gebhart/patrepeval huggingface dataset:
Whole genome duplications, multi-break rearrangements, and genome halving problem (2007)

The Genome Halving Problem, motivated by the whole genome duplication events in molecular evolution, was solved by El-Mabrouk and Sankoff. The El-Mabrouk-Sankoff algorithm is rather complex inspiring a quest for a simpler solution. An alternative approach to Genome Halving Problem based on the notion of the contracted breakpoint graph was recently proposed in [2]. This new technique reveals that while the El-Mabrouk-Sankoff result is correct in most cases, it does not hold in the case of unichromosomal genomes. This raises a problem of correcting El-Mabrouk-Sankoff analysis and devising an algorithm that deals adequately with all genomes. In this paper we efficiently classify all genomes into two classes and show that while the El-Mabrouk-Sankoff theorem holds for the first class, it is incorrect for the second class. The crux of our analysis is a new combinatorial invariant defined on duplicated permutations. Using this invariant we were able to come up with a full proof of the Genome Halving theorem and a polynomial algorithm for Genome Halving Problem (for unichromosomal genomes). We also give the first short proof of the original El-Mabrouk-Sankoff result for multichromosomal genomes. Finally, we discuss a generalization of Genome Halving Problem for a more general set of rearrangement operations (including transpositions) and propose an efficient algorithm for solving this problem.
Unarmoured and thin-walled dinoflagellates from the Gulf of Naples, with the description of<i>Woloszynskia cincta</i>sp. nov. (Dinophyceae, Suessiales) (2009)

R. Siano, W.H.C.F. Kooistra, M. Montresor and A. Zingone. 2009. Unarmoured and thin-walled dinoflagellates from the Gulf of Naples, with the description of Woloszynskia cincta sp. nov. (Dinophyceae, Suessiales). Phycologia 48: 44–65. DOI: 10.2216/08-61.1.The unarmoured dinoflagellate assemblage of the Gulf of Naples has been investigated in the frame of a 1-year sampling of natural surface samples collected weekly at a coastal station c. 2 miles offshore. Twenty-six strains of unarmoured dinoflagellates were brought into culture by means of serial dilution. Observations at both light and scanning electron microscopy (SEM) together with molecular phylogenetic analyses allowed identification of eight dinoflagellate species. Gymodinium aureolum, Karlodinium veneficum, Protodinium simplex and Takayama acrotrocha were previously reported in the Mediterranean; whereas, Karlodinium ballantinum and Lepidodinium viride together with a taxon identified as Karenia cf. longicanalis are recorded in the basin for the first time. A new thin-walled dinoflagellate is described as Woloszynskia cincta sp. nov. on the basis of morphological results. Molecular analysis showed that Woloszynskia cincta is closely related to W. halophila and W. pseudopalustris and only distantly related to W. pascheri. In Protodinium simplex, a straight acrobase and an arrangement of the amphiesmal vesicles in latitudinal series were revealed by SEM observations, demonstrating the relatedness of this species with woloszynskioid dinoflagellates. Based on new morphological information on Karlodinium species, Gyrodinium corsicum is transferred to Karlodinium corsicum. New morphological features are identified for the recognition of Takayama acrotrocha, such as the arrangement of the acrobase and the presence of a pore on the ventral side of the cell. The latter species was found to be genetically distinct from other species in the genus Takayama, which is monophyletic.
T-cell Responses in Individuals Infected with Zika Virus and in Those Vaccinated Against Dengue Virus (2017)

Background: The outbreak of Zika virus (ZIKV) infection in Brazil has raised concerns that infection during pregnancy could cause microcephaly and other severe neurodevelopmental malformations in the fetus. The mechanisms by which ZIKV causes fetal abnormalities are largely unknown. The importance of pre-infection with dengue virus (DENV), or other flaviviruses endemic to Brazil, remains to be investigated. It has been reported that antibodies directed against DENV can increase ZIKV infectivity by antibody dependent enhancement (ADE), suggesting that a history of prior DENV infection might worsen the outcome of ZIKV infection.Methods: We used bioinformatics tools to design 18 peptides from the ZIKV envelope containing predicted HLA-I T-cell epitopes and investigated T-cell cross-reactivity between ZIKV-infected individuals and DENV-vaccinated subjects by IFNg ELISPOT.Results: Three peptides induced IFNg production in both ZIKV-infected subjects and in DENV-vaccinated individuals. Flow cytometry indicated that 1 ZIKV peptide induced a CD4+ T-cell response in DENV-vaccinated subjects.Conclusions: We demonstrated that vaccination against DENV induced a T-cell response against ZIKV and identified one such CD4+ T-cell epitope. The ZIKV-reactive CD4+ T cells induced by DENV vaccination and identified in this study could contribute to the appearance of cross-reactive antibodies mediating ADE.
RF requirements of an HSPA terminal (2006)

This chapter contains sections titled: Transmitter requirements Receiver requirements Frequency bands and multiband terminals References
A CD8+ NK cell transcriptomic signature associated with clinical outcome in relapsing remitting multiple sclerosis (2021)

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system (CNS) with the majority of cases characterised by relapsing/remitting (RRMS) attacks of neurologic dysfunction followed by variable resolution. Improving clinical outcomes in RRMS requires both a better understanding of the immunological mechanisms driving recurrent demyelination and better means of predicting future disease course to facilitate early targeted therapy. Here, we apply hypothesis-generating network transcriptomics to CD8<sup>+</sup> cells isolated from patients in RRMS, identifying a signature reflecting expansion of a subset of CD8<sup>+</sup> natural killer cells (NK8<sup>+</sup>) associated with favourable outcome. NK8<sup>+</sup> are capable of regulating CD4<sup>+</sup> T cell activation and proliferation in vitro, with reduced expression of HLA-G binding inhibitory receptors and consequent reduced sensitivity to HLA-G-mediated suppression. We identify surrogate markers of the NK8<sup>+</sup> signature in peripheral blood leucocytes and validate their association with clinical outcome in an independent cohort, suggesting their measurement may facilitate early, targeted therapy in RRMS.
Glucocorticoid Potentiation of Cytochrome P4501A1 Induction by 2,3,7,8-Tetrachlorodibenzo-p-dioxin in Porcine and Human Endothelial Cells in Culture (1997)

Cytochrome P4501A1 (CYP1A1) induction was examined in cultures of porcine aorta endothelial cells (PAEC) and of human aorta endothelial cells (HAEC) exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) with or without the glucocorticoid receptor (GR) agonist cortisol or dexamethasone (DEX). In PAEC exposed to 0.1 nM TCDD + 10 microM cortisol the level of CYP1A1 protein and the degree of ethoxyresorufin-O-deethylase (EROD) activity induction were 2- to 3-fold greater than with 0.1 nM TCDD alone. A similar enhancement of EROD induction was obtained when 0.1 or 1 nM TCDD was added together with 0.1, 1, or 10 microM DEX in the media. Cultures of HAEC also showed potentiation of EROD induction when 1 nM TCDD was co-administered with 10 microM DEX. This potentiation caused by DEX was abolished by addition of 10 microM of the GR antagonist RU38486. These data suggest that potentiation of CYP1A1 induction in endothelial cells proceeds by a GR dependent mechanism.
Achievement of alternative configurations of vehicles on multiple lanes (2009)

Heavy traffic congestion occurs daily at merging sections on a highway. For relieving this congestion, possibility of alternative configuration of vehicles on multiple-lane road at a merging area is discussed in this paper. This is the configuration where no vehicles move aside on the other lane. It has merit in making a smooth merging at an intersection or a junction due to the so-called "zipper effect." We show, by developing a cellular automaton model for multiple lanes, that this configuration is achieved by simple local interactions between vehicles neighboring each other. The degree of the alternative configuration in terms of the spatial increase in parallel driving length is studied by using both numerical simulations and mean-field theory. We successfully construct a theoretical method for calculating this degree of the alternative configuration by using cluster approximation. It is shown that the theoretical results coincide with those of the simulations very well.
Analysis of packet loss in a large-scale DSRC field operational test (2016)

Dedicated Short-Range Communication (DSRC) intends to improve transportation safety by using wireless technology to allow vehicles to exchange safety-awareness message between them. Using a large empirical dataset collected from a field operational test of nearly 3000 vehicles operating around Ann Arbor, Michigan, we characterize the packet-level performance of safety messages exchanged among vehicular encounters. Specifically, to better understand the real-world operating conditions of the vehicular wireless channel, the characteristics of Packet Reception Ratio (PRR) and Inter-Packet Gap (IPG) behaviors and temporal and spatial correlations are examined. Analysis of vehicle-pair encounters shows DSRC packet losses differing from other, static-node wireless beaconing networks, due mainly to the vehicles' high mobility and the possibilities of signal scatterers and/or obstructers that may come between them. As long bursts of consecutively lost packets could jeopardize vehicle safety awareness, IPG is explored further, with short-gapped consecutive losses commonly uncorrelated and longer gaps exhibiting temporal correlation tendencies. The findings of this paper can be used to inform channel models for DSRC systems, which in turn can produce meaningful simulation results.
Thin and small form factor cells: Simulated behavior (2010)

Thin and small form factor cells have been researched lately by several research groups around the world due to possible lower assembly costs and reduced material consumption with higher efficiencies. Given the popularity of these devices, it is important to have detailed information about the behavior of these devices. Simulation of fabrication processes and device performance reveals some of the advantages and behavior of solar cells that are thin and small. Three main effects were studied: the effect of surface recombination on the optimum thickness, efficiency, and current density, the effect of contact distance on the efficiency for thin cells, and lastly the effect of surface recombination on the grams per Watt-peak. Results show that high efficiency can be obtained in thin devices if they are well-passivated and the distance between contacts is short. Furthermore, the ratio of grams per Watt-peak is greatly reduced as the device is thinned.
Calculation of penalties due to polarization effects in a long-haul WDM system using a Stokes parameter model (2001)

We derive a Stokes parameter model to calculate the penalties due to the combination of polarization mode dispersion (PMD), polarization dependent loss (PDL), and polarization dependent gain (PDG) in long-haul, dense wavelength division multiplexed (WDM) systems. In this model, we follow the Stokes parameters for the signal and the noise in each channel instead of following the full time domain behavior of each channel. This approach allows us to determine the statistical distribution of penalties with up to 10/sup 5/ fiber realizations and 40 channels. We validate this model to the extent possible by comparison to full numerical simulations. Using this model, we find that the interaction of PMD and PDL is the major source of penalties and that the effect of PDG is negligible in WDM systems with more than ten channels.
Loblolly Pine (Pinus taeda L.) Contains Multiple Expressed Genes Encoding Light-Dependent NADPH:Protochlorophyllide Oxidoreductase (POR) (1998)

NADPH:protochlorophyllide oxidoreductase (POR) catalyzes the light-dependent reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), a key regulatory step in chlorophyll biosynthesis. In most angiosperms, POR is encoded by a small nuclear gene family, containing at least two differentially-expressed genes designated porA and porB. We have demonstrated that the PORs of loblolly pine (Pinus taeda L.), a gymnosperm, are encoded by a large multigene family, composed of two distinct subfamilies encoding porA and porB genes similar to those previously described in angiosperms. DNA gel blot analysis of genomic DNA showed that the two por subfamilies of loblolly pine have duplicated at different rates, with the porA subfamily containing two members, and the porB subfamily containing at least 11 potential members. DNA sequence analysis and gel blot hybridization studies also showed that a subset of the por genes present in the loblolly pine genome are pseudogenes. Based on the results of 5'- and 3'-RACE analysis, it appears that multiple porA and porB genes are expressed in loblolly pine cotyledons and stems during development. Using gene specific probes, no difference was observed in the steady-state levels of the different porA and porB transcripts in cotyledons of dark-grown seedlings before and following illumination. However, the steady state levels of the porA and porB transcripts were found to increase at different rates in the stems of dark-grown seedlings following illumination. The phylogenetic relationship between the por gene family members in P. taeda and other pine species and the potential significance of the two por subfamilies to the evolution of por gene function are discussed.
Laboratory Simulation of Blue Jets with Apokampic Discharge in the Hz Frequency Range (2019)

It is shown that the channel of apokampic discharge is a source of streamers at low air pressure and low frequencies (7–16 Hz) of high-voltage positive-polarity pulses and voltage amplitudes from 26 to 35 kV. The maximal starting speed of laboratory streamers was 560 km/s. A hypothesis about blue jet origination in nature is suggested based on experimental data. For their start, high frequencies of voltage pulses are not required, breakdowns in the Hz range are sufficient, but the discharge channel should bend and the field intensity should be high at the bending point.
Data from Synchronous Detection of Circulating Tumor Cells in Blood and Disseminated Tumor Cells in Bone Marrow Predicts Adverse Outcome in Early Breast Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;We examined the prognostic impact of circulating tumor cells (CTCs) and disseminated tumor cells (DTCs) detected at the time of surgery in 742 untreated patients with early breast cancer.&lt;/p&gt;Experimental Design:&lt;p&gt;DTCs in bone marrow were enumerated using the EPCAM-based immunomagnetic enrichment and flow cytometry (IE/FC) assay. CTCs in blood were enumerated either by IE/FC or CellSearch. Median follow-up was 7.1 years for distant recurrence-free survival (DRFS) and 9.1 years for breast cancer–specific survival (BCSS) and overall survival (OS). Cox regressions were used to estimate hazard ratios for DRFS, BCSS, and OS in all patients, as well as in hormone receptor–positive (HR-positive, 87%) and HR-negative (13%) subsets.&lt;/p&gt;Results:&lt;p&gt;In multivariate models, CTC positivity by IE/FC was significantly associated with reduced BCSS in both all (&lt;i&gt;n&lt;/i&gt; = 288; &lt;i&gt;P&lt;/i&gt; = 0.0138) and HR-positive patients (&lt;i&gt;n&lt;/i&gt; = 249; &lt;i&gt;P&lt;/i&gt; = 0.0454). CTC positivity by CellSearch was significantly associated with reduced DRFS in both all (&lt;i&gt;n&lt;/i&gt; = 380; &lt;i&gt;P&lt;/i&gt; = 0.0067) and HR-positive patients (&lt;i&gt;n&lt;/i&gt; = 328; &lt;i&gt;P&lt;/i&gt; = 0.0002). DTC status, by itself, was not prognostic; however, when combined with CTC status by IE/FC (&lt;i&gt;n&lt;/i&gt; = 273), double positivity (CTC+/DTC+, 8%) was significantly associated with reduced DRFS (&lt;i&gt;P&lt;/i&gt; = 0.0270), BCSS (&lt;i&gt;P&lt;/i&gt; = 0.0205), and OS (&lt;i&gt;P&lt;/i&gt; = 0.0168). In HR-positive patients, double positivity (9% of 235) was significantly associated with reduced DRFS (&lt;i&gt;P&lt;/i&gt; = 0.0285), BCSS (&lt;i&gt;P&lt;/i&gt; = 0.0357), and OS (&lt;i&gt;P&lt;/i&gt; = 0.0092).&lt;/p&gt;Conclusions:&lt;p&gt;Detection of CTCs in patients with HR-positive early breast cancer was an independent prognostic factor for DRFS (using CellSearch) and BCSS (using IE/FC). Simultaneous detection of DTCs provided additional prognostic power for outcome, including OS.&lt;/p&gt;&lt;/div&gt;
Transforming growth factors type‐β and dexamethasone attenuate group II phospholipase A<sub>2</sub> gene expression by interleukin‐1 and forskolin in rat mesangial cells (1992)

Treatment of rat mesangial cells with interleukin-1 beta (IL-1 beta) and forskolin induced, in a synergistic fashion, the expression of group II phospholipase A2 (PLA2) mRNA, with subsequent increased synthesis and secretion of PLA2. In contrast, interleukin-6 did not increase PLA2 mRNA levels of PLA2 activity. Transforming growth factor (TGF) beta 1, TGF beta 2 and TGF beta 3 equipotently attenuated the IL-1 beta- and forskolin-induced elevation of PLA2 mRNA, as well as PLA2 synthesis and secretion. The glucocorticoid dexamethasone only partially suppressed the IL-1 beta- and forskolin-induced elevation of PLA2 mRNA, but totally inhibited PLA2 synthesis and secretion.
Empirical virtual machine models for performance guarantees (2010)

Existing Virtual Machine (VM) management systems rely on host resource utilization metrics to allocate and schedule VMs. Many management systems only consolidate and migrate VMs based on hosts ’ CPU utilizations. However, the performance of delay-sensitive workloads, such as web services and online transaction processing, can be severely degraded by contention on numerous of the hosts’ components. Current VM management systems typically use threshold based rules to decide when to migrate VMs, rather than using application-level performance. This means that they cannot easily provide application-level service level objective (SLO) guarantees. Providing SLO guarantees is even more difficult when considering that today’s enterprise applications often consist of multiple VM tiers. In this paper we show how the performance of a multi-tiered VM application can be empirically captured, modeled and scaled. This allows our management system to guarantee application-level performance, despite variable host utilization and VM workload levels. Additionally, it can predict the performance of an application at host utilization levels that have not been previously observed. This is achieved by performing regression analysis on the previously observed values and scaling the applications performance model. This allows the performance of a VM to be predicted before it is migrated to or from a new host. We have found that by dynamically, rather than statically, allocating resources, average response time can be improved by 30%. Additionally, we found that resource allocations can be reduced by 20%, with no degradation in response time. 1.
A New Portal to SuFEx Click Chemistry: A Stable Fluorosulfuryl Imidazolium Salt Emerging as an “F−SO<sub>2</sub>+” Donor of Unprecedented Reactivity, Selectivity, and Scope (2017)

Abstract Sulfuryl fluoride, SO 2 F 2 , has been found to derivatize phenols in all kinds of environments, even those in highly functional molecules. We now report that a solid fluorosulfuryl imidazolium triflate salt delivers the same “F−SO 2 + ” fragment to Nu−H acceptor groups in the substrates. However, this triflate salt is a far more reactive fluorosulfurylating agent than SO 2 F 2 and displays selectivity preferences of its own. Moreover, the new azolium triflate reagent reacts once with primary amines and anilines before the reaction stops. On the other hand, with triethylamine and two equivalents of the “F−SO 2 + ” donor present, it proceeds on to the bis(fluorosulfuryl)imides in good yield—two important conversions that we have never seen with sulfuryl fluoride as the electrophile.
Oral microbial ecology in chronic periodontitis and periodontal health (2005)

Our aim was to find out differences between chronic periodontitis (CP) and periodontally healthy subjects with respect to oral lactic acid bacteria (LAB) as well as subgingival microbial relations. Clinical data, salivary levels of lactobacilli and mutans streptococci, and subgingival microbial samples were obtained from 26 CP and 15 periodontally healthy subjects. Antimicrobial activity of LAB against periodontal pathogens was assessed. We found Actinobacillus actinomycetemcomitans , Porphyromonas gingivalis and Prevotella intermedia/nigrescens in 54%, 23% and 73% of CP patients, respectively; the latter was also found in 47% of healthy subjects. The mean proportion of streptococci (27.0 vs 15.2%), particularly S. mutans group (5.7 vs 0.8%) and S. mitis group (18.1 vs 5.0%), as well as aerobic coryneforms (24.7 vs 11.9%) was higher in healthy persons (p< 0.05). An inverse relationship of subgingival streptococci and aerobic coryneforms with periodontal pathogens and deteriorated clinical parameters were seen. Salivary counts of mutans streptococci were higher in healthy persons. Inhibition of periodontal pathogens by LAB was observed. In conclusion, the proportions of oral LAB were significantly lower in CP than in healthy subjects, whilst being important antagonists against periodontal pathogens. These oral commensals may play an important role in the suppression of periodontal pathogens and maintenance of microecological balance in the oral cavity. Key words: Chronic periodontitis, periodontal health, lactic acid bacteria, subgingival microflora, antimicrobial activity, microbial ecology
Reduction of azo dyes by redox mediators originating in the naphthalenesulfonic acid degradation pathway of Sphingomonas sp. strain BN6 (1997)

The anaerobic reduction of azo dyes by Sphingomonas sp. strain BN6 was analyzed. Aerobic conversion of 2-naphthalenesulfonate (2NS) by cells of strain BN6 stimulated the subsequent anaerobic reduction of the sulfonated azo dye amaranth at least 10-fold. In contrast, in crude extracts, the azo reductase activity was not stimulated. A mutant of strain BN6 which was not able to metabolize 2NS showed increased amaranth reduction rates only when the cells were resuspended in the culture supernatant of 2NS-grown BN6 wild-type cells. The same increase could be observed with different bacterial strains. This suggested the presence of an extracellular factor which was formed during the degradation of 2NS by strain BN6. The addition of 1,2-dihydroxynaphthalene, the first intermediate of the degradation pathway of 2NS, or its decomposition products to cell suspensions of the mutant of strain BN6 (2NS-) increased the activity of amaranth reduction. The presence of bacterial cells was needed to maintain the reduction process. Thus, the decomposition products of 1,2-dihydroxynaphthalene are suggested to act as redox mediators which are able to anaerobically shuttle reduction equivalents from the cells to the extracellular azo dye.
Analysis of range ambiguity suppression in SAR by up and down chirp modulation for point and distributed targets (2004)

This Paper provides a demonstrative derivation of the effect of up and down chirp modulation on point and extended target signals. Analysis has been performed with respect to signal amplitude, signal extension, modulation rate and phase behavior. The suppression of "point target" range ambiguities is investigated for the a possible TerraSAR-X parameter setting. Extended targets have been simulated and filtered. A Range-Ambiguity Simulator is under development which is based on airborne X-band data from the Experimental SAR (E-SAR) of DLR. The simulator concept is presented.