gebhart/patrepeval huggingface dataset:
Optimizing Matrix Multiplication on Intel® Xeon Phi TH x200 Architecture (2017)

Matrix multiplication is ubiquitous in scientific computing. From computational science to machine learning, a large and diverse set of applications rely on the performance of general matrix-matrix multiplication (GEMM) subroutines. The Intel <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> Math Kernel Library(R) provides highly optimized GEMM subroutines that take full advantage of the available parallelism and vectorization in both Intel <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> Xeon <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> and Intel <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> Xeon Phi(TM) processors. In this paper we discuss the optimization of GEMM subroutines for the Intel <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">®</sup> Xeon Phi <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> x200 (code-named Knights Landing).
Extracellular Vesicles from Different Pneumococcal Serotypes Are Internalized by Macrophages and Induce Host Immune Responses (2021)

Bacterial extracellular vesicles are membranous ultrastructures released from the cell surface. They play important roles in the interaction between the host and the bacteria. In this work, we show how extracellular vesicles produced by four different serotypes of the important human pathogen, <i>Streptococcus pneumoniae</i>, are internalized by murine J774A.1 macrophages via fusion with the membrane of the host cells. We also evaluated the capacity of pneumococcal extracellular vesicles to elicit an immune response by macrophages. Macrophages treated with the vesicles underwent a serotype-dependent transient loss of viability, which was further reverted. The vesicles induced the production of proinflammatory cytokines, which was higher for serotype 1 and serotype 8-derived vesicles. These results demonstrate the biological activity of extracellular vesicles of clinically important pneumococcal serotypes.
Anisotropic Saturable and Excited‐State Absorption in Bulk ReS2 (2018)

Abstract The intensity‐scan (I‐scan) technique to study the polarization‐dependent, nonlinear processes in exfoliated bulk ReS 2 is utilized. The polarization‐dependent reflection and transmission of ReS 2 , from which the absorption coefficients are extracted using the transfer matrix method, are measured. Absorption coefficients under high laser peak power show a transition from saturable absorption (SA) to reverse saturable absorption when rotating the laser polarization with respect to the b ‐axis. It is found that SA and excited‐state absorption (ESA) contribute to the nonlinear optical processes. Both the SA and ESA show strong dependence on the polarization angle, which is attributed to the anisotropic optical transition probability and electronic band structure in ReS 2 . The anisotropic nonlinear optical properties of ReS 2 may find applications as saturable absorbers in lasers and optical modulators.
Broadband global acoustic cloaking experiments (2021)

Rendering objects invisible to impinging acoustic waves (i.e., acoustic cloaking), is a mature topic in the acoustic community and has diverse applications. Nevertheless, existing approaches and physical demonstrations still exhibit a large range of assumptions and limitations. Passive approaches, which surround the scattering object with a suitable (meta-)material, are usually only effective in a narrow frequency-band and cannot adapt to changing incident fields. Active approaches, which rely on the emission of a secondary wavefield that destructively interferes with the scattered field, have the potential to respond dynamically and be broad band. However, without knowledge of the primary or scattered field, the signals for the secondary sources need to be estimated from wavefield measurements in real-time. To our knowledge, this was never demonstrated beyond 1D acoustic experiments to achieve global broadband control of forward- and backscattered waves. Here, we present experimental results of active, broadband 2D acoustic cloaking without any assumptions of the primary or scattered wavefields. Using a low-latency control system and a dense array of control microphones, the signals for 20 control sources surrounding the scatterer are estimated and applied in real-time to achieve fully deterministic, global acoustic cloaking.
Enantioselective Synthesis of α-(Hetero)aryl Piperidines through Asymmetric Hydrogenation of Pyridinium Salts and Its Mechanistic Insights (2018)

