gebhart/patrepeval huggingface dataset:
Nanobody-Based Quantification of GTP-Bound RHO Conformation Reveals RHOA and RHOC Activation Independent from Their Total Expression in Breast Cancer (2021)

As key regulators of the actin cytoskeleton, RHO GTPase expression and/or activity are deregulated in tumorigenesis and metastatic progression. Nevertheless, the vast majority of experiments supporting this conclusion was conducted on cell lines but not on human tumor samples that were mostly studied at the expression level only. Up to now, the activity of RHO proteins remains poorly investigated in human tumors. In this article, we present the development of a robust nanobody-based ELISA assay, with a high selectivity that allows an accurate quantification of RHO protein GTP-bound state in the nanomolar range (1 nM; 20 μg/L), not only in cell lines after treatment but also in tumor samples. Of note, we present here a fine analysis of RHOA-like and RAC1 active state in tumor samples with the most comprehensive study of RHOA-GTP and RHOC-GTP levels performed on human breast tumor samples. We revealed increased GTP-bound RHOA and RHOC protein activities in tumors compared to normal tissue counterparts, and demonstrated that the RHO active state and RHO expression are two independent parameters among different breast cancer subtypes. Our results further highlight the regulation of RHO protein activation in tumor samples and the relevance of directly studying RHO GTPase activities involvement in molecular pathways.
Deep Neural Networks as Gaussian Processes (2017)

It has long been known that a single-layer fully-connected neural network with an i.i.d. prior over its parameters is equivalent to a Gaussian process (GP), in the limit of infinite network width. This correspondence enables exact Bayesian inference for infinite width neural networks on regression tasks by means of evaluating the corresponding GP. Recently, kernel functions which mimic multi-layer random neural networks have been developed, but only outside of a Bayesian framework. As such, previous work has not identified that these kernels can be used as covariance functions for GPs and allow fully Bayesian prediction with a deep neural network. In this work, we derive the exact equivalence between infinitely wide deep networks and GPs. We further develop a computationally efficient pipeline to compute the covariance function for these GPs. We then use the resulting GPs to perform Bayesian inference for wide deep neural networks on MNIST and CIFAR-10. We observe that trained neural network accuracy approaches that of the corresponding GP with increasing layer width, and that the GP uncertainty is strongly correlated with trained network prediction error. We further find that test performance increases as finite-width trained networks are made wider and more similar to a GP, and thus that GP predictions typically outperform those of finite-width networks. Finally we connect the performance of these GPs to the recent theory of signal propagation in random neural networks.
The Adaptive Projection Forest: Using adjustable exclusion and parallelism in metric space indexes (2014)

This paper introduces an indexing method for searching diverse data types that is easily parallelizable for use with large data sets. This method, the Adaptive Projection Forest (APF) is a partition-based metric-space indexing method, which provides generic retrieval solutions for data sets for which similarity is defined by a metric-distance function. The APF is uniquely suited to alleviate problems typically encountered in metric-space indexing because it adaptively incorporates exclusion, a method that removes data near a partition boundary and creates multiple trees for use in parallel computing. The use of exclusion allows the index to be more effective when data falls near partition boundaries, where traditional pruning is not always possible. The APF's use of exclusion also allows it to have greater success in parallel environments, meaning that the APF algorithm can be more effectively used on large data sets with diverse data types. In the APF index, the proportion of excluded data is adjusted dynamically at each index node by locally determining the dimension, k, of the projection of the metric space onto the real numbers. The algorithm, which provides asymptotic algorithmic guarantees for nearest neighbor search, is presented along with a parallel implementation of the APF. Across a suite of real-world and synthetic benchmarks the APF demonstrates favorable empirical results, measured in number of calculations, when compared with the emVP, MVP, and SA indexes. Experiments also reveal that number of calculations can be minimized when a critical parameter, the width of the exclusion region, is set much smaller than the value suggested by asymptotic algorithmic analysis.
On the linear dynamic range of integrated electrooptical modulators (1986)

