gebhart/patrepeval huggingface dataset:
Maternal and fetal antibrain antibodies in development and disease (2012)

Recent evidence has emerged indicating that the maternal immune response can have a substantial deleterious impact on prenatal development (Croen et al., [2008]: Biol Psychiatry 64:583-588). The maternal immune response is largely sequestered from the fetus. Maternal antibodies, specifically immunoglobulin G (IgG), are passed to the fetus to provide passive immunity throughout much of pregnancy. However, both protective and pathogenic autoantibodies have equal access to the fetus (Goines and Van de Water [2010]: Curr Opin Neurol 23:111-117). If the mother has an underlying autoimmune disease or has reactivity to fetal antigens, autoantibodies produced before or during pregnancy can target tissues in the developing fetus. One such tissue is the fetal brain. The blood brainbarrier (BBB) is developing during the fetal period allowing maternal antibodies to have direct access to the brain during gestation (Diamond et al. [2009]: Nat Rev Immunol; Braunschweig et al. [2011]; Neurotoxicology 29:226-231). It has been proposed that brain injury by circulating brain-specific maternal autoantibodies might underlie multiple congenital, developmental disorders (Lee et al. [2009]: Nat Med 15:91-96). In this review, we will discuss the current state of research in the area of maternal autoantibodies and the development of autism.
Characterization of Asphalt Mixture Homogeneity Based on X-ray Computed Tomography (2012)

Abstract The mechanical performance and life span of asphalt pavement depend largely on the homogeneity of the asphalt mixture. Inhomogeneity of asphalt mixtures is due to the non-uniform segregation of air voids and aggregates in mixtures. In order to evaluate the homogeneity of an asphalt mixture during lab compaction, computed tomography (CT) images of the specimen were obtained based on x-ray CT. The image was virtually cut into slices of various sizes, and the vertical air void distributions and aggregate gradations were quantified. Research results reveal that the air void content in the middle part of the specimen was lower than those on both ends. Also, the homogeneity was better under high compaction levels. The results from aggregate gradations were in good agreement with air void distribution calculations. Therefore, it is feasible to characterize an asphalt mixture’s homogeneity based on the air void distributions and aggregate gradations as determined via x-ray CT.
Synthesis of 3′‐deoxy‐3′‐[18F]fluoro‐1‐β‐D‐xylofuranosyluracil ([18F]‐FMXU) for PET (2005)

Abstract The synthesis of a pyrimidine analog, 3′‐deoxy‐3′‐[ 18 F]‐fluoro‐1‐ β ‐ D ‐xylofuranosyluracil ([ 18 F]‐FMXU) is reported. 5‐Methyluridine 1 was converted to its di‐methoxytrityl derivatives 2 and 3 as a mixture. After separation the 2′,5′‐di‐methoxytrityluridine 2 was converted to its 3′‐triflate 4 followed by derivatization to the respective N 3 ‐ t ‐Boc product 5 . The triflate 5 was reacted with tetrabutylammonium[ 18 F]fluoride to produce 6 , which by acid hydrolysis yielded compound 7 . The crude preparation was purified by HPLC to obtain the desired product [ 18 F]‐FMXU. The radiochemical yields were 25–40% decay corrected (d. c.) with an average of 33% in four runs. Radiochemical purity was &gt;99% and specific activity was &gt;74 GBq/µmol at the end of synthesis (EOS). The synthesis time was 67–75 min from the end of bombardment (EOB). Copyright © 2005 John Wiley &amp; Sons, Ltd.
P11-M Comprehensive and Reliable Proteome Analysis Using Bioinformatic Strategies for Automated Result Validation (2007)

