gebhart/patrepeval huggingface dataset:
P4‐222: NEW FORMULATION OF LITHIUM IMPROVES COGNITIVE PERFORMANCE IN EARLY STAGES OF ALZHEIMER‐LIKE AMYLOID PATHOLOGY IN TRANSGENIC RATS (2014)

Lithium, a drug widely used for treatment of bipolar disorder, has disease-modifying properties both in patients at risk for developing Alzheimer disease and in AD transgenic animal models. However, an understanding of the exact active mechanisms underlying lithium-mediated neuroprotection remains elusive. Moreover, conventional lithium has a narrow therapeutic window and many significant adverse neurotoxic side effects, making it inappropriate for long-term treatment. We have developed a transgenic rat model of Alzheimer-like Aβ pathology (coded McGill-R-Thy1-APP) that incorporates Swedish and Indiana human APP gene mutations. These rats develop Aβ plaques as early as 6-9 months of age, and display intraneuronal Aβ accumulation of the toxic oligomeric soluble form before plaque formation - as has been shown to occur in human AD and Down's syndrome. It is significant that McGill-R-Thy1-APP rats present progressive behaviour impairments starting at 3 months of age, while no amyloid plaques are yet present, when subjected to Morris water maze, auditory fear conditioning, and Novel Object Recognition and Location tasks. In this project, we have evaluated the therapeutic efficacy of a recently developed transmucosal formulation of lithium whose lower dose achieves therapeutic effects in the absence of associated side effects. Prior to the onset of Aβ plaque deposition in the transgenic animals, Mcgill-R-Thy1-APP transgenic rats and non-transgenic littermate controls were treated and cognitively assessed. Both groups received a novel formulation of lithium or vehicle control for six weeks and were assessed using the cognitive tests described above. Modifications of the APP cascade, markers of synaptic plasticity and neuroinflammatory processes were examined by ELISA, Western blotting and immunohistochemistry. Lithium-treated transgenic rats displayed notable improvements on Morris water maze and fear-conditioning paradigms compared to vehicle-treated transgenic animals. Improvements in cognition were accompanied by modulation of synaptic and inflammatory markers, APP processing, and occurred in the absence of the regular negative side effects previously observed following treatment with standard lithium. We conclude that this novel formulation of lithium has a therapeutic effect in APP transgenic rats at the earliest stages of Alzheimer-like amyloid pathology.
Barrett's metaplasia glands are clonal, contain multiple stem cells and share a common squamous progenitor (2011)

In normal oesophageal squamous epithelium, a single stem cell clone can populate large areas of epithelium. Barrett's metaplasia glands are clonal units, contain multiple multipotential stem cells and most likely divide by fission. Furthermore, a single cell of origin can give rise to both squamous and glandular epithelium suggesting oesophageal plasticity.
Network Modeling Reveals Prevalent Negative Regulatory Relationships between Signaling Sectors in Arabidopsis Immune Signaling (2010)

Biological signaling processes may be mediated by complex networks in which network components and network sectors interact with each other in complex ways. Studies of complex networks benefit from approaches in which the roles of individual components are considered in the context of the network. The plant immune signaling network, which controls inducible responses to pathogen attack, is such a complex network. We studied the Arabidopsis immune signaling network upon challenge with a strain of the bacterial pathogen Pseudomonas syringae expressing the effector protein AvrRpt2 (Pto DC3000 AvrRpt2). This bacterial strain feeds multiple inputs into the signaling network, allowing many parts of the network to be activated at once. mRNA profiles for 571 immune response genes of 22 Arabidopsis immunity mutants and wild type were collected 6 hours after inoculation with Pto DC3000 AvrRpt2. The mRNA profiles were analyzed as detailed descriptions of changes in the network state resulting from the genetic perturbations. Regulatory relationships among the genes corresponding to the mutations were inferred by recursively applying a non-linear dimensionality reduction procedure to the mRNA profile data. The resulting static network model accurately predicted 23 of 25 regulatory relationships reported in the literature, suggesting that predictions of novel regulatory relationships are also accurate. The network model revealed two striking features: (i) the components of the network are highly interconnected; and (ii) negative regulatory relationships are common between signaling sectors. Complex regulatory relationships, including a novel negative regulatory relationship between the early microbe-associated molecular pattern-triggered signaling sectors and the salicylic acid sector, were further validated. We propose that prevalent negative regulatory relationships among the signaling sectors make the plant immune signaling network a "sector-switching" network, which effectively balances two apparently conflicting demands, robustness against pathogenic perturbations and moderation of negative impacts of immune responses on plant fitness.
HLA DQB1*0602 is associated with cataplexy in 509 narcoleptic patients. (1997)