Linear dynamic range depends on both the nonlinearities of electrooptic modulators and the system details. Nonlinearities of electrooptical modulators should be specified by a Taylor series representation of their output versus input characteristic, not by their linear dynamic range. Several examples of the linear dynamic range in different types of systems are given.
Optical component modelling and circuit simulation using SERENADE suite (2002)

Conférence URSI-GA 2002, Maastricht.
Phenotypic defects in Gamamrus fossarum (Amphipoda) exposed to fenoxycarb as embryo (2017)

The use of embryos in ecotoxicology can be useful not only for understanding the mode of action of a toxic compound but also to detect subtle toxic effects as embryos could be the most vulnerable stages within the life history of an organism. Despite these advantages, ecotoxicological studies dealing with embryos of aquatic arthropods remained rare and many use hatching success as the endpoint of interest. The toxicity of environmental compounds in early life stages is of importance since embryo toxicity has been shown implicated in population decline. Since ontogeny is under the regulation of numerous morphogenetic factors and endocrine signaling pathways, toxic exposure experienced during embryogenesis could cause an increase of phenotypic defects in new-born individuals. This is the hypothesis we tested in the present study. For that purpose, embryos of the amphipod Gammarus fossarum were directly exposed throughout the entire embryo cycle to increasing fenoxycarb concentrations. Fenoxycarb is a growth regulator insecticide, analog of the arthropod juvenile hormone, used for controlling lepidopteran, mosquito, cockroach and bug. In the present study, three types of phenotypic defects were measured in newly hatched individuals from exposed embryos: i) eye pigmentation impairment, ii) appendage shape variations by geometric morphometrics and iii) tissue damages.
Inhibitory effects of crude alpha-mangostin, a xanthone derivative, on two different categories of colon preneoplastic lesions induced by 1, 2-dimethylhydrazine in the rat. (2005)

The purpose of this study was to examine whether crude alpha-mangostin (a major xanthone derivative in mangosteen pericarp (Garcinia mangostana)) has short-term chemopreventive effects on putative preneoplastic lesions involved in rat colon carcinogenesis. The crude preparation was obtained by simple recrystallization of an ethylacetate extract of mangosteen pericarps. A total of 33 five-week-old male F344 rats were randomly divided into 5 experimental groups. Rats in groups 1-3 were given a subcutaneous injection of 1,2-dimethylhydrazine (DMH)(40 mg/kg body weight) once a week for 2 weeks. Starting one week before the first injection of DMH, rats in groups 2 and 3 were fed a diet containing 0.02% and 0.05% crude alpha-mangostin, respectively, for 5 weeks. Rats in group 4 also received the diet containing 0.05% crude alpha-mangostin, while rats in group 5 served as untreated controls. The experiment was terminated 5 weeks after the start. Dietary administration of crude alpha-mangostin at both doses significantly inhibited the induction and/or development of aberrant crypt foci (ACF) (P<0.05 for 0.02% crude alpha-mangostin, P<0.01 for 0.05% crude alpha-mangostin), when compared to the DMH-treated group (group 1). Moreover, treatment of rats with 0.05% crude alpha-mangostin significantly decreased dysplastic foci (DF) (P<0.05) and beta-catenin accumulated crypts (BCAC) (P<0.05), to below the group 1 values. The proliferating cell nuclear antigen (PCNA) labeling indices of colon epithelium and focal lesions in groups 2 and 3 were also significantly lower than in group 1 and this effect occurred in a dose dependent manner of the crude alpha-mangostin. This finding that crude alpha-mangostin has potent chemopreventive effects in our short-term colon carcinogenesis bioassay system suggests that longer exposure might result in suppression of tumor development.
A scalable explicit multicast protocol for MANETs (2005)