Enantioselective synthesis of α-aryl and α-heteroaryl piperidines is reported. The key step is an iridium-catalyzed asymmetric hydrogenation of substituted N-benzylpyridinium salts. High levels of enantioselectivity up to 99.3:0.7 er were obtained for a range of α-heteroaryl piperidines. DFT calculations support an outersphere dissociative mechanism for the pyridinium reduction. Notably, initial protonation of the final enamine intermediate determines the stereochemical outcome of the transformation rather than hydride reduction of the resultant iminium intermediate.
In vivo confocal microendoscopy : "from the proximal bronchus down to the pulmonary acinus" (2009)

International audience
Long-haul "hut-skipped" transmission of mixed 10 &amp; 40 Gb/s signals over deployed SSMF fiber in MCI's Dallas fiber loop using hybrid Raman-erbium doped fiber amplifiers (2005)

This paper reports results of the first field-deployed "hut-skipping" line architecture using hybrid Raman-erbium doped fiber amplifiers (EDFA) and SSMF. Total transmission distance reached 640 km at 40 Gb/s with deployable lifetime margin using MCI's metro fiber ring.
Mercury-Free Automated Synthesis of Guanidinium Backbone Oligonucleotides (2019)

A new method for synthesizing deoxynucleic guanidine (DNG) oligonucleotides that uses iodine as a mild and inexpensive coupling reagent is reported. This method eliminates the need for the toxic mercury salts and pungent thiophenol historically used in methods aimed at preparing DNG oligonucleotides. This coupling strategy was readily translated to a standard MerMade 12 oligonucleotide synthesizer with coupling yields of 95% and has enabled the synthesis of a 20-mer DNG oligonucleotide, the longest DNG strand to date, in addition to mixed DNA-DNG sequences with 3-9 DNG inserts. Importantly, DNG oligonucleotides exhibit robust unaided cellular uptake as compared to unmodified oligonucleotides without apparent cellular toxicity. Taken together, these findings should greatly increase the accessibility of cationic backbone modifications and assist in the development of oligonucleotide-based drugs.
Diastereoselective Synthesis of Pyranoquinolines on Zirconium‐Containing UiO‐66 Metal‐Organic Frameworks (2016)

The Zr terephthalate MOFs UiO‐66 and UiO‐66‐NH 2 have been found to be highly diastereoselective catalysts for the synthesis of a pyrano[3,2‐ c ]quinoline through an inverse electron‐demand aza‐Diels–Alder [4+2] cycloaddition of an aryl imine (formed in situ from aniline and benzaldehyde) and 3,4‐dihydro‐2 H ‐pyran in one pot, affording the corresponding trans isomer in diastereomeric excesses of 90–95 %. The solids are stable under the reaction conditions and can be reused at least three times without significant loss of activity or diastereoselectivity.
Azaserine Affinity Labelling of γ-Glutamyl Transferase of Hydra Attenuata Without Inactivation of the Glutathione Receptor (1982)

ABSTRACT Intrigued by similar specificities of the hydra feeding receptor and γ-glutamyl transferase activity toward GSH, we examined the possibility that these two GSH-binding activities might reside in the same protein. We find that the two activities differ in specificity toward the γ-glutamyl moiety of GSH. The hydra transferase recognizes L-azaserine, L-GlU, D-GlU and L-Gln. The feeding receptor recognizes only L-GlU and L-Gln; L-azaserine and D-GlU have no effect. L-azaserine, known to bind covalently to the γ-glutamyl donor site of mammalian transferase, irreversibly inactivates hydra transferase activity. The transferase affinity label, however, has no effect on the GSH-stimulated feeding response, permitting us to demonstrate that these two activities have different GSH recognition sites and appear to reside in different proteins.
Developing a virtual reality environment for petrous bone surgery: a state-of-the-art review (2001)

