gebhart/patrepeval huggingface dataset:
Molecular biology of tick acetylcholinesterases (2017)

Ticks vector many pathogens with major health and economic impacts and have developed resistance to most acaricides used for tick control. Organophosphate (OP) acaricides target acetylcholinesterase (AChE) critical to tick central nervous system function. Mutations producing tick AChEs resistant to OPs were characterized; but tick OP-resistance is not fully elucidated, due to remarkable complexity of tick cholinergic systems. Three paralogous tick AChEs exhibiting differences in primary structure and biochemical kinetics are encoded by amplified genes with developmentally regulated expression. Gene silencing data suggest tick AChEs are functional complements <i>in vivo,</i> and transcriptomic and genomic data suggest existence of additional tick AChEs. Cholinergic systems are crucial in neural transmission and are also regulators of vertebrate immune function. Ticks exhibit prolonged intimate host contact, suggesting adaptive functions for tick cholinergic system complexity. AChE was recently reported in tick saliva and a role in manipulation of host immune responses was hypothesized. Physiological roles and genetic control of multiple tick AChEs requires further elucidation and may provide unique opportunities to understand and manipulate cholinergic involvement in biological systems.
Biological markers for early detection and pharmacological treatment of Alzheimer's disease. (2009)

The introduction of biological markers in the clinical management of Alzheimer's disease (AD) will not only improve diagnosis relating to early detection of neuropathology with underlying molecular mechanisms, but also provides tools for the assessment of objective treatment benefits. In this review, we identify a number of in vivo neurochemistry and neuroimaging techniques, which can reliably assess aspects of physiology, pathology, chemistry, and neuroanatomy of AD, and hold promise as meaningful biomarkers in the early diagnostic process, as well as for the tracking of disease-modifying pharmacological effects. These neurobiological measures appear to relate closely to pathophysiological, neuropathological, and clinical data, such as hyperphosphorylation of tau, abeta metabolism, lipid peroxidation, pattern and rate of atrophy, loss of neuronal integrity, and functional and cognitive decline, as well as risk of future decline. As a perspective, the important role of biomarkers in the development of innovative drug treatments for AD and the related regulatory process is discussed.
Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia (2019)

Abstract Active retrotransposons in the human genome (L1, Alu and SVA elements) can create genomic mobile element insertions (MEIs) in both germline and somatic tissue 1 . Specific somatic MEIs have been detected at high levels in human cancers 2 , and at lower to medium levels in human brains 3 . Dysregulation of somatic retrotransposition in the human brain has been hypothesized to contribute to neuropsychiatric diseases 4, 5 . However, individual somatic MEIs are present in small proportions of cells at a given anatomical location, and thus standard whole-genome sequencing (WGS) presents a difficult signal-to-noise problem, while single-cell approaches suffer from limited scalability and experimental artifacts introduced by enzymatic whole-genome amplification 6 . Previous studies produced widely differing estimates for the somatic retrotransposition rates in human brain 3, 6–8 . Here, we present a highly precise machine learning method (RetroSom) to directly identify somatic L1 and Alu insertions in &lt;1% cells from 200× deep WGS, which allows circumventing the restrictions of whole-genome amplification. Using RetroSom we confirmed a lower rate of retrotransposition for individual somatic L1 insertions in human neurons. We discovered that anatomical distribution of somatic L1 insertion is as widespread in glia as in neurons, and across both hemispheres of the brain, indicating retrotransposition occurs during early embryogenesis. We characterized two of the detected brain-specific L1 insertions in great detail in neurons and glia from a donor with schizophrenia. Both insertions are within introns of genes active in brain ( CNNM2 , FRMD4A ) in regions with multiple genetic associations with neuropsychiatric disorders 9–11 . Gene expression was significantly reduced by both somatic insertions in a reporter assay. Our results provide novel insights into the potential for pathological effects of somatic retrotransposition in the human brain, now including the large glial fraction. RetroSom has broad applicability in all disease states where somatic retrotransposition is expected to play a role, such as autoimmune disorders and cancer.
X Pinches in Frames (2005)