Proteomic analyses typically produce massive amounts of mass spectrometric data, which are analyzed in an automated way by database search engines for retrieval of peptide sequences and subsequent inference on the corresponding protein sequences. However, this process turned out to be error prone, producing false positives and multiple hits for the same proteins for various reasons. In this study we analyzed the human serum glycosubproteome. For this, glycoproteins were produced in five separate extractions by affinity interaction chromatography using magnetic beads coated with the lectins ConA, WGA, LCA, and AIA, as well as with boronic acid. The eluates from the beads were digested using trypsin and subsequently analyzed by LC-MALDI-MS/MS as well as LC-ESI-MS/MS. The analyses were carried out as up to triple replicates. All the data were submitted to the ProteinScape database system. Within ProteinScape, the datasets were searched against Mascot and Phenyx. The resulting peptide identifications were analyzed by the ProteinExtractor tool to reduce the list by the false positives using a decoy strategy, and subsequently merged into a combined list of identified proteins for the respective sample preparations. This allows the combination of data from different search engines as well as from different experiments (ESI and MALDI). The use of decoy strategies as well as application of the ProteinExtractor to overcome the protein inference problem minimizes the need for manual validation (which is nevertheless easily possible using raw spectra information). In parallel, the use of a single data repository allows for easy access to the combined information from different work-flows and links to external tools complement the system for project-spanning comparisons of datasets.
Development of lightweight x-ray mirrors for the Constellation-X mission (2005)

The Constellation-X mission's Spectroscopic X-Ray Telescopes (SXT) require an angular resolution of 15" half-power diameter (HPD) with extremely lightweight grazing incidence mirrors. The areal density of the mirror must be about 1 kg/m<sup>2</sup> or less. In comparison with the state of the art X-ray mirrors represented by the XMM/Newton telescopes, this is approximately an order of magnitude less in mass areal density while maintaining the same angular resolution. We use a precision glass forming technique to fabricate mirrors that are 0.4mm thick and optical metrology to demonstrate that these mirrors can meet the stringent figure and micro-roughness requirements of the Constellation-X mission. We expect in the next few years to significantly improve the production yield and mirror quality to meet the goal of the mission, which is 5" HPD for two reflections at the same mass.
ChemInform Abstract: Tetradehydrodinaphtho[10]annulene and Its Transformation into Zethrene: A Hitherto Unknown Dehydroannulene and a Forgotten Aromatic Hydrocarbon (2010)

Abstract Review: 47 refs.
Solid-to-fluid–like DNA transition in viruses facilitates infection (2014)

Releasing the packaged viral DNA into the host cell is an essential process to initiate viral infection. In many double-stranded DNA bacterial viruses and herpesviruses, the tightly packaged genome is hexagonally ordered and stressed in the protein shell, called the capsid. DNA condensed in this state inside viral capsids has been shown to be trapped in a glassy state, with restricted molecular motion in vitro. This limited intracapsid DNA mobility is caused by the sliding friction between closely packaged DNA strands, as a result of the repulsive interactions between the negative charges on the DNA helices. It had been unclear how this rigid crystalline structure of the viral genome rapidly ejects from the capsid, reaching rates of 60,000 bp/s. Through a combination of single-molecule and bulk techniques, we determined how the structure and energy of the encapsidated DNA in phage λ regulates the mobility required for its ejection. Our data show that packaged λ-DNA undergoes a solid-to-fluid-like disordering transition as a function of temperature, resulting locally in less densely packed DNA, reducing DNA-DNA repulsions. This process leads to a significant increase in genome mobility or fluidity, which facilitates genome release at temperatures close to that of viral infection (37 °C), suggesting a remarkable physical adaptation of bacterial viruses to the environment of Escherichia coli cells in a human host.
Poly(acrylates) via SET-LRP in a continuous tubular reactor (2013)

A simple, easy to construct, bench-top plug flow reactor consisting of PTFE tubing with a Cu(0) threaded core (wire) was used to perform SET-LRP of methyl acrylate. The reaction was optimized by changing the residence time within the flow reactor. Both changing the flow reactor length and changing the flow rate was seen to control the resultant polymer molecular weight. Using a 20 cm reactor length, 95% conversion of monomer was seen at a flow rate of 0.1 mL min−1. The polymers formed had narrow molecular weight distributions (PDI< 1.2), and very high ω-chain end fidelity, as seen by both 1H NMR and MALDI-TOF MS.
Symbiotic genes of Rhizobium meliloti (1988)

National audience
Towards an Automated Acoustic Detection Algorithm for Wood-Boring Beetle Larvae (Coleoptera: Cerambycidae and Buprestidae) (2019)

