gebhart/patrepeval huggingface dataset:
Antibody responses to the RTS,S/AS01E vaccine and Plasmodium falciparum antigens after a booster dose within the phase 3 trial in Mozambique (2020)

The RTS,S/AS01<sub>E</sub> vaccine has shown consistent but partial vaccine efficacy in a pediatric phase 3 clinical trial using a 3-dose immunization schedule. A fourth-dose 18 months after the primary vaccination was shown to restore the waning efficacy. However, only total IgG against the immunodominant malaria vaccine epitope has been analyzed following the booster. To better characterize the magnitude, nature, and longevity of the immune response to the booster, we measured levels of total IgM, IgG, and IgG<sub>1-4</sub> subclasses against three constructs of the circumsporozoite protein (CSP) and the hepatitis B surface antigen (HBsAg, also present in RTS,S) by quantitative suspension array technology in 50 subjects in the phase 3 trial in Manhiça, Mozambique. To explore the impact of vaccination on naturally acquired immune responses, we measured antibodies to <i>P. falciparum</i> antigens not included in RTS,S. We found increased IgG, IgG1, IgG3 and IgG4, but not IgG2 nor IgM, levels against vaccine antigens 1 month after the fourth dose. Overall, antibody responses to the booster dose were lower than the initial peak response to primary immunization and children had higher IgG and IgG1 levels than infants. Higher anti-Rh5 IgG and IgG<sub>1-4</sub> levels were detected after the booster dose, suggesting that RTS,S partial protection could increase some blood stage antibody responses. Our work shows that the response to the RTS,S/AS01<sub>E</sub> booster dose is different from the primary vaccine immune response and highlights the dynamic changes in subclass antibody patterns upon the vaccine booster and with acquisition of adaptive immunity to malaria.
Novel Extension of SBR–PO Method for Solving Electrically Large and Complex Electromagnetic Scattering Problem in Half-Space (2017)

To extend hybrid high-frequency shooting and bouncing rays-physical optics (SBR-PO) method to the modeling of electromagnetic (EM) scattering from an object in half-space, this paper focuses on addressing two key issues: 1) how to accurately obtain the induced electric currents on the object surface by taking into account the EM interactions between the object and half-space and 2) how to accurately calculate far-fields in half-space configuration. First, by introducing virtual interface of half-space, the proposed method avoids physically modeling the underlying ground, and only induced electric currents on the object are effectively taken into account in the SBR process. Second, the closed-form half-space Green's function is used to calculate scattered far-fields to avoid the time-consuming evaluation of the Sommerfeld integrals. The computational errors are only from the approximation of induced electric currents with the same level of the SBR-PO method for the solution of the free-space problem, so the proposed method is more accurate than the conventional SBR-PO technique. Besides, performing the proposed method on the graphics processing unit platform to further accelerate the ray-tracing process makes the method even more powerful to solve the extra-large-scale scattering problems in the half-space.
Performance bounds on state-feedback controllers with network delay (2008)

This paper describes a convex optimization approach to bound the performance degradation of control systems subject to network loop delay. We consider a linear time-invariant continuous-time plant connected over a communication network to a remote controller. The network introduces bounded but time-varying delays between the controller and plant. We establish an upper bound on the worst-case performance degradation due to the network delays as a function of the delay bound, which can be used as a design parameter for the networked implementation. Numerical simulation results illustrate the degree of conservativeness of the bound.
Bound and Conquer: Improving Triangulation by Enforcing Consistency (2018)

Code to reproduce the results from "Bound and conquer: Improving Triangulation by Enforcing Consistency" published in IEEE Transactions on Pattern Analysis and Machine Intelligence in 2019. Paper abstract: We study the accuracy of triangulation in multi-camera systems with respect to the number of cameras. We show that, under certain conditions, the optimal achievable reconstruction error decays quadratically as more cameras are added to the system. Furthermore, we analyze the error decay-rate of major state-of-the-art algorithms with respect to the number of cameras. To this end, we introduce the notion of consistency for triangulation, and show that consistent reconstruction algorithms achieve the optimal quadratic decay, which is asymptotically faster than some other methods. Finally, we present simulations results supporting our findings. Our simulations have been implemented in MATLAB and the resulting code is available in the supplementary material.
Endotoxin induction of plasminogen activator and plasminogen activator inhibitor type 1 mRNA in rat tissues in vivo. (1990)

