Radiation Information from 1958 δ2

The telemetered radiation information from the satellite 1958 δ2 (Sputnik III) has been analyzed for sixty-two separate passes recorded in College, Alaska. The data indicate a dependence of radiation intensity on altitude in the range 250-500 km. Both the high and low energy components apparently contribute to the overall increase of intensity with altitude, but the presence of a continuous afterglow in the scintillating crystal prevented detailed interpretation of the results.IGY Project No. 32.42 NSF Grant No. Y/32.42/268Ye

Predictors of tonsillectomy after previous adenoidectomy for upper airway obstruction [abstract]

One of the main indications for adenotonsillectomy in children is upper airway obstruction, including obstructive sleep apnea. Previous research has suggested an increased risk for requiring subsequent tonsillectomy when adenoidectomy alone is performed for upper airway obstruction. The purpose of this study is to further characterize potential risk factors for subsequent tonsillectomy in pediatric patients undergoing adenoidectomy for upper airway obstruction

Regular and Irregular Boundary Conditions in the AdS/CFT Correspondence

We expand on Klebanov and Witten's recent proposal for formulating the AdS/CFT correspondence using irregular boundary conditions. The proposal is shown to be correct to any order in perturbation theory.Comment: 7 pages, typos correcte

Deriving Boltzmann Equations from Kadanoff-Baym Equations in Curved Space-Time

To calculate the baryon asymmetry in the baryogenesis via leptogenesis scenario one usually uses Boltzmann equations with transition amplitudes computed in vacuum. However, the hot and dense medium and, potentially, the expansion of the universe can affect the collision terms and hence the generated asymmetry. In this paper we derive the Boltzmann equation in the curved space-time from (first-principle) Kadanoff-Baym equations. As one expects from general considerations, the derived equations are covariant generalizations of the corresponding equations in Minkowski space-time. We find that, after the necessary approximations have been performed, only the left-hand side of the Boltzmann equation depends on the space-time metric. The amplitudes in the collision term on the right--hand side are independent of the metric, which justifies earlier calculations where this has been assumed implicitly. At tree level, the matrix elements coincide with those computed in vacuum. However, the loop contributions involve additional integrals over the the distribution function.Comment: 14 pages, 5 figures, extended discussion of the constraint equations and the solution for the spectral functio

reComBat: Batch effect removal in large-scale, multi-source omics data integration

With the steadily increasing abundance of omics data produced all over the world, some-times decades apart and under vastly different experimental conditions residing in public databases, a crucial step in many data-driven bioinformatics applications is that of data integration. The challenge of batch effect removal for entire databases lies in the large number and coincide of both batches and desired, biological variation resulting in design matrix singularity. This problem currently cannot be solved by any common batch correction algorithm. In this study, we present reComBat , a regularised version of the empirical Bayes method to overcome this limitation. We demonstrate our approach for the harmonisation of public gene expression data of the human opportunistic pathogen Pseudomonas aeruginosa and study a several metrics to empirically demonstrate that batch effects are successfully mitigated while biologically meaningful gene expression variation is retained. reComBat fills the gap in batch correction approaches applicable to large scale, public omics databases and opens up new avenues for data driven analysis of complex biological processes beyond the scope of a single study

reComBat: batch-effect removal in large-scale multi-source gene-expression data integration

With the steadily increasing abundance of omics data produced all over the world under vastly different experimental conditions residing in public databases, a crucial step in many data-driven bioinformatics applications is that of data integration. The challenge of batch-effect removal for entire databases lies in the large number of batches and biological variation, which can result in design matrix singularity. This problem can currently not be solved satisfactorily by any common batch-correction algorithm.; We present; reComBat; , a regularized version of the empirical Bayes method to overcome this limitation and benchmark it against popular approaches for the harmonization of public gene-expression data (both microarray and bulkRNAsq) of the human opportunistic pathogen; Pseudomonas aeruginosa; . Batch-effects are successfully mitigated while biologically meaningful gene-expression variation is retained.; reComBat; fills the gap in batch-correction approaches applicable to large-scale, public omics databases and opens up new avenues for data-driven analysis of complex biological processes beyond the scope of a single study.; The code is available at https://github.com/BorgwardtLab/reComBat, all data and evaluation code can be found at https://github.com/BorgwardtLab/batchCorrectionPublicData.; Supplementary data are available at; Bioinformatics Advances; online

