinciples for the successful implementation of motor augmentation.\n
EFFECT OF COSMOS CAUDATUS KUNTH LEAVES ON THE LIPID PROFILE OF A HYPERLIPIDEMIA-INDUCED ANIMAL MODEL (2014)

Hyperlipidemia, a metabolic disorder closely associated with the modern life-style and eating habits, is increasingly prevalent among the world population. This study was conducted on obese rats to evaluate the efficacy of Cosmos caudatus leaves as a treatment of hyperlipidemia. Hyperlipidemic conditions were induced in rats by submitting them to a high-fat diet during 3 months. After this, the rats were administered 200 mg/kg body weight of an ethanolic C. caudatus leaf extract or 35 mg/kg body weight atorvastatin for four weeks. The rats treated with the C. caudatus extract showed a significant (P<0.05) reduction of plasma triglycerides, total cholesterol, low density lipoprotein-cholesterol and glucose, and a significant (P< 0.05) increase in high density lipoprotein-cholesterol and Atherogenic Index values. The study indicated that supplementation with C. caudatus has a potential for the treatment of hyperlipidemia.
Design through the looking glass [digital twins of real products] (2016)

What they do is test it virtually, in order to tell the doctor what he needs to do for the patient. You don't want the doctor to open you up and say, OK, what do I need to do here?'. They provide the virtual capability, so a doctor operating on your knee, before he goes knows exactly what hardware he needs to put in, Michael Grieves describes the use in healthcare of a digital twin, the concept he developed more than a decade ago. Although he first proposed the idea in 2003 as a way of developing products more cheaply with the help of computer models, it has since found wider uses.
Estimation of Phase Noise for QPSK Modulation over AWGN Channels (2003)

Every oscillator used in bandpass communication suffers from an instability of their phase (a.k.a. phase noise) that, if left unaddressed, can lead to great degradation of the system performance. In this paper, we tackle the problem of minimising the effect of oscillator phase noise on the coherent detection of a quadrature phase shift keying (QPSK) modulation operating on an Additive White Gaussian Noise (AWGN) channel. The phase noise process is modeled as a Wiener-Levy (random walk) process. Our approach uses maximum likelihood (ML) estimation of phase noise. Thorough analysis and derivation for Decision Directed (DD), Non-Data Aided (NDA), used with and without symbol differential encoding, and pilot based estimators are presented. We compare these estimators with respect to their main features and evaluate their bit error rate (BER) performances throught simulations. Results show that for low signal to noise ratio (SNR) applications, the use of differential encoding along with the proposed DD or NDA estimator yields performances with an SNR penalty below the two dB imposed by the non coherent detection methods, while pilot based estimation using wiener interpolation makes it possible to detect a QPSK modulation with SNR penalty around two dB.
Influence of cell isolation method on the optimization of CD4+ T cell expansion using anti-CD3/CD28 coated beads (2013)

The results demonstrate that purified CD4+ T lymphocytes from immunorosette formation provided the highest CD4+ T lymphocyte expansion when stimulated with anti-CD3/CD28 coated beads. This method can be used to obtain a large number of expanded CD4+ T cells for adoptive immunotherapy.
Theoretical study of the X‐ray photoionization spectra of polycycloalkanes (1996)

The dependence of X-ray photoionization spectra on structural characteristics is assessed by one-particle Green's function calculations on the nearly isomeric adamantane, 1,4-dimethyl bicyclo [2,2,2] octane and 1,1,4,4-tetramethyl cyclohexane compounds. These calculations are carried out using the quasi-particle approximation and the diagonal 2ph-TDA renormalization scheme for the self-energy. The simulated spectra fingerprint remarkably the atomic connectivity from their inner valence part, through the interplay of energy degeneracies and the influence of torsional strains on electron binding energies. The boundary region between the inner and outer valence bands provides also specific signatures for molecular characteristics pertaining to conformational questions, namely the enforced conversion from the chair to the boat form of the cyclohexane units generating these compounds. © 1996 John Wiley & Sons, Inc.
The K252a Derivatives, Inhibitors for the PAK/MLK Kinase Family, Selectively Block the Growth of HAS Transformants (2002)

These bulky adenosine triphosphate antagonists derived from K252a or related indolocarbazole compounds such as staurosporine would be potentially useful for the treatment of RAS/ PAK1-induced cancers, once their anti-PAK1 activity is significantly potentiated by a few additional chemical modifications at the sugar ring suggested in this paper.
A Review of Proper Modeling Techniques (2008)