Summary form only given. The X-pinch plasma has established itself as an extraordinarily useful tool for studying the dynamics and kinetics of hot, dense plasmas as well as for high resolution imaging. An X-pinch plasma is formed when two or more fine wires, which cross at a point to form an "X," are used as the load of a pulse power machine. When this configuration is exploded to form a plasma, a Z-pinch forms near the original cross point of the wires. This process produces small, bright plasmas that emit nanosecond scale X-ray bursts in the 1-15 keV range. For our experiments the X pinches were driven with Cornell's XP pulser, which reaches a peak current of about 450 kA in 40-50 ns. The small (micron scale) X-ray sources produced are useful for point projection X-ray imaging. Thus, in order to maximize the usefulness of X pinches we must find ways to control the unstable process that produces the X-ray bright spots. Furthermore, in order to advance the study of X-pinch plasmas it would be helpful to find a way to increase the rate at which X-pinch pulses can be taken. Consequently, we have devised a setup to improve both of these situations. Initially, we designed an X-pinch "frame" to increase the repetition rate for X-pinch pulses since many frames can be loaded in advance, reducing the setup time for each experiment. In addition, we imagine using several frames chained together in order to change the load under vacuum. In testing we found that many of the frame materials used would conduct too much of the current as result of UV induced flashover. We found that of the materials tested, fiberglass was able to hold off the UV flashover the longest without a need for additional shielding. The fiberglass frames allowed enough load current to produce a high quality bright spot while the conduction due to UV flashover prevented subsequent bursts and minimized the production of energetic electrons. All of these conditions lead to increased image quality. We also found that the intensity of higher energy X-rays (above 8 keV) was significantly reduced. Therefore, these X pinches are most useful for soft X-ray imaging. Additionally, we tested various geometries, including several X pinches in series, which can give us information from multiple X pinches in a single shot
Supplementary Tables S1-S13 from Cancer Cell Intrinsic and Immunologic Phenotypes Determine Clinical Outcomes in Basal-like Breast Cancer (2023)

&lt;p&gt;Excel file containing Tables S1 through S13&lt;/p&gt;
Rho1p-Bni1p-Spa2p Interactions: Implication in Localization of Bni1p at the Bud Site and Regulation of the Actin Cytoskeleton inSaccharomyces cerevisiae (1998)

Rho1p is a yeast homolog of mammalian RhoA small GTP-binding protein. Rho1p is localized at the growth sites and required for bud formation. We have recently shown that Bni1p is a potential target of Rho1p and that Bni1p regulates reorganization of the actin cytoskeleton through interactions with profilin, an actin monomer-binding protein. Using the yeast two-hybrid screening system, we cloned a gene encoding a protein that interacted with Bni1p. This protein, Spa2p, was known to be localized at the bud tip and to be implicated in the establishment of cell polarity. The C-terminal 254 amino acid region of Spa2p, Spa2p(1213-1466), directly bound to a 162-amino acid region of Bni1p, Bni1p(826-987). Genetic analyses revealed that both the bni1 and spa2 mutations showed synthetic lethal interactions with mutations in the genes encoding components of the Pkc1p-mitogen-activated protein kinase pathway, in which Pkc1p is another target of Rho1p. Immunofluorescence microscopic analysis showed that Bni1p was localized at the bud tip in wild-type cells. However, in the spa2 mutant, Bni1p was not localized at the bud tip and instead localized diffusely in the cytoplasm. A mutant Bni1p, which lacked the Rho1p-binding region, also failed to be localized at the bud tip. These results indicate that both Rho1p and Spa2p are involved in the localization of Bni1p at the growth sites where Rho1p regulates reorganization of the actin cytoskeleton through Bni1p.
High-Speed Fiber Placement on Large Complex Structures (2007)

&lt;div class="htmlview paragraph"&gt;Automated Fiber Placement (AFP) equipment has been developed capable of laying fiber in excess of 2000 inches per minute on full-size, complex parts. Two such high-speed machines will be installed for production of a nose section for a large twin-aisle commercial aircraft fuselage at Spirit AeroSystems in Wichita, Kansas along with a rotator for the fuselage mandrel. The problem of cutting and adding on the fly at these speeds requires thorough re-evaluation of all aspects of the technology, including the mechanical, controls, servos systems, and programming systems. Factors to be considered for high speed cut and add on the fly are discussed.&lt;/div&gt;
Peculiarities of the Dynamics of Ion Exchange in Supersaturated Solutions and Colloid Systems (2003)