Narcolepsy is a sleep disorder associated with HLA DR15 (DR2) and DQB1*0602. We HLA typed 509 patients enrolled in a clinical trial for the drug modafinil and analyzed the results in relation to cataplexy, a symptom of narcolepsy characterized by muscle weakness triggered by emotions. The patients were either subjects with cataplexy who had a mean sleep latency (SL) of less than 8 minutes and two or more sleep onset rapid eye movement (REM) periods (SOREMPs) during a multiple sleep latency test, or narcoleptic patients without cataplexy but with a mean SL shorter than 5 minutes and two or more SOREMPs. The respective values of DRB1*15 (DR2) and DQB1*0602 as markers for narcolepsy were first compared in different ethnic groups and in patients with and without cataplexy. DQB1*0602 was found to be a more sensitive marker for narcolepsy than DRB1*15 across all ethnic groups. DQB1*0602 frequency was strikingly higher in patients with cataplexy versus patients without cataplexy (76.1% in 421 patients versus 40.9% in 88 patients). Positivity was highest in patients with severe cataplexy (94.8%) and progressively decreased to 54.2% in patients with the mildest cataplexy. A voluntary 50-item questionnaire focusing on cataplexy was also analyzed in 212 of the 509 HLA-typed patients. Subjects with definite cataplexy as observed by an experienced clinician were more frequently HLA DQB1*0602-positive than those with doubtful cataplexy, and the manifestations of cataplexy were clinically more typical in DQB1*0602-positive patients. These results show that the HLA association is as tight as previously reported (85-95%) when cataplexy is clinically typical or severe. We also found that patients with mild, atypical, or no cataplexy have a significantly increased DQB1*0602 frequency (40-60%) in comparison with ethnically matched controls (24%). These results could be explained by increased disease heterogeneity in the noncataplexy group or by a direct effect of the HLA DQB1*0602 genotype on the clinical expression of narcolepsy.
Evolution and Regulation of the <i>Lotus japonicus LysM Receptor</i> Gene Family (2010)

LysM receptor kinases were identified as receptors of acylated chitin (Nod factors) or chitin produced by plant-interacting microbes. Here, we present the identification and characterization of the LysM receptor kinase gene (Lys) family (17 members) in Lotus japonicus. Comprehensive phylogenetic analysis revealed a correlation between Lys gene structure and phylogeny. Further mapping coupled with sequence-based anchoring on the genome showed that the family has probably expanded by a combination of tandem and segmental duplication events. Using a sliding-window approach, we identified distinct regions in the LysM and kinase domains of recently diverged Lys genes where positive selection may have shaped ligand interaction. Interestingly, in the case of NFR5 and its closest paralog, LYS11, one of these regions coincides with the predicted Nod-factor binding groove and the suggested specificity determining area of the second LysM domain. One hypothesis for the evolutionary diversification of this receptor family in legumes is their unique capacity to decipher various structures of chitin-derived molecules produced by an extended spectrum of interacting organisms: symbiotic, associative, endophytic, and parasitic. In a detailed expression analysis, we found several Lotus Lys genes regulated not only during the symbiotic association with Mesorhizobium loti but also in response to chitin treatment.
Area Optimization of Slicing Floorplans in Parallel (1994)