The increasing power of computers has led to the development of sophisticated systems that aim to immerse the user in a virtual environment. The benefits of this type of approach to the training of physicians and surgeons are immediately apparent. Unfortunately the implementation of “virtual reality” (VR) surgical simulators has been restricted by both cost and technical limitations. The few successful systems use standardized scenarios, often derived from typical clinical data, to allow the rehearsal of procedures. In reality we would choose a system that allows us not only to practice typical cases but also to enter our own patient data and use it to define the virtual environment. In effect we want to re-write the scenario every time we use the &#13;\nenvironment and to ensure that its behavior exactly duplicates the behavior of the real tissue. If this can be achieved then VR systems can be used not only to train surgeons but also to rehearse individual procedures where variations in anatomy or pathology present specific surgical problems. The European Union has recently funded a multinational 3-year project (IERAPSI, Integrated &#13;\nEnvironment for Rehearsal and Planning of Surgical Interventions) to produce a virtual reality &#13;\nsystem for surgical training and for rehearsing individual procedures. Building the IERAPSI system will bring together a wide range of experts and combine the latest technologies to produce a true, patient specific virtual reality surgical simulator for petrous/temporal bone &#13;\nprocedures. This article presents a review of the “state of the art” technologies currently available to construct a system of this type and an overview of the functionality and specifications such a system requires.
Control Mechanisms in Standing while Simultaneously Receiving Perturbations and Active Assistance from the Robotic Upright Stand Trainer (RobUST) (2020)

In people with severe neuromotor deficits of trunk and lower extremities, rehabilitation of standing postural control is limited to rigid body support. To expand postural control training in standing, we have recently developed a Robotic Upright Stand Trainer (RobUST). In this study, we use RobUST to deliver body perturbations on the trunk while simultaneously providing direction-specific postural assistance on the pelvis. We study the effect that assist-as-needed forces has on postural imbalance on 10 able-bodied adults. We characterize postural imbalance with center of pressure (COP) variables such as excursion and root mean square COP. Surface electromyography (sEMG) was also applied to investigate muscle strategies. RobUST was designed for future training of participants with profound postural standing deficits. A common postural strategy, applied in such population, is to encourage the use of handlebars to maintain balance. Thus, we additionally investigate COP changes during trunk perturbations when ablebodied adults stood and held a handlebar. Results show that during perturbations, pelvic assistive forces decreased postural excursions and postural variability compared to quiet standing with no support. Interestingly, participants showed a similar level of postural stability, but with fewer muscle activity, with the use of an external fixed handlebar. Although, the maximum level of postural stability was observed when participants used the handlebar and received assistive forces. Our results show a significant promise of RobUST for future training of individuals with severe postural standing deficits.
Advanced sorption chillers for gas cooling (1995)

The power demand peak caused by compression climatization may be reduced by using direct-fired sorption chillers. Commercial absorption chillers reach a coefficient of performance (COP) of about 1.2, which often is not high enough to compete with compression chillers. Using high-temperature driving heat, the COP of absorption chillers can be improved by multistaging. But at high temperatures, currently used working pairs tend to cause heavy corrosion of the construction materials. Solid sorption systems as high-temperature topping cycles can avoid these problems. In a French-German cooperation a cascading triple-effect system is being realized, consisting of a bottoming double-effect machine working with LiBr/water and a topping solid-reaction machine working with NiCl{sub 2}/ammonia. A COP of 1.35 is expected in this experiment, equivalent to an improvement of about 13% compared to the industrial standard. The solid-reaction topping cycle also can be realized as a two-reaction system. Then a COP of 1.55 can be expected, which means a 28% improvement. Even quadruple-effect operation is possible with a COP of 1.8. Several possible cycle configurations are discussed in this paper. The advantages and problems of the envisaged combined cycles are presented and the principle design of the experiment is outlined.
Visualization of neonatal lung injury associated with mechanical ventilation using x-ray dark-field radiography (2016)