The tissue-specific distribution of tissue-type and urokinase-type plasminogen activator (t-PA and u-PA) and their inhibitor type 1 (PAI-1) was analyzed at mRNA level in five major rat organ tissues. t-PA mRNA was detected in lung, kidney, heart, and liver. u-PA mRNA was detected in kidney and lung. Presence of PA mRNA correlated with the detection of PA activity in extracts of these tissues. PAI-1 mRNA was detected predominantly in heart and lung. Although PAI activity could not be measured directly in tissue extracts, the presence of PAI-1 mRNA correlated with the occurrence of PA.PAI complex in fibrin autography of tissue extracts. Endotoxin injection caused a very large increase in plasma PAI activity. This increase correlated with a marked increase in PAI-1 mRNA in nearly all tissues studied. The increase in PAI-1 mRNA is most pronounced in lung and liver. Endotoxin injection also caused an increased level of t-PA mRNA in heart and kidney, and an increased u-PA mRNA level in kidney. mRNA analysis of freshly isolated and separated subfractionated liver cells showed that the marked increase in PAI-1 mRNA in the liver after endotoxin injection may be due mainly to a strong increase of PAI-1 mRNA in the liver endothelial cells.
Translational Animal Models of Atopic Dermatitis for Preclinical Studies. (2017)

There is a medical need to develop new treatments for patients suffering from atopic dermatitis (AD). To improve the discovery and testing of novel treatments, relevant animal models for AD are needed. Generally, these animal models mimic different aspects of the pathophysiology of human AD, such as skin barrier defects and Th2 immune bias with additional Th1 and Th22, and in some populations Th17, activation. However, the pathomechanistic characterization and pharmacological validation of these animal models are generally incomplete. In this paper, we review animal models of AD in the context of preclinical use and their possible translation to the human disease. Most of these models use mice, but we will also critically evaluate dog models of AD, as increasing information on disease mechanism show their likely relevance for the human disease.
Comparative analysis of genetic diversity among the maize inbred lines (Zea mays L.) obtained by RAPD and SSR markers (2008)

The RAPD and SSR markers were used to compare the genetic diversity among the 16 maize inbred lines. Twenty-two primers were used in the RAPD reactions, resulting in the amplification of 265 fragments, while 16 pairs of SSR primers resulted in 75 fragments. The similarity based on Dice coefficient for the RAPD ranged from 53 to 84% and for the SSR from 11 to 82%. The dendrogram obtained by the RAPD showed five groups, while dendrogram obtained by the SSR showed three groups and one isolated line. The association constructed from the markers and the principal coordinate’s analysis separated lines into two groups according to endosperm color, either orange or yellow. The RAPD were effective to validate pedigree data, while the SSR were effective to recognize the differences between the quantitative characters. Because they assess the distinct regions of the genome, the selection of one or other marker would depend on the characteristics of the material used and the objectives of the project.
Dynamics at Surfaces: Probing the Dynamics of Polar and A-Polar Liquids at Silica and Vapour Surfaces (2008)

Recent studies by Nuclear Magnetic Resonance and Neutron Scattering of the dynamics and phase-fractions of water/ice systems in templated porous silicas (SBA-15) indicate that what was believed to be a non-frozen surface water layer is actually plastic ice, the quantity varying (continuously and reversibly) with temperature, and converting to a brittle (mainly cubic) ice at lower temperatures. Current research relates to the study the dynamics of polar water/ice and a-polar organics at both solid and vapour interfaces. The polar results are significant for water/ice systems in the environment, where snow-packs, glaciers and icebergs are common examples of water/ice systems with extensive air/vapour interfaces. This research also points the way forward for wide-range cryoporometric metrology in 'difficult' systems such as high iron content clays and rocks, as well as aged concrete. Results are presented for cryoporometric measurements on meteorite samples with a significant metallic content, exhibiting T2* relaxation times down to 2.5ms.
Neural mechanisms of selective listening to pitch and timbre in musical sounds (2018)