Group oriented multicast applications are becoming increasingly popular in mobile ad hoc networks (MANETs). Due to dynamic topology of MANETs, stateless multicast protocols are finding increased acceptance since they do not require maintenance of state information at intermediate nodes. Recently, several multicast schemes have been proposed which scale better with the number of multicast sessions than traditional multicast strategies. These schemes are also known as explicit multicast (Xcast; explicit list of destinations in the packet header) or small group multicast (SGM). In this paper, we propose a new scheme for small group multicast in MANETs named extended explicit multicast (E2M), which is implemented on top of Xcast and introduces mechanisms to make it scalable with number of group members for a given multicast session. Unlike other schemes, E2M does not make any assumptions related to network topology or node location. It is based on the novel concept of dynamic selection of Xcast forwarders (XFs) between a source and its potential destinations. The XF selection is based on group membership and the processing overhead involved in supporting the Xcast protocol at a given node. If the number of members in a given session is small, E2M behaves just like the basic Xcast scheme with no intermediate XFs. As group membership increases, nodes may dynamically decide to become an XF. This scheme, which can work with few E2M aware nodes in the network, provides transparency of stateless multicast, reduces header processing overhead, minimizes Xcast control traffic, and makes Xcast scalable with the number of group members.
Impaired 17,20-Lyase Activity in Male Mice Lacking Cytochrome b5 in Leydig Cells (2016)

Androgen and estrogen biosynthesis in mammals requires the 17,20-lyase activity of cytochrome P450 17A1 (steroid 17-hydroxylase/17,20-lyase). Maximal 17,20-lyase activity in vitro requires the presence of cytochrome b5 (b5), and rare cases of b5 deficiency in human beings causes isolated 17,20-lyase deficiency. To study the consequences of conditional b5 removal from testicular Leydig cells in an animal model, we generated Cyb5(flox/flox):Sf1-Cre (LeyKO) mice. The LeyKO male mice had normal body weights, testis and sex organ weights, and fertility compared with littermates. Basal serum and urine steroid profiles of LeyKO males were not significantly different than littermates. In contrast, marked 17-hydroxyprogesterone accumulation (100-fold basal) and reduced testosterone synthesis (27% of littermates) were observed after human chorionic gonadotropin stimulation in LeyKO animals. Testis homogenates from LeyKO mice showed reduced 17,20-lyase activity and a 3-fold increased 17-hydroxylase to 17,20-lyase activity ratio, which were restored to normal upon addition of recombinant b5. We conclude that Leydig cell b5 is required for maximal androgen synthesis and to prevent 17-hydroxyprogesterone accumulation in the mouse testis; however, the b5-independent 17,20-lyase activity of mouse steroid 17-hydroxylase/17,20-lyase is sufficient for normal male genital development and fertility. LeyKO male mice are a good model for the biochemistry but not the physiology of isolated 17,20-lyase deficiency in human beings.
Present and future therapies of hepatitis B: From discovery to cure (2015)

With growing interest in developing and efforts to develop more effective therapies for HBV, the challenging goal of a cure may be well within reach in the near future.
ChemInform Abstract: Enzyme‐Catalyzed Stereoselective Synthesis of (S)‐Propanolamines. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
The Elusive Evidence of Volcanic Lightning (2017)

Lightning strikes are known to morphologically alter and chemically reduce geologic formations and deposits, forming fulgurites. A similar process occurs as the result of volcanic lightning discharge, when airborne volcanic ash is transformed into lightning-induced volcanic spherules (LIVS). Here, we adapt the calculations used in previous studies of lightning-induced damage to infrastructure materials to determine the effects on pseudo-ash samples of simplified composition. Using laboratory high-current impulse experiments, this research shows that within the lightning discharge channel there is an ideal melting zone that represents roughly 10% or less of the total channel radius at which temperatures are sufficient to melt the ash, regardless of peak current. The melted ash is simultaneously expelled from the channel by the heated, expanding air, permitting particles to cool during atmospheric transport before coming to rest in ash fall deposits. The limited size of this ideal melting zone explains the low number of LIVS typically observed in volcanic ash despite the frequent occurrence of lightning during explosive eruptions.
Critical Review—Narrow-Band Nitride Phosphors for Wide Color-Gamut White LED Backlighting (2017)