We first present a parallel algorithm for finding the optimal implementations for the modules of a slicing floorplan that respects a given slicing tree. The algorithm runs in O( n ) time and requires O( n ) processors, where n is the number of modules. It is based on a new O( n 2 ) sequential algorithm for solving the above problem. We then present a parallel algorithm for finding a set of optimal implementations for a slicing floorplan whose corresponding slicing tree has height O(log n ). This algorithm runs in O( n ) time using O(log n ) processors. Our parallel algorithms do not need shared memory and can be implemented in a distributed system.
Microscopic frictional forces on molecular motion in liquids. Picosecond rotational diffusion in alkanes and alcohols (1987)

The rotational diffusion times of the nonpolar solutes p-terphenyl, p-quaterphenyl, and 9,10-diphenylanthracene dissolved in n-alkane and n-alcohol solvents are reported. The observed microscopic frictional coefficients approximate the predictions of ‘‘slip’’ hydrodynamics in n-alkanes. Substantially lower friction is found in n-alcohols of comparable viscosity. Large deviations are also observed in branched alkane and dialcohol solvents. These differences are interpreted as an indication of nonhydrodynamic behavior in the microscopic rotational friction. Comparison with the results of other recent studies supports this interpretation and also indicate that charged solutes experience higher friction than the neutral solutes used in this study. The difference between charged and uncharged solutes is attributed to the larger effective volume of charged species, as well as to dielectric friction and solvation environment effects. A new picosecond spectroscopic technique based on stimulated emission gain anisotropy relaxation is used to perform the experiments.
Learning to Rank Learning Curves (2020)

Many automated machine learning methods, such as those for hyperparameter and neural architecture optimization, are computationally expensive because they involve training many different model configurations. In this work, we present a new method that saves computational budget by terminating poor configurations early on in the training. In contrast to existing methods, we consider this task as a ranking and transfer learning problem. We qualitatively show that by optimizing a pairwise ranking loss and leveraging learning curves from other datasets, our model is able to effectively rank learning curves without having to observe many or very long learning curves. We further demonstrate that our method can be used to accelerate a neural architecture search by a factor of up to 100 without a significant performance degradation of the discovered architecture. In further experiments we analyze the quality of ranking, the influence of different model components as well as the predictive behavior of the model.
Identification of Small Amounts of Coal Tar Dyes in Foods by Reversed-Phase TLC/Scanning Densitometry with Sample Concentration Techniques (1998)

We have investigated the applicability of TLC/scanning densitometry (TLC/SCAN) to the analysis of small amounts of coal tar dyes in foods. The use of a combination of reversed-phase C18 TLC and sample concentration techniques on the TLC plate enabled us to measure the visible absorption spectra of small amounts of coal tar dyes in foods with good accuracy. The sample concentration techniques improved the detection limits 10-20-fold. The TLC/SCAN was successfully applied to the identification of coal tar dyes in 48 food samples which were suspected to be in violation of the Japanese Food Sanitation Law. The present method is convenient for the rapid identification of small amounts of coal tar dyes in foods.
Validation of Modulation Transfer Functions and Noise Power Spectra from Natural Scenes (2019)

The Modulation Transfer Function (MTF) and the Noise Power Spectrum (NPS) characterize imaging system sharpness/resolution and noise, respectively. Both measures are based on linear system theory. However, they are applied routinely to scene-dependent systems applying non-linear, content-aware image signal processing. For such systems, MTFs/NPSs are derived inaccurately from traditional test charts containing edges, sinusoids, noise or uniform luminance signals, which are unrepresentative of natural scene signals. The dead leaves test chart delivers improved measurements from scene-dependent systems but still has its limitations. In this article, the authors validate novel scene-and-process-dependent MTF (SPD-MTF) and NPS (SPD-NPS) measures that characterize (i) system performance concerning one scene, (ii) average real-world performance concerning many scenes or (iii) the level of system scene dependency. The authors also derive novel SPD-NPS and SPD-MTF measures using the dead leaves chart. They demonstrate that the proposed measures are robust and preferable for scene-dependent systems to current measures.
Solution treatment of AC1A aluminum alloy reinforced with aluminum borate whiskers. (1996)

