gebhart/patrepeval huggingface dataset:
The GP‐protein of Marburg virus contains the region similar to the ‘immunosuppressive domain’ of oncogenic retrovirus P15E proteins (1993)

cDNA was synthesized and cloned on the template of the genomic RNA of Marburg virus (strain Popp). Recombinant plasmids with specific cDNA inserts were selected and sequenced. The length of the open reading frame encoding the GP-protein is 681 amino acids. GP-protein is proposed to be an integral membrane protein. Computer-assisted comparison of the deduced amino acid sequence with those of different viruses revealed significant homology with the GP-protein of Ebola virus and with the 'immunosuppressive domain' of the P15E envelope proteins of some oncogenic retroviruses.
Protein synthesis in distal axons is not required for axon growth in the embryonic spinal cord (2007)

It is now well established that new proteins are synthesized in the distal segments of elongating axons, where they may play an essential role in some guidance decisions. It remains unclear, however, whether distal protein synthesis also plays an essential role in axon growth per se. Previous in vitro experiments have shown that blocking protein synthesis in distal axons has no effect on the rate of axonal advance. However, because these experiments were performed in vitro and over a relatively short time period, the role of distal protein synthesis over longer periods and in a native tissue environment remained untested. Here, we tested whether protein synthesis in distal axons plays an essential role in the elongation of descending axons in the embryonic spinal cord. We developed an in situ model of the brainstem-spinal projection of the embryonic chick, and developed a split-chamber method in which inhibitors of proteins synthesis could be applied independently to cell bodies in the brainstem or to distal axons in the spinal cord. When protein synthesis was blocked in distal axons, axon growth remained robust for 2 days, which is the length of the experiment. However, when protein synthesis was blocked only in the brainstem, axonal elongation in the spinal cord ceased within 6 h. These data showed that protein synthesis in the distal axon is not essential to continue the advance of axons. Rather, essential proteins are synthesized more proximally and then transported rapidly to the distal axon.
Analytical Study of QoS-Oriented Multicast in Wireless Networks (2011)

Multicast is a very popular bandwidth-conserving technology exploited in many multimedia applications. However, existing standards of high rate wireless networks provide no error recovery mechanism (ARQ) for multicast traffic. ARQ absence in wireless networks unreliable by their nature leads to frequent packet losses, which is inappropriate for most of multimedia applications. In this paper, we study new reliable multicast mechanism proposed recently to support multimedia QoS (packet loss ratio, latency, and throughput) with various wireless technologies. This mechanism is based on the concept of multiple ACK-leaders, that is, multicast recipients responsible for acknowledging data packets. We develop analytical models of the mechanism with various leader selection schemes and use the models to study the schemes efficiency and to optimize them. Numerical results show that the novel multicast mechanism with multiple ACK-leaders can be easily tuned to meet specific QoS requirements of multimedia or any other multicast applications.
Detection of a regulatory idiotype on a spontaneous neonatal self-reactive hybridoma antibody. (1986)

To investigate the physiologic relevance of an idiotype-driven regulation of the immune system, we began a search for spontaneous self-reactive hybridomas in neonatal BALB/c mice. We sought hybridoma antibodies reactive with thyroglobulin (Tg) and expressing Id62, a recurrent idiotype with regulatory properties borne on induced adult autoantibodies to Tg. We describe herein such a neonatal Tg binding/Id62-positive monoclonal antibody (mAb) B10H2, and compare it with prototype mAb 62, an adult Tg-binding/Id62-positive mAb. Both mAb react with the same Tg epitope, as demonstrated by their abilities to totally inhibit the binding of the other to Tg. Moreover, as assessed by a double-reciprocal plot of their binding to Tg, their relative affinities for Tg are comparable. Likewise, mAb B10H2 appears idiotypically similar to mAb 62 because it totally inhibits the binding of mAb 62 to homologous anti-idiotype. Finally, as previously shown for mAb 62, mAb B10H2 expresses Id62 independently on both heavy (H) and light (L) chains, as evidenced by the immunoblot binding of a specific anti-Id62 probe to separated H and L chains. By molecular genetic analysis both antibodies appear to have made use of a member of the same VH 7183 gene family. Altogether, these findings suggest that neonatal mAb B10H2 and adult mAb 62 are very similar if not identical, and regulatory idiotype Id62 may be germline encoded. Furthermore this observation supports, in general, the concept of an idiotype-driven regulation for autoimmune responses.
Focal Points in Mass Spectrometry (1987)

