gebhart/patrepeval huggingface dataset:
Exploring Alternative Transcript Structure in the Human Genome Using BLOCKS and InterPro (2003)

Understanding how alternative splicing affects gene function is an important challenge facing modern-day molecular biology. Using homology-based, protein sequence analysis methods, it should be possible to investigate how transcript diversity impacts protein function. To test this, high-quality exon-intron structures were deduced for over 8000 human genes, including over 1300 (17 percent) that produce multiple transcript variants. A data mining technique (DiffMotif) was developed to identify genes in which transcript variation coincides with changes in conserved motifs between variants. Applying this method, we found that 30 percent of the multi-variant genes in our test set exhibited a differential profile of conserved InterPro and/or BLOCKS motifs across different mRNA variants. To investigate these, a visualization tool (ProtAnnot) that displays amino acid motifs in the context of genomic sequence was developed. Using this tool, genes revealed by the DiffMotif method were analyzed, and when possible, hypotheses regarding the potential role of alternative transcript structure in modulating gene function were developed. Examples of these, including: MEOX1, a homeobox-containing protein; AIRE, involved in auto-immune disease; PLAT, tissue type plasminogen activator; and CD79b, a component of the B-cell receptor complex, are presented. These results demonstrate that amino acid motif databases like BLOCKS and InterPro are useful tools for investigating how alternative transcript structure affects gene function.
The Anglo-Soviet Treaty (1986)

British public opinion strongly favoured the closest possible cooperation with the Soviets, thus making the Russian card a tempting one for ambitious politicians to play. Shortly after the German attack the British Institute of Public Opinion conducted a survey on the question 'Do you feel that Britain has taken or has not taken full advantage offered by the German attack on Russia?' The replies were: Has taken 29%; Not taken 49%; Don't know 22%.1 The Home Intelligence Weekly Reports, based on an extensive survey of public opinion, continued to show concern that Russia was fighting the war for Britain with insufficient help. One such report stated that 'People realise that every Russian killed is one Englishman less to die, and they are not only thankful, they are grateful.' There were also widespread complaints that there was not nearly as much enthusiasm at the top to help the Soviet Union as there was among the working class.2 Another report spoke of annoyance at 'persons in high position who are not one hundred per cent in favour of assisting the Russians'. It was pointed out that such people still refused to sit on the same platforms as Communists even though the Soviets were now comrades-in-arms.3 At least until the end of October 1941 there was a strong desire for a second front to be opened as soon as possible.KeywordsPrime MinisterBaltic StateBritish TroopPeace ConferenceSoviet SupportThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Relations between verb and noun in the domain of motion: arrive/arrival in English and French. (2021)

International audience
Recombinant tissue-type plasminogen activator and immediate angioplasty in acute myocardial infarction. One-year follow-up. The European Cooperative Study Group. (1992)

Benefit from treatment with alteplase, heparin, and aspirin is not diminished at 1 year. Routine immediate PTCA does not confer additional benefit. Prognosis after hospital discharge mainly is determined by coronary anatomy and residual left ventricular function and is unrelated to initial treatment assignment.
Coadsorption of TbIII–Porphyrin Double-decker Single-molecule Magnets in a Porous Molecular Network: Toward Controlled Alignment of Single-molecule Magnets on a Carbon Surface (2016)

© 2016 The Chemical Society of Japan. A self-assembled monolayer of a mixture of radical 2,3,7,8,12,13,17,18-octaethylporphyrin (OEP)TbIII doubledecker (TbIII(OEP)2) single-molecule magnets and alkoxylated dehydrobenzo[12]annulene (DBA) at the 1-phenyloctane/highly oriented pyrolytic graphite interface was investigated using scanning tunneling microscopy. The observations revealed that single TbIII(OEP)2 molecules were incorporated in the 2D pores of the honeycomb structure formed by a DBA derivative containing octyloxy chains. The number of TbIII(OEP)2 molecules coadsorbed in the porous DBA networks increased with increasing concentration of the TbIII(OEP)2 radical solution.
A DASH 360° immersive video streaming control system (2020)