To achieve a brilliant image with high color saturation in white LED backlighting technology, innovative phosphor materials with narrow-band emission in the green and red spectral region are continuously pursed. Nitride phosphors are so far accepted as the most suitable phosphors for white LED backlights due to their high efficiency and excellent robustness. In this perspective, we will present an overview about the recent developments of state-of-the-art and newly-emerging nitride phosphors with a narrow emission band, and the emphasis would be placed on the relationships between the crystal structure and luminescence properties. Finally, some empirical rules for designing novel narrow-band phosphors for backlighting technologies would be summarized.
Online Estimation of Lithium-Ion Battery Capacity Using Sparse Bayesian Learning (2015)

Lithium-ion (Li-ion) rechargeable batteries are used as one of the major energy storage components for implantable medical devices. Reliability of Li-ion batteries used in these devices has been recognized as of high importance from a broad range of stakeholders, including medical device manufacturers, regulatory agencies, patients and physicians. To ensure a Li-ion battery operates reliably, it is important to develop health monitoring techniques that accurately estimate the capacity of the battery throughout its life-time. This paper presents a sparse Bayesian learning method that utilizes the charge voltage and current measurements to estimate the capacity of a Li-ion battery used in an implantable medical device. Relevance Vector Machine (RVM) is employed as a probabilistic kernel regression method to learn the complex dependency of the battery capacity on the characteristic features that are extracted from the charge voltage and current measurements. Owing to the sparsity property of RVM, the proposed method generates a reduced-scale regression model that consumes only a small fraction of the CPU time required by a full-scale model, which makes online capacity estimation computationally efficient. 10 years’ continuous cycling data and post-explant cycling data obtained from Li-ion prismatic cells are used to verify the performance of the proposed method.
Automated CO2 Composite Spray Cleaning System for HDD Rework Parts (2009)

Many advanced assemblies require high-volume and cost-effective selective cleaning during various stages of assembly or rework operations. Due to component compatibility problems and drying challenges, partially assembled devices cannot be immersed in or sprayed with aqueous cleaners or solvents. Newer dry cleaning techniques such as carbon dioxide (CO 2 ) aerosol spray cleaning processes (snow cleaning) have proven to be challenging to implement in automated high-volume manufacturing operations. Issues associated with conventional snow cleaning include high costs of operation, lack of process consistency, ineffective controls, and the requirements for a supply of high-purity liquid CO 2 . Advanced CO 2 composite spray [CO 2 (solid)-compressed dry air (CDA)(gas)] cleaning is an effective alternative to traditional spray and immersion cleaning processes and to conventional snow cleaning for selectively removing contaminants and films from partially assembled hard disk drive (HDD) components during the remanufacturing or rework process. CO 2 consumption is reduced using a composite spray, while spray cleaning control and performance is improved. CO 2 composite spray cleaning performance is dependent on the position, speed, and motions of the spray applicator, which are matched to comply with HDD factory output. Stored spray cleaning programs deliver precise cleaning seven days a week, 24 hours per day, with uptimes exceeding 99.9% over a 6-month period. Monitoring and controlling composite spray cleaning process parameters including spray pressure and composition, scanning speed, and pallet/part identification are done automatically. Operator interaction is limited to loading and unloading pallets for continuous system operation.
Use of Diels–Alder Chemistry for Thermoreversible Cross-Linking of Rubbers: The Next Step toward Recycling of Rubber Products? (2015)

A proof of principle for the use of Diels–Alder chemistry as a thermoreversible cross-linking tool for rubber products is demonstrated. A commercial ethylene-propylene rubber grafted with maleic anhydride has been thermoreversibly cross-linked in two steps. The pending anhydride rings were first modified with furfurylamine to graft furan groups onto the rubber backbone. These pending furans were cross-linked with a bismaleimide via a Diels–Alder coupling reaction. The newly formed Diels–Alder cross-links break at elevated temperatures (>150 °C) and can be re-formed by thermal annealing (50–70 °C). Reversibility of the rubber network was proven with infrared spectroscopy and on the basis of the mechanical properties. Furthermore, reversibility was also shown in a practical way, i.e., by cutting the used material into pieces and pressing them into new samples displaying comparable mechanical properties (impossible for conventionally cross-linked rubbers). The physical properties of the resulting products are comparable to those of conventionally cross-linked EPDM rubber and superior compared to those of their non-cross-linked precursors.
Can GCSF-stimulated donor lymphocyte infusions improve outcomes for relapsed disease following allogeneic hematopoietic cell transplantation? A systematic review and meta-analysis (2022)

