gebhart/patrepeval huggingface dataset:
magnetiza- tion dynamics in heterogeneous granular FePt media PATRICK GRAN- (2014)

URR, SIMES/SLAC — Granular FePt in the L10 phase is a key material for future magnetic data storage devices, supporting the smallest stable magnetic domains. Precessional eigenmodes have recently been studied with fs laser pump-probe techniques[Becker, et al APL 104, 152412 (2014)]. Large 400 GHz eigenfrequencies are observed due to the huge FePt magnetic anisotropy. However, such optical techniques only measure the collective spin precession of all grains without spatial resolution. Here we investigate the nanoscale aspects of magnetization dynamics in FePt with fs X-ray pulses from the Linac Coherent Light Source at Stanford. We show that optical excitation leads to distinctly different magnetic responses due to the size distribution of FePt grains. While part of the laser-excited magnetic grains follow a small applied magnetic field, others do not. The former display heat assisted magnetic recording. In contrast, the magnetic anisotropy of the latter is not significantly affected by laser excitation. Such grains display the typical high-frequency magnetization precession modes. We show that the interplay of “weak” and “hard” grains leads to magnetic frustration in the ground state causing heterogeneity that is partially lifted by laser excitation.
Electric loads characterization in an aircraft carrier with ring-bus distribution system (2015)

The increase in installed power onboard ships and the adoption of electric propulsion led to the need of a rather complex power system. The so-called Integrated Power System (IPS) feeds all the ship loads, integrating into a single entity the functions of generation, regulation, distribution and utilization of the electric power. The integration, thus being a powerful tool to increase vessel's performance, reliability and efficiency, permits also the propagation of disturbances to all the users fed by the IPS. Being Power Quality a primary need for the loads (and especially for some particular military ones) it is needed an assessment of the disturbances that can occur in the power system, both in terms of voltage and frequency transients and in terms of harmonic distortion. In this paper is presented a measurement campaign to assess disturbance levels and performance of a Naval vessel.
Small Cell Carcinoma Presenting as an Extrapulmonary Neoplasm: Sites of Origin and Response to Chemotherapy<xref ref-type="fn" rid="fn2">2</xref> (1981)

Eight (4%) of 203 consecutive prospectively staged and treated patients with small cell carcinoma (SCC) had no evidence of pulmonary or mediastinal tumor on chest roentgenogram or at fiberoptic bronchoscopy at the time of diagnosis. There were two distinct clinical presentations in these SCC patients with exclusively extrapulmonary tumors. Four had discrete localized extrapulmonary neoplasms, presumably originating in these sites. In the other 4 cases with either regional or widely metastatic disease, no obvious primary tumor could be documented in the lungs or elsewhere. One complete and two partial responses to chemotherapy (duration 6 to greater than 11 mo) occurred in 6 evaluable patients. Two remaining patients were inevaluable for response because they received adjuvant chemotherapy after irradiation or excision of the primary tumor and are free of disease at 15 and 28 months. Results document two clinicopathologic entities of extrapulmonary SCC, more firmly establish that it can be responsive to chemotherapy, and encourage systemic therapy as part of initial treatment planning.
Using Transposon Tn5 Insertions to Sequence Bacteriophage T4 Gene 11 (1989)

A simple and rapid method of creating an overlapping set of deletions in cloned DNA in preparation for sequencing has been developed. The method is based on a positive selection for Tn5 transposition into the cloned DNA fragment on a high-copy-number filamid, resolution of potential filamid dimers by filamentous phage infection, and the use of Tn5 both as a "portable" restriction enzyme site for in vitro DNA deletion and a "portable" sequencing primer binding site to initiate DNA sequencing reactions using a custom primer complementary to the outside ends of IS50. This new method has been utilized to sequence bacteriophage T4 gene 11, encoding the T4 baseplate protein gp11. The coding sequence of gene 11 is 657 bp in length, and predicts a primary structure of 219 amino acids that agrees well with the biochemical data previously obtained. DNA sequence around gene 11 suggests that the expression of genes 10, 11, and 12 of phage T4 are translationally coupled. Plasmids carrying deletions generated using this method have been used to map genetically five amber alleles of gene 11. These amber alleles were sequenced to confirm the proposed reading frame. The five amber alleles actually represent two different mutational changes at either codon 206 or 207, changing these adjacent glutamine codons to amber. The position of these amber alleles lends support to earlier studies identifying the carboxyl terminus of gp11 as essential in the interaction of P11 with baseplate protein P10 (Plishker and Berget, 1984).
Figure S4 from Detection of Promoter DNA Methylation in Urine and Plasma Aids the Detection of Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Figure S4&lt;/p&gt;
H2O on Pt(111): structure and stability of the first wetting layer (2012)

