gebhart/patrepeval huggingface dataset:
Discovering Selective Binders for Photoswitchable Proteins Using Phage Display (2018)

Nature provides an array of proteins that change conformation in response to light. The discovery of a complementary array of proteins that bind only the light-state or dark-state conformation of their photoactive partner proteins would allow each light-switchable protein to be used as an optogenetic tool to control protein-protein interactions. However, as many photoactive proteins have no known binding partner, the advantages of optogenetic control-precise spatial and temporal resolution-are currently restricted to a few well-defined natural systems. In addition, the affinities and kinetics of native interactions are often suboptimal and are difficult to engineer in the absence of any structural information. We report a phage display strategy using a small scaffold protein that can be used to discover new binding partners for both light and dark states of a given light-switchable protein. We used our approach to generate binding partners that interact specifically with the light state or the dark state conformation of two light-switchable proteins: PYP, a test case for a protein with no known partners, and AsLOV2, a well-characterized protein. We show that these novel light-switchable protein-protein interactions can function in living cells to control subcellular localization processes.
Deep-learning-based extraprostatic nodal lesion segmentation on 18F-fluciclovine PET (2022)

We propose a learning-based method to automatically segment extraprostatic nodal lesion from 18F-fluciclovine (anti-1- amino-3-[18F] fluorocyclobutane-1-carboxylic acid) PET images. Our proposed method, named hierarchical activation network, consists of three main subnetworks: a fully convolutional one-stage object detection (FCOS) network and a mask module, and a hierarchical convolutional block. While FCOS is employed to detect the view-of-interests (VOIs) of extraprostatic nodal lesion. Hierarchical convolutional block is used to derive activation map to boost the classification accuracy around lesion boundary. This is followed by the binary segmentation of extraprostatic nodal lesion within the detected VOI by mask module. To evaluate the proposed method, we retrospectively investigated 92 lesions with 18F- fluciclovine PET acquired. On each dataset, the extraprostatic lesions were delineated by physicians and was served as ground truth and training target. The proposed method was trained and evaluated by a five-fold cross validation strategy. The average DSC among all lesions is close to 0.7. The proposed method has great potential in improving the efficiency and mitigating the observer-dependence in extraprostatic lesion contouring for radiation therapy.
MPICH. Portable Implementation of the Standard Message Passing Interface (1992)

MPICH is a portable implementation of the MPI Message Passing Interface standard. A general-purpose library, it contains routines with which to write message-passing programs for a variety of parallell computers and workstation networks.
Ab initio study of the O(1D)+CH4(X 1A1)→OH(X 2Π)+CH3(X 2A2″) reaction: Ground and excited potential energy surfaces (2003)

The two potential energy surfaces (1 1A and 2 1A PESs) adiabatically correlating the reactants and products asymptotes of the title reaction were studied by means of the CASSCF and CASPT2 ab initio methods. The minimum energy path determined for the ground PES evolved through the barrierless insertion of the O(1D) atom into a C–H bond. The OH+CH3 products result from the dissociation of the CH3OH methanol intermediate formed. Reactivity on the excited 2 1A PES was found to proceed via an abstraction pathway. The energy barrier involved is low enough to expect the 2 1A PES to play a non-negligible role in the title reaction, even at the usual conditions attained in the experiments. The crossing between the 1 1A and 3 1A PESs was also investigated, the latter surface correlating with the excited OH(A 2Σ+) product.
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C–miRNA complexes and the degradation of miRNA targets (2009)

How miRNAs recognize their target sites is a puzzle that many experimental and computational studies aimed to solve. Several features, such as perfect pairing of the miRNA seed, additional pairing in the 3' region of the miRNA, relative position in the 3' UTR, and the A/U content of the environment of the putative site, have been found to be relevant. Here we have used a large number of previously published data sets to assess the power that various sequence and structure features have in distinguishing between putative sites that do and those that do not appear to be functional. We found that although different data sets give widely different answers when it comes to ranking the relative importance of these features, the sites inferred from most transcriptomics experiments, as well as from comparative genomics, appear similar at this level. This suggests that miRNA target sites have been selected in evolution on their ability to trigger mRNA degradation. To understand at what step in the miRNA-induced response individual features play a role, we transfected human HEK293 cells with miRNAs and analyzed the association of Argonaute/EIF2C-miRNA complexes with target mRNAs and the degradation of these messages. We found that structural features of the target site are only important for Argonaute/EIF2C binding, while sequence features such as the A/U content of the 3' UTR are important for mRNA degradation.
Proteoglycans in the microvasculature. I. Histochemical localization in microvessels of the rabbit eye. (1981)

The ultrastructural organization of ruthenium red (RR) stainable material within small blood vessels located in the limbus of the rabbit eye was studied. Proteoglycans were identified in this material by digesting tissues with Streptomyces hyaluronidase, testicular hyaluronidase, chondroitinase ABC, or heparinase before ruthenium red staining. Neuraminidase digestion enabled separate identification of sialoglycoprotein. The luminal surface of endothelial cells demonstrates an RR-stained glycocalyx containing both sialoglycoprotein and proteoglycans, which are removed by testicular hyaluronidase and crude heparinase. The basal coat of endothelial cells and small granules (10-20 nm in diameter) located within the basal lamina stain with RR and are removed only by crude heparinase. The surface coat of smooth muscle cells and small granules (10-20 nm) within their basal laminas are also digested by crude heparinase. Large proteoglycan granules (20-50 nm), which are completely removed by testicular hyaluronidase and partially digested by Streptomyces hyaluronidase, are deposited between the connective tissue fibers of the media and adventitia. Other large granules that are attached to collagen fibers contain enzyme-resistant anionic materials. The surface coat of adventitial fibroblasts is removed only by crude heparinase. Thin filaments (3-5 nm in diameter) interconnect the cell coat material, basal lamina granules, and large connective tissue granules, to form a network of proteoglycans that traverses the intima, media, and adventitia. The highly ordered arrangement of proteoglycans in the microvascular wall suggests that these macromolecules play several roles in microvascular function.
High-Luminance Blue-Emitting BaAl2S4:Eu Thin-Film Electroluminescent Devices (1999)

The high-luminance blue emitting electroluminescent (EL) devices which have been satisfied with the requirement for full color displays were obtained. BaAl 2 S 4 :Eu thin-film EL devices as the new blue emitting EL phosphor was prepared by the two targets pulse-electron-beam evaporation. The maximum luminance level was 65 cd/m 2 under the 50 Hz-pulse voltage. The EL spectrum had a blue emission band with a peak around 475 nm due to the 5d-4f transition for Eu 2+ ion. The Commission Internationale de l'Eclairage (CIE) color coordinates of BaAl 2 S 4 :Eu EL device were x =0.12 and y =0.10.
Genetic and antigenic characteristics of a human influenza C virus clinical isolate (2019)

Unlike influenza A and B viruses that infect humans and cause severe diseases in seasonal epidemics, influenza C virus (ICV) is a ubiquitous childhood pathogen typically causing mild respiratory symptoms. ICV infections are rarely diagnosed and less research has been performed on it despite the virus being capable of causing severe disease in infants. Here we report on the isolation of a human ICV from a child with acute respiratory disease, provisionally designated C/Victoria/2/2012 (C/Vic). The full-length genome sequence and phylogenetic analysis revealed that the hemagglutinin-esterase-fusion (HEF) gene of C/Vic was derived from C/Sao Paulo lineage, while its PB2 and P3 genes evolved separately from all characterized historical ICV isolates. Furthermore, antigenic analysis using the hemagglutination inhibition (HI) assay found that 1947 C/Taylor virus (C/Taylor lineage) was antigenically more divergent from1966 C/Johannesburg (C/Aichi lineage) than from 2012 C/Vic. Structure modeling of the HEF protein identified two mutations in the 170-loop of the HEF protein around the receptor-binding pocket as a possible antigenic determinant responsible for the discrepant HI results. Taken together, results of our studies reveal novel insights into the genetic and antigenic evolution of ICV and provide a framework for further investigation of its molecular determinants of antigenic property and replication.
On information measures based on particle mixture for optimal bearings-only tracking (2009)

In this work we consider a target tracking scenario where a moving observer with a bearings-only sensor is tracking a target. The tracking performance is highly dependent on the trajectory of the sensor platform, and the problem is to determine how it should maneuver for optimal tracking performance. The problem is considered as a stochastic optimal control problem and two sub-optimal control strategies are presented based on the Information filter and the determinant of the information matrix as the optimization objective. Using the determinant of the information matrix as an objective function in the planning problem is equivalent to using differential entropy of the posterior target density when it is Gaussian. For the non-Gaussian case, an approximation of the differential entropy of a density represented by a particle mixture is proposed. Furthermore, a gradient approximation of the differential entropy is derived and used in a stochastic gradient search algorithm applied to the planning problem.
Pilot Scale Evaluation of Peroxone for Treatment of Contaminated Groundwater. (1994)