This letter proposes a DASH‐compliant video streaming control system for 360 ° immersive videos. The overall system is composed of two control algorithms which cooperate both to adapt the video bitrate to match the time‐varying end‐to‐end network bandwidth and to select the most appropriate view of the panoramic scene in response to the varying point of view of the user. The proposed system has been implemented and an extensive experimental evaluation has been carried out in a realistic emulated network scenario to assess the obtainable performances in terms of visual quality and bitrate reduction.
Alternative choices in measurement systems for artificial river aeration (1980)

Artificial in‐stream aeration is an economical and, under appropriate conditions, desirable method for alleviating symptoms of water pollution in rivers. Some measurement of the degree of pollution is generally required for this and other aquatic reclamation applications. Our objective is to optimize the selection of such measurements for use as feedback in aeration systems in order to improve performance under variable conditions. A special case of our mathematical results can also give the optimized measurement selection for water quality estimators. Two widely accepted measures of water quality are dissolved oxygen and biochemical oxygen demand, the latter being available only through time‐consuming and rather inaccurate observations. This time delay can be avoided by correlating biochemical oxygen demand with measurements of total organic carbon but only with a further sacrifice of accuracy. We examine a hierarchy of feedback structures, which includes the measurement of a variety of water quality parameters, and compare these structures to determine their relative performance. Finally, a trade‐off between time lag and accuracy of biochemical oxygen demand measurements is developed to optimize per formance.
Cover Picture: Hexaphyrin as a Potential Theranostic Dye for Photothermal Therapy and 19F Magnetic Resonance Imaging (ChemBioChem 10/2017) (2017)

The cover picture shows a hexaphyrin as a potential theranostic expanded porphyrin for use in both sustained photothermal heat generation and 19F magnetic resonance imaging (MRI). Expanded porphyrins have two potential key features suitable for theranostic agents, excellent absorption in the near infrared (NIR) region and the possibility of introducing multiple fluorine atoms at structurally nearly equivalent positions. Under NIR light, the hexaphyrin showed intense photothermal and weak photodynamic effects, which were most likely due to its low-lying excited states close to that of singlet oxygen. This sustained photothermal effect caused the ablation of cancer cells more effectively than the photodynamic effect of indocyanine green, a clinically used dye. In addition, the hexaphyrin that has 12 trifluoromethyl groups showed potential for use in the visualization of tumors by 19F MRI due to the presence of these multiple fluorine atoms. More information can be found in the full paper by T. Matsuda, M. Shirakawa, T. Murakami, H. Imahori et al. on page 951 in Issue 10, 2017 (DOI: 10.1002/cbic.201700071).
Estimation for paired binomial data with application to radiation therapy (2001)

We compare and contrast several different methods for estimating the effect of treatment when responses are paired binomial observations. The ratio of binomial probabilities is the parameter of interest, while the binomial probabilities are nuisance parameters which may vary between pairs. The application is a meta-analysis of the treatment of rectal cancer, with observations in each study indicating the number of recurrences of the cancer in each of two groups, one with radiation therapy and one without. The ratio of the probabilities of recurrence in the radiation to non-radiation groups is of substantive interest, and is modelled as a logistic or complementary log-log function of an unknown linear combination of the covariates. The three methods we consider are maximum likelihood, a Bayesian approach and an approach based on estimating equations. For the MLE and Bayesian approach the potentially large number of nuisance parameters are estimated together with the parameters of interest, whereas for the estimating equation approach only the parameters of interest are estimated. A simulation study is performed to compare the methods and evaluate the impact of overdispersion.
DIFICULDADES PARA O INGRESSO E PERMANENCIA NA CIENCIA E ENGENHARIA DA COMPUTACAO: UM OLHAR FEMININO (2014)