We study the structure and stability of the first water layer on Pt(111) by variable-temperature scanning tunneling microscopy. We find that a high Pt step edge density considerably increases the long-range order of the equilibrium √37 × √37R25.3°- and √39 × √39R16.1°-superstructures, presumably due to the capability of step edges to trap residual adsorbates from the surface. Passivating the step edges with CO or preparing a flat metal surface leads to the formation of disordered structures, which still show the same structural elements as the ordered ones. Coadsorption of Xe and CO proves that the water layer covers the metal surface completely. Moreover, we determine the two-dimensional crystal structure of Xe on top of the chemisorbed water layer which exhibits an Xe-Xe distance close to the one in bulk Xe and a rotation angle of 90° between the close-packed directions of Xe and the close-packed directions of the underlying water layer. CO is shown to replace H(2)O on the Pt(111) surface as has been deduced previously. In addition, we demonstrate that tunneling of electrons into the antibonding state or from the bonding state of H(2)O leads to dissociation of the molecules and a corresponding reordering of the adlayer into a √3 × √3R30°-structure. Finally, a so far not understood restructuring of the adlayer by an increased tunneling current has been observed.
Anti-insect Screening of Medicinal Plants from Kukrail Forest, Lucknow, India (2003)

Ten medicinal plants were evaluated at a dose of 10mg/ml for insecticidal, ovicidal, feeding-deterrence, growth inhibition and morphogenetic effects against various life stages of a noxious lepidopteran insect-pest, Spilarctia obliqua Walker. The acetone extract of Ageratum conyzoides, methanol extract of Justicia adhatoda, and chloroform extract of Plumbago zeylanica showed strong feeding-deterrence, growth inhibition and ovicidal effects against eggs and larvae of S. obliqua. In addition, the chloroform extract of P. zeylanica also created strong morphogenetic disorders in treated pupae of S. obliqua. The methanol extracts of Chenopodium ambrosioides and Ailanthus excelsa showed only feeding-deterrence and growth inhibitory effects but no ovicidal effect, whereas all the five extracts (hexane, chloroform, acetone, methanol and water) of Catharanthus roseus exhibited strong growth inhibition towards larvae of S. obliqua. The acetone extract of Vitex negundo was found to exhibit all the activities tested against S. obliqua. Other plants tested, Ajuga remota, Andrographis paniculata and Clerodendrum inermre, were found to have low to moderate effects towards S. obliqua.
A sátira na poesia e na poética de Jorge de Sena (2008)

The satire of Jorge de Sena is an accusation worded in a language which is one of the richest and fullest in self-awareness of all the satirical poetry written in Portuguese. From this evidence, the essay moves into the analysis of the markedly intellectual meaning of a creation investing in the diversification of verbal styles -from the most erudite to the most colloquial and obscene -and in the coexistence of states of mind: melancholy and anger are brought together in a compound whose emphasis varies in accordance with the play of forces acting in the poem.
Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm (2023)

In this study, genomic and plasmid characteristics of Escherichia coli were determined with the aim of deducing how mcr genes may have spread on a colistin withdrawn pig farm. Whole genome hybrid sequencing was applied to six mcr-positive E. coli (MCRPE) strains isolated from pigs, a farmworker and wastewater collected between 2017 and 2019. Among these, mcr-1.1 genes were identified on IncI2 plasmids from a pig and wastewater, and on IncX4 from the human isolate, whereas mcr-3 genes were found on plasmids IncFII and IncHI2 in two porcine strains. The MCRPE isolates exhibited genotypic and phenotypic multidrug resistance (MDR) traits as well as heavy metal and antiseptic resistance genes. The mcr-1.1-IncI2 and IncX4 plasmids carried only colistin resistance genes. Whereas, the mcr-3.5-IncHI2 plasmid presented MDR region, with several mobile genetic elements. Despite the MCRPE strains belonged to different E. coli lineages, mcr-carrying plasmids with high similarities were found in isolates from pigs and wastewater recovered in different years. This study highlighted that several factors, including the resistomic profile of the host bacteria, co-selection via adjunct antibiotic resistance genes, antiseptics, and/or disinfectants, and plasmid-host fitness adaptation may encourage the maintenance of plasmids carrying mcr genes in E. coli.
Tomato Pto encodes a functional N‐myristoylation motif that is required for signal transduction in Nicotiana benthamiana (2005)

