gebhart/patrepeval huggingface dataset:
Escherichia coli transcription factor NusG binds to 70S ribosomes (2018)

Transcription and translation are coupled processes in bacteria. A role of transcription elongation cofactor NusG in coupling has been suggested by in vitro structural studies. NMR revealed association of the NusG carboxy-terminal domain with S10 (NusE), implying a direct role for NusG as a bridge linking RNAP and the lead ribosome. Here we present the first in vitro and in vivo evidence of full-length NusG association with mature 70S ribosomes. Binding did not require accessory factors in vitro. Mutating the NusG:S10 binding interface at NusG F165 or NusE M88 and D97 residues weakened NusG:S10 association in vivo and completely abolished it in vitro, supporting the specificity of this interaction. Mutations in the binding interface increased sensitivity to chloramphenicol. This phenotype was suppressed by rpoB*35, an RNAP mutation that reduces replisome-RNAP clashes. We propose that weakened NusG:S10 interaction leads to uncoupling when translation is inhibited, with resulting RNAP backtracking, replication blocks and formation of lethal DNA double-strand breaks.
A novel, fast and sensitive supercritical fluid chromatography-tandem mass spectrometry (SFC-MS/MS) method for analysis of arachidonic acid metabolites (2018)

The development of a rapid, sensitive and reliable method for the quantification of bioactive arachidonic acid metabolites (AA-metabolites) in biological samples is quite challenging due to the minute concentration, short half-life and their structural complexity arising from different isomers. In this study, a simple, fast and environmentally friendly supercritical fluid chromatography-tandem mass spectrometry (SFC-MS/MS) method was developed and validated for simultaneous measurement of five (PGD2, PGE2, PGF2α, 6KetoPGF1α and LTB4) AA-metabolites in biological samples. These analytes were extracted by protein precipitation followed by separation and quantification. The analysis was completed within 3 minutes. The matrix matched linear calibration ranged from 0.5-100 ng mL-1 (r2 ≥ 0.995), whilst, the limit of quantification of PGD2, PGE2, PGF2α, and LTB4 was 0.5 ng mL-1 and was 2.5 ng mL-1 for 6KetoPGF1α. The interday and intraday precisions of the method were less than 15% while the accuracy of most of the analytes varied between 83 and 109%. Finally, as a proof of concept, the method was successfully applied for the determination of eicosanoids in human samples, which expands the possibility to explore physiological states, disease phenotypes, and novel biomarkers.
Thickness dependency of mechanical properties for thin-walled titanium parts manufactured by Electron Beam Melting (EBM®) (2014)

Metal powder bed additive manufacturing technologies, such as the Electron Beam Melting process, facilitate a high degree of geometric flexibility and have been demonstrated as useful production te ...
Thin infrared imaging systems through multichannel sampling (2008)

The size of infrared camera systems can be reduced by collecting low-resolution images in parallel with multiple narrow-aperture lenses rather than collecting a single high-resolution image with one wide-aperture lens. We describe an infrared imaging system that uses a three-by-three lenslet array with an optical system length of 2.3 mm and achieves Rayleigh criteria resolution comparable with a conventional single-lens system with an optical system length of 26 mm. The high-resolution final image generated by this system is reconstructed from the low-resolution images gathered by each lenslet. This is accomplished using superresolution reconstruction algorithms based on linear and nonlinear interpolation algorithms. Two implementations of the ultrathin camera are demonstrated and their performances are compared with that of a conventional infrared camera.
Indium(III)-Catalyzed Addition of Diethyl Acetamidomalonate to Terminal Alkynes:  An Efficient Approach to β-Branched α-Amino Acids (2007)

The indium(III)-catalyzed Markovnikov addition of active methylene compounds to terminal alkynes has been expanded further to include diethyl acetamidomalonate. This reaction has been studied, and a practical approach to beta-branched alpha-amino acids was developed.
Stickler: Defending Against Malicious CDNs in an Unmodified Browser (2015)