The development of acoustic systems for detection of wood-boring larvae requires knowledge of the features of signals produced both by insects and background noise. This paper presents analysis of acoustic/vibrational signals recorded in tests using tree bolts infested with Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae) (Asian longhorn beetle) and Agrilus planipennis Fairmaire (Coleoptera: Buprestidae) (emerald ash borer) larvae. Based on features found, an algorithm for automated insect signal detection was developed. The algorithm automatically detects pulses with parameters typical for the larva-induced signals and rejects noninsect signals caused by ambient noise. The decision that a wood sample is infested is made when the mean rate of detected insect pulses per minute exceeds a predefined threshold. The proposed automatic detection algorithm demonstrated the following performance: 12 out of 15 intact samples were correctly classified as intact, 23 out of 25 infested samples were correctly classified as infested, and five samples out of the total 40 were classified as ‘unknown.’ This means that a successful wood-sample classification of 87.5% was achieved, with the remaining 12.5% classified as ‘unknown,’ requiring a repeat of the test in a less noisy environment, or manual inspection.
Characterization of a type IIb sodium-phosphate cotransporter from zebrafish(Danio rerio)kidney (2003)

Zebrafish (Danio rerio) express two isoforms of the type IIb Na-dependent P(i) cotransporter (NaPi). Type NaPi-IIb1 has previously been cloned and characterized. Here, we report the cloning of the NaPi-IIb2 transcript from zebrafish kidney, its localization, and its functional characterization. RT-PCR with renal RNA and degenerate NaPi-IIb-specific primers resulted in a specific fragment. 3'-Rapid amplification of cDNA ends yielded a product that contained typical NaPi-IIb characteristics such as a cysteine-rich COOH terminus and a PDZ (PSD95- Dlg-zona occludens-1) binding motif. Several approaches were unsuccessful at cloning the 5' end of the transcript; products lacked an in-frame start codon. The missing information was obtained from an EST (GenBank accession number ). The combined clone displayed a high degree of homology with published type IIb cotransporter sequences. Specific antibodies were raised against a COOH-terminal epitope of both NaPi-IIb1 and NaPi-IIb2 isoforms. Immunohistochemical mapping revealed apical expression of both isoforms in zebrafish renal and intestinal epithelia, as well as in bile ducts. The novel clone was expressed in oocytes, and function was assayed by the two-electrode voltage-clamp technique. The function of the new NaPi-IIb2 clone was found to be significantly different from NaPi-IIb1 despite strong structural similarities. NaPi-IIb2 was found to be strongly voltage sensitive, with higher affinities for both sodium and phosphate than NaPi-IIb1. Also, NaPi-IIb2 was significantly less sensitive to external pH than NaPi-IIb1. The strong structural similarity but divergent function makes these zebrafish transporters ideal models for the molecular mapping of functionally important regions in the type II NaPi-cotransporter family.
Interrelations between Hypothalamic Somatostatin and Proopiomelanocortin Neurons (1998)

Somatostatin receptors were visualized by [125I]-Tyr0-DTrp8-somatostatin radioautography on 35% of arcuate neurons containing proopiomelanocortin (POMC) mRNA, as identified by in situ hybridization using a [35S] labelled riboprobe on 5 microm-thick consecutive sections. Furthermore, double immunohistochemical staining revealed contacts of beta-endorphin or alpha-MSH containing fibres with a majority of somatostatin perikarya in the anterior hypothalamic periventricular nucleus. Taken together, these data indicate that hypothalamic somatostatin and POMC neurons are interconnected. The results are discussed in term of intrahypothalamic control of GH secretion.
Microfluidic devices fabricated in poly(methyl methacrylate) using hot-embossing with integrated sampling capillary and fiber optics for fluorescence detection (2002)