Previous research showed that different dimensions of sound such as pitch and timbre elicit distinct patterns of neural activities. Here, we report event related potential (ERP) along with functional magnetic resonance imaging (fMRI) data during a selective listening task of musical sounds. The participants were 12 normal adults. The stimuli were 4 musical tones with timbre (piano vs. violin) and pitch (high vs. low) contrasts. The stimuli were normalized for duration and intensity. In the timbre condition, the listener needed to indicate the instrument category. In the pitch condition, the listener needed to indicate the pitch level. While both conditions reached the ceiling-level accuracy, the pitch condition required significantly longer reaction time. Significant fMRI activations were found in the superior temporal gyri with right dominance for both conditions. The right superior temporal gyrus and left inferior frontal regions were important for coding pitch whereas the anterior cingulate cortex was exclusively active in selectively attending to timbre. These data demonstrate how different cortical networks contribute to selective listening. The ERP data further showed larger N1 and N2 peaks for the timbre condition than the pitch condition, suggesting that attentional modulation operates at both early and later stages of processing for selective listening.
Substrate specificity of SARS-CoV-2 nsp10-nsp16 methyltransferase (2020)

Abstract The ongoing COVID-19 pandemic exemplifies the general need to better understand viral infections. The positive single strand RNA genome of its causative agent, the SARS coronavirus 2 (SARS-CoV-2) encodes all viral enzymes. In this work, we focus on one particular methyltransferase (MTase), nsp16, which in complex with nsp10 is capable of methylating the first nucleotide of a capped RNA strand at the 2′-O position. This process is part of a viral capping system and is crucial for viral evasion of the innate immune reaction. In light of recently discovered non-canonical RNA caps, we tested various dinucleoside polyphosphate-capped RNAs as substrates for nsp10-nsp16 MTase. We developed an LC-MS-based method and discovered five types of capped RNA (m 7 Gp 3 A(G)-, Gp 3 A(G)- and Gp 4 A-RNA) that are substrates of the nsp10-nsp16 MTase. Our technique is an alternative to the classical isotope labelling approach for measurement of 2′-O-MTase activity. Further, we determined the IC 50 value of sinefungin (286 ± 66 nM) to illustrate the value of our approach for inhibitor screening. In the future, this approach can be used for screening inhibitors of any type of 2′-O-MTase.
Approximating the stationary distribution of an infinite stochastic matrix (1991)

We are given a Markov chain with states 0, 1, 2, ···. We want to get a numerical approximation of the steady-state balance equations. To do this, we truncate the chain, keeping the first n states, make the resulting matrix stochastic in some convenient way, and solve the finite system. The purpose of this paper is to provide some sufficient conditions that imply that as n tends to infinity, the stationary distributions of the truncated chains converge to the stationary distribution of the given chain. Our approach is completely probabilistic, and our conditions are given in probabilistic terms. We illustrate how to verify these conditions with five examples.
Influence of the Vagus Nerves on Pancreatic Insulin Secretion (1967)

The effect of short and long-term faradic stimulation of the vagus nerves on pancreatic immunoreactive insulin (IRI) release was assessed in dogs. In the present study stimulation of the vagus nerves at the level of the diaphragm or in the neck did not enhance pancreatic IRI release. The only significant effect was a transient fall in pancreatic vein IRI values immediately after stimulation was begun.
Community participation in Afghan refugee camps in Pakistan. (1985)

Community participation is regarded by many as the key to the primary health care (PHC) approach; that is the most essential factor in determining the success of failure of a PHC programme. In September 1983, UNICEF and Save the Children Fund (SCF) signed an agreement for a pilot PHC project in Badaber refugee camp, Pakistan, as the first phase in development of PHC in areas settled by Afghan refugees, under the supervision of the United Nations High Commission for Refugees (UNHCR) ant the government of Pakistan. This paper reviews the factors enhancing and inhibiting the formation of a community, describes how community participation was achieved in Badaber and discusses the prospects for replication of the model in the 86 camps in North West Frontier Province which are funded by UNHCR.
Supplementary Table 1 from Genome-Wide Array-Based Comparative Genomic Hybridization Reveals Multiple Amplification Targets and Novel Homozygous Deletions in Pancreatic Carcinoma Cell Lines (2023)