Website publishers can derive enormous performance benefits and cost savings by directing traffic to their sites through content distribution networks (CDNs). However, publishers who use CDNs today must trust their CDN not to modify the site's JavaScript, CSS, images or other media en route to end users. A CDN that violates this trust could inject ads into websites, downsample media to save bandwidth or, worse, inject malicious JavaScript code to steal user secrets it could not otherwise access. We present Stickler, a system for website publishers that guarantees the end-to-end authenticity of content served to end users while simultaneously allowing publishers to reap the benefits of CDNs. Crucially, Stickler achieves these guarantees without requiring modifications to the browser.
The Dagstuhl Beginners Guide to Reproducibility for Experimental Networking Research (2019)

Reproducibility is one of the key characteristics of good science, but hard to achieve for experimental disciplines like Internet measurements and networked systems. This guide provides advice to researchers, particularly those new to the field, on designing experiments so that their work is more likely to be reproducible and to serve as a foundation for follow-on work by others.
Supplementary Table S2 from The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints (2023)

&lt;p&gt;Supplementary Table S2. Exome sequencing of MSS tumor outlier.&lt;/p&gt;
A phase 1b/2, open label, dose-escalation study of margetuximab (M) in combination with pembrolizumab (P) in patients with relapsed/refractory advanced HER2+ gastroesophageal (GEJ) junction or gastric (G) cancer. (2017)

TPS219 Background: Prognosis for advanced HER2+ GEJ and G cancers remains poor, with median survival just beyond one year. Trastuzumab (T) in combination with chemotherapy is the initial treatment of choice, but therapeutic options targeting HER2 beyond T are poorly defined. M is an Fc-enhanced monoclonal antibody (Mab) to HER2 that recognizes with similar affinity the same epitope as T and whose Fc domain, compared to T, binds with increased affinity to the activating CD16A Fc-receptor (FcR) and decreased affinity to the inhibitory CD32B FcR. Preliminary data shows that M monotherapy has clinical activity against HER2+ tumors in GEJ and G cancer patients previously treated with T or other anti-HER2 agents. P is a Mab that blocks the interaction of the immune checkpoint molecule, PD-1, with its ligands, facilitating tumor cell elimination by releasing tumor-associated T cells from exhaustion. Monotherapy P has demonstrated remarkable and durable clinical activity in a Phase I study. Safety profiles of M and P are acceptable and non-overlapping. Methods: This study advances a chemotherapy free combination of M + P treatment for advanced HER2+ GEJ and G cancer patients. Enrolled patients will have relapsed/refractory HER2+ GEJ or G adenocarcinoma with measurable disease that has progressed on T plus first line chemotherapy. HER2+ (IHC 3+ or ISH+) will be confirmed by central review. Two dose levels of M (10mg/kg and 15mg/kg) and a fixed dose of P (200mg) will be evaluated for safety and tolerability. Patients will receive combination treatment once every 21 days for up to 24 months, until confirmed disease progression or intolerable toxicity. Dose expansion will enroll up to 60 patients, with 20 undergoing pre- and on-treatment biopsy. Response will be assessed every 6 weeks for the first 6 months and every 12 weeks thereafter per RECIST v1.1 and immune RECIST to account for response patterns observed with immunotherapies. Primary endpoint is ORR and duration of response, and secondary endpoints include PFS and OS. The study was initiated on January 2016 and is ongoing in North America and Asia. Clinical trial information: NCT02689284.
Automated detection of smuggled high-risk security threats using Deep\n Learning (2016)