High-aspect-ratio microstructures have been prepared using hot-embossing techniques in poly(methyl methacrylate) (PMMA) from Ni-based molding dies prepared using LIGA (Lithographie, Galvanoformung, Abformung). Due to the small amount of mask undercutting associated with X-ray lithography and the high energy X-ray beam used during photoresist patterning, deep structures with sharp and smooth sidewalls have been prepared. The Ni-electroforms produced devices with minimal replication errors using hot-embossing at a turn around time of approximately 5 min per device. In addition, several different polymers (with different glass transition temperatures) could be effectively molded with these Ni-electroforms and many devices (>300) molded with the same master without any noticeable degradation. The PMMA devices consisted of deep and narrow channels for insertion of a capillary for the automated electrokinetic loading of sample into the microfluidic device and also, a pair of optical fibers for shuttling laser light to the detection zone and collecting the resulting emission for fluorescence analysis. Electrophoretic separations of double-stranded DNA ladders Phi X174 digested with Hae III) were performed with fluorescence detection accomplished using near-IR excitation. It was found that the narrow width of the channels did not contribute significantly to electrophoretic zone broadening and the plate numbers generated in the extended length separation channel allowed sorting of the 271/281 base pair fragments associated with this sizing ladder when electrophoresed in methylcellulose entangled polymer solutions. The dual fiber detector produced sub-attomole detection limits with the entire detector, including laser source, electronics and photon transducer, situated in a single box measuring 3'' x 10" x 14".
Naked mole rat cells display more efficient DNA excision repair and higher resistance to toxic impacts than mouse cells (2020)

Naked mole rat is the long-lived and tumor-resistant rodent. Naked mole rat possesses multiple adaptations that may contribute to longevity and cancer-resistance. Higher activity of DNA excision repair systems and their faster recovery after genotoxic impact as compare with Mus musculus directly demonstrated in our previous investigation contribute to longevity and cancer resistance of naked mole rat. In the present study the DNA-damage-induced apoptosis in naked mole rat fibroblasts was studied using conventional methods. The ability of naked mole rat cells to undergo regulated cell death in response to genotoxic stress is another group of cell defense mechanisms. Naked mole rat skin fibroblasts were demonstrated to be much more resistant towards proapoptotic reagents methyl methanesulfonate, 5-fluorouracil and etoposide as compared with fibroblasts of Mus musculus . Naked mole rat cells have demonstrated limited apoptotic response and seem to undergo also other-type regulated cell death under severe genotoxic stress.
Neutrophil Gelatinase–Associated Lipocalin and Contrast-Induced Acute Kidney Injury (2015)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT01098032.
Data from A Long-term Prospective Study of Type-Specific Human Papillomavirus Infection and Risk of Cervical Neoplasia Among 20,000 Women in the Portland Kaiser Cohort Study (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Human papillomavirus (HPV) DNA testing is more sensitive than cytology for detection of cervical intraepithelial neoplasia grade 3 and cancer (≥CIN3). Adding HPV testing to cytology is recommended for women ≥30 but long-term prospective studies of HPV testing are rare.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; Beginning in 1989–1990, ∼20,000 women in a prepaid health maintenance organization (median age = 34) were followed passively by recommended annual cytology. We tested archived cervicovaginal lavage specimens collected at enrollment, primarily by MY09-MY11 PCR-based methods, for carcinogenic HPV types. We calculated positive and negative predictive values for the entire study period, and Kaplan–Meier estimates of cumulative probability for ≥CIN3, up to 18 years of follow-up.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We observed 15 cases of invasive cervical cancer during the study period, and 189 cases of CIN3. Predictive values and Kaplan–Meier analyses yielded the same conclusions. In women 30 and older, the reassurance against ≥CIN3 following a single negative HPV test was long-lasting (cumulative probability = 0.7% during follow-up). In this age group, a single HPV test (positive vs. negative, hazard ratio of 8.5, 95% CI = 4.8–15.1) provided greater long-term risk stratification than a single cytologic result (abnormal vs. normal, HR = 2.9, 95% CI = 1.2–6.6). The risk for ≥CIN3 was higher for HPV16 than for the average of the other carcinogenic types (hazard ratio = 2.7).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion and Impact:&lt;/b&gt; The data from this cohort study show the long-term predictive value of HPV testing, particularly in women ≥30, and a possible role for distinguishing particularly carcinogenic types like HPV16. &lt;i&gt;Cancer Epidemiol Biomarkers Prev; 20(7); 1398–409. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Universally Composable Symbolic Analysis for Two-Party Protocols Based on Homomorphic Encryption (2014)