Mechanical ventilation (MV) and supplementation of oxygen-enriched gas, often needed in postnatal resuscitation procedures, are known to be main risk factors for impaired pulmonary development in the preterm and term neonates. Unfortunately, current imaging modalities lack in sensitivity for the detection of early stage lung injury. The present study reports a new imaging approach for diagnosis and staging of early lung injury induced by MV and hyperoxia in neonatal mice. The imaging method is based on the Talbot-Lau x-ray grating interferometry that makes it possible to quantify the x-ray small-angle scattering on the air-tissue interfaces. This so-called dark-field signal revealed increasing loss of x-ray small-angle scattering when comparing images of neonatal mice undergoing hyperoxia and MV-O2 with animals kept at room air. The changes in the dark field correlated well with histologic findings and provided superior differentiation than conventional x-ray imaging and lung function testing. The results suggest that x-ray dark-field radiography is a sensitive tool for assessing structural changes in the developing lung. In the future, with further technical developments x-ray dark-field imaging could be an important tool for earlier diagnosis and sensitive monitoring of lung injury in neonates requiring postnatal oxygen or ventilator therapy.
Disparity between prostate tumor interior versus peripheral vasculature in response to verteporfin‐mediated vascular‐targeting therapy (2008)

Photodynamic therapy (PDT) is a light-based cancer treatment modality. Here we employed both in vivo and ex vivo fluorescence imaging to visualize vascular response and tumor cell survival after verteporfin-mediated PDT designed to target tumor vasculature. EGFP-MatLyLu prostate tumor cells, transduced with EGFP using lentivirus vectors, were implanted in athymic nude mice. Immediately after PDT with different doses of verteporfin, tumor-bearing animals were injected with a fluorochrome-labeled albumin. The extravasation of fluorescent albumin along with tumor EGFP fluorescence was monitored noninvasively with a whole-body fluorescence imaging system. Ex vivo fluorescence microscopy was performed on frozen sections of tumor tissues taken at different times after treatment. Both in vivo and ex vivo imaging demonstrated that vascular-targeting PDT with verteporfin significantly increased the extravasation of fluorochrome-labeled albumin in the tumor tissue, especially in the tumor periphery. Although PDT induced substantial vascular shutdown in interior blood vessels, some peripheral tumor vessels were able to maintain perfusion function up to 24 hr after treatment. As a result, viable tumor cells were typically detected in the tumor periphery in spite of extensive tumor cell death. Our results demonstrate that vascular-targeting PDT with verteporfin causes a dose- and time-dependent increase in vascular permeability and decrease in blood perfusion. However, compared to the interior blood vessels, peripheral tumor blood vessels were found less sensitive to PDT-induced vascular shutdown, which was associated with subsequent tumor recurrence in the tumor periphery.
Development of a Synthetic Poxvirus-Based SARS-CoV-2 Vaccine (2020)

Modified Vaccinia Ankara (MVA) is a highly attenuated poxvirus vector that is widely used to develop vaccines for infectious diseases and cancer. We developed a novel vaccine platform based on a unique three-plasmid system to efficiently generate recombinant MVA vectors from chemically synthesized DNA. In response to the ongoing global pandemic caused by SARS coronavirus-2 (SARS-CoV-2), we used this novel vaccine platform to rapidly produce fully synthetic MVA (sMVA) vectors co-expressing SARS-CoV-2 spike and nucleocapsid antigens, two immunodominant antigens implicated in protective immunity. Mice immunized with these sMVA vectors developed robust SARS-CoV-2 antigen-specific humoral and cellular immune responses, including potent neutralizing antibodies. These results demonstrate the potential of a novel vaccine platform based on synthetic DNA to efficiently generate recombinant MVA vectors and to rapidly develop a multi-antigenic poxvirus-based SARS-CoV-2 vaccine candidate.
The European Lead Extraction ConTRolled (ELECTRa) study: a European Heart Rhythm Association (EHRA) Registry of Transvenous Lead Extraction Outcomes (2017)

The ELECTRa study is the largest prospective registry on TLE and confirmed the safety and efficacy of the current practice of TLE. Lead extraction was associated with a higher success rate with lower all cause complication and mortality rates in high volume compared with low volume centres.
Long term follow-up of patients with ventricular high rate events detected on remote monitoring of pacemakers (2018)

VHRE are frequently encountered on remote monitoring of pacemakers and not associated with increased risk of mortality or need for downstream device upgrade.
Detecting Goal-Oriented vs. Browsing Users Through Behavior Analysis (2023)