Disparidades nas carreiras relacionadas a Ciencia da Computacao acontecem em todo o mundo. De acordo com JUNG & APEDOE (2013), nos Estados Unidos a media de mulheres que cursam Bacharelado em Ciencia da Computacao e menor do que 20%, e a presenca das mulheres nas carreiras relacionadas a Ciencia da Computacao so chega a 25%. No Brasil, verifica-se que os cursos ligados as areas de Informatica, Dados e Informacao apresentam o menor porcentual de matriculas de estudantes do sexo feminino (IPEA, 2011). A Paraiba acompanha esta tendencia. Os cursos de Bacharelado em Ciencia da Computacao e Engenharia da Computacao do Campus I da UFPB em Joao Pessoa-PB apresentam uma predominância masculina, sendo que apenas cerca de 13% de mulheres estudam nas areas citadas contra 87% de homens, evidenciando a baixa presenca feminina e reproduzindo as relacoes de genero que sao caracteristicas das areas de ciencia e tecnologia (NTI, 2012; BARBOSA, 2013); CARVALHO e RABAY,2013). Atraves de questionarios estruturados e entrevistas, este trabalho realiza um diagnostico das principais dificuldades enfrentadas pelas alunas tanto para o ingresso como para a permanencia nos cursos da area de Ciencia da Computacao da UFPB.
Invisible Metasurface-Bound Volumes (2018)

Here we discuss possibilities to enclose a volume of space by some penetrable metasurfaces so that the fields outside this volume are not perturbed by the metasurfaces while the fields induced inside the volume can be controlled: for example, made very large or very small. We restrict the analysis to a one-dimensional scenario where the incident field is a single plane wave and focus on realizations using purely reactive metasurfaces. The study is relevant to such applications as low-observable sensors or non-linear devices, and the studied physical phenomena have links to recent research on embedded eigenstates in continuum.
Simple laser accelerator: Optics and particle dynamics (1991)

When a laser is focused it develops a longitudinal component. This could be used to develop a laser particle accelerator. A lens waveguide array is discussed, and it is shown that such a system could generate high-energy particle beams. The possibility of using a ``diffraction-free'' Bessel beam is discussed, and a possible configuration is suggested. To accelerate electrons from one to a few MeV seems possible using a well-focused, 1-J, 1-ps laser pulse. This would provide a simple proof-of-principle experiment. In order to accelerate heavier particles, such as protons, the injected particle beam would have to be ultrarelativistic such as that produced by the superconducting supercollider.
Plasma Extracellular Superoxide Dismutase is Decreased in High-Altitude Mountaineers who are Endurance Trained (2006)

Restricted accessAbstractFirst published March 2006Plasma Extracellular Superoxide Dismutase is Decreased in High-Altitude Mountaineers who are Endurance TrainedE.A. Regan, R.P. Bowler, and J.D. CrapoView all authors and affiliationsVolume 54, Issue 2_supplhttps://doi.org/10.1177/108155890605402s137
Hot Corrosion of an Electrodeposited Ni-11 wt % Cr Nanocomposite under Molten Na[sub 2]SO[sub 4]–K[sub 2]SO[sub 4]–NaCl (2005)

A Ni–Cr nanocomposite with an average Cr concentration of was deposited onto nickel plate by simultaneous electrodeposition of Ni and Cr nanoparticles from a nickel sulfate bath. The nanocomposite consisted of a nanocrystalline Ni matrix and dispersed Cr nanoparticles with a mean size of . For comparison, two Ni–Cr alloys, one with similar Cr content and the other with much higher Cr content , were prepared using electro-arc melting. Hot corrosion testing under molten in air at showed that rapid formation of a continuous chromia-rich scale is essential for hot corrosion protection. This was the case only for the nanocomposite. Internal sulfidation was observed for arc-melted alloys, but not for the nanocomposite. The results demonstrate that it was not primarily the Cr content but the unique structure of the nanocomposite that was responsible for its superior hot corrosion resistance. The protection mechanism lies in the fast formation of a continuous chromia scale on the nanocomposite, due to the easy nucleation of chromia on both chromium nanoparticles and abundant nickel grain boundaries, and then fast linking of the nuclei as a result of enhanced diffusion of Cr through those grain boundaries.
Preliminary results in the development of a multi-colour pulsed laser for holography (2013)

This paper presents the development of a pulsed, high coherence multi-wavelength laser for colour holography. The laser operates in five different wavelengths to provide a very good coverage of the chromatic range. All the wavelengths are simultaneously derived from a single Nd:YAG laser source through Raman wavelength shifting and harmonic conversion processes, making the system fairly compact and robust.
Real‐Time Quantitative Monitoring of Specific Peptide Cleavage by a Proteinase for Cancer Diagnosis (2012)