The conditions for solution and aging treatments of AC1A aluminum alloy reinforced with aluminum borate whiskers were investigated. When the composite was solution treated at 843 K for 100 ks, the whiskers reacted with AC1A and γ–Al2O3 was formed on the surfaces of the whiskers. At a lower temperature of 773 K, θ phase did not dissolve and no age hardening was obtained. On the other hand, the solution treatment at 788 K for 10 ks or longer dissolved these θ phase, resulting in age hardening. As an increase of aging time to 100 ks did not increase hardness, the temperature of 733 K and time of 10 ks are recommend for the conditions for solution treatment. It was found that surface reaction between the whiskers and AC1A did not reduced the amount of Cu in the alloy; thus this finding can explain the age hardening. In age hardening, the composite reached its highest hardness faster than the alloy, due to the acceleration effect in the composite for precipitation of θ' phase. The tensile strength of the composite showed a change with aging time similar to the hardness. The age treatment at 433 K for 72 ks resulted in the improvement of tensile strength to the similar extent to the alloy.
ChemInform Abstract: Nucleophilic Additions to (4S)‐1‐Alkylidene‐2,4‐dihydro‐1H‐pyrazino[2,1‐b]quinazoline‐3,6‐diones. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Oxygen Attenuates Atelectasis-induced Injury in the In Vivo  Rat Lung (2005)

Although supplemental oxygen worsened atelectasis in this model, it prevented the pathologic effects of atelectasis, including microvascular leak and pulmonary hypertension. Atelectasis-induced lung injury seems to be mediated by hypoxia rather than by the direct mechanical effects of atelectasis.
Antiviral-Activated Dendritic Cells: A Paracrine-Induced Response State (2008)

Infection of immature dendritic cells (DCs) by virus stimulates their maturation into APC. Infected DCs can also expose uninfected DCs to a panoply of cytokines/chemokines via paracrine signaling. Mathematical modeling suggests that a high rate of paracrine signaling is likely to occur among DCs located in three-dimensional space. Relatively little is known about how secreted factors modify the early response to virus infection. We used a transwell experimental system that allows passage of secreted factors, but not direct contact, between virus-infected DCs and uninfected DCs to investigate paracrine signaling responses. Paracrine signaling from infected DCs induced an antiviral-primed DC state distinct from that of mature virus-infected DCs that we refer to as antiviral-activated DCs (AVDCs). AVDCs had increased surface MHC class II and CD86 levels, but in contrast to virus-infected DCs, their MHC class I levels were unchanged. Imaging flow cytometry showed that AVDCs had an increased rate of phagocytosis compared with naive DCs. Experiments with IFN-beta cytokine indicated that it may be responsible for CD86, but not MHC class II regulation in AVDCs. Both IFN-inducible and IFN-independent genes are up-regulated in AVDCs. Notably, AVDCs are relatively resistant to virus infection in comparison to naive DCs and achieve accelerated and augmented levels of costimulatory molecule expression with virus infection. AVDCs show a distinct antiviral-primed state of DC maturation mediated by DC paracrine signaling. Although further in vivo study is needed, the characteristics of the AVDC suggest that it is well suited to play a role in the early innate-adaptive transition of the immune system.
Implementation of Ternary Weights with Resistive RAM Using a Single\n Sense Operation per Synapse (2020)