Abstract : Advance oxidation processes (AOPs) are treatment processes that rely on the hydroxyl radical to destroy contaminants in polluted waters. Peroxone is an advanced oxidation process that utilizes the reaction of ozone and hydrogen peroxide to produce hydroxyl radicals without the requirement of ultraviolet light. The USAE Waterways Experiment Station (WES) evaluated the use of peroxone at Rocky Mountain Arsenal (RMA) for treatment of groundwater contaminated with diisopropylmethylphosphonate (DIMP) and low levels of pesticides. This evaluation was performed at RMA using a pilot scale treatment system. Results indicate that DIMP was easily oxidized to below detection limit levels. Optimization of the process indicated that a 250 m1/1 hydrogen peroxide dose in four columns plumbed in series that were all sparged with 2.2% ozonated air at a rate of 2.5 scfm.
Simultaneous measurement of surface geometry and material distribution by focusing ellipsotopometry (2002)

A new method for total surface measurement based on reflection ellipsometry is presented. By scanning the surface of the target under test with a focused laser beam, one can measure the surface topography and its material distribution simultaneously with high lateral resolution. Target topography is determined by ellipsometric measurement of local gradient angles gamma(x) and gamma(y) of the target's scanned surface elements. To identify the material, one measures the local complex refractive index n, too. The influence of beam focusing on the measurement results is discussed. We describe successful tests with various dielectric and metallic surfaces by use of He-Ne (632-nm) and He-Cd (442-nm) lasers.
Impact of VCO and PLL Phase Noise on Distributed Beamforming Arrays With Periodic Synchronization (2021)

Distributed beamforming between separate wireless nodes in a distributed antenna array requires significant coordination of the relative electrical states of the systems to achieve and maintain a phase-coherent state. A principal factor impacting distributed phase coherence is the relative stability of the local oscillators on each node. Ensuring a coherent state requires the distribution of a reference frequency such that all nodes are operating on the same basis frequency. To support distributed beamforming, the reference frequency must furthermore be distributed wirelessly, typically using a phase-locked loop (PLL) on the secondary nodes. In large arrays, the wireless link used for frequency distribution will have limited capacity, necessitating intermittent updates during which the oscillators are locked, and between which their frequencies will drift. The stability of the oscillator therefore plays an important role in the overall performance relative to the update time. In this paper, we discuss the sources of phase noise generated by the reference oscillator and the PLL, and analyze the impacts of phase noise and update interval on distributed beamforming performance. We provide a framework for analyzing distributed beamforming performance from oscillator and PLL parameters in general, and we analyze beamforming performance for two specific cases using nominal high-stability and low-stability voltage-controlled oscillators, with a parametric comparison between their impact on beamforming performance.
Reversed Conductance Decay of 1D Topological Insulators by Tight-Binding Analysis (2022)

Reversed conductance decay describes increasing conductance of a molecular chain series with increasing chain length. Realizing reversed conductance decay is an important step toward making long and highly conducting molecular wires. Recent work has shown that one-dimensional topological insulators (1D TIs) can exhibit reversed conductance decay due to their nontrivial edge states. The Su-Schrieffer-Heeger (SSH) model for 1D TIs relates to the electronic structure of these isolated molecules but not their electron transport properties as single-molecule junctions. Herein, we use a tight-binding approach to demonstrate that polyacetylene and other diradicaloid 1D TIs show a reversed conductance decay at the short chain limit. We explain these conductance trends by analyzing the impact of the edge states in these 1D systems on the single-molecule junction transmission. Additionally, we discuss how the self-energy from the electrode-molecule coupling and the on-site energy of the edge sites can be tuned to create longer wires with reversed conductance decays.
Toward Understanding the Design of Intertwined Human–Computer Integrations (2023)

Human–computer integration is an HCI trend in which computational machines can have agency, i.e., take control. Our work focuses on a particular form of integration in which the user and the computational machine share agency over the user's body, that is, can simultaneously (in contrast to a traditional turn-taking approach) control the user's body. The result is a user experience where the agency of the user and the computational machine is so intertwined that it is often no more discernable who contributed what to what extent; we call this “intertwined integration”. Due to the recency of advanced technologies enabling intertwined integration systems, we find that little understanding and documented design knowledge exist. To begin constructing such an understanding, we use three case studies to propose two key dimensions (“awareness of machine's agency” and “alignment of machine's agency”) to articulate a design space for intertwined integration systems. We differentiate four roles that computational machines can assume in this design space (angel, butler, influencer, and adversary). Based on our craft knowledge gained through designing such intertwined integration systems, we discuss strategies to help designers create future systems. Ultimately, we aim at advancing the HCI field's emerging understanding of sharing agency.
Towards fast quantum key distribution with quantum frames (2008)

We propose and investigate a fibre-based quantum key distribution system, which employs polarization qubits encoded into faint laser pulses. As a novel feature, it allows sending of classical framing information via sequences of strong laser pulses that precede the quantum data. This allows synchronization, sender and receiver identification, and compensation of time-varying birefringence in the communication channel. Furthermore, this method also provides a platform to communicate implementation specific information such as encoding and protocol in view of future optical quantum networks. All optical components can be operated at Gbps rates, which is a first requirement for Mbps secret key rates.
Foundations of neurobiology (1997)

Foundations of Neurobiology is the first book on the subject conceived and written exclusively for undergraduate biology students--a concise, principles-oriented text that spans the entire field of neurobiology from molecules to the mind. With only general biology as a prerequisite, the book takes a broad, conceptual, comparative approach, introducing the principles of vertebrate and invertebrate neural function in all sensory systems.
An Augmented Reality Mobile Application for Skin Lesion Data Visualization (2020)

Melanoma is the deadliest form of skin cancer. It mainly requires a visual diagnosis by dermatologists. However, a dermatologist's recognition of melanoma may be subject to errors and may take some time to diagnose correctly it. To this aim, in the last twenty years, Computer-Aided Diagnosis systems based on artificial vision are increasingly adopted to support dermatologists in the early diagnosis of melanoma. However, these systems exploits only a reduced set of parameters or they implement a melanoma classifier that tries to substitute the dermatologists, without supporting their experience in the classification of skin lesions. This paper proposes a mobile application for supporting the clinician decision in the diagnosis of melanoma directly in the dermatologist environment by using Augmented Reality technology. In particular, computer-generated perceptual information is added to the image of patient skin reporting the values of various parameters and the lesion classification based on deep learning approach for analyzing skin lesions and identifying melanoma.
An efficient algorithm for the implementation of fingerprint authentication on smartcards (2007)

In recent years, biometrics has become established as the pinnacle of reliable authentication, able to overcome the limitations of traditional methods. With the ability to securely store data and execute functions on-card, smartcards can play an important role in providing secure solutions that are both highly usable and trusted, while preserving user privacy. However technological constraints currently prohibit computationally intensive applications on-card, making implementation a challenging problem: to date, current 'match-on-card' applications work by releasing a portion of the template into the off-card environment, thereby reintroducing significant security vulnerabilities.

With the aim of developing a secure implementation of a biometric matching algorithm within a resource constrained environment, this paper establishes a disturbance rejection methodology capable of differentiating between equivalent and extraneous data. Initial studies demonstrate this novel concept is capable of yielding significant reductions in the magnitude of computation through the refinement of the feature search-space, opening up the prospect of truly secure 'match-on-card' systems.
Isoﬂavones supplementation of a probiotic fermented soy product: effects on quality characteristics and isoﬂavones proﬁle (2010)

The aim of the present study was to investigate the effect of isoflavones supplementation of a fermented soy product on its sensory acceptance, physicochemical properties and probiotic cell viable count. Additionally we also investigated the ability of the mixed starter cultures (Enterococcus faecium CRL 183 and Lactobacillus helveticus 416) to modify the isofl avones profi le of soy product during the fermentation process. Three products were analysed: soy product fermented with E. faecium CRL 183 and L. helveticus 416, isofl avonessupplemented soy product (fermented with E. faecium CRL 183 and L. helveticus 416; 50 mg/100g, Isofl avin®, Galena, Brazil) and unfermented soy product. A panel of judges evaluated the acceptability of the samples on a nine point structured hedonic scale. The chemical composition namely fat, protein, ash and total carbohydrate contents, pH, enumeration of viable Lactobacillus spp. and Enterococcus spp. and quantifi cation of isofl avones using HPLC were investigated. All determinations were conducted after 7 days storage at 10°C. The sensorial acceptance was reduced in the isofl avones-supplemented soy product, but this effect was not signifi cant compared to the sample without isofl avones addition. Chemical composition did not differ ..
Synthesis of nanocrystalline Y 2 O 3 :Eu phosphor through different chemical methods: studies on the chromaticity dependence and phase conversion (2012)

In this study, Y2O3:Eu nanocrystals (NCs) were prepared through the combustion, Pechini and hydrothermal methods followed by the heat treatment of samples at 873 K. The resultant NCs were investigated by X-ray diffractometery, scanning electron microscopy, transmission electron microscopy, selected area electron diffractometery and photoluminescence (PL) spectroscopy. The obtained sample by the Pechini method presents cubic phase, whereas the hydrothermal sample consists of different phases (cubic, monoclinic and hexagonal phases of Y2O3 besides yttrium nitrate hydrate phase). Cubic and monoclinic phases of Y2O3 as well as tetragonal phase of yttrium oxide nitride (YO(NO3)3) phases were observed in combustion sample before heat treatment, whereas just the cubic phase stayed after heat treatment of this sample. The morphological investigations demonstrated that the hydrothermal sample has flower-like morphology with micron-size petals, whereas other samples have rounded particles. The PL intensity and chromaticity of Pechini sample are not as good as combustion and hydrothermal samples, but low agglomeration of the Pechini sample makes it good candidate for biological applications as a luminescence sensors and tags.