Good vibrations: A bioassay using a resonant peptide-functionalized microcantilever enables the quantitative characterization of the proteolytic activity of membrane type-1 matrix metalloproteinase (MT1-MMP). In this assay, shifts in the frequency of the cantilever after specific proteolytic cleavage of the target peptides by MT1-MMP are measured (see picture).
Performance comparison of spectrum-narrowing equalizations with maximum likelihood sequence estimation and soft-decision output (2014)

Maximum likelihood sequence estimation (MLSE) offers effective equalizations for bandwidth-limited optical signal on mitigation towards inter-symbol-interference (ISI) impairment. In this paper, we provide the first comprehensive comparisons and analysis of three post-compensation algorithms on the same modeling platform for high spectral-efficiency (SE) optical systems employing the spectral prefiltering. Those algorithms include 1-tap constant modulus algorithm (CMA) and 3-tap MLSE, regular CMA and digital filter with 2-tap MLSE, and constant multi-modulus algorithm (CMMA) with 2-tap MLSE. Furthermore, a novel and effective approach is proposed and verified for the generation of both hard value and soft value at the output of MLSE in order to be compatible with the implementation of soft-decision forward error correction (SD-FEC) decoding process.
Improving Perfusion Bioreactor Yields by Using Particle Swarm Optimization (2016)

peer reviewed
Effects of combination M40403 and dexamethasone therapy on joint disease in a rat model of collagen‐induced arthritis (2005)

This study shows that combination therapy with M40403 and DEX reduced the degree of chronic inflammation and tissue and bone damage associated with CIA in the rat. It supports the possible use of SODm in combination with steroids to reduce the dose necessary and the side effects related to the use of steroids in the management of chronic diseases such as rheumatoid arthritis.
The surfactant co-formulant POEA in the glyphosate-based herbicide RangerPro but not glyphosate alone causes necrosis in Caco-2 and HepG2 human cell lines and ER stress in the ToxTracker assay (2022)

The toxicity of co-formulants present in glyphosate-based herbicides (GBHs) has been widely discussed leading to the European Union banning the polyoxyethylene tallow amine (POEA). We identified the most commonly used POEA, known as POE-15 tallow amine (POE-15), in the widely used US GBH RangerPro. Cytotoxicity assays using human intestinal epithelial Caco-2 and hepatocyte HepG2 cell lines showed that RangerPro and POE-15 are far more cytotoxic than glyphosate alone. RangerPro and POE-15 but not glyphosate caused cell necrosis in both cell lines, and that glyphosate and RangerPro but not POE-15 caused oxidative stress in HepG2 cells. We further tested these pesticide ingredients in the ToxTracker assay, a system used to evaluate a compound's carcinogenic potential, to assess their capability for inducing DNA damage, oxidative stress and an unfolded protein response (endoplasmic reticulum, ER stress). RangerPro and POE-15 but not glyphosate gave rise to ER stress. We conclude that the toxicity resulting from RangerPro exposure is thus multifactorial involving ER stress caused by POE-15 along with oxidative stress caused by glyphosate. Our observations reinforce the need to test both co-formulants and active ingredients of commercial pesticides to inform the enactment of more appropriate regulation and thus better public and environmental protection.
Engineering Antibody Specificity Using Combinatorial Antibody Libraries (2009)