This paper reports the results obtained by experimental and theoretical study of the dynamics of ion exchange accompanied by the ion-exchange isothermal supersaturation (IXISS) effect. This effect is observed for a number of ion-exchange systems where the frontal or the reverse frontal separation is accompanied by the formation of extremely stable supersaturated solutions of low solubility substances in the interstitial space of ion-exchange columns. After leaving the column, a supersaturated solution crystallizes spontaneously, which allows for designing a practically ideal ion-exchange process where a crystalline product is obtained directly after the ion-exchange treatment cycle. The paper comprises results on the experimental investigation of IXISS of magnesium carbonate on carboxylic resins, which is observed in desorption of Mg2+ from the resin in the Mg form with Na2CO3 solutions or with solutions of Na2CO3−NaHCO3 mixtures. The physical and mathematical models of the kinetics and the dynamics of the ion-exchange processes proceeding in a colloid system comprising a supersaturated solution and an ion exchanger, which surface is partially blocked by adsorbed precrystalline aggregated (micelles), are proposed, and their validity is experimentally confirmed.
Intra- and Early Postoperative Complications of the LeFort I Osteotomy (1991)

de Mol van Otterloo, J. J.; Tuinzing, D. B.; Greebe, R. B.; vanderKnwast, W. A. M.; Eppley, Barry L. MD, DMD
CACNA1C hypermethylation is associated with bipolar disorder (2016)

The CACNA1C gene, encoding a subunit of the L-type voltage-gated calcium channel is one of the best-supported susceptibility genes for bipolar disorder (BD). Genome-wide association studies have identified a cluster of non-coding single-nucleotide polymorphisms (SNPs) in intron 3 to be highly associated with BD and schizophrenia. The mechanism by which these SNPs confer risk of BD appears to be through an altered regulation of CACNA1C expression. The role of CACNA1C DNA methylation in BD has not yet been addressed. The aim of this study was to investigate if CACNA1C DNA methylation is altered in BD. First, the methylation status of five CpG islands (CGIs) across CACNA1C in blood from BD subjects (n=40) and healthy controls (n=38) was determined. Four islands were almost completely methylated or completely unmethylated, while one island (CGI 3) in intron 3 displayed intermediate methylation levels. In the main analysis, the methylation status of CGI 3 was analyzed in a larger sample of BD subjects (n=582) and control individuals (n=319). Out of six CpG sites that were investigated, five sites showed significant hypermethylation in cases (lowest P=1.16 × 10(-7) for CpG35). Nearby SNPs were found to influence the methylation level, and we identified rs2238056 in intron 3 as the strongest methylation quantitative trait locus (P=2.6 × 10(-7)) for CpG35. In addition, we found an increased methylation in females, and no difference between bipolar I and II. In conclusion, we find that CACNA1C methylation is associated with BD and suggest that the regulatory effect of the non-coding risk variants involves a shift in DNA methylation.
ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses (2018)

Endogenous retroviruses (ERVs) are integrated retroviral elements that make up 8% of the human genome. However, the impact of ERVs on human health and disease is not well understood. While select ERVs have been implicated in diseases, including autoimmune disease and cancer, the lack of tools to analyze genome-wide, locus-specific expression of proviral autonomous ERVs has hampered the progress in the field. Here we describe a method called ERVmap, consisting of an annotated database of 3,220 human proviral ERVs and a pipeline that allows for locus-specific genome-wide identification of proviral ERVs that are transcribed based on RNA-sequencing data, and provide examples of the utility of this tool. Using ERVmap, we revealed cell-type-specific ERV expression patterns in commonly used cell lines as well as in primary cells. We identified 124 unique ERV loci that are significantly elevated in the peripheral blood mononuclear cells of patients with systemic lupus erythematosus that represent an IFN-independent signature. Finally, we identified additional tumor-associated ERVs that correlate with cytolytic activity represented by granzyme and perforin expression in breast cancer tissue samples. The open-source code of ERVmap and the accompanied web tool are made publicly available to quantify proviral ERVs in RNA-sequencing data with ease. Use of ERVmap across a range of diseases and experimental conditions has the potential to uncover novel disease-associated antigens and effectors involved in human health that is currently missed by focusing on protein-coding sequences.
DESIGN CONSIDERATIONS FOR AN EDXRF SYSTEM FOR IN VIVO ELEMENTAL ANALYSIS (1999)

An outline is given of the general considerations involved in designing and implementing Energy Dispersive XRF systems for in vivo elemental analysis. These considerations are more of a guidance than specific solutions. For example, some factors and constraints that need to be considered include patient dosimetry, geometrical configuration of the system, selection of the x-ray-source type and energy, and the counting time allowed to accomplish the measurement. Although a system’s specific design strongly depends on the element being analyzed, nevertheless, there are a few basic considerations that maximize the signal-to-noise ratio, thus minimizing the counting time and, consequently, the patient’s dose, regardless of the element being analyzed.
Supramolecular Structure of inclusion complexes of $\beta $-cyclodextrin with PEO-b-PPO-b-PEO Triblock Copolymer (2010)

A mini-review of the literature concerning epigenetic gene regulation in cancer.
Unidirectional emission from a cardioid-shaped microcavity laser (2016)

We find unidirectional emission in a cardioid-shaped microcavity laser. When a deformation parameter is well adjusted, rays starting around a period-5 unstable periodic orbit emit unidirectionally. To confirm the emission direction, we fabricate a laser by using an InGaAsP semiconductor and investigate emission characteristics. When the laser is excited by current injection with a dc current, resonances localized on the period-5 unstable periodic orbit emit unidirectionally.
Mission Report on The Solar Power Sail Deployment Demonstration of IKAROS (2011)

Hirokata Sawada Japan Aerospace Exploration Agency, Kanagawa, 252-5210, JAPAN Osamu Mori 2 Japan Aerospace Exploration Agency, Kanagawa, 252-5210, JAPAN Nobukatsu Okuizumi Japan Aerospace Exploration Agency, Kanagawa, 252-5210, JAPAN Yoji Shirasawa University of Tokyo, Tokyo, JAPAN Yasuyuki Miyazaki Nihon University, Chiba, 274-8501, JAPAN Michihiro Natori Waseda University, Tokyo, 169-8555, JAPAN Saburo Matunaga Tokyo Institute of Technology, Tokyo, 152-8552, JAPAN Hiroshi Furuya Tokyo Institute of Technology, Tokyo, 152-8552, JAPAN Hiraku Sakamoto Tokyo Institute of Technology, Tokyo, 152-8552, JAPAN
Construction of Polycation‐Based Non‐Viral DNA Nanoparticles and Polyanion Multilayers via Layer‐by‐Layer Self‐Assembly (2005)

Abstract Summary: The multilayers of polycation‐based non‐viral DNA nanoparticles and biodegradable poly( L ‐glutamic acid) (PGA) were constructed by a layer‐by‐layer (LbL) technique. Poly(ethyleneimine) (PEI) was used to condense DNA to develop non‐viral DNA nanoparticles. AFM, UV‐visible spectrometry, and TEM measurements revealed that the PEI‐DNA nanoparticles were successfully incorporated into the multilayers. The well‐structured, easily processed multilayers with the non‐viral DNA nanoparticles may provide a novel approach to precisely control the delivery of DNA, which may have great potential for gene therapy applications in tissue engineering, medical implants, etc. A TEM image of the cross section of a (PGA/PEI‐DNA nanoparticle) 20 multilayer. image A TEM image of the cross section of a (PGA/PEI‐DNA nanoparticle) 20 multilayer.
Compact grating coupler between vertically stacked silicon-on-insulator waveguides (2004)