Mass spectrometry has advanced with the renaissance of time-of-flight mass analysis, the use of ion traps as analyzers and reactors, the application of tandem mass spectrometers to problems in ionic reaction mechanisms and chemical analysis, and the development of new desorption ionization techniques. These developments have allowed determination of the molecular weight distributions for polymers through the 10,000-dalton range, as well as the molecular weight and partial sequence of biopolymers of similar size. Surfaces can be characterized by use of the mass, energy, and angle distributions of particles ejected by sputtering or by laser-induced desorption. Mass spectrometry has yielded new information on the kinetics of catalytic surface reactions and on the reactivity of metal clusters.
Single-mode instability in optical bistability (1989)

This paper gives a detailed description of the plane-wave Gaussian models of optical bistability and of the experimental investigations of the single-mode instability induced on a beam of sodium atoms in a cavity by an external driving field. Our goal is to provide a careful comparison of the theoretical and experimental results. We focus on the shape of the instability domain, the nature and behavior of the spontaneous output oscillations produced by the instability, and their frequency dependence on the control parameters. We carry out this comparison using both the plane-wave and Gaussian models. Our analysis shows that the latter is in good quantitative agreement with the experimental results. We investigate in detail the main assumption of the Gaussian model, namely, that the internal cavity field retains the same radial profile as the input field.
Detection of new fumonisin mycotoxins and fumonisin‐like compounds by reversed‐phase high‐performance liquid chromatography/electrospray ionization ion trap mass spectrometry (2006)

Fumonisins were produced in a rice culture infected with Fusarium verticillioides. To decrease the possibility of the formation of artifacts, the fumonisins were analyzed by reversed-phase high-performance liquid chromatography with electrospray ionization ion trap tandem mass spectrometry (RP-HPLC/ESI-IT-MS2) immediately after the extraction of the culture material without any sample clean-up. In addition to already known fumonisins, numerous new fumonisin mycotoxins and fumonisin-like compounds were detected. On the basis of the IT-MS2 data, detailed fragmentation pathways including new mechanisms were proposed for the different series of fumonisins. The retention times, the masses of the protonated molecules and of the product ions including the backbones and the characteristic neutral mass losses from the protonated molecules of the new compounds suggested their structures (applying the well-known designation): iso-FA1a,b, iso-FB1a-d, iso-FB2,3a-e, PHFB2a-c, PHFB4a-d, FB5/iso-FB5a-d, FBK1 2TCA, FBK4 2TCA, FC2, iso-FC2,3, PHFC4, FD and FBX series. The relative quantities of fumonisins and fumonisin-like compounds found in the sample extract were expressed as percentages of FB1 (0.02-100%). The backbone of the compound denoted FD contained fewer carbon atoms than the well-known fumonisins with the C19 or C20 backbone and may well be a precursor of the longer compounds. For the compounds denoted FBX (12 compounds), one or two OH groups attached to the fumonisin backbone were esterified by carboxylic acids other than tricarballylic acid, such as cis-aconitic acid, oxalylsuccinic acid and oxalylfumaric acid.
Safe Control for Nonlinear Systems with Stochastic Uncertainty via Risk Control Barrier Functions (2022)