The research presented in this thesis investigates antibody specificity, antibody-antigen and protein-protein interactions using combinatorial antibody libraries, phage-display and bacterial display technology. One goal was to develop a method to generate antibodies that bind two protein antigens with high affinity using a single-antigen binding site, and to investigate the molecular and thermodynamic requirements for antibody multispecificity. The thesis describes how naïve combinatorial antibody libraries with diversity in the light chain can be used to generate antibodies of different antigen-binding specificities. A variant of the HERCEPTIN® antibody, a therapeutic monoclonal antibody that binds the human epidermal growth factor receptor 2 (HER2), was isolated on the basis of its ability to simultaneously interact with vascular endothelial growth factor (VEGF). Crystallographic and mutagenesis studies revealed that distinct amino acids of this antibody, called bH1, engage HER2 and VEGF energetically, but there is extensive overlap between the antibody surface areas contacting the two antigens. By selectively mutating residues of the complementarity determining regions (CDRs), the binding affinity of bH1 was improved for both antigens 100-fold (KD = 0.2 nM and 3 nM for HER2 and VEGF, respectively). This affinity-improved version of bH1 specifically inhibits both HER2- and VEGF-mediated cell proliferation in vitro and tumor progression in mouse models with activity similar to the Herceptin® antibody and the anti-VEGF antibody bevacizumab, respectively. While the structural and mutagenesis studies highlight the differences of the interfaces between the dual specific antibody and its two antigens in surface topology and energetic engagement of CDR residues, the two interactions share a common thermodynamic signature: favorable entropy and enthalpy. The positive entropy change upon binding and large negative heat capacities suggests that the hydrophobic effect plays an important role in the dual specific interactions. Finally we show that by mutation of merely two residues in the CDRs, the high affinity dual specific antibodies can be converted back to essentially monospecific HER2 or VEGF antibodies. The described dual specific “two-in-one” antibodies challenge the paradigm of monoclonal antibodies being one binding site/one antigen, and they could provide new opportunities for antibody-based therapies.
Enhanced performance of plasmid DNA polyplexes stabilized by a combination of core hydrophobicity and surface PEGylation (2014)

Nonviral gene therapy has high potential for safely promoting tissue restoration and for treating various genetic diseases. One current limitation is that conventional transfection reagents such as polyethylenimine (PEI) form electrostatically stabilized plasmid DNA (pDNA) polyplexes with poor colloidal stability. In this study, a library of poly(ethylene glycol-b-(dimethylaminoethyl methacrylate-co-butyl methacrylate)) [poly(EG-b-(DMAEMA-co-BMA))] polymers were synthesized and screened for improved colloidal stability and nucleic acid transfection following lyophilization. When added to pDNA in the appropriate pH buffer, the DMAEMA moieties initiate formation of electrostatic polyplexes that are internally stabilized by hydrophobic interactions of the core BMA blocks and sterically stabilized against aggregation by a PEG corona. The BMA content was varied from 0% to 60% in the second polymer block in order to optimally tune the balance of electrostatic and hydrophobic interactions in the polyplex core, and polymers with 40 and 50 mol% BMA achieved the highest transfection efficiency. Diblock copolymers were more stable than PEI in physiologic buffers. Consequently, diblock copolymer polyplexes aggregated more slowly and followed a reaction-limited colloidal aggregation model, while fast aggregation of PEI polyplexes was governed by a diffusion-limited model. Polymers with 40% BMA did not aggregate significantly after lyophilization and produced up to 20-fold higher transfection efficiency than PEI polyplexes both before and after lyophilization. Furthermore, poly(EG-b-(DMAEMA-co-BMA)) polyplexes exhibited pH-dependent membrane disruption in a red blood cell hemolysis assay and endosomal escape as observed by confocal microscopy.Lyophilized polyplexes made with the lead candidate diblock copolymer (40% BMA) also successfully transfected cells <i>in vitro</i> following incorporation into gas-foamed polymeric scaffolds. In summary, the enhanced colloidal stability, endosomal escape, and resultant high transfection efficiency of poly(EG-b-(DMAEMA-co-BMA))-pDNA polyplexes underscores their potential utility both for local delivery from scaffolds as well as systemic, intravenous delivery.
Fault Tree Analysis Aimed to Design and Implement On-Field Fault Detection and Isolation Schemes for SOFC Systems (2010)

The paper focuses on a methodological study oriented towards the development of diagnostic tools for on-field operating solid oxide fuel cell (SOFC) systems. This work is motivated by the increasing demand for diagnostic techniques aimed at both increasing durability and fully exploiting SOFC benefits throughout system lifetime. Nowadays many SOFC diagnostic applications are available in lab-controlled environment, but few studies are proposed for on-field use. Main contribution of this work is thus the development of suited methodologies for detection and isolation of typical SOFC system faults. Fault tree analysis (FTA) is proposed as a tool for the isolation process. For each specific component, the most significant faults are correlated, via a top-down approach, to the corresponding symptom(s). The knowledge gained through the FTA is exploited to understand the mutual interactions among all devices within the entire SOFC system. Such an approach resulted in the definition of a fault signature matrix that conveniently links system-level symptoms to specific component faults. Such an approach is therefore suitable to perform fault detection and isolation (FDI) of an SOFC system as a whole.