The security infrastructure is ill-equipped to detect and deter the smuggling\nof non-explosive devices that enable terror attacks such as those recently\nperpetrated in western Europe. The detection of so-called "small metallic\nthreats" (SMTs) in cargo containers currently relies on statistical risk\nanalysis, intelligence reports, and visual inspection of X-ray images by\nsecurity officers. The latter is very slow and unreliable due to the difficulty\nof the task: objects potentially spanning less than 50 pixels have to be\ndetected in images containing more than 2 million pixels against very complex\nand cluttered backgrounds. In this contribution, we demonstrate for the first\ntime the use of Convolutional Neural Networks (CNNs), a type of Deep Learning,\nto automate the detection of SMTs in fullsize X-ray images of cargo containers.\nNovel approaches for dataset augmentation allowed to train CNNs from-scratch\ndespite the scarcity of data available. We report fewer than 6% false alarms\nwhen detecting 90% SMTs synthetically concealed in stream-of-commerce images,\nwhich corresponds to an improvement of over an order of magnitude over\nconventional approaches such as Bag-of-Words (BoWs). The proposed scheme offers\npotentially super-human performance for a fraction of the time it would take\nfor a security officers to carry out visual inspection (processing time is\napproximately 3.5s per container image).\n
Research report Improved bioavailability to the brain of glycosylated Met-enkephalin (2000)

The blood‐brain barrier prevents the entry of many potentially therapeutic peptide drugs to the brain. Glycosylation has shown potential as a methodology for improving delivery to the CNS. Previous studies have shown improved bioavailability and improved centrally mediated analgesia of glycosylated opioids. In this study we investigate the effect of glycosylation on the cyclic opioid peptide 2,5 6 7 6 [D-Cys ,Ser ,Gly ] enkephalin. The peptide was glycosylated on the Ser via an O-linkage with various sugar moieties and alignments. The peptides were then investigated for receptor binding, physiochemical attributes, in situ brain uptake in female Sprague‐Dawley rats and antinociception in male ICR mice. Glycosylation resulted in a slight decrease in affinity to the d-opioid receptor, and mixed effect on binding to the m-opioid receptor. There was a significant decrease in lipophilicity resulting from glycosylation and a slight reduction in binding to bovine serum albumin. In situ perfusion showed that brain uptake was improved by up to 98% for several of the glycosylated peptides, and the nociceptive profiles of the peptides, in general, followed the rank order of peptide entry to the brain with up to a 39-fold increase in A.U.C. © 2000 Elsevier Science B.V. All rights reserved. Theme: Cellular and molecular biology Topic: Blood‐brain barrier
Role of incorporated hydrogen on performance and photo-bias instability of indium gallium zinc oxide thin film transistors (2012)

This study examined the effects of hydrogen incorporation in amorphous indium gallium zinc oxide (IGZO) on the performance and photo-bias stability of the resulting thin-film transistors (TFTs). It was found that the threshold voltage of IGZO TFTs was negatively shifted without significant loss of the field-effect mobility and ION/OFF ratio with increasing hydrogen concentration, suggesting that interstitial hydrogen can act as a shallow donor. The hydrogen-doped device, however, showed more negative bias illumination stress (NBIS) instability than the undoped device, which cannot be explained by the simple shallow donor model. This NBIS-induced degradation might be associated with the increased tailing state distribution, which may stem from a hydrogen-related complex defect or compensation.
Une approche variationnelle pour la reconnaissance d'objets (1989)

Dans cette these, nous proposons une formulation variationnelle du probleme de la reconnaissance d'objets qui nous permet, d'une part, d'unifier les differents elements de notre approche dans un meme cadre theorique et, d'autre part, de developper des methodes de calcul realistes pour le traitement d'images complexes. Nous decrivons les objets en termes d'un langage qui inclut les contraintes tant photometriques que geometriques ou semantiques auxquelles ces objets et leur apparence dans l'image sont soumis. Nous definissons un critere de nature statistique qui mesure la qualite d'une telle description; reconnaitre les objets equivaut alors a trouver la description optimale de l'image en termes de notre langage. Nous avons valide notre approche dans le cadre de la reconnaissance de routes et bâtiments dans des images aeriennes et avons implemente un systeme qui identifie avec succes la majorite des objets cible dans des images difficiles. Dans le premier chapitre nous introduisons et motivons notre approche. Nous presentons ensuite des articles qui documentent son evolution. Dans le dernier chapitre, nous decrivons en detail notre fonction (objectif) ? et les procedures d'optimisation que nous avons implementees.
Self-trapping in a weakly saturated medium (1989)