Understanding user personas in e-commerce is important for promoting successful online interactions. Two common personas include goal-oriented and browsing users. A goal-oriented user has the intention of completing a specific task as efficiently as possible (e.g., purchasing a product). A browsing user explores for information that will ultimately determine the next objective (e.g., to purchase or look elsewhere). A website that customizes content to a goal-oriented versus browsing user will improve the user experience and ultimately maximize conversion. In this research, we provide a methodology for differentiating between goal-oriented and browsing users by monitoring users’ behavior on the website. We conducted a study where participants were randomly assigned to either a goal-oriented task to find a product or told to simply browse the website. Based on the study’s results, we discuss suggestions to assist future human-computer interaction (HCI) researchers on how to design behavior-monitoring studies to accurately portray goal-oriented versus browsing users. We also provide insights into the need for considering the motivation of Amazon’s Mechanical Turk workers to appropriately utilize them as a sample population in future behavior-monitoring studies.
Apoptosis in Gastric Epithelial Cells Is Induced byHelicobacter pyloriand Accompanied by Increased Expression of BAK (1997)

Carriage of the bacterium H. pylori in the human stomach is associated with evidence of increased epithelial cell apoptosis. This may be of significance in the etiology of gastritis, peptic ulcers, and neoplasia. The ability of H. pylori to directly induce epithelial apoptosis was examined in vitro by fluorescence and electron microscopy, flow cytometry, and DNA fragmentation ELISA. The induction of apoptosis by H. pylori was time and concentration-dependent and inhibited by preventing direct bacterial-epithelial cell contact. Apoptosis was accompanied by increased expression of Bak, with little change in expression of other Bcl-2 family proteins. The expression of Bak was also increased in gastric biopsies from patients colonized by H. pylori. Thus, H. pylori induces gastric epithelial cell apoptosis, by a Bak-dependent pathway.
Electronic transitions in hydrogen bonded dimers of carboxylic acids in the vapour phase: an electron energy loss spectroscopic study (1989)

An electron energy loss spectroscopic study of the formic acid dimer has shown bands centred around 7.2, 8.5, 9.8, and 11.1 eV, of which the first and the third bands are assigned to n–π* transitions and the other two to π–π* transitions; similar transitions are found in the acetic acid dimer.
Optical diffusion tomography by iterative-coordinate-descent optimization in a Bayesian framework (1999)

Frequency-domain diffusion imaging uses the magnitude and phase of modulated light propagating through a highly scattering medium to reconstruct an image of the spatially dependent scattering or absorption coefficients in the medium. An inversion algorithm is formulated in a Bayesian framework and an efficient optimization technique is presented for calculating the maximum a posteriori image. In this framework the data are modeled as a complex Gaussian random vector with shot-noise statistics, and the unknown image is modeled as a generalized Gaussian Markov random field. The shot-noise statistics provide correct weighting for the measurement, and the generalized Gaussian Markov random field prior enhances the reconstruction quality and retains edges in the reconstruction. A localized relaxation algorithm, the iterative-coordinate-descent algorithm, is employed as a computationally efficient optimization technique. Numerical results for two-dimensional images show that the Bayesian framework with the new optimization scheme outperforms conventional approaches in both speed and reconstruction quality.
Nonlinear Bayesian Filtering for Denoising of Electrocardiograms Acquired in a Magnetic Resonance Environment (2010)

ECGs are currently acquired during magnetic resonance examinations. This "hostile" environment highly distorts ECG signals, due to the high-static magnetic field, RF pulses and fast switching magnetic gradients. Specific signal processing is then required since the ECG signal is used for image synchronization with heart activity (or triggering) and for patient monitoring. A new set of two magnetic field gradient (MFG) artifact reduction methods, based on ECG and MFG artifact modelings and Bayesian filtering, is herein presented and will be called Bayesian gradient artifact reduction monitoring (BAGARRE-M) and BAGARRE-triggering. These algorithms overcome the limitations of state-of-the-art methods and enable accurate processing of very noisy ECG acquisitions during MRI. Whether for triggering or monitoring purposes, the presented methods overcome state-of-the-art techniques with both better QRS detection accuracy and signal denoising quality.