gebhart/patrepeval huggingface dataset:
Inhibition of Ebola Virus by a Molecularly Engineered Banana Lectin (2019)

Ebolaviruses cause an often rapidly fatal syndrome known as Ebola virus disease (EVD), with average case fatality rates of ~50%. There is no licensed vaccine or treatment for EVD, underscoring the urgent need to develop new anti-ebolavirus agents, especially in the face of an ongoing outbreak in the Democratic Republic of the Congo and the largest ever outbreak in Western Africa in 2013-2016. Lectins have been investigated as potential antiviral agents as they bind glycans present on viral surface glycoproteins, but clinical use of them has been slowed by concerns regarding their mitogenicity, i.e. ability to cause immune cell proliferation. We previously engineered a banana lectin (BanLec), a carbohydrate-binding protein, such that it retained antiviral activity but lost mitogenicity by mutating a single amino acid, yielding H84T BanLec (H84T). H84T shows activity against viruses containing high-mannose N-glycans, including influenza A and B, HIV-1 and -2, and hepatitis C virus. Since ebolavirus surface glycoproteins also contain many high-mannose N-glycans, we assessed whether H84T could inhibit ebolavirus replication. H84T inhibited Ebola virus (EBOV) replication in cell cultures. In cells, H84T inhibited both virus-like particle (VLP) entry and transcription/replication of the EBOV mini-genome at high micromolar concentrations, while inhibiting infection by transcription- and replication-competent VLPs, which measures the full viral life cycle, in the low micromolar range. H84T did not inhibit assembly, budding, or release of VLPs. These findings suggest that H84T may exert its anti-ebolavirus effect(s) by blocking both entry and transcription/replication. In a mouse model, H84T partially (maximally, ~50-80%) protected mice from an otherwise lethal mouse-adapted EBOV infection. Interestingly, a single dose of H84T pre-exposure to EBOV protected ~80% of mice. Thus, H84T shows promise as a new anti-ebolavirus agent with potential to be used in combination with vaccination or other agents in a prophylactic or therapeutic regimen.
Chemical, structural, and transport properties ofNa1−xCoO2 (2003)

We report measurements of room-temperature compressibility, thermal expansion, thermoelectric power \ensuremath{\alpha}(T) at various pressures $P&lt;~20\mathrm{kbar},$ basal-plane resistivity ${\ensuremath{\rho}}_{\mathrm{ab}}(T),$ magnetic susceptibility, and thermal conductivity $\ensuremath{\kappa}(T)$ taken on single-crystal or cold-pressed ${\mathrm{Na}}_{1\ensuremath{-}x}{\mathrm{CoO}}_{2},$ $(1\ensuremath{-}x)\ensuremath{\approx}0.57.$ Whereas the c-axis thermal expansion is large, the basal-plane thermal expansion remains negligible for all temperatures $T&lt;300\mathrm{K}.$ We propose here that pinning of the nominal Co(IV)/Co(III) redox couple at the top of the ${\mathrm{O}}^{2\ensuremath{-}}{:2p}^{6}$ bands, and a schematic location of the ${a}_{1}^{T}$ and ${e}^{T}$ antibonding bands of this couple with respect to the Fermi energy are responsible for the large thermoelectric power found in this compound. On the other hand, the phonon contribution to the thermal conductivity measured on a dense cold-pressed ceramic sample is not as small as previously reported.
Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint (2022)

<i>N</i>-Substituted peptides, such as peptoids and β-peptoids, have been reported to have unique structures with diverse functions, like catalysis and manipulation of biomolecular functions. Recently, the preorganization of monomer shape by restricting bond rotations about all backbone dihedral angles has been demonstrated to be useful for <i>de novo</i> design of peptoid structures. Such design strategies are hitherto unexplored for β-peptoids; to date, no preorganized β-peptoid monomers have been reported. Here, we report the first design strategy for β-peptoids, in which all four backbone dihedral angles (<i>ω</i>, <i>ϕ</i>, <i>θ</i>, <i>ψ</i>) are rotationally restricted on a per-residue basis. The introduction of a cyclopentane constraint realized the preorganized monomer structure and led to a β-peptoid with a stable twisted strand shape.
Progression of basal cell carcinoma through loss of chromosome 9q and inactivation of a single p53 allele. (1994)