Pto kinase of tomato (Lycopersicon esculentum) confers resistance to bacterial speck disease caused by Pseudomonas syringae pv. tomato expressing avrPto or avrPtoB. Pto interacts directly with these type-III secreted effectors, leading to induction of defence responses including the hypersensitive response (HR). Signalling by Pto requires the nucleotide-binding site-leucine-rich repeat (NBS-LRR) protein Prf. Little is known of how Pto is controlled prior to or during stimulation, although kinase activity is required for Avr-dependent activation. Here we demonstrate a role for the N-terminus in signalling by Pto. N-terminal residues outside the kinase domain were required for induction of the HR in Nicotiana benthamiana. The N-terminus also contributed to both AvrPto-binding and phosphorylation abilities. Pto residues 1-10 comprise a consensus motif for covalent attachment of myristate, a hydrophobic 14-carbon saturated fatty acid, to the Gly-2 residue. Several lines of evidence indicate that this motif is important for Pto function. A heterologous N-myristoylation motif complemented N-terminal deletion mutants of Pto for Prf-dependent signalling. Signalling by wild-type and mutant forms of Pto was strictly dependent on the Gly-2 residue. The N-myristoylation motif of Pto complemented the cognate motif of AvrPto for avirulence function and membrane association. Furthermore, Pto was myristoylated in vivo dependent on the presence of Gly-2. The subcellular localization of Pto was independent of N-myristoylation, indicating that N-myristoylation is required for some function other than membrane affinity. Consistent with this idea, AvrPtoB was also found to be a soluble protein. The data indicate an important role(s) for the myristoylated N-terminus in Pto signalling.
Conformational analysis and helical preferences of normal and α,α‐dialkyl amino acids (1990)

Abstract Energy calculations have been performed on right‐handed helical structures of L ‐alanine and α‐methylalanine oligomers. A new ′3.6 10 ′‐helix is described for α‐methylalanine peptides. The dependence of the relative stability of the α, 3 10 , and 3.6 10 structural forms on helix length, dielectric, and force‐field, in the gas phase, has been studied. Potential energy surfaces for the interconversion of helices have been generated. The 3 10 ‐helix in α‐methylalanine oligomers exhibits a degree of enthalpic and entropic stabilization not observed for alanine. The relevance of the results to the formation of voltage‐sensitive ion channels is discussed.
Cyclosporine-Induced Nephrotoxicity (1984)

Cyclosporine is a unique immunosuppressive agent that inhibits activation of both B and T lymphocytes as well as certain macrophage functions; however, the predominant effect of the drug appears to reside in its interference with the release of interleukin-2, which stimulates antigen-activated helper and cytotoxic T cells to commence DNA synthesis.1 On the other hand, the drug does not grossly interfere with the activation of antigen-specific suppressor T cells in vivo2 or in vitro.3 Despite the remarkable effectiveness of cyclosporine in experimental models and in the clinic, as well as the absence of potent myelosuppressive effects, cyclosporine-induced nephrotoxicity remains a . . .
HSF2 cooperates with HSF1 to drive a transcriptional program critical for the malignant state (2022)

Heat shock factor 1 (HSF1) is well known for its role in the heat shock response (HSR), where it drives a transcriptional program comprising heat shock protein (HSP) genes, and in tumorigenesis, where it drives a program comprising HSPs and many noncanonical target genes that support malignancy. Here, we find that HSF2, an HSF1 paralog with no substantial role in the HSR, physically and functionally interacts with HSF1 across diverse types of cancer. HSF1 and HSF2 have notably similar chromatin occupancy and regulate a common set of genes that include both HSPs and noncanonical transcriptional targets with roles critical in supporting malignancy. Loss of either HSF1 or HSF2 results in a dysregulated response to nutrient stresses in vitro and reduced tumor progression in cancer cell line xenografts. Together, these findings establish HSF2 as a critical cofactor of HSF1 in driving a cancer cell transcriptional program to support the anabolic malignant state.
Quantitative ultrasound imaging of the uterus for improved embryo implantation: Preliminary study (2015)

Enhanced by the modern trend in postponing conception, infertility problems touch nowadays an increasing number of women. Many couples are therefore referred for in vitro fertilization procedures. Despite representing the most advanced option, in vitro fertilization still counts for a low success rate of about 30%. There is evidence that uterine movement may play an important role influencing the procedure outcome. Until now, no objective means of measuring uterine movement is available. Therefore, in this work we present the first method for quantitative analysis of the uterine movement. Given its widespread availability and relatively low cost, ultrasound imaging is employed for the analysis. In particular, a speckle-tracking algorithm has been implemented that is based on block matching by normalized cross correlation. Wiener deconvolution is used to regularize the image resolution prior to speckle tracking. The method feasibility was tested for its ability to distinguish between active and non-active phase of a natural menstrual cycle in eight women. Two pairs of sites were manually defined on the uterine muscle and automatically tracked over time. Variance and mean frequency of the strain and distance between these sites were the features extracted and evaluated for classification. The results are promising, showing significant class separation by Student t-test (p <; 0.05), and sensitivity and specificity both equal to 75% for the strain variance and distance mean frequency. Extensive validation is however required to confirm this result, also involving the evaluation of additional features. Once fully validated, this method will be tested for quantitative evaluation of uterine movement in the context of in vitro fertilization.
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells (2013)

High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE
EXPERIMENTAL EVOLUTION OF HSP70 EXPRESSION AND THERMOTOLERANCE IN DROSOPHILA MELANOGASTER (1999)

To examine whether recent evolutionary history affects the expression of Hsp70, the major heat-induced-heat shock protein in Drosophila melanogaster, we measured Hsp70 expression, thermotolerance, and hsp70 gene number in replicate populations undergoing laboratory evolution at different temperatures. Despite Hsp70's ancient and highly conserved nature, experimental evolution effectively and replicably modified its expression and phenotype (thermotolerance). Among five D. melanogaster populations founded from a common ancestral population and raised at three different temperatures (one at 18°C, two each at 25°C and 28°C) for twenty years, Hsp70 expression varies in a consistent pattern: the replicate 28°C lines expressed 30-50% less Hsp70 than the other lines at a range of inducing temperatures. This modification was refractory to acclimation, and correlated with thermotolerance: the 28°C lines had significantly lower inducible tolerance of 38.5°C and 39°C. We verified the presence of five hsp70 genes in the genome of each line, excluding copy number variation as a candidate molecular basis of the evolved difference in expression. These findings support the ability of Hsp70 levels in D. melanogaster populations to change over microevolutionary time scales and implicate constancy of environmental temperature as a potentially important selective agent.
Representing Formal Languages: A Comparison Between Finite Automata and Recurrent Neural Networks (2019)

We investigate the internal representations that a recurrent neural network (RNN) uses while learning to recognize a regular formal language. Specifically, we train a RNN on positive and negative examples from a regular language, and ask if there is a simple decoding function that maps states of this RNN to states of the minimal deterministic finite automaton (MDFA) for the language. Our experiments show that such a decoding function indeed exists, and that it maps states of the RNN not to MDFA states, but to states of an {\em abstraction} obtained by clustering small sets of MDFA states into "superstates". A qualitative analysis reveals that the abstraction often has a simple interpretation. Overall, the results suggest a strong structural relationship between internal representations used by RNNs and finite automata, and explain the well-known ability of RNNs to recognize formal grammatical structure.
Automated discovery of structural features of the optic nerve head on the basis of image and genetic data (2014)

Evaluation of optic nerve head (ONH) structure is a commonly used clinical technique for both diagnosis and monitoring of glaucoma. Glaucoma is associated with characteristic changes in the structure of the ONH. We present a method for computationally identifying ONH structural features using both imaging and genetic data from a large cohort of participants at risk for primary open angle glaucoma (POAG). Using 1054 participants from the Ocular Hypertension Treatment Study, ONH structure was measured by application of a stereo correspondence algorithm to stereo fundus images. In addition, the genotypes of several known POAG genetic risk factors were considered for each participant. ONH structural features were discovered using both a principal component analysis approach to identify the major modes of variance within structural measurements and a linear discriminant analysis approach to capture the relationship between genetic risk factors and ONH structure. The identified ONH structural features were evaluated based on the strength of their associations with genotype and development of POAG by the end of the OHTS study. ONH structural features with strong associations with genotype were identified for each of the genetic loci considered. Several identified ONH structural features were significantly associated (p &lt; 0.05) with the development of POAG after Bonferroni correction. Further, incorporation of genetic risk status was found to substantially increase performance of early POAG prediction. These results suggest incorporating both imaging and genetic data into ONH structural modeling significantly improves the ability to explain POAG-related changes to ONH structure.
Molecular Therapeutic Strategies Targeting Duchenne Muscular Dystrophy (2010)

Since the discovery of the gene for Duchenne muscular dystrophy more than 20 years ago, scientists have worked to apply molecular principles for restoration of the dystrophin protein and correction of the underlying physiologic defect that predisposes muscle fibers to injury. Recent studies provide realistic hope that molecular therapies may help patients who have this disorder. At present, only corticosteroids can improve walking ability and increase quality of life for boys with this disease. The results are modest and encumbered by side effects. The authors review 3 molecular therapeutic approaches that have been introduced into the clinic: (1) gene replacement therapy, (2) mutation suppression, and (3) exon skipping.
Simultaneous SPECT studies of pre- and postsynaptic dopamine binding sites in baboons. (1999)

This is the first example that clearly demonstrates the feasibility of simultaneous imaging of both pre- and postsynaptic sites of the dopaminergic system in baboons with dual-isotope SPECT studies. With or without corrections for cross-contamination of 123I into the 99mTc window, striatum-to-cerebellum ratios (target-to-nontarget) of dual-isotope experiments did not differ significantly from single-isotope experiments. This method may be a valuable and cost-effective tool for gaining comprehensive information about the dopaminergic system in one SPECT imaging session.