Supplementary Table 1 from Genome-Wide Array-Based Comparative Genomic Hybridization Reveals Multiple Amplification Targets and Novel Homozygous Deletions in Pancreatic Carcinoma Cell Lines
Ketogenic diet slows down mitochondrial myopathy progression in mice (2010)

Mitochondrial dysfunction is a major cause of neurodegenerative and neuromuscular diseases of adult age and of multisystem disorders of childhood. However, no effective treatment exists for these progressive disorders. Cell culture studies suggested that ketogenic diet (KD), with low glucose and high fat content, could select against cells or mitochondria with mutant mitochondrial DNA (mtDNA), but proper patient trials are still lacking. We studied here the transgenic Deletor mouse, a disease model for progressive late-onset mitochondrial myopathy, accumulating mtDNA deletions during aging and manifesting subtle progressive respiratory chain (RC) deficiency. We found that these mice have widespread lipidomic and metabolite changes, including abnormal plasma phospholipid and free amino acid levels and ketone body production. We treated these mice with pre-symptomatic long-term and post-symptomatic shorter term KD. The effects of the diet for disease progression were followed by morphological, metabolomic and lipidomic tools. We show here that the diet decreased the amount of cytochrome c oxidase negative muscle fibers, a key feature in mitochondrial RC deficiencies, and prevented completely the formation of the mitochondrial ultrastructural abnormalities in the muscle. Furthermore, most of the metabolic and lipidomic changes were cured by the diet to wild-type levels. The diet did not, however, significantly affect the mtDNA quality or quantity, but rather induced mitochondrial biogenesis and restored liver lipid levels. Our results show that mitochondrial myopathy induces widespread metabolic changes, and that KD can slow down progression of the disease in mice. These results suggest that KD may be useful for mitochondrial late-onset myopathies.
Silicon Solar Cell with Nanoporous Structure Formed on a Textured Surface (2009)

A nanoporous silicon (Si) surface was formed on monocrystalline silicon solar cells by electrochemical etching. The galvanostatic mode was applied to conventional n–p–p + solar cells, which were fabricated by pyramidal texturing, phosphorous diffusion, screen‐printing, rapid thermal firing, and laser isolation (effective area of 144.7 cm 2 ). Without an additional antireflection layer such as SiN x , the anodic reaction of the Si wafer could provide uniform porous layers on a pyramidal surface (111) with relatively low reflectance, and it would improve the photovoltaic performance.
[Posterior fracture-dislocation of the shoulder. A study of 11 cases (author's transl)]. (1981)

The authors have observed 11 cases of posterior fracture-dislocation of the shoulder. All were recognised easily except one. The lesions are described and the mechanism of the lesion is considered. Treatment was conservative in most cases, and gave satisfactory results.
Coupleur directionnel compact à ligne de transmission tensorielle, et application aux formateurs de faisceau (2013)

National audience
Practical Training Framework for Fitting a Function and Its Derivatives (2011)

This paper describes a practical framework for using multilayer feedforward neural networks to simultaneously fit both a function and its first derivatives. This framework involves two steps. The first step is to train the network to optimize a performance index, which includes both the error in fitting the function and the error in fitting the derivatives. The second step is to prune the network by removing neurons that cause overfitting and then to retrain it. This paper describes two novel types of overfitting that are only observed when simultaneously fitting both a function and its first derivatives. A new pruning algorithm is proposed to eliminate these types of overfitting. Experimental results show that the pruning algorithm successfully eliminates the overfitting and produces the smoothest responses and the best generalization among all the training algorithms that we have tested.
Taste-masked tacrolimus-phospholipid nanodispersions: dissolution enhancement, taste masking and reduced gastric complications (2016)