Optimized RNA isolation of FFPE uterine scar tissues for RNA expression analyses delineated by laser microdissection

ABSTRACT Samples for histological analyses are often formalin-fixed paraffin-embedded (FFPE) and slide-mounted, which complicates RNA extraction for many downstream molecular applications. Furthermore, when the region of interest is extremely small due to isolation with lasermicrodissection (LMD), extracting RNA of adequate quality and quantity is difficult. We describe an optimized protocol for maximizing RNA output from FFPE tissue devised to identify and analyze gene expression of humanmaternal uterine scar tissue obtained fromuterotomy scars resulting from prior cesarean deliveries. Gomori trichrome staining allowed for region identification for LMD. Successful RNA isolation, reverse transcription and, importantly, quantitative real-time PCR (qRT-PCR) were performed. This report provides an optimized step-by-step protocol yielding sufficient RNA for qRT-PCR analyses from challenging tissue/LMD-FFPE samples. METHOD SUMMARY FFPE sample sections weremounted on glass slides and stained with hematoxylin and eosin (HE). A corresponding slide was stained according to Gomori trichrome for orientation. Regions of interest in HE-stained samples weremarked using lasermicrodissection (LMD) and subsequently scratched off the slide with a sterile scalpel. RNA extraction and cDNA synthesis were carried out, and quantitative real-time PCR with TaqMan probes was performed. TWEETABLE ABSTRACT We describe a protocol for maximized RNA output from FFPE tissue delineated by laser microdissection devised to analyze gene expression of human maternal uterine scar tissue obtained from uterotomy scars of prior cesarean deliveries

Topoisomerase II inhibitors induce DNA damage-dependent interferon responses circumventing Ebola virus immune evasion

Ebola virus (EBOV) protein VP35 inhibits production of interferon alpha/beta (IFN) by blocking RIG-I-like receptor signaling pathways, thereby promoting virus replication and pathogenesis. A high-throughput screening assay, developed to identify compounds that either inhibit or bypass VP35 IFN-antagonist function, identified five DNA intercalators as reproducible hits from a library of bioactive compounds. Four, including doxorubicin and daunorubicin, are anthracycline antibiotics that inhibit topoisomerase II and are used clinically as chemotherapeutic drugs. These compounds were demonstrated to induce IFN responses in an ATM kinase-dependent manner and to also trigger the DNA-sensing cGAS-STING pathway of IFN induction. These compounds also suppress EBOV replication in vitro and induce IFN in the presence of IFN-antagonist proteins from multiple negative-sense RNA viruses. These findings provide new insights into signaling pathways activated by important chemotherapy drugs and identify a novel therapeutic approach for IFN induction that may be exploited to inhibit RNA virus replication

Avalanche of Bifurcations and Hysteresis in a Model of Cellular Differentiation

Cellular differentiation in a developping organism is studied via a discrete bistable reaction-diffusion model. A system of undifferentiated cells is allowed to receive an inductive signal emenating from its environment. Depending on the form of the nonlinear reaction kinetics, this signal can trigger a series of bifurcations in the system. Differentiation starts at the surface where the signal is received, and cells change type up to a given distance, or under other conditions, the differentiation process propagates through the whole domain. When the signal diminishes hysteresis is observed

THEORY OF PHASE-LOCKING IN SMALL JOSEPHSON JUNCTION CELLS

Within the RSJ model, we performed a theoretical analysis of phase-locking in elementary strongly coupled Josephson junction cells. For this purpose, we developed a systematic method allowing the investigation of phase-locking in cells with small but non-vanishing loop inductance.The voltages across the junctions are found to be locked with very small phase difference for almost all values of external flux. However, the general behavior of phase-locking is found to be just contrary to that according to weak coupling. In case of strong coupling there is nearly no influence of external magnetic flux on the phases, but the locking-frequency becomes flux-dependent. The influence of parameter splitting is considered as well as the effect of small capacitive shunting of the junctions. Strongly coupled cells show synchronization even for large parameter splitting. Finally, a study of the behavior under external microwave radiation shows that the frequency locking-range becomes strongly flux-dependent, whereas the locking frequency itself turns out to be flux-independent.Comment: 26 pages, REVTEX, 9 PS figures appended in uuencoded form at the end, submitted to Phys. Rev. B