A dynamic system model is proper for a particular application if it achieves the accuracy required by the application with minimal complexity. Because model complexity often—but not always—correlates inversely with simulation speed, a proper model is often alternatively defined as one balancing accuracy and speed. Such balancing is crucial for applications requiring both model accuracy and speed, such as system optimization and hardware-in-the-loop simulation. Furthermore, the simplicity of proper models conduces to control system analysis and design, particularly given the ease with which lower-order controllers can be implemented compared to higher-order ones. The literature presents many algorithms for deducing proper models from simpler ones or reducing complex models until they become proper. This paper presents a broad survey of the proper modeling literature. To simplify the presentation, the algorithms are classified into frequency, projection, optimization, and energy based, based on the metrics they use for obtaining proper models. The basic mechanics, properties, advantages, and limitations of the methods are discussed, along with the relationships between different techniques, with the intention of helping the modeler to identify the most suitable proper modeling method for a given application.
Developement of magnetic pulse welding process for welding dissimilar materials and joining polymeric composites to metals (2018)

La réduction des émissions CO2 et l'amélioration de la performance restent toujours les grands objectifs de l'industrie automobile. Pour atteindre ces objectif, les équipementiers automobiles cherchent toujours à alléger les structures à travers l'emploie des matériaux hétérogènes qui a évolué au cours des dernières décennies où nous trouvons aujourd'hui à la fois des aciers doux, des aciers à très hautes résistances, des alliages légers tels que les alliages d'aluminium et de magnésium ainsi que des composites à fibre de verre ou de carbone. Cette tendance pose aujourd'hui plusieurs défis concernant à la fois l'assemblage bimétallique et l'assemblage hybride métal/composite. Les difficultés de réaliser ce type d’assemblage est lié surtout à la différence des propriétés mécaniques, thermiques et chimiques des divers matéiaux. Ces différences limitent l’utilisation des techniques d’assemblage traditionnelles, c’est-à-dire l’assemblage mécanique, le soudage par fusion et le collage, et nécessitent ainsi le développement de nouvelles solutions d’assemblage. Dans ce contexte, cette étude vise à répondre aux défis des soudages hétérogènes ainsi qu' à développer deux nouvelles solutions originales d'assemblage hybride métal/composite en utilisant le procédé de soudage par impulsion magnétique.
A formal verification of dynamic updating in a Java-based embedded system (2017)

Dynamic software updating (DSU) consists in updating running programs on the fly without any downtime. This feature is interesting in critical applications that must run continuously. Because updates may lead to safety errors and security breaches, the question of their correctness is raised. Formal methods are a rigorous means to ensure the correctness required by applications using DSU. In this paper, we present a formal verification of correctness of DSU in a Java-based embedded system. Our approach is based on three major contributions. First, a formal interpretation of the semantic of update operations to ensure type safety of the update. Secondly, we rely on a functional representation of bytecode, the predicate transformation calculus and a functional model of the update mechanism to ensure the behavioural correctness of the updated programs. It is based on the use of Hoare predicate transformation to derive a specification of an updated bytecode. Thirdly, we use the functional representation to model the safe update point detection mechanism. This mechanism guarantees that none of the updated methods are active. This property is called activeness safety. We propose a functional specification that allows to derive proof obligations that guarantee the safety of the mechanism.
MicroRNA-146a acts as a guardian of the quality and longevity of hematopoietic stem cells (P4467) (2013)

Abstract During inflammation and infection, hematopoietic stem and progenitor cells (HSPCs) are stimulated to proliferate and differentiate into mature immune cells, especially of the myeloid lineage. MicroRNA-146a (miR-146a) is a critical negative regulator of inflammation. Deletion of miR-146a produces effects that appear as dysregulated inflammatory hematopoiesis, leading to a decline in the number and quality of hematopoietic stem cells (HSCs), excessive myeloproliferation, and, ultimately, to exhaustion of the HSCs and hematopoietic neoplasms. In the absence of miR-146a, LPS-mediated serial inflammatory stimulation accelerates the effects of aging. The chronic inflammatory stress on HSCs in deleted mice involves a molecular axis consisting of upregulation of TRAF6 leading to excessive activity of NF-κB and overproduction of the cytokine IL-6. At the cellular level, we show that the defects are attributable to both an intrinsic problem in the miR-146a-deficient HSCs and extrinsic effects of miR-146a-deficient lymphocytes and non-hematopoietic cells. This study has identified a microRNA, miR-146a, to be a critical regulator of HSC homeostasis during chronic inflammatory challenge in mice and has provided a molecular connection between chronic inflammation and the development of bone marrow failure and myeloid malignancies. This may have implications for human hematopoietic malignancies, such as myelodysplastic syndrome, which frequently displays downregulated miR-146a expression.
Diffuse ocular metastasis of ductal breast carcinoma following vitreoretinal surgery (2010)

A 65-year-old female presented to our hospital for enucleation of her painful and blind left eye. During the last 2 years, she had been operated on several times for recurrent retinal detachment of unknown aetiology and proliferative vitreoretinopathy including repeat vitrectomy with instillation and removal of silicone oil. On examination, she presented with an inflamed left eye without any light perception and complained of an intermittent left-sided headache. The cornea was cloudy with neovascularisation and band keratopathy which obscured any further details of the intraocular structures (figure 1A). Ultrasound OS revealed a non-specific thickening of the choroid and hyper-reflective membranes near the posterior pole consistent with a persistent retinal detachment (figure 1B). The medical history was remarkable for metastatic breast carcinoma diagnosed 23 years previously in 1986. Subsequently, the patient underwent radiotherapy and breast-saving therapy. In 1994, the patient developed a metastasis to the pleura and received chemotherapy with tamoxifen for 5 years. This metastasis was thought to develop from the original cancer. The patient also received radiotherapy and surgery (complete excision of the infiltrated part of the pleura and reduction of the infiltrated breast) in the mean time. In 2004, the patient had a new metastasis in the pleura and again underwent excisional surgery of the metastasis and pleurodesis as well as radiotherapy for bone metastases.



Figure 1 
(A) Clinical appearance of the phthisical eye with band keratopathy and corneal neovascularisation. (B) Sonography of the left globe showing an old bullous retinal detachment as well as hyper-reflectivity of the slightly thickened choroid.



Enucleation was performed subsequently. The procedure was unexpectedly difficult due to strong adhesions between the conjunctiva, the sclera and the posterior periocular tissues.

The tissue was fixed in formalin and submitted for ophthalmopathological evaluation. Macroscopic examination showed a small part (10×20 mm) and the remaining main part of the globe (23×17×14 mm). In order …
Speech-codec detection by spectral harmonic-plus-noise decomposition (2005)

This paper presents a new method for speech-codec detection providing reliable information about the perceived quality of a telephone link. Our specific decomposition of the short-time speech-spectrum into a harmonic and a noise component reveals codec-specific distortions of the speech signal. In conjunction with an appropriate classifier, we thus can identify five different codecs with an error rate of less than 8%.
MATLANG (2019)

We investigate the expressive power of MATLANG, a formal language for matrix manipulation based on common matrix operations and linear algebra. The language can be extended with the operation inv for inverting a matrix. In MATLANG + inv we can compute the transitive closure of directed graphs, whereas we show that this is not possible without inversion. Indeed we show that the basic language can be simulated in the relational algebra with arithmetic operations, grouping, and summation. We also consider an operation eigen for diagonalizing a matrix. It is defined such that for each eigenvalue a set of orthogonal eigenvectors is returned that span the eigenspace of that eigenvalue. We show that inv can be expressed in MATLANG + eigen. We put forward the open question whether there are boolean queries about matrices, or generic queries about graphs, expressible in MATLANG+eigen but not in MATLANG+inv. Finally, the evaluation problem for MATLANG + eigen is shown to be complete for the complexity class 9R.
Observation of Photon-driven Electronic Transport in Quantum Cascade Lasers (2007)

We report a series of femtosecond pump-probe measurements on quantum cascade lasers operating below and above threshold; the gain recovery dynamics reveal how quantum stimulated emission drives the current through the cascade heterostructure, which we refer to as photon-driven transport.
NG Broadband Access – A Total-Cost-of-Ownership Analysis (2009)

TCO of access networks is determined by operational expenditures, with energy cost being one of the major contributors. We show that WDM-PON, although not lowest in capital expenditures, is a future-proof solution which minimizes TCO.
Conservative Garbage Collection on DSM Systems. (1996)

Kidneys from cattle at slaughter were examined for the presence of leptospires. Of 218 (8.3%) kidneys leptospires were isolated from 18; all were identified as Leptospira interrogans serovar hardjo. None of the leptospire-infected kidneys had histopathological lesions indicative of leptospirosis and leptospires were demonstrated in only 2 by immunogold silver staining. Leptospires infected kidneys remained viable for at least 21 days when stored at 4 degrees but became non-viable within 14 days when stored frozen at -15 degrees.
Interleukin-1B Induces Interleukin-6 Production through the Production of Prostaglandin E2 in Human Osteoblasts, MG-63 Cells (1999)