Basal cell carcinoma (BCC) of the skin represents a unique group of tumors strongly associated with exposure to UV light. Unlike squamous carcinoma of the skin, BCC is generally indolent, noninvasive, and rarely metastatic. To study the involvement of tumor suppressor genes in these neoplasms, we analyzed 36 BCCs for p53 mutations and a subset of these tumors for loss of chromosomes 17p and 9q. Sixty-nine % of sporadic BCCs had lost a 9q allele, with the common area of loss surrounding the putative gene for nevoid BCC or Gorlin's syndrome. Forty-four % (16 of 36) of BCCs had a mutated p53 allele, usually opposite pyrimidine tracts, which is consistent with UV-induced mutations. Surprisingly, only one tumor had lost a 17p allele, and in all BCCs only one p53 allele was inactivated. This is in direct contrast to other epithelial tumors, which usually progress by the inactivation of both p53 alleles.
GPU-Based Artificial Neural Network Configuration and Training for Water Distribution System Analysis (2012)

Previous research by the authors has confirmed that GPU-based Artificial Neural Network (ANN) construction offers significant computational speed-up over the CPU-based ANN implementation for water distribution system meta-modeling. Further research showed that for real-world scale systems, however, the hydraulic prediction accuracy achieved by the previously trained ANN is inadequate when the ANN is employed as a surrogate model to replace the hydraulic simulator for pump scheduling optimization. This paper improves the GPU-based ANN meta-modeling approach for constructing the ANN model of adequate accuracy in an efficient manner. This includes system decomposition, ANN configuration and training specifications to achieve a reliable surrogate model for pump scheduling optimization. The technique is successfully applied to a real-world water distribution system, and the GPU-based ANN predicted the hydraulic responses with a Root-Mean-Square Error (RMSE) of less than 1% for tank levels and pump energy consumption.
Antibodies against HIV-1 from Phage Display Libraries: Mapping of an Immune Response and Progress towards Antiviral Immunotherapy (Part 2 of 2) (1996)

The last decade has witnessed remarkable developments in antibody research and its therapeutic applications. With the methods of molecular biology it is now possible to manipulate the specificities and activities of antibody molecules to generate an almost limitless array of structures for both basic investigations and the clinical setting. The contributions to this volume cover all three domains of the antibody: the variable regions, the relatively neglected but crucial hinge, and the constant region. These studies provide critical structural and functional information about antibodies, while also pointing the way to the construction of molecules with enhanced or even novel properties. Bringing together major experts on antibody engineering, this book is highly recommended to faculty, postdoctoral fellows and graduate students in molecular biology, microbiology, immunology, cancer research and genetics.
On the correlation of TCP traffic in backbone networks (2004)

We study the second order statistics of traffic in an Internet backbone. We model the traffic at the flow level by a Poisson shot noise process. This model is quite parasimonious, and is driven only by variables that can be easily obtained from measurements, namely flow sizes, durations and arrival rate. We consider the auto-correlation of TCP traffic where the loss process of each TCP connection is assumed to be Poisson. Using a stochastic differential equation, we are able to provide an upper bound on the auto-covariance function of the aggregated TCP traffic whose tightness is shown by simulations with the network simulator-ns.
Oncology education in primary health care (2014)

Potrebne su minimalne izmjene i dopune Zakona o zdravstvenoj zastiti i samo treba dodati: „U sklopu centara za palijativnu medicinu, kao posebne zdravstvene ustanove mogu se osnivati Ustanove za palijativnu skrb. One sklapaju ugovore s HZZO i placene su na temelju posebnih propisa koje izrađuje HZZO“ „U postojecim opcim i specijalnim bolnicama, uz prethodnu suglasnost ili po nalogu Ministra zdravstva prenamjenjuju se dijelovi postojecih kapaciteta i u kapacitete (postelje) za palijativnu skrb, maksimalno do 5% postojeceg kapaciteta. Ovi kapaciteti ne organiziraju se kao posebni odjel ili odsjek nego se prema odluci managementa bolnice raspoređuju kao posebni kreveti unutar postojecih odjela gdje se pojavljuju velike potrebe za palijativnom skrbi (onkologija, pulmologija, interna medicina, psihijatrija, kirurgija itd.). Rad ovih kapaciteta placa se na temelju posebnih propisa koje izrađuje HZZO“ „Postojeci kapaciteti stacionara u okvirima domova zdravlja prenamjenjuju se u ustanove za palijativnu skrb u zajednici, Rad ovih kapaciteta placa se na temelju posebnih propisa koje izrađuje HZZO“.
Serine-Selective Bioconjugation (2020)