Guaranteeing safety for robotic and autonomous systems in real-world environments is a challenging task that requires the mitigation of stochastic uncertainties. Control barrier functions have, in recent years, been widely used for enforcing safety related set-theoretic properties, such as forward invariance and reachability, of nonlinear dynamical systems. In this paper, we extend this rich framework to nonlinear discrete-time systems subject to stochastic uncertainty and propose a framework for assuring risk-sensitive safety in terms of coherent risk measures. To this end, we introduce risk control barrier functions (RCBFs), which are compositions of barrier functions and dynamic, coherent risk measures. We show that the existence of such barrier functions implies invariance in a coherent risk sense. Furthermore, we formulate conditions based on finite-time RCBFs to guarantee finite-time reachability to a desired set in the coherent risk. Conditions for risk-sensitive safety and finite-time reachability of sets composed of Boolean compositions of multiple RCBF are also formulated. We show the efficacy of the proposed method through its application to a cart-pole system in a safety-critical scenario.
Methods to determine the kinetic performance limit of contemporary chromatographic techniques (2020)

By combining separation efficiency data as a function of flow rate with the column permeability, the kinetic plot method allows to determine the limits of separation power (time vs. efficiency) of different chromatographic techniques and methods. The technique can be applied for all different types of chromatography (liquid, gas, or supercritical fluid), for different types of column morphologies (packed beds, monoliths, open tubular, micromachined columns), for pressure and electro-driven separations and in both isocratic and gradient elution mode. The present contribution gives an overview of the methods and calculations required to correctly determine these kinetic performance limits and their underlying limitations.
Low-Frequency Vibrations of Soft Colloidal Glasses (2010)

We conduct experiments on two-dimensional packings of colloidal thermosensitive hydrogel particles whose packing fraction can be tuned above the jamming transition by varying the temperature. By measuring displacement correlations between particles, we extract the vibrational properties of a corresponding "shadow" system with the same configuration and interactions, but for which the dynamics of the particles are undamped. The vibrational properties are very similar to those predicted for zero-temperature sphere packings and found in atomic and molecular glasses; there is a boson peak at low frequency that shifts to higher frequency as the system is compressed above the jamming transition.
Macromol. Chem. Phys. 4/2015 (2015)

Back Cover: Ionic liquids have been widely successful in many applications; here, 1-butyl-3-methylimidazolium tetrafluoroborate is demonstrated to be an effective initiator for electro-induced polymerization of vinyl ethers. This reaction was studied by the versatile technique Fourier-transform near-infrared spectroscopy, offering advantages over other, more complicated and more time-consuming methods. Using ionic liquids as electro-polymerization initiators has potential applications in the development of anti-corrosion coatings for metal pipes. Further details can be found in the article by F. Yang, J. L. Yang, K. J. Zheng, J. W. Stansbury, and J. Nie* on page 380.
Muscle Atrophy and Hypertrophy Signaling in Patients with Chronic Obstructive Pulmonary Disease (2007)

An increase in atrogin-1 and MuRF1 mRNA and FoxO-1 protein content was observed in the quadriceps of patients with COPD. The transcriptional regulation of atrogin-1 and MuRF1 may occur via FoxO-1, but independently of AKT. The overexpression of the muscle hypertrophic signaling pathways found in patients with COPD with muscle atrophy could represent an attempt to restore muscle mass.
Relative Height Estimation by Cross-Correlating Ground-Range Synthetic Aperture Sonar Images (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The relative height of the seafloor can be estimated by using two vertically displaced receivers. In this paper, we propose techniques to improve the accuracy of the estimated height. Our results are based on the use of synthetic aperture sonar (SAS) imaging, which implies coherent addition of complex images acquired from a moving platform. The SAS processing improves the along-track (or azimuth) resolution, as well as the signal-to-noise ratio (SNR), which in turn improves the estimated height accuracy. We show that the shift of the <emphasis emphasistype="boldital">effective</emphasis> center frequency induced by coherent, frequency-dependent scattering affect the time-delay estimates from complex cross correlations, and we propose a correction technique for broadband signals with uneven magnitude spectra. To reduce the effect of geometrical decorrelation and increase the coherence between the images, we beamform the sonar images onto an <emphasis emphasistype="bold"><emphasis>a priori</emphasis></emphasis> estimate of the seafloor height before correlating. We develop a mathematical model for the imaging geometry. Finally, we demonstrate our proposed estimators by providing relative seafloor height estimates from real aperture and SAS images, obtained during the InSAS-2000 experiment at Elba Island in Italy. In particular, we demonstrate that the SAS image quality is significantly improved by inclusion of the height estimates as <emphasis emphasistype="bold"><emphasis>a priori</emphasis></emphasis> information. </para>
Diagnostic procedures for non-small-cell lung cancer (NSCLC): recommendations of the European Expert Group (2015)