We consider a class of two-party function evaluation protocols in which the parties are allowed to use ideal functionalities as well as a set of powerful primitives, namely commitments, homomorphic encryption, and certain zero-knowledge proofs. With these it is possible to capture protocols for oblivious transfer, coin-flipping, and generation of multiplication-triples. We show how any protocol in our class can be compiled to a symbolic representation expressed as a process in an abstract process calculus, and prove a general computational soundness theorem implying that if the protocol realises a given ideal functionality in the symbolic setting, then the original version also realises the ideal functionality in the standard computational UC setting. In other words, the theorem allows us to transfer a proof in the abstract symbolic setting to a proof in the standard UC model. Finally, we have verified that the symbolic interpretation is simple enough in a number of cases for the symbolic proof to be partly automated using the ProVerif tool.
Design of the injection beamline for the Californium Rare Isotope Breeder Upgrade electron beam ion source charge breeder (2012)

The design of the ion injection line connecting the electron beam ion source (EBIS) charge breeder and the Californium Rare Isotope Breeder Upgrade radio frequency quadrupole cooler-buncher at the Argonne Tandem Linear Accelerator System was investigated with particle tracking simulations. The injection line was configured to accommodate several differential pumping sections, individual optical components were optimized to minimize emittance growth, and the ion beam parameters were matched with the EBIS electron beam acceptance to minimize losses upon injection.
Application of plant‐based antimicrobials for the growth inhibition of clostridia in pressed beet pulp silage (2011)

Abstract BACKGROUND: In this study the inhibition of hop beta acids on the growth of clostridia in soil‐contaminated pressed sugar beet pulp silages was investigated. Hop beta acids are natural substances which display their effect at low concentrations. Fresh pressed beet pulp material was mixed with soil to artificially contaminate it with clostridia. Laboratory silos were filled with the substrate, stored at 25 °C and opened for sampling at 0, 2, 8, 15, 30, 60, and 90 days. The impact on clostridial growth during silage fermentation was monitored by determination of the pH value and dry matter content, as well as chemical analysis of the fermentation products. Throughout the experiments, the effect of a commercial silage inoculant based on lactic acid bacteria (LAB) and hop‐resistant LAB were examined with and without the combination of plant‐based antimicrobials. RESULTS: Results indicate that in contaminated silage samples without any additives high butyric acid contents occurred due to clostridial growth. This spoilage could not be suppressed by the application of LAB, whereas the combined application of LAB and hop beta acids significantly improved silage quality, which was reflected by favourable organic acid composition ( P &lt; 0.05). CONCLUSION: The experimental data indicate that the application of hop beta acids improves the preservation effect of LAB in suppressing clostridial growth in silages and thus demonstrates some potential for the combined use of plant‐based antimicrobials and LAB. Copyright © 2011 Society of Chemical Industry
<title>Multivariate segmentation of fMRI for human brain mapping</title> (2000)

fMRI has provided a new option to study cognitive phenomena. Recent developments in medical image processing and analysis allow researchers to study more elaborate cognitive tasks from a wide perspective. These techniques include Statistical Parametric Mapping, Subspace Modeling and Maximum Likelihood Estimation, and Spatio-temporal Analysis using Random Fields. Their common weakness is the assumption of the statistical independence among the image pixels. We have developed a multivariate segmentation method to functional MRI analysis for human brain function study based on the second-order statistics of images. It consists of four steps: (1) detecting the number of the distinctive image regions, (2) generating the scores and determining their rank, (3) forming score plots and clustering in the feature space, (4) projecting clusters from the feature space to the image space to generate object images. We have validated this method on the simulated and fMRI images. The theoretical and experimental results obtained by using this method were in good agreement. The relations between this method and other multivariate image analysis methods are discussed.
Association of Sarcoidosis With Endothelial Function, Arterial Wall Properties, and Biomarkers of Inflammation (2011)

In the present study, we have shown that sarcoidosis patients have impaired endothelial function and increased arterial stiffness. Sarcoidosis patients on cortisone treatment had no differences compared to controls on the vascular parameters. Moreover, there was a significant correlation between inflammatory process and vascular function impairment. These findings indicate that sarcoidosis patients have impaired vascular function and increased inflammatory status, which may improve with cortisone treatment.