Through the integration of orthogonal central composite design and desirability function, this work aimed to explore the potential of quality by design in understanding the formulation of phospholipid-stabilized tacrolimus nanodispersions by microfluidization. The influence of homogenization pressure, microfluidization time and phospholipid concentration (X1-X3) on nanodispersion performance was studied. Nanodispersions were characterized by differential scanning calorimetric (DSC), X-ray diffractometer (XRD) and Fourier transform infrared (FTIR) analysis. Moreover, masking the unpalatable taste of tacrolimus and reducing the gastric complications were also evaluated. FTIR analysis indicated its interaction with phospholipid. DSC and XRD analysis revealed the amorphous transformation of tacrolimus within nanodispersions. The dissolution was enhanced by 35 folds and 15 folds after 0.5 and 2 h, respectively. Maximum tacrolimus content, yield, polydispersity index, percentages dissolved after 0.5 and 2 h of 99.3%, 100%, 0.864, 39.7% and 95.3%, respectively, with particle size of 160 nm were obtained at X1, X2 and X3 values of 20 000 psi, 6 min and 30%, respectively. The Euclidean distance values demonstrated masking the unpalatable taste and taste perversion to stimuli of tacrolimus in its optimized nanodispersion. Moreover, the ulcerative indices following raw tacrolimus and its optimized nanodispersion oral administration were 6.73 and 2.45, respectively, to indicate that nanodispersion was significantly less irritating to the gastric mucosa.
Use of Mixtures of Mesotrione, Imazethapyr, and Imazethapyr plus Imazapyr in Imidazolinone-Resistant Corn (Zea mays)1 (2003)

Field studies were conducted in 1999, 2000, and 2001 to evaluate mesotrione at 105 and 210 g ai/ha alone and in mixtures with imazethapyr at 70 g ai/ha and the prepackage mixture of imazethapyr at 47 g/ha plus imazapyr at 16 g ai/ha postemergence. Mixtures of mesotrione with imazethapyr and imazethapyr plus imazapyr controlled common ragweed, common lambsquarters, and morningglory species better than imazethapyr or imazethapyr plus imazapyr alone. Similarly, mixtures of mesotrione with these imidazolinone herbicides improved the control of giant foxtail over that by mesotrione alone. Crop injury did not exceed 11% with all treatments and appeared as transient stunting. Yields of corn treated with mixtures of mesotrione plus imidazolinone herbicides were highest in 2000 and 2001, when rainfall was higher than in 1999.Nomenclature: Imazapyr; imazethapyr; mesotrione; common lambsquarters, Chenopodium album L. #3 CHEAL; common ragweed, Ambrosia artemisiifolia L. # AMBEL; giant foxtail, Setaria faberi Herrm. # SETFA; morningglory species, Ipomoea spp. # IPOSS; corn, Zea mays L. ‘Pioneer 3395 IR’, ‘Pioneer 32Z1B IR’.Additional index words: Imidazolinone herbicides, Ipomoea hederacea (L.) Jacq., Ipomoea lacunosa L., Ipomoea purpurea (L.) Roth, IPOHE, IPOLA, IPOPU, total postemergence, triketone herbicides.Abbreviations: DAT, days after treatment; POST, postemergence; WAT, weeks after treatment.
Intratumoral Administration of Anti-KITENIN shRNA-Loaded PEI-<I>alt</I>-PEG Nanoparticles Suppressed Colon Carcinoma Established Subcutaneously in Mice (2010)

Biodegradable gene carrier, termed as PEI-alt-PEG, has been synthesized based on Michael addition reaction between lower Mw PEI and poly(ethylene glycol) (PEG) diacrylate and tested its potential of anti-metastatic cancer gene therapy by using anti-KITENIN short hairpin RNA. KITENIN is known to promote invasion of mouse colon adenocarcinoma in vivo. Intratumoral administration of anti-KITENIN shRNA-loaded PEI-alt-PEG nanoparticles has shown suppressed proliferlation and enhanced apoptosis signal in tumor compared to commercial available liposome, leading to delayed tumor growth.
Managed video services over multi-domain software defined networks (2016)

We introduce a framework for provisioning end-to-end (E2E) managed video services over a multi-domain SDN, where different domains may be operated by different network providers. The proposed framework enables efficient dynamic management of network resources for network providers and ability to request the desired level of quality of experience (QoE) for end users. In the proposed fully-distributed E2E service framework, controllers of different domains negotiate with each other for the service level parameters of specific flows. The main contributions of this paper are a framework to provide E2E video services over multi-domain SDN, where functions that manage E2E services can collaborate with functions that manage network resources of respective domains, and a procedure for optimization of service parameters within each domain. The proposed framework and procedure have been verified over a newly developed large-scale multi-domain SDN emulation environment.