gebhart/patrepeval huggingface dataset:
A New Strategy to Photoactivate Green Fluorescent Protein (2010)

Eine glänzende Idee: Ein photoaktivierbares GFP wurde durch Mutagenese des Fluorophors Tyrosin zu einem photoaktivierbaren o-Nitrobenzyltyrosin entwickelt. Dieses Protein ist praktisch nichtfluoreszierend, und bei Bestrahlung mit Licht von 365 nm steigt die Fluoreszenz fast um den Faktor 100. Kristallographie und zeitaufgelöste UV/Vis-Spektroskopie geben Einblick in den Mechanismus der Fluoreszenzlöschung, der wohl ein photoinduzierter Elektronentransfer auf die Nitrobenzylgruppe zugrunde liegt. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Two Models for Noisy Feedback in MIMO Channels (2008)

Two distinct models of feedback, suited for FDD (Frequency Division Duplex) and TDD (Frequency Division Duplex) systems respectively, have been widely studied in the literature. In this paper, we compare these two models of feedback in terms of the diversity multiplexing tradeoff for varying amount of channel state information at the terminals. We find that, when all imperfections are accounted for, the maximum achievable diversity order in FDD systems matches the diversity order in TDD systems. TDD systems achieve better diversity order at higher multiplexing gains. In FDD systems, the maximum diversity order can be achieved with just a single bit of feedback. Additional bits of feedback (perfect or imperfect) do not affect the diversity order if the receiver does not know the channel state information.
Single-cell stable isotope probing in microbial ecology (2022)

Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.
Task-related activity in sensorimotor cortex in Parkinson's disease and essential tremor: changes in beta and gamma bands (2015)

In Parkinson's disease patients in the OFF medication state, basal ganglia local field potentials exhibit changes in beta and gamma oscillations that correlate with reduced voluntary movement, manifested as rigidity and akinesia. However, magnetoencephalography and low-resolution electrocorticography (ECoG) studies in Parkinson's patients suggest that changes in sensorimotor cortical oscillations differ from those of the basal ganglia. To more clearly define the role of sensorimotor cortex oscillatory activity in Parkinson's, we performed intraoperative, high-resolution (4 mm spacing) ECoG recordings in 10 Parkinson's patients (2 females, ages 47-72) undergoing deep brain stimulation (DBS) lead placement in the awake, OFF medication state. We analyzed ECoG potentials during a computer-controlled reaching task designed to separate movement preparation from movement execution and compared findings to similar invasive recordings in eight patients with essential tremor (3 females, ages 59-78), a condition not associated with rigidity or akinesia. We show that (1) cortical beta spectral power at rest does not differ between Parkinson's and essential tremor patients (p = 0.85), (2) early motor preparation in Parkinson's patients in the OFF medication state is associated with a larger beta desynchronization compared to patients with essential tremor (p = 0.0061), and (3) cortical broadband gamma power is elevated in Parkinson's patients compared to essential tremor patients during both rest and task recordings (p = 0.004). Our findings suggest an oscillatory profile in sensorimotor cortex of Parkinson's patients that, in contrast to the basal ganglia, may act to promote movement to oppose the anti-kinetic bias of the dopamine-depleted state.
ChemInform Abstract: Bio‐Inspired Synthetic Pathways and Beyond: Integrative Chemistry (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Organic Vapor-Phase Deposition* (2009)

Shadow Masks .................................................................................. 41 2.5.4 The Breakdown of the Continuous Medium Assumptionfor Kn &lt; 10 ..........................................................................................42 2.5.5 Modeling of Gas Transport in Confi ned Geometries .................43 2.5.6 Monte-Carlo Simulation of OVPD through Apertures ..............44
Comparison of local feature descriptors for mobile visual search (2010)

We evaluate the performance of MPEG-7 image signatures, Compressed Histogram of Gradients descriptor (CHoG) and Scale Invariant Feature Transform (SIFT) descriptors for mobile visual search applications. We observe that SIFT and CHoG outperform MPEG-7 image signatures greatly in terms of feature-level Receiver Operating Characteristic (ROC) performance and image-level matching. Moreover, CHoG descriptors demonstrate such gains while being comparable with MPEG-7 image signatures in bit-rate.
Low Loss Optical Waveguides in the Blue and Ultraviolet Spectrum (2018)

We present a low-loss waveguide platform in the visible and near ultraviolet regime. Fully-etched waveguides based on atomic layer deposition (ALD) of aluminum oxide operate in a single transverse mode with $<$3 dB/cm propagation loss at a wavelength of 371 nm. Ring resonators with intrinsic quality factors exceeding 470,000 are demonstrated at 405 nm, and the thermo optic coefficient of ALD aluminum oxide is estimated. Absorption loss is sufficiently low to allow on-resonance operation with intra-cavity powers up to 12.5 mW. Experimental and simulated data suggests the propagation loss is dominated by sidewall roughness, suggesting lower loss in the blue and UV is achievable.
All-Printed Thin-Film Transistor Based on Purified Single-Walled Carbon Nanotubes with Linear Response (2011)

We report an all-printed thin-film transistor (TFT) on a polyimide substrate with linear transconductance response. The TFT is based on our purified single-walled carbon nanotube (SWCNT) solution that is primarily consists of semiconducting carbon nanotubes (CNTs) with low metal impurities. The all-printed TFT exhibits a high ON/OFF ratio of around 10 3 and bias-independent transconductance over a certain gate bias range. Such bias-independent transconductance property is different from that of conventional metal-oxide-semiconductor field-effect transistors (MOSFETs) due to the special band structure and the one-dimensional (1D) quantum confined density of state (DOS) of CNTs. The bias-independent transconductance promises modulation linearity for analog electronics.
Identification of Stabilizing Mutations in an H5 Hemagglutinin Influenza Virus Protein (2015)

We have identified mutations in HA that increase its heat stability and affect the pH that triggers an irreversible conformational change (a prerequisite for virus infectivity). These mutations were identified in the genetic background of an H5 HA protein that was mutated to bind to human cells. The ability to bind to human-type receptors, together with physical stability and an altered pH threshold for HA conformational change, may facilitate avian influenza virus transmission via respiratory droplets in mammals.
Modéliser les processus de création de la musique avec dispositif numérique : représenter pour rejouer et préserver les œuvres contemporaines (2012)

National audience
Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases (2019)

Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class <i>Agaricomycetes</i>, associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, <i>Ls</i>AA9B, a naturally occurring protein from <i>Lentinus similis</i> The <i>Ls</i>AA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of <i>Ls</i>AA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass.
Secondary Amyloidosis Presenting as Ischemic Proctitis (2021)

A 49-year-old man presented with abdominal pain and rectal bleeding for two days associated with a 50-pound unintentional weight loss. History was notable for hypertension, chronic kidney disease, obesity, gout, and acute cholecystitis status post cholecystectomy. Computed tomography (CT) of the abdomen and pelvis showed rectal wall thickening. Colonoscopy showed proctitis with superficial ulcerations. In the setting of renal insufficiency, malabsorption, and low-voltage QRS complexes on electrocardiogram (ECG), amyloidosis was considered in the differential diagnosis. Rectal and renal biopsies with subsequent retrospective staining of gallbladder tissue confirmed amyloid deposition. Gastrointestinal involvement of amyloidosis is relatively uncommon. Particularly, amyloid deposition in the gallbladder and rectum is very rare. The development of AA amyloidosis in our patient may have been related to gout, obesity, and the presence of a heterozygous complex variant for the MEFV (familial Mediterranean fever) gene. Awareness of this atypical presentation of amyloidosis is important, as additional staining of biopsy samples is necessary, and diagnosis allows for directed treatment.
Spotlight SAR Data Collection Geometry from ECEF Coordinates (2020)

High-performance spotlight Synthetic Aperture Radar (SAR) requires measurement of the radars motion during the synthetic aperture. A convenient coordinate frame for motion measurement is often not the convenient coordinate frame for motion compensation during the SAR data generation and image formation processing. A convenient frame for radar motion measurement is the Earth-Centered Earth-Fixed (ECEF) coordinate frame, whereas spotlight SAR processing typically require s polar coordinates from a selected Scene Reference Point (SRP). This report presents the conversion from ECEF coordinates to appropriate parameters for SAR processing.
Shear thinning behavior of heavy oil samples: Laboratory measurements and modeling (2008)

Viscoelastic measurements of four heavy and extra‐heavy oil samples were carried out to analyze the dependence of complex viscosity, loss and storage modulus with temperature and frequency. The dynamic rheological tests showed a shear thinning phenomenon typical of non‐Newtonian fluids, highly pronounced for seismic and sonic frequencies and for temperatures below 50°C. The Power‐Law method that explains the shear thinning behavior was modified to incorporate the liquid crystal theory and the viscosity dependence on temperature based on the concept of activation energy. An expression was derived to predict complex viscosity based on frequency and temperature changes.
Capacity region of multi-resolution streaming in peer-to-peer networks (2013)

We consider multi-resolution streaming in fully-connected peer-to-peer networks, where transmission rates are constrained by arbitrarily specified upload capacities of the source and peers. We fully characterize the capacity region of rate vectors achievable with arbitrary coding, where an achievable rate vector describes a vector of throughputs of the different resolutions that can be supported by the network. We then prove that all rate vectors in the capacity region can be achieved using pure routing strategies. This shows that coding has no capacity advantage over routing in this scenario.
MRD Detection in B-Cell Non-Hodgkin Lymphomas Using Ig Gene Rearrangements and Chromosomal Translocations as Targets for Real-Time Quantitative PCR (2012)

Minimal residual disease (MRD) diagnostics is of high clinical relevance in patients with indolent B-cell Non-Hodgkin lymphomas (B-NHL) and serves as a surrogate parameter to evaluate treatment effectiveness and long-term prognosis. MRD diagnostics performed by real-time quantitative PCR (RQ-PCR) is the gold-standard and currently the most sensitive and the most broadly applied method in follicular lymphoma (FL) and mantle cell lymphoma (MCL). RQ-PCR analysis of the junctional regions of the rearranged immunoglobulin heavy-chain gene (IgH) serves as the most broadly applicable MRD target in B-NHL (∼80%). Chromosomal translocations as t(14;18) translocation in FL and t(11;14) translocation in MCL can be used in selected lymphoma subtypes. In patients with B-cell chronic lymphocytic leukemia, both flow-cytometry as well as RQ-PCR are equally suitable for MRD assessment as long as a sensitivity of ≤10(-4) shall be achieved.MRD diagnostics targeting the IgH gene is complex and requires extensive knowledge and experience because the junctional regions of each lymphoma have to be identified before the patient-specific RQ-PCR assays can be designed for MRD monitoring. Furthermore, somatic mutations of the IgH region occurring during B-cell development of germinal center and post-germinal center lymphomas may hamper appropriate primer binding leading to false negative results. The translocations mentioned above have the advantage that consensus forward primers and probes, both placed in the breakpoint regions of chromosome 18 in FL and chromosome 11 in MCL, can be used in combination with a reverse primer placed in the IgH joining region of chromosome 14. RQ-PCR-based methods can reach a good sensitivity (≤10(-4)). This chapter provides all relevant background information and technical aspects for the complete laboratory process from detection of the clonal IgH gene rearrangement and the chromosomal translocations at diagnosis to the actual MRD measurements in clinical follow-up samples of B-NHL. However, it should be noted that MRD diagnostics for clinical treatment protocols has to be accompanied by regular international quality control rounds to ensure the reproducibility and reliability of the MRD results.
Advances in Tip-Enhanced Spectroscopy from Optical Nano-Crystallography to Ultrafast Spectroscopy (2011)

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.
Rücktitelbild: Promoted Fixation of Molecular Nitrogen with Surface Oxygen Vacancies on Plasmon‐Enhanced TiO2 Photoelectrodes (Angew. Chem. 19/2018) (2018)

Die Ammoniak-Synthese …… durch photoelektrochemische N2-Reduktion benötigt nur wenig Energie und gelingt bei Umgebungsbedingungen oder leicht erhöhten Temperaturen und Drücken. O-Fehlstellen an der Oberfläche haben großes Potenzial für die N2-Adsorption und -Aktivierung, ihre Einführung ohne Veränderung der Materialeigenschaften ist aber nach wie vor eine Herausforderung. In ihrer Zuschrift auf S. 5380 zeigen J. Gong und Mitarbeiter, wie O-Fehlstellen in äußeren Schichten von dünnen Filmen aus amorphem TiO2 die Reduktion von N2 zu NH3 vereinfachen.
Patch map: A benchmark for occupancy grid algorithm evaluation (2012)

Mobile robots have been using two-dimensional discrete occupancy grid maps for more than 25 years to represent a continuous environment. Occupancy grids discretize the environment into a grid of cells and seek to determine the occupancy of each cell. These maps are generally used to determine the degree to which each cell is occupied.
Synthesis of Silicon-Based Infrared Semiconductors in the Ge−Sn System Using Molecular Chemistry Methods (2001)

Growth reactions based on a newly developed deuterium-stabilized Sn hydride [(Ph)SnD(3)] with Ge(2)H(6) produce a new family of Ge-Sn semiconductors with tunable band gaps and potential applications in high-speed, high-efficiency infrared optoelectronics. Metastable diamond-cubic films of Ge(1-x)Sn(x) alloys are created by chemical vapor deposition at 350 degrees C on Si(100). These exhibit unprecedented thermal stability and superior crystallinity despite the 17% lattice mismatch between the constituent materials. The composition, crystal structure, electronic structure, and optical properties of these materials are characterized by Rutherford backscattering, high-resolution electron microscopy, and X-ray diffraction, as well as Raman, IR, and spectroscopic ellipsometry. Electron diffraction reveals monocrystalline and perfectly epitaxial layers with lattice constants intermediate between those of Ge and alpha-Sn. X-ray diffraction in the theta-2theta mode shows well-defined peaks corresponding to random alloys, and in-plane rocking scans of the (004) reflection confirm a tightly aligned spread of the crystal mosaics. RBS ion-channeling including angular scans confirm that Sn occupies substitutional lattice sites and also provide evidence of local ordering of the elements with increasing Sn concentration. The Raman spectra show bands corresponding to Ge-Ge and Sn-Ge vibrations with frequencies consistent with random tetrahedral alloys. Resonance Raman and ellipsometry spectra indicate a band-gap reduction relative to Ge. The IR transmission spectra suggest that the band gap decreases monotonically with increasing Sn fraction. The synthesis, characterization, and gas-phase electron diffraction structure of (Ph)SnD(3) are also reported.
Evaluation of Multi-Walled Carbon Nanotube Scaffolds for Osteoblast Growth (2007)

The development of carbon nanotubes (CNTs) for tissue engineering and regenerative medicine has attracted a great deal of attention. Multi‐walled carbon nanotube (MWCNT) scaffolds have been used for the successful proliferation of osteoblasts. In this study, osteoblast cells were cultured on prepared scaffolds in vitro and the characteristics of each scaffold were evaluated in an effort to investigate the effect of surface properties such as roughness and the adsorption of albumin on MWCNT scaffolds with different diameters.
Movie S5 from Induction of Telomere Dysfunction Prolongs Disease Control of Therapy-Resistant Melanoma (2023)

&lt;p&gt;Time-lapse imaging of A375(Fucci2)-CR cells treated with the control.&lt;/p&gt;
Toxicity and Biodistribution of a First-Generation Recombinant Adenoviral Vector, Encoding Aquaporin-1, After Retroductal Delivery to a Single Rat Submandibular Gland (2006)

Before conducting a phase 1/2 clinical trial of a serotype 5 adenovirus encoding human aquaporin-1 (AdhAQP1) for the treatment of radiation-damaged salivary glands, we have conducted a detailed toxicity and biodistribution study in adult rats. AdhAQP1 (2x108-2x1011 particles) was delivered to a single submandibular gland by retroductal cannulation. Administration of this vector resulted in no animal mortality or morbidities, and no adverse signs of clinical toxicity. In addition, over the 92-day time course of the study, with both male and female rats, there were no consistent treatment-related changes in serum indicators of hepatic, renal, and cardiac functions. Importantly, we also observed no vector-associated effects on either water consumption by, or hematocrit levels in, study animals. However, three suggestive mild gender-related response differences were seen. Female, but not male, rats exhibited small reductions in food consumption (10-15%) and body weight gain (5-10%), and evidence of persistent inflammation, after vector treatment. These were vector, but not dose, related. Three days after delivery of 2x1011 particles of AdhAQP1, vector was detected primarily in the targeted gland; 9 of 10 samples from the targeted gland were positive, whereas only 5 of 90 nonoral samples were positive. There was no evidence of the generation of replication-competent adenovirus in saliva or blood samples. In aggregate, these findings show that localized delivery of AdhAQP1 to salivary glands appears to occur without significant toxicity.
Effect of Image Artifacts, Organ Motion, and Poor Segmentation on the Reliability and Accuracy of Three-Dimensional Chamfer Matching (1997)

Our objective was to investigate the influence of various image artifacts on three-dimensional chamfer matching. A number of artificial and natural artifacts (for instance, as a model for CT-MR matching) were introduced or suppressed in pairs of pelvic CT scans, and a perturbation study was used to determine reliability and accuracy in a well known ground truth situation. in general, chamfer matching is extremely robust against missing data, low resolution, and poor segmentation of the images. in the presence of artifacts, minimization of the average distance outperformed minimization of the root-mean-square distance. Outliers in the scan from which the point list is obtained must be avoided. For example, rotation of the femurs reduces CT-CT registration accuracy by 1–2 mm. The robustness of chamfer matching is confirmed by a limited perturbation study of CT-MR registration for the pelvic region. in conclusion, chamfer matching is extremely accurate and reliable if outliers are avoided in the scan from which the point list is derived, and the average distance is used as a cost function.