Donor lymphocyte infusions (DLI) can produce graft-versus tumor effects to treat relapse after allogeneic hematopoietic cell transplantation, however, durable responses remain uncommon. A systematic review and meta-analysis are needed to clarify whether DLI collected after stimulation with granulocyte colony-stimulating factor (GCSF; G-DLI) can improve clinical outcomes. Sixteen studies (4 controlled) involving 585 patients were identified in a systematic search up to 17 September 2020. A meta-analysis demonstrated no significant difference in the risk of all-cause mortality (RR: 0.94, 95% CI 0.52-1.68, <i>p</i> = 0.82; <i>n</i> = 3 studies) or relapse-related mortality (RR: 0.72, 0.44-1.18, <i>p</i> = 0.19; <i>n</i> = 3 studies) between G-DLI and conventional DLI (C-DLI) groups. G-DLI products had similar mean CD3+ cells compared to C-DLI products, but median CD34+ cells/kg were increased. No improvement in disease progression, complete response rates, or risk of developing GVHD was observed with G-DLI, however, greater non-relapse mortality was observed compared to C-DLI. Alternative approaches to enhancing graft-versus-tumor effects are needed.
Radiation Effects Introduced by X-Ray Lithography in MOS Devices (1982)

The effects of low energy ionizing irradiation on MOS structures, with doses typical of those encountered in x-ray lithography, were studied in capacitors and transistors. The capacitor studies indicated the irradiations induced a slow trapping instability and an increase in surface state density. This surface state density increase was partially annealed at 450C in N2 after 1/2 hour. Transistor threshold shifts were largely annealed away under these conditions. However, a shift of 250 mV was observed in 1000 Å oxides which was not annealed away. In the 250 Å case, 50 mV remained after anneal. Even in the thinnest oxides studied (250 Å oxides) increases in subthreshold swing as large as 35% were encountered. This degradation was only partially annealed away under the conditions listed above. No channel length dependence to the effect was uncovered (down to 1 μm channel length).
Binding of beta gamma subunits of heterotrimeric G proteins to the PH domain of Bruton tyrosine kinase. (1994)

Bruton tyrosine kinase (Btk) has been implicated as the defective gene in both human and murine B-cell deficiencies. The identification of molecules that interact with Btk may shed light on critical processes in lymphocyte development. The N-terminal unique region of Btk contains a pleckstrin homology domain. This domain is found in a broad array of signaling molecules and implicated to function in protein-protein interactions. By using an in vitro binding assay and an in vivo competition assay, the pleckstrin homology domain of Btk was shown to interact with the beta gamma dimer of heterotrimeric guanine nucleotide-binding proteins (G proteins). A highly conserved tryptophan residue in subdomain 6 of the pleckstrin homology domain was shown to play a critical role in the binding. The interaction of Btk with beta gamma suggests the existence of a unique connection between cytoplasmic tyrosine kinases and G proteins in cellular signal transduction.
Advances in Polycarbonates (2005)

Polycarbonates (1) are an interesting and commercially successful class of polymers. Known for useful properties such as high heat capability, optical clarity, and incredible toughness, polycarbonates continue to generate academic interest as well as finding new avenues for commercial utilization. Although aromatic polycarbonates were first reported in the literature just over 100 years ago, the number of patents and publications continues to climb each year. The field of polycarbonate research is very diverse, with novel work covering the entire range of theoretical calculations, synthesis, physical measurements and analysis, as well as new additives, blends and applications. This volume is based on a symposium, "Advances in Polycarbonates," held at the National ACS Meeting in New Orleans, in March, 2003. It collects chapters from a variety of authors describing recent work or reviews on an assortment of polycarbonate topics.