To optimise diagnosis and treatment of patients with NSCLC, it is essential to establish SOPs that are adaptable to the local situation. In addition, a continuous QC system and a local multidisciplinary tumour-type-oriented board are essential.
Reaction Development for DNA-Encoded Library Technology: Expanding the Toolkit on DNA Chemistry (2021)

Medicinal Chemistry Reviews is an outstanding 965 page volume providing timely and critical reviews of important topics in medicinal chemistry. It is provided free of charge to MEDI members in electronic format. Members can also order a print copy, for the cost of printing, shipping and handling
Efficient tracking with the bounded hough transform (2004)

The Bounded Hough Transform is introduced to track objects in a sequence of sparse range images. The method is based upon a variation of the General Hough Transform that exploits the coherence across image frames that results from the relationship between known bounds on the object's velocity and the sensor frame rate. It is extremely efficient, running in O(N) for N range data points, and effectively trades off localization precision for runtime efficiency. The method has been implemented and tested on a variety of objects, including freeform surfaces, using both simulated and real data from Lidar and stereovision sensors. The motion bounds allow the inter-frame transformation space to be reduced to a reasonable, and indeed small size, containing only 729 possible states. In a variation, the rotational subspace is projected onto the translational subspace, which further reduces the transformation space to only 54 states. Experimental results confirm that the technique works well with very sparse data, possibly comprising only tens of points per frame, and that it is also robust to measurement error and outliers.
Direct observation of 3D topological spin textures and their interactions using soft x-ray vector ptychography (2021)

Magnetic topological defects are energetically stable spin configurations characterized by symmetry breaking. Vortices and skyrmions are two well-known examples of 2D spin textures that have been actively studied for both fundamental interest and practical applications. However, experimental evidence of the 3D spin textures has been largely indirect or qualitative to date, due to the difficulty of quantitively characterizing them within nanoscale volumes. Here, we develop soft x-ray vector ptychography to quantitatively image the 3D magnetization vector field in a frustrated superlattice with 10 nm spatial resolution. By applying homotopy theory to the experimental data, we quantify the topological charge of hedgehogs and anti-hedgehogs as emergent magnetic monopoles and probe their interactions inside the frustrated superlattice. We also directly observe virtual hedgehogs and anti-hedgehogs created by magnetically inert voids. We expect that this new quantitative imaging method will open the door to study 3D topological spin textures in a broad class of magnetic materials. Our work also demonstrates that magnetically frustrated superlattices could be used as a new platform to investigate hedgehog interactions and dynamics and to exploit optimized geometries for information storage and transport applications.
In-line dispersion–precipitation method for the synthesis of metal-substituted dawsonites. Genesis of oxide materials with superior properties (2006)

Thermal activation of metal-substituted dawsonite-type compounds synthesized by a novel in-line dispersion–precipitation (ILDP) method leads to oxide materials with superior properties of component dispersion, porosity, thermal stability, and improved catalytic performance.
3D Thermal-ADI - An Efficient Chip-Level Transient Thermal Simulator (2002)