The design of systems implementing low precision neural networks with\nemerging memories such as resistive random access memory (RRAM) is a\nsignificant lead for reducing the energy consumption of artificial\nintelligence. To achieve maximum energy efficiency in such systems, logic and\nmemory should be integrated as tightly as possible. In this work, we focus on\nthe case of ternary neural networks, where synaptic weights assume ternary\nvalues. We propose a two-transistor/two-resistor memory architecture employing\na precharge sense amplifier, where the weight value can be extracted in a\nsingle sense operation. Based on experimental measurements on a hybrid 130 nm\nCMOS/RRAM chip featuring this sense amplifier, we show that this technique is\nparticularly appropriate at low supply voltage, and that it is resilient to\nprocess, voltage, and temperature variations. We characterize the bit error\nrate in our scheme. We show based on neural network simulation on the CIFAR-10\nimage recognition task that the use of ternary neural networks significantly\nincreases neural network performance, with regards to binary ones, which are\noften preferred for inference hardware. We finally evidence that the neural\nnetwork is immune to the type of bit errors observed in our scheme, which can\ntherefore be used without error correction.\n
The aggregated form of an AAMP derived peptide behaves as a heparin sensitive cell binding agent (1997)

A peptide termed P189, derived from the sequence of a newly discovered protein, AAMP (angio-associated migratory cell protein), contains a motif that is predicted to a bind heparin. It occurs near the amino terminal end of AAMP. Previous studies have shown that in its solubilized form P189 (RRLRRMESESES) binds heparin and melanoma cells. The peptide is bipolar in that it contains positive charges at its amino end and negative charges at its carboxyl end. It forms strongly aggregated particles that require exposure to 50% DMSO and 100 degrees C for solubilization to occur. Now heparin and cell binding (heparin sensitive) are also demonstrated for the peptide in its particular form. Cell binding/clustering to the peptide particles is strong and resists exposure to various reagents (sugars and inhibitors of glycolysis and protein synthesis) except heparin. Tumor cell migration is partially inhibited by the presence of the peptide. On electron photomicrographs the peptide is seen in close apposition to cell membranes. Heparin sensitivity of the cell binding indicates that cell surface glycosaminoglycans are involved. The aggregated peptide binds heparin in a saturable manner with a dissociation constant, K(d), of 306 pmol. Cell binding/clustering studies using peptide variants of P189, which have substitutions in either the charged and/or nonpolar residues, show that the specific sequence of P189 optimizes heparin-sensitive cell aggregation. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 365-372, 1997.
D6.22- 4th periodic report on PhDs (2022)

12-month progress of the One Health EJP PhD students between January and December 2021
Infection with retroviral vectors leads to perturbed DNA replication increasing vector integrations into fragile sites (2013)

Genome instability is a hallmark of cancer. Common fragile sites (CFSs) are specific regions in the human genome that are sensitive to replication stress and are prone to genomic instability in different cancer types. Here we molecularly cloned a new CFS, FRA11H, in 11q13. The genomic region of FRA11H harbors a hotspot of chromosomal breakpoints found in different types of cancer, indicating that this region is unstable during cancer development. We further found that FRA11H is a hotspot for integrations of Murine Leukemia Virus (MLV)-based vectors, following CD34+ infections in vitro as well as ex-vivo during gene therapy trials. Importantly, we found that the MLV-based vector infection in-vitro leads to replication perturbation, DNA damage and increased CFS expression. This suggests that infection by MLV-based vectors leads to replication-induced genome instability, raising further concerns regarding the use of retroviral vectors in gene therapy trials.
Molecular dynamics of the primary photochemical event in bacteriorhodopsin. Theoretical evidence for an excited singlet state assignment for the J intermediate (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular dynamics of the primary photochemical event in bacteriorhodopsin. Theoretical evidence for an excited singlet state assignment for the J intermediateRobert R. Birge, Leonore A. Findsen, and Brian M. PierceCite this: J. Am. Chem. Soc. 1987, 109, 16, 5041–5043Publication Date (Print):August 1, 1987Publication History Published online1 May 2002Published inissue 1 August 1987https://pubs.acs.org/doi/10.1021/ja00250a056https://doi.org/10.1021/ja00250a056research-articleACS PublicationsRequest reuse permissionsArticle Views69Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts