gebhart/patrepeval huggingface dataset:
Nucleomorph genome of <i>Hemiselmis andersenii</i> reveals complete intron loss and compaction as a driver of protein structure and function (2007)

Nucleomorphs are the remnant nuclei of algal endosymbionts that took up residence inside a nonphotosynthetic eukaryotic host. The nucleomorphs of cryptophytes and chlorarachniophytes are derived from red and green algal endosymbionts, respectively, and represent a stunning example of convergent evolution: their genomes have independently been reduced and compacted to <1 megabase pairs (Mbp) in size (the smallest nuclear genomes known) and to a similar three-chromosome architecture. The molecular processes underlying genome reduction and compaction in eukaryotes are largely unknown, as is the impact of reduction/compaction on protein structure and function. Here, we present the complete 0.572-Mbp nucleomorph genome of the cryptophyte Hemiselmis andersenii and show that it is completely devoid of spliceosomal introns and genes for splicing RNAs-a case of complete intron loss in a nuclear genome. Comparison of H. andersenii proteins to those encoded in the slightly smaller (0.551-Mbp) nucleomorph genome of another cryptophyte, Guillardia theta, and to their homologs in the unicellular red alga Cyanidioschyzon merolae reveal that (i) cryptophyte nucleomorph genomes encode proteins that are significantly smaller than those in their free-living algal ancestors, and (ii) the smaller, more compact G. theta nucleomorph genome encodes significantly smaller proteins than that of H. andersenii. These results indicate that genome compaction can eliminate both coding and noncoding DNA and, consequently, drive the evolution of protein structure and function. Nucleomorph proteins have the potential to reveal the minimal functional units required for basic eukaryotic cellular processes.
On the Mechanism of the Hofmeister Effect (2004)

Vibrational sum frequency spectroscopy was used to probe fatty amine monolayers spread on various electrolyte solutions. The spectra revealed ion specific changes in both monolayer ordering and water structure with the former following the Hofmeister series. Separate measurements of the surface potential as a function of ion tracked closely to changes in alkyl chain structure, but less closely to changes in water structure. The disruption of the monolayer ordering could be ascribed to the relative ability of the ions to penetrate past the hydrophilic surface of the monolayer's headgroups and into the more hydrophobic portion of the thin film. The corresponding trends observed in the surface water structure showed significant deviations from the Hofmeister series, leading to the conclusion that the changes in surface water structure, often credited with being the origin of Hofmeister effects, are probably not of primary importance. On the other hand, dispersion forces almost certainly play a large role in the order of the Hofmeister series.
Activation of Antibiotic Biosynthesis by Specified Mutations in the <i>rpoB</i> Gene (Encoding the RNA Polymerase β Subunit) of <i>Streptomyces lividans</i> (2002)

We found that the biosynthesis of actinorhodin (Act), undecylprodigiosin (Red), and calcium-dependent antibiotic (CDA) are dramatically activated by introducing certain mutations into the rpoB gene that confer resistance to rifampin to Streptomyces lividans 66, which produces less or no antibiotics under normal growth conditions. Activation of Act and/or Red biosynthesis by inducing mutations in the rpoB gene was shown to be dependent on the mutation's position and the amino acid species substituted in the beta-subunit of the RNA polymerase. Mutation analysis identified 15 different kinds of point mutations, which are located in region I, II, or III of the rpoB gene and, in addition, two novel mutations (deletion of nucleotides 1287 to 1289 and a double substitution at nucleotides 1309 and 1310) were also found. Western blot analyses and S1 mapping analyses demonstrated that the expression of actII-ORF4 and redD, which are pathway-specific regulatory genes for Act and Red, respectively, was activated in the mutants able to produce Act and Red. The ActIV-ORF1 protein (an enzyme for Act biosynthesis) and the RedD protein were produced just after the upregulation of ActII-ORF4 and RedZ, respectively. These results indicate that the mutation in the rpoB gene of S. lividans, resulting in the activation of Act and/or Red biosynthesis, functions at the transcription level by activating directly or indirectly the key regulatory genes, actII-ORF4 and redD. We propose that the mutated RNA polymerase may function by mimicking the ppGpp-bound form in activating the onset of secondary metabolism in STREPTOMYCES:
Open-loop deep brain stimulation for the treatment of epilepsy: a systematic review of clinical outcomes over the past decade (2008–present) (2018)