Recent studies show that the nonuniform thermal distribu-tion on the substrate and interconnects has impact on the circuit reliability and performance. Hence three-dimensional (3-D) thermal analysis is crucial to analyze these effects. In this paper, we present and develop an efficient 3-D tran-sient thermal simulator based on the alternating direction implicit (ADI) method for large scale temperature estima-tion problems. Our simulator, 3D Thermal-ADI, not only has a linear runtime and memory requirement, but also is unconditionally stable. Detailed analysis of the 3-D nonho-mogeneous cases and boundary conditions for on-chip VLSI applications are introduced and presented. Extensive exper-imental results show that our algorithm is not only orders of magnitude faster than the traditional thermal simulation algorithms, but is also highly accurate and memory efficient. The temperature profile of steady state can be reached in few iterations. The software is avaiable on the web [1].
Ynones Merge Activation/Conjugate Addition of Chalcogenoborates ArE‐Bpin (E=Se, S) (2015)

Abstract The “pull–push” effect of the Bpin moiety in ArE‐Bpin reagents (E=Se, S) is demonstrated by the Lewis acid interaction with the carbonyl group of ynones and the concomitant delivery of ArSe or ArS to the electron‐deficient alkyne with impressive stereoselectivity. The two component reactivity is carried out in methanol to generate ( Z )‐β‐(arylseleno)‐α,β‐unsaturated ketones and ( Z )‐β‐(arylsulfuro)‐α,β‐unsaturated ketones with a consensus between experimental and theoretical understanding of the mechanism. magnified image
The human-baited host decoy trap (HDT) is an efficient sampling device for exophagic malaria mosquitoes within irrigated lands in southern Malawi (2021)

Abstract Irrigation schemes provide an ideal habitat for Anopheles mosquitoes particularly during the dry season. Reliable estimates of outdoor host-seeking behaviour are needed to assess the impact of vector control options and this is particularly the case for Anopheles arabiensis which displays a wide range of behaviours that circumvent traditional indoor-insecticide based control. In this study we compared the Host Decoy Trap (HDT) with the Human Landing Catch (HLC) and Suna trap in a repeated Latin square design in two villages on an irrigated sugar estate in southern Malawi. Over the course of 18 trapping nights we caught 379 female Anopheles , the majority of which were identified as An. arabiensis . Overall, the HDT and HLC caught a similar number of Anopheles per night with both methods catching significantly higher densities than the Suna trap across both villages. Regardless of the density of Anopheles mosquitoes in each village the HLC and HDT demonstrated broadly similar sampling efficacy. We conclude that the HDT is an effective sampling device for outdoor host seeking An. arabiensis in southern Malawi. The presence of An. arabiensis in irrigated lands during the dry season poses a challenge for ongoing indoor vector control efforts.
The Phaseolus vulgaris PvTRX1h gene regulates plant hormone biosynthesis in embryogenic callus from common bean (2015)

Common bean is the most important grain legume in the human diet. Bean improvement efforts have been focused on classical breeding techniques because bean is recalcitrant to both somatic embryogenesis and in vitro regeneration. This study was undertaken to better understand the process of somatic embryogenesis in the common bean. We focused on the mechanisms by which somatic embryogenesis in plants is regulated and the interaction of these mechanisms with plant hormones. Specifically, we examined the role of the gene PvTRX1h, an ortholog of a major known histone lysine methyltransferase in plants, in somatic embryo generation. Given the problems with regeneration and transformation, we chose to develop and use regeneration-competent callus that could be successively transformed. Embryogenic calli of common bean were generated and transformed with the PvTRX1hRiA construction to down-regulate, by RNA interference, expression of the PvTRX1h gene. Plant hormone content was measured by mass spectrometry and gene expression was assessed by q-PCR. Detailed histological analysis was performed on selected transgenic embryogenic calli. It was determined that down-regulation of PvTRX1h gene was accompanied by altered concentrations of plant hormones in the calli. PvTRX1h regulated the expression of genes involved in auxin biosynthesis and embryogenic calli in which PvTRX1h was down-regulated were capable of differentiation into somatic embryos. Also, down-regulation of PvTRX1h showed increased transcript abundance of a gene coding for a second histone lysine methyltransferase, PvASHH2h. Accordingly, the PvTRX1h gene is involved in the synthesis of plant hormones in common bean callus. These results shed light on the crosstalk among histone methyltransferases and plant hormone signaling and on gene regulation during somatic embryo generation.