The area of integrated optical circuits has been undergoing rapid development due to the important applications of fiber communication systems and optical interconnects. A significant challenge of photonic circuits is to increase circuit density and to miniaturize these devices. The vertical integration of stacked waveguides for photonic circuits onto a single substrate is a promising configuration to enable the dense monolithic integration of three-dimensional photonic devices. Application of high-index-contrast waveguides, such as silicon-on-insulator waveguides, is another important way to increase the density of optical circuits due to their small sizes. These waveguides produce high confinement in the guiding layers and have the advantages of compactness and immunity of cross-talk between different waveguides. It is thus expected that efficient coupling of light between vertically integrated waveguides where no direct field-overlap of guided modes exists is a key issue. We propose a compact double-grating coupler to realize efficient coupling through radiation modes between two vertically stacked SOI waveguides. The grating is strong enough to be considered as a onedimensional photonic bandgap structure which facilitates a very short coupling length. Simulations suggest that a 22% efficiency is achievable in coupling light from one waveguide to another with a 12.9&mu;m long grating. We find that the coupling efficiency is enhanced by Fabry-Perot resonance between two gratings. Coupling efficiency can be dramatically increased by incorporating a reflective under-layer structure or using blazed grating.
Impact of the surface properties of lactic bacteria on the stability of emulsions (2005)

Bacteria have physicochemical surface properties which depend on the chemical composition of the cell surface. These characters proceed from several type of physicochemical interactions and are involved in attachment processes of microorganisms to surfaces. Thus they are of interest in several areas, as biomedicine, formation of biofilms and adhesion to apolar surfaces. Moreover, food matrix are complex heterogeneous media, which structure settles on interaction forces between molecules (van der Waals, electrostatic or structural forces…). When bacteria are present in a matrix, it is probable that their surface interacts with the other constituents. So far, few studies have mentioned this subject. In order to understand the involvement of cells surface properties in a food matrix, the effect of surface properties of lactic bacteria on the stability of model emulsions were studied. The results showed that the choice of a bacterium according to its surface properties may have a strong impact on the stability and on the behavior of an emulsion.
Phylogenomics resolves the timing and pattern of insect evolution (2014)

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Direct Synthesis of Thiols from Halides and Epoxides Using Hydrosulfide Exchange Resin in Methanol (1995)

Various thiols are prepared directly from the corresponding alkyl halides and epoxides using hydrosulfide exchange resin in methanol in the presence of equimolar amounts of triethylammonium chloride at room temperature. The reaction not only proceeds with unique chemoselectivity, but also gives better yields of thiols than most commonly used indirect methods and has an additional advantage of a simple workup.
Optimal Spectrum Fragmentation in NC-OFDMA based Multi-hop Networks. (2013)

Wireless transmission using non-contiguous chunks of spectrum is becoming increasingly important due to a variety of scenarios such as: secondary users avoiding incumbent users in TV white space; anticipated spectrum sharing between commercial and military systems; and spectrum sharing among uncoordinated interferers in unlicensed bands. Multi-Channel Multi-Radio (MCMR) platforms and Non-Contiguous Orthogonal Frequency Division Multiple Access (NC-OFDMA) technology are the two commercially viable transmission choices to access these non-contiguous spectrum chunks. Fixed MC-MRs do not scale with increasing number of non-contiguous spectrum chunks due to their fixed set of supporting radio front ends. NC-OFDMA allows nodes to access these non-contiguous spectrum chunks and put null sub-carriers in the remaining chunks. However, nulling sub-carriers increases the sampling rate (spectrum span) which, in turn, increases the power consumption of radio front ends. Our work characterizes this trade-off from a cross-layer perspective, specifically by showing how the slope of ADC/DAC power consumption versus sampling rate curve influences scheduling decisions in a multi-hop network. Specifically, we provide a branch and bound algorithm based mixed integer linear programming solution that performs joint power control, spectrum span selection, scheduling and routing in order to minimize the system power of multi-hop NC-OFDMA networks. We also provide a low complexity (O(E^2 M^2)) greedy algorithm where M and E denote the number of channels and links respectively. Numerical simulations suggest that our approach reduces system power by 30% over classical transmit power minimization based cross-layer algorithms.