OBJECTIVE The field of deep brain stimulation (DBS) for epilepsy has grown tremendously since its inception in the 1970s and 1980s. The goal of this review is to identify and evaluate all studies published on the topic of open-loop DBS for epilepsy over the past decade (2008 to present). METHODS A PubMed search was conducted to identify all articles reporting clinical outcomes of open-loop DBS for the treatment of epilepsy published since January 1, 2008. The following composite search terms were used: ("epilepsy" [MeSH] OR "seizures" [MeSH] OR "kindling, neurologic" [MeSH] OR epilep* OR seizure* OR convuls*) AND ("deep brain stimulation" [MeSH] OR "deep brain stimulation" OR "DBS") OR ("electric stimulation therapy" [MeSH] OR "electric stimulation therapy" OR "implantable neurostimulators" [MeSH]). RESULTS The authors identified 41 studies that met the criteria for inclusion. The anterior nucleus of the thalamus, centromedian nucleus of the thalamus, and hippocampus were the most frequently evaluated targets. Among the 41 articles, 19 reported on stimulation of the anterior nucleus of the thalamus, 6 evaluated stimulation of the centromedian nucleus of the thalamus, and 9 evaluated stimulation of the hippocampus. The remaining 7 articles reported on the evaluation of alternative DBS targets, including the posterior hypothalamus, subthalamic nucleus, ventral intermediate nucleus of the thalamus, nucleus accumbens, caudal zone incerta, mammillothalamic tract, and fornix. The authors evaluated each study for overall epilepsy response rates as well as adverse events and other significant, nonepilepsy outcomes. CONCLUSIONS Level I evidence supports the safety and efficacy of stimulating the anterior nucleus of the thalamus and the hippocampus for the treatment of medically refractory epilepsy. Level III and IV evidence supports stimulation of other targets for epilepsy. Ongoing research into the efficacy, adverse effects, and mechanisms of open-loop DBS continues to expand the knowledge supporting the use of these treatment modalities in patients with refractory epilepsy.
A clinico-pathological study of adult histiocytosis X involving the brain. (1993)

Adult histiocytosis X involving the CNS caused progressive spastic paraparesis. The diagnosis was made by immunoreactive anti-S100 protein antibody staining and from the presence of Birbeck granules in biopsy specimens of skin lesions. Neuropathological examination showed massive proliferation and infiltration of S-100 containing histiocyte-like cells and reactive astrocytes throughout the CNS.
Thermomechanical analyses of metal solidification processes (1995)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1995.
CONSTRUCTION, OPTIMIZATION, AND APPLICATIONS OF A SMALL TRAPPED-ION QUANTUM COMPUTER (2019)

A large-scale quantum computer will have the ability to solve many computational problems beyond the capabilities of today's most powerful computers. Significant efforts to build such a computer are underway, many of which are small prototypes that are believed to be extensible to larger systems. Such systems, like the one in this thesis built off of 171Yb+ ions, are enticing scientific endeavors for their potential to inform the production of large-scale systems, as well as the interesting experiments they can perform. In this work, experimental research is presented on both topics: scalability as well as compelling computations. The first half of this thesis discusses building and optimizing a quantum computer to have high-fidelity qubit operations. An experimental architecture that allows for individual addressing and individual detection of qubits is presented alongside a discussion of errors and error-reduction. We derive the coherent manipulation of qubits using Raman lasers for rotational gates and the criteria necessary for multi-qubit entangling gates. Methods for efficiently fulfilling these criteria are presented with experimental data. Lastly, we consider coherence-related properties of the system necessary to perform these operations and how they can be experimentally improved. The second half of the thesis features three experimental applications of the quantum computer: quantifying quantum scrambling, applying a quantum error correction code, and measuring Renyi entropy. Quantum scrambling is the coherent delocalization of information through a quantum system and is notably difficult to quantify experimentally. We present an efficient scheme to measure it using quantum teleportation. Quantum error correction is a set of techniques for mitigating the effect of imperfect operations performed on a quantum computer, and we demonstrate some of these techniques in order to fault-tolerantly prepare a logical qubit. Lastly, \renyi entropy is an information theoretic quantity that can be used to directly quantify the amount of entanglement in a system. We present a method for measuring it efficiently using a quantum gate known as a Fredkin gate.
Encuentro entre Sonia Livingston e Peter Lewis: Educomunicación e medios comunitarios en Europa. De barreiras invisíbeis e conceptos irmáns : Conversa entre Sonia Livingstone e Peter Lewis (2015)

Desde a RICD puxemos en comun os conecementos e a experiencia de dous referentes nos seus campos de investigacion no ambito anglosaxon, Sonia Livingston e Peter Lewis. Tanto unha, mais enfocada a exploracion de estratexias de educomunicacion coa infancia e xuventude, como o outro, centrado nas posibilidades do medio radiofonico como instrumento comunicativo das comunidades, comparten a necesidade de artellar formulas que acheguen a investigacion e o traballo educativo nas escolas e universidades a sociedade, e en especial aos grupos en situacion de vulnerabilidade. E isto leva aparellada unha maior atencion as preocupacions e problematicas deses grupos, alen do xeito no que se achegan habitualmente aos medios de comunicacion.
Thermolysis of Benzannulated Enyne‐Carbodiimides. Application in the Synthesis of Pyrido[1′,2′:1,2]pyrimido[4,5‐b]indoles and Related Heteroaromatic Compounds. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Evaluation of a Methodology for Quantifying the Effect of Room Air Ultraviolet Germicidal Irradiation on Airborne Bacteria (2000)

As a result of the recent resurgence in tuberculosis (TB) and the increasing incidence of multidrug-resistant TB, there has been renewed interest in engineering controls to reduce the spread of TB and other airborne infectious diseases in high-risk settings. Techniques such as the use of lamps that produce ultraviolet germicidal radiation may reduce exposure to infectious agents by inactivating or killing microorganisms while they are airborne. We designed and evaluated a test method to quantitatively estimate the efficacy of germicidal lamps, in conjunction with dilution ventilation, for reducing the concentration of viable airborne bacteria. Bacterial particles were generated in a 36m3 room and collected with midget impingers at 5-7 locations. The effectiveness of the control technique was determined by comparing concentrations of culturable airborne bacteria with and without the control in operation. Results for a single, 15 W germicidal lamp showed reductions of 50% for Bacillus subtilis (B. subtilis) and Micrococcus luteus (M. luteus); tests with Escherichia coli (E. coli) showed nearly 100% reduction (E. coli were isolated only from the sampler nearest the aerosol source when the lamp was operating). The addition of louvers to a lamp greatly reduced its efficacy. Decay experiments showed that roughly 4-6 equivalent air changes per hour were achieved for B. subtilis with one or two lamps operating. These preliminary experiments demonstrated that this methodology was well suited for these evaluations and identified factors that could be modified to refine the study design for future work.
Hydration of Lithium Ion in Aqueous Solutions (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydration of Lithium Ion in Aqueous SolutionsWolfram Rudolph, Murray H. Brooker, and Cory C. PyeCite this: J. Phys. Chem. 1995, 99, 11, 3793–3797Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/j100011a055https://doi.org/10.1021/j100011a055research-articleACS PublicationsRequest reuse permissionsArticle Views1137Altmetric-Citations128LEARN 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 options Get e-Alerts
Application of GPS and Infrared for Car Navigation in Foggy Condition to Avoid Accident (2010)

The paper describes about the application of GPS card meant for navigational system by infra-red control of the cars in foggy condition to avoid accident along with microcontrol system. After an exhaustive review of GPS card for various applications, the paper plans to present the experimental details of the system. As a part of theoretical work related with the system it plans to discuss about ambiguity function of the matched filter of the moving target.
The Selection of Appropriate Bacterial Strains in Preclinical Evaluation of Infection-Resistant Biomaterials (2008)

Implant-related infections are broadly recognized as one of the most serious and devastating complications associated with the use of biomaterials in medical practice. The growing interest and need for the development of implant materials with reduced susceptibility to microbial colonization and biofilm formation has necessitated the development of a series of in vitro and in vivo models for evaluation and preclinical testing. Current technologies provide these investigations with an ample choice of qualitative and quantitative techniques for an accurate assessment of the bioactivity and anti-infective efficacy of any new compound or device. These tests are typically performed using a reference bacterial strain designated as the test or reference strain. Recent molecular epidemiological studies have identified the complex clonal nature of most prevalent etiological agents implicated in implant-associated infections. New information which is continually emerging on the identity and the characteristics of both sporadic and epidemic clones must be considered when selecting a reference. A new emerging requirement is that the strain should be representative of the clones causing clinically relevant infections; they should, therefore, belong to the most prevalent epidemic clones rather than to sporadic ones, which may occur in only 1 out of 200 infections or even fewer. The correct choice of reference strain for preclinical tests is of crucial importance for the clinical significance of the achieved results. In this paper we report our experience and recommendations regarding this issue.
Induction and identification of polyploids in Cattleya intermedia Lindl. (orchidaceae) by in vitro techniques (2000)

The effect of colchicine on the protocorm-like bodies of Cattleya intermedia L. (Orchidaceae) cultured in vitro was studied. Different concentrations of the drug (0.00, 0.05, 0.10 and 0.20%) as well as two times of culture (4 or 8 days) were tested to determine the best treatment for the induction of tetraploid plants. Of the 3 colchicine levels applied, 0.05 and 0.10% of drug treatments appeared to be effective on the production of mixoploids and tetraploids and could be further used in breeding programs. The suitability of stomatal area and stomata density as criteria for the distinction between diploids and tetraploids was also tested. The results suggested that tetraploid plants could be identified with a fair amount of certainty when the screening was based on the density of stomata.
Oscillations in Cerebral Blood Flow Detected with a Transcranial Doppler Index (1999)

Although transcranial Doppler ultrasound (TCD) has been used to detect oscillations in CBF, interpretation is severely limited, since only blood velocity and not flow is measured. Oscillations in vessel diameter could, therefore, mask or alter the detection of those in flow by TCD velocities. In this report, the authors use a TCD-derived index of flow to detect and quantify oscillations of CBF in humans at rest. A flow index (FI) was calculated from TCD spectra by averaging the intensity weighted mean in a beat-by-beat manner over 10 seconds. Both FI and TCD velocity were measured in 16 studies of eight normal subjects at rest every 10 seconds for 20 minutes. End tidal CO2 and blood pressure were obtained simultaneously in six of these studies. The TCD probe position was meticulously held constant. An index of vessel area was calculated by dividing FI by velocity. Spectral estimations were obtained using the Welch method. Spectral peaks were defined as peaks greater than 2 dB above background. The frequencies and magnitudes of spectral peaks of FI, velocity, blood pressure, and CO2 were compared with t tests. The Kolmogorov-Smirnov test was used to further confirm that the data were not white noise. In most cases, three spectral peaks (a, b, c) could be identified, corresponding to periods of 208+/-93, 59+/-31, and 28+/-4 (SD) seconds for FI, and 196+/-83, 57+/-20, and 28+/-6, (SD) seconds for velocity. The magnitudes of the spectral peaks for FI were significantly greater (P<0.02) than those for velocity. These magnitudes corresponded to variations of at least 15.6%, 9.8%, and 6.8% for FI, and 4.8%, 4.2%, and 2.8% for velocity. The frequencies of the spectral peaks of CO2 were similar to those of FI with periods of 213+/-100, 60+/-46, and 28+/-3.6 (SD) seconds. However, the CO2 spectral peak magnitudes were small, with an estimated maximal effect on CBF of (+/-) 2.5+/-0.98, 1.5+/-0.54, and 1.1+/-0.31 (SD) percent. The frequencies of the blood pressure spectral peaks also were similar, with periods of 173+/-81, 44+/-8, and 26+/-2.5 (SD) seconds. Their magnitudes were small, corresponding to variations in blood pressure of (+/-) 2.1+/-0.55, 0.97+/-0.25, and 0.72+/-0.19 (SD) percent. Furthermore, coherence analysis showed no correlation between CO2 and FI, and only weak correlations at isolated frequencies between CO2 and velocity, blood pressure and velocity, or blood pressure and FI. The Kolmogorov-Smirnov test distinguished our data from white noise in most cases. Oscillations in vessel flow occur with significant magnitude at three distinct frequencies in normal subjects at rest and can be detected with a TCD-derived index. The presence of oscillations in blood velocity at similar frequencies but at lower magnitudes suggests that the vessel diameters oscillate in synchrony with flow. Observed variations in CO2 and blood pressure do not explain the flow oscillations. Ordinary TCD velocities severely underestimate these oscillations and so are not appropriate when small changes in flow are to be measured.
Elucidating the role of free polycationic chains in polycation gene carriers by free chains of polyethylenimine or N,N,N-trimethyl chitosan plus a certain polyplex (2014)

Polycations as gene carriers have attracted considerable attention over the past decade. Generally, polyplexes between polycations and deoxyribonucleic acid (DNA) are formed at low N/P ratios (the ratios of the numbers of nitrogen atoms in a polycation to the numbers of phosphorus atoms in DNA), but high transfection efficiency can only be obtained at much higher N/P ratios. Thus, many polycationic chains are still free in solution. In this study, we investigated the detailed functions of free polyethylenimine chains (PEI-F) and free N,N,N-trimethyl chitosan chains (TMC-F) using the same polyplex, ie, TMC polyplex (TMC-P), which has high stability in Dulbecco's Modified Eagle's Medium (DMEM). Meanwhile, PEI polyplex (PEI-P)/PEI-F was also evaluated rather than PEI-P/TMC-F because the stability of PEI-P is low in DMEM and, in the latter case, the TMC-F may replace the bound PEI chain in PEI-P to form TMC-P. The transfection results show that both TMC-F and PEI-F can significantly increase the transfection efficiency of TMC-P; however, PEI-F can upregulate the gene expression of TMC-P more efficiently than TMC-F. Further investigations on the endocytosis and intracellular trafficking show that PEI-P/PEI-F, TMC-P/PEI-F, and TMC-P/TMC-F exhibit similar cellular uptake efficiency. However, by shutting down the clathrin-mediated endocytosis or vacuolar proton pump, the transfection efficiency decreases in the order of PEI-P/PEI-F > TMC-P/PEI-F > TMC-P/TMC-F. These findings indicate that PEI-F and TMC-F may promote the transfection efficiency of the polyplex by affecting its cellular uptake pathway and intracellular trafficking.