This Communication reports the first general method for rapid, chemoselective, and modular functionalization of serine residues in native polypeptides, which uses a reagent platform based on the P(V) oxidation state. This redox-economical approach can be used to append nearly any kind of cargo onto serine, generating a stable, benign, and hydrophilic phosphorothioate linkage. The method tolerates all other known nucleophilic functional groups of naturally occurring proteinogenic amino acids. A variety of applications can be envisaged by this expansion of the toolbox of site-selective bioconjugation methods.
Comic Story Analysis Based on Genre Classification (2017)

People who are reading comics are interested not only by the estheticism of the graphics but also by interesting stories. Therefore, understanding the detail of comic story is an important step to build comic retrieval systems based on readers' interest. As a method of understanding comic story, we propose to convert comic story into a novel formatted narrative structure, which uses comic genres as the representation of the contents of story. Each page of a comic volume is classified into a genre by using convolutional neural network. Generally, in machine learning, labeling ground truth on a large number of training samples is necessary, which costs time and money. In this paper, we propose a story analysis method which can describe a comic story as the sequence of genres with relatively low manual cost. The experimental results show the effectiveness of our proposed method.
Protein Recognition and Denaturation by Self‐Assembling Fragments on a DNA Quadruplex Scaffold. (2007)

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, please click on HTML or PDF.
A Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data (2022)

T-cell receptor (TCR) analysis is relevant for the study of immune system diseases. The expression of TCRs is usually measured with targeted sequencing approaches where TCR genes are selectively amplified. However, many non-targeted RNA-seq experiments also contain reads of TCR genes, which could be leveraged for TCR expression analysis while reducing sample requirements and costs. Moreover, a step-by-step pipeline for the processing of transcriptome RNA-seq reads to deliver immune repertoire data is missing, and these types of analyses are usually not included in RNA-seq studies of immunological conditions. This represents a missed opportunity for complementing them with the analysis of the immune repertoire. We present a Nextflow pipeline for T-cell receptor repertoire reconstruction and analysis from RNA sequencing data. We used a case study where TCR repertoire profiles were recovered from bulk RNA-seq of isolated CD4 T cells from control patients, cirrhotic patients without and with Minimal Hepatic Encephalopathy (MHE). MHE is a neuropsychiatric syndrome, mediated by peripheral inflammation, that may affect cirrhotic patients. After the recovery of 498-1,114 distinct TCR beta chains per patient, repertoire analysis of patients resulted in few public clones, high diversity and elevated within-repertoire sequence similarity, independently of immune status. Additionally, TCRs associated with celiac disease and inflammatory bowel disease were significantly overrepresented in MHE patient repertoires. The provided computational pipeline functions as a resource to facilitate TCR profiling from RNA-seq data boosting immunophenotype analyses of immunological diseases.
Effect of Mn doping on the electronic and optical properties of Dy2Ti2O7: a combined spectroscopic and theoretical study (2023)

Electronic and optical studies on Dy<sub>2</sub>Ti<sub>2-</sub>Mn<i><sub>x</sub></i>O<sub>7</sub>(<i>x</i>= 0.00, 0.05, 0.10, 0.15, & 0.20) have been presented through both, theoretical (density functional theory (DFT) calculations) and experimental (ultraviolet-visible absorption and photoluminescence emission spectroscopy) approaches. DFT calculations were employed considering the local density approximation (LDA) and LDA-1/2 for exchange-correlation interactions. Computed crystallographic parameters and energy band-gap using theoretical formulations are in good agreement with experimental results. The band-gap value obtained through the LDA-1/2 approach indicates insulated ground state of Dy<sub>2</sub>Ti<sub>2-<i>x</i></sub>Mn<i><sub>x</sub></i>O<sub>7</sub>(<i>x</i>= 0.00, 0.05, 0.10, 0.15, 0.20) system. Experimentally obtained band gap value reduces from 3.82 eV to 2.45 eV with increase in positive chemical pressure as<i>x</i>increases from 0 to 0.20. Reduction in band gap value is attributed to the fact that there exists a lack of hybridization between the O-2p orbital and Ti-3d orbital, which is well correlated with the crystallographic data. Jahn-Teller effect is likely to be responsible for the presence of a mixed state of Mn (explained using x-ray photoelectron spectroscopy results), resulting in the intermediate Mn state between the valence band and the conduction band with immediate inclusion of Mn at Ti site in Dy<sub>2</sub>Ti<sub>2-<i>x</i></sub>Mn<i><sub>x</sub></i>O<sub>7</sub>system.
Power Balancing in Multiple Spot-Beam Satellite Systems for Multicast Support (2004)