This study was conducted to investigate the mechanism of interleukin-1beta (IL-1beta)-induced IL-6 production in human osteoblasts (MG-63 cells). Stimulation with IL-1beta resulted in the production of IL-6 and prostaglandin E(2) (PGE(2)). IL-6 production gradually increased and peaked 96 h after stimulation. IL-6 mRNA was detected between 4 and 72 h after IL-1beta stimulation. The patterns of PGE(2) production and the expression of cyclooxygenase-2 (COX-2) mRNA were biphasic after stimulation. Actinomycin D, cycloheximide, indomethacin, and NS-398 (COX-2 inhibitor) suppressed the production of IL-6 and PGE(2). Anti-PGE(2) antibody markedly reduced the production of IL-6. In addition, stimulation with 17-phenyl-PGE(2), a PGE receptor-1 (EP-1 receptor) agonist, led to the expression of IL-6 mRNA after pretreatment with IL-1beta. These findings indicate that IL-1beta-induced IL-6 production in MG-63 cells involves the following sequence of steps: IL-1beta-induced COX-2 activation, PGE(2) production, and EP-1 receptor signaling prior to IL-6 production.
Highly Stable and Strongly Emitting N-Heterocyclic Carbene Platinum(II) Biaryl Complexes (2018)

C^C cyclometalated platinum(II) triplet emitters bearing electronically different N-heterocyclic carbenes-(1,3-diisopropyl-4-(trifluoromethyl)-imidazol-2-ylidene (d), 1,3-diisopropyl-benzimidazol-2-ylidene (e), and 1,3-diisopropyl-imidazol-2-ylidene (f))-as neutral ligands and biphenyl (bph) as well as its fluorinated derivative octafluorobiphenyl (oFbph) as dianionic cyclometalating ancillary ligand were synthesized and structurally characterized by <sup>1</sup>H, <sup>13</sup>C, <sup>19</sup>F, and <sup>195</sup>Pt NMR, single crystal X-ray diffraction, and HR-ESI-MS studies. Detailed photophysical investigations carried out reveal a strong influence on the excited-state properties exerted by the electronic nature of the N-heterocyclic carbenes as well as the fluorine functional groups on the ancillary biphenyl moiety. The solid-state structures of all complexes reveal a nearly planar and slightly distorted square planar geometry around the platinum center. Introduction of fluorine groups into the ligand framework leads to a less structured emission centered at 513 nm in poly(methyl methacrylate) (PMMA) thin films, compared to the highly structured emission profile of the bph analogues. Additionally, a hypsochromic shift of approximately 10-12 nm was found in the absorption as well as in the emission profiles and is attributed to the electron deficient nature of the oFbph ligand. Three wt % of the compounds doped in PMMA exhibit photoluminescence efficiencies as high as 92% in thin films. DFT and TD-DFT calculations on selected molecules revealed the charge transfer to be an admixture of intraligand (<sup>3</sup>ILCT) and metal-to-ligand charge transfer (<sup>3</sup>MLCT) and the frontier orbitals corresponding to the emission to be mainly localized on the bph and oFbph ligands, which is consistent with the observations from the photophysical investigations. The thermal stability of the complexes evaluated by thermogravimetric analysis (TGA) shows an enhanced thermal stability for the complexes bearing fluorine functional groups.
Microservice-Based Unsupervised Anomaly Detection Loop for Optical Networks (2022)

Unsupervised learning (UL) is a technique to detect previously unseen anomalies without needing labeled datasets. We propose the integration of a scalable UL-based inference component in the monitoring loop of an SDN-controlled optical network. © 2022 The Author(s)
Birefringence-controlled anti-Stokes line emission from a microstructurefiber (2004)

Microstructure fibers with a specially designed form birefringence are shown to be ideally suited for the creation of highly efficient frequency-tunable sources of short pulses in the visible range. We use unamplified 35-fs pulses of 820-nm Ti: sapphire laser radiation to demonstrate efficient generation of an intense anti-Stokes signal in an elliptical-core fused silica microstructure fiber. The central wavelength of this anti-Stokes signal can be switched between 490 and 510 nm by coupling the pump pulses into the fast and slow modes of the microstructure fiber.