The phenomenon of self-trapping has been extensively studied in the past for both cubic and saturable nonlinearity. 1 In this paper, by using a modified nonlinear Schrodinger equation, we analyze the possibility of a self-trapped beam propagating in a weakly saturated amplifying/absorb- ing medium. We consider the case of only one transverse dimension (for example, a semiconductor laser medium or a nonlinear planar waveguide structure such as the one used by Maneuf and Reynaud 2 for their recent observation of spatial solitary waves). A simple exact analytical solution is obtained with a sechlike amplitude profile and a nonuniform phase front. Near this axis, this wavefront is parabolic but becomes progressively linear off-axis. Selftrapping is also predicted for a defocusing nonlinearity. The stability of the solution is investigated by using the adiabatic approximation as well as by solving the equation of propagation numerically.
Domains of quality of life affecting elderly patients with hand osteoarthritis: a qualitative study in the Asian perspective (2016)

The domains of concepts important to people with HOA in an Asian socio-cultural context are not fully represented in the most commonly used instruments. Further studies on the selection of main domains relevant to HOA patients are necessary.
Smart Grid Research: Vehicular - IEEE Smart Grid Vision for Vehicular Technology: 2030 and Beyond (2014)

Vehicle electrification is envisioned to be a significant component of the forthcoming Smart Grid. In this document, a Smart Grid vision of electric vehicle technology for the next 30 years and beyond is presented from six different perspectives: 1) social, economic, and political implications, 2) intelligent vehicles and grid interaction, 3) infrastructure, 4) travelers, 5) communications, and 6) systems, operations, and scenarios.
Non-Invasive Transcranial Brain Therapy Guided by CT Scans: an In Vivo Monkey Study (2007)

Brain therapy using focused ultrasound remains very limited due to the strong aberrations induced by the skull. A minimally invasive technique using time‐reversal was validated recently in‐vivo on 20 sheeps. But such a technique requires a hydrophone at the focal point for the first step of the time‐reversal procedure. A completely noninvasive therapy requires a reliable model of the acoustic properties of the skull in order to simulate this first step. 3‐D simulations based on high‐resolution CT images of a skull have been successfully performed with a finite differences code developed in our Laboratory. Thanks to the skull porosity, directly extracted from the CT images, we reconstructed acoustic speed, density and absorption maps and performed the computation. Computed wavefronts are in good agreement with experimental wavefronts acquired through the same part of the skull and this technique was validated in‐vitro in the laboratory. A stereotactic frame has been designed and built in order to perform non invasive transcranial focusing in vivo. Here we describe all the steps of our new protocol, from the CT‐scans to the therapy treatment and the first in vivo results on a monkey will be presented. This protocol is based on protocols already existing in radiotherapy.
High Resolution Molecular Imaging with Čerenkov-Excited Luminscence Scanned Imaging (ČELSI) (2015)

Using high energy x-rays to excite Čerenkov emission in tissue, it is possible to achieve high resolution optical molecular imaging at depths of a few centimeters, while delivering low radiation doses.
Comparability of Raman Spectroscopic Configurations: A Large Scale Cross-Laboratory Study (2020)

The variable configuration of Raman spectroscopic platforms is one of the major obstacles in establishing Raman spectroscopy as a valuable physicochemical method within real-world scenarios such as clinical diagnostics. For such real world applications like diagnostic classification, the models should ideally be usable to predict data from different setups. Whether it is done by training a rugged model with data from many setups or by a primary-replica strategy where models are developed on a 'primary' setup and the test data are generated on 'replicate' setups, this is only possible if the Raman spectra from different setups are consistent, reproducible, and comparable. However, Raman spectra can be highly sensitive to the measurement conditions, and they change from setup to setup even if the same samples are measured. Although increasingly recognized as an issue, the dependence of the Raman spectra on the instrumental configuration is far from being fully understood and great effort is needed to address the resulting spectral variations and to correct for them. To make the severity of the situation clear, we present a round robin experiment investigating the comparability of 35 Raman spectroscopic devices with different configurations in 15 institutes within seven European countries from the COST (European Cooperation in Science and Technology) action Raman4clinics. The experiment was developed in a fashion that allows various instrumental configurations ranging from highly confocal setups to fibre-optic based systems with different excitation wavelengths. We illustrate the spectral variations caused by the instrumental configurations from the perspectives of peak shifts, intensity variations, peak widths, and noise levels. We conclude this contribution with recommendations that may help to improve the inter-laboratory studies.
Detailed mapping of a congenital heart disease gene in chromosome 3p25 (2000)