Abstract — We address the problem of optimizing resource sharing and flow control in a multiple spot-beam broadband satellite system that supports both unicast and multicast flows. Satellite communication systems, with their wide-area coverage and ubiquitous access to large number of users, clearly have an inherent advantage in supporting distributed applications that require concurrent transmission of content to multiple users. In order to remain competitive against other broadband technologies, next generation satellite systems will be required to support both unicast and multicast flows and offer optimal sharing of system resources between these flows. We show that a high load variation across the spot-beam queues may significantly under-utilize the system and be perceived unsatisfactory by potential users when both unicast and multicast flows are active in the system. We propose an optimization based-approach to balance the load in the system and conclude that it is possible to increase the average session rates of all active flows by up to 30% after this optimization is applied. Index Terms — System design, multicast delivery, satellite networks, power allocation, mathematical optimization. I.
Synthesis of n-Type Perylene Bisimide Derivatives and Their Orthogonal Self-Assembly with p-Type Oligo(p-phenylene vinylene)s (2004)

Four different (chiral) electron-deficient (n-type) perylene bisimides containing aliphatic, aromatic, or ethyleneoxide side chaines have been synthesized and fully characterized. All of them form supramolecular stacks in apolar methylcyclohexane (MCH) solution as demonstrated by concentration- and temperature-dependent absorption, circular dichroism, and fluorescence studies. One derivative was investigated in more detail in the solid state and proven to be liquid crystalline and capable of forming nanometer-sized fiberlike networks when drop-cast from MCH. Optical spectroscopy techniques show that perylene bisimide and an oligo(p-phenylene vinylene) (p-type) derivative orthogonally self-assemble into separate nanosized p-and n-type stacks in MCH. In contrast in toluene only molecularly dissolved species are present. In films deposited from MCH as well as from toluene photoinduced electron transfer takes place from the p-type material to the n-type material. As a result of the orthogonal self-assembly process, in films from MCH an ordered network of fibers was formed, whereas in films from toluene no ordering was observed. However, probably due to the lateral orientation on the surface and the presence of long aliphatic chains pointing toward the electrodes, efficient bulk heterojunction solar cells could not be constructed.
Modulation of Cancer Patients' Immune Responses by Administration of Anti-Idiotypic Antibodies (1989)

Thirty patients with Dukes stage D colon carcinoma who had undergone operative removal of the primary tumor and had growing hepatic metastases each received four intradermal injections of 0.5-4 mg of alum-precipitated goat anti-idiotypic antibodies (anti-Id). The anti-Id had been produced against murine monoclonal antibody (mAb) CO17-1A, which defines a human colon carcinoma associated antigen. All patients elaborated anti-anti-Id that shared idiotopes with mAb CO17-1A, bound to tumor cells and isolated tumor antigen, and competed with the mAb for binding to tumor cells. The clinical response was monitored by ultrasonography, CT, radionuclide scanning, and serum marker assays. Six patients had partial tumor responses; five of these had received additional booster anti-Id injections along with chemotherapy. Seven patients had stabilized tumor; six had received additional anti-Id, with chemotherapy also in four. Conclusions about the clinical role of such immunization await further study, but in demonstrating a specific response to anti-Id, our results support the use of this approach in human immunotherapy against tumors or pathogens.
Gold-Catalyzed Addition of N-Hydroxy Heterocycles to Alkynes and Subsequent 3,3-Sigmatropic Rearrangement (2013)

Gold-catalyzed intermolecular addition of hydroxybenzotriazole derivatives to alkynes at room temperature, gives vinyl ethers 3 in high yields and with excellent regioselectivity. Unlike many other vinyl ethers, 3 can easily be purified by regular silica-gel chromatography. On heating, 3,3-sigmatropic rearrangement of 3 gives access to highly functionalized benzotriazoles. This two-step sequence represents an efficient oxygen transfer protocol which incorporates a nucleophilic oxygen atom into an alkyne group. Reaction of 3 with an electrophilic fluorinating reagent (Selectfluor) gives a fluorinated ketone regioselectively and in high yield.
Bayesian Optimization-Based Global Optimal Rank Selection for Compression of Convolutional Neural Networks (2020)

Recently, convolutional neural network (CNN) compression via low-rank decomposition has achieved remarkable performance. Finding the optimal rank is a crucial problem because rank is the only hyperparameter for controlling computational complexity and accuracy in compressed CNNs. In this paper, we propose a global optimal rank selection method based on Bayesian optimization (BayesOpt), which is a machine learning based global optimization technique. By utilizing both a simple objective function and a proper optimization scheme, the proposed method produces a global optimal rank that provides a good trade-off between computational complexity and accuracy degradation. In addition, our method also reflects the correlation of each rank in multi-rank selection, and is able to flexibly yield an optimal rank with a given fixed compression ratio. Experimental results indicate that the proposed algorithm can identify the global optimal rank regardless of the huge size of dataset or the various structural features of CNNs. In all experiments on multi-rank selection, the proposed method produces the rank with higher accuracy and lower computational complexity than the state-of-the-art rank selection method, variational Bayesian matrix factorization (VBMF).
Data mining at NASA (2009)

NASA has some of the largest and most complex data sources in the world, with data sources ranging from the earth sciences, space sciences, and massive distributed engineering data sets from commercial aircraft and spacecraft. This talk will discuss some of the issues and algorithms developed to analyze and discover patterns in these data sets. We will also provide an overview of a large research program in Integrated Vehicle Health Management. The goal of this program is to develop advanced technologies to automatically detect, diagnose, predict, and mitigate adverse events during the flight of an aircraft. A case study will be presented on a recent data mining analysis performed to support the Flight Readiness Review of the Space Shuttle Mission STS-119.
Fluid tolerance while running: effect of repeated trials (2008)

This study assessed tolerance to fluid ingestion with repeated sessions of drinking while running. Seven trained distance runners (age 22 ± 2 yr; VO 2 max = 54.4 ± 7.1 ml/kg/min) performed six 90 min treadmill runs (~1/week) at 65% VO 2 max while ingesting a glucose‐electrolyte solution. During run 1 , subjects drank ad libitum every 10 min and sweat rate was determined. On runs 2‐6 , subjects drank every 10 min at a rate to match the sweat rate determined in run 1 . Stomach comfort (1–4 scale) and other gastrointestinal symptoms were also assessed every 10 min. Gastric emptying rate was determined in runs 2 and 6 . Subjects consumed significantly (P &lt; 0.05) more fluid during runs 2–6 (mean ± SD; 1247 ± 162 ml), than during run 1 (508 ± 476 ml). Stomach comfort improved (P &lt; 0.05) on runs 5 and 6 (1.7 ± 0.5 units) compared to run 2 (2.3 ± 0.5 units). Gastric emptying rate was not different between runs 2 and 6 (12.0 ± 1.9 ml/min vs. 12.3 ± 2.3 ml/min, respectively). These results indicate repeated sessions of drinking at a rate that matches sweat rate improves stomach comfort, however, gastric emptying rate does not change under such conditions. Supported by the Gatorade Sports Science Institute
CCR2 Regulates Vaccine-Induced Mucosal T-Cell Memory to Influenza A Virus (2021)

While antibody-based immunity to influenza A virus (IAV) is type and sub-type specific, lung and airway-resident memory T cells that recognize conserved epitopes in the internal viral proteins are known to provide heterosubtypic immunity. Hence, broadly protective IAV vaccines need to elicit robust T-cell memory in the respiratory tract. We have developed a combination adjuvant-based IAV nucleoprotein vaccine that elicits strong CD4 and CD8 T cell memory in lungs and protects against H1N1 and H5N1 strains of IAV. In this study, we examined the mechanisms that control vaccine-induced protective memory T cells in the respiratory tract. We found that trafficking of monocytes into lungs might limit the development of anti-viral lung-resident memory T cells, following intranasal vaccination. These findings suggested that strategies that limit monocyte infiltration can potentiate vaccine-induced frontline T-cell immunity to respiratory viruses such as IAV and SARS-CoV-2.