Distal deletion of chromosome 3p25-pter (3p- syndrome) produces a distinct clinical syndrome characterised by low birth weight, mental retardation, telecanthus, ptosis, and micrognathia. Congenital heart disease (CHD), typically atrioventricular septal defect (AVSD), occurs in about a third of patients. In total, approximately 25 cases of 3p- syndrome have been reported world wide. We previously analysed five cases and showed that (1) the 3p25-pter deletions were variable and (2) the presence of CHD correlated with the proximal extent of the deletion, mapping a CHD gene centromeric to D3S18. To define the molecular pathology of the 3p- syndrome further, we have now proceeded to analyse the deletion region in a total of 10 patients (five with CHD), using a combination of FISH analysis and polymorphic markers, for up to 21 loci from 3p25-p26. These additional investigations further supported the location of an AVSD locus within 3p25 and refined its localisation. Thus, the critical region was reduced to an interval between D3S1263 and D3S3594. Candidate 3p25 CHD genes, such as PMCA2 (ATP2B2), fibulin 2, TIMP4, and Sec13R, were shown to map outside the target interval. Additionally, the critical region for the phenotypic features of the 3p- phenotype was mapped to D3S1317 to D3S17 (19-21 cM). These findings will accelerate the identification of the 3p25 CHD susceptibility locus and facilitate investigations of the role of this locus in non-syndromic AVSDs, which are a common form of familial and isolated CHD.
Optics development for micro-cell based CPV modules (2011)

Semprius' two-stage pupil imaging concentrated photovoltaic (CPV) module design incorporates extremely costeffective glass ball secondary lenses in addition to plano-convex primary lens arrays. Optimization of the optical concentrator design involves modeling the illumination uniformity of the primary aperture (the 'pupil') on the multijunction solar cell in response to the secondary lens index, diameter, surface quality, location, and tolerance offsets. We reconcile our theoretical model with experimental results from a single fully adjustable 'concentrating unit cell', and we thereby create a robust model for design updates, for tolerance and sensitivity modeling, and for prediction of full module and on-sun tracker performance based on receiver placement relative to our primary lens array. In this paper, we discuss the rationale behind our optics approach, our criteria for optimizing our optics, and our tolerancing approach. Then we discuss our experimental approach, including our universally adjustable 'concentrating unit' fixture, our light source, and our primary and secondary optics. We show sensitivity curves of our 'concentrating unit' performance to receiver placement, and ball lens size. We reconcile these with our ray-traced model, and, finally, we show predicted module performance based on receiver tolerance data and receiver wiring in the module using a parameter driven high level circuit model.
ASIC design and data communications for the Boston retinal prosthesis (2012)

We report on the design and testing of a custom application-specific integrated circuit (ASIC) that has been developed as a key component of the Boston retinal prosthesis. This device has been designed for patients who are blind due to age-related macular degeneration or retinitis pigmentosa. Key safety and communication features of the low-power ASIC are described, as are the highly configurable neural stimulation current waveforms that are delivered to its greater than 256 output electrodes. The ASIC was created using an 0.18 micron Si fabrication process utilizing standard 1.8 volt CMOS transistors as well as 20 volt lightly doped drain FETs. The communication system receives frequency-shift keyed inputs at 6.78 MHz from an implanted secondary coil, and transmits data back to the control unit through a lower-bandwidth channel that employs load-shift keying. The design's safety is ensured by on-board electrode voltage monitoring, stimulus charge limits, error checking of data transmitted to the implant, and comprehensive self-test and performance monitoring features. Each stimulus cycle is initiated by a transmitted word with a full 32-bit error check code. Taken together, these features allow researchers to safely and wirelessly tailor retinal stimulation and vision recovery for each patient.