gebhart/patrepeval huggingface dataset:
Efficient estimation of compressible state-space models with application to calcium signal deconvolution (2016)

In this paper, we consider linear state-space models with compressible innovations and convergent transition matrices in order to model spatiotemporally sparse transient events. We perform parameter and state estimation using a dynamic compressed sensing framework and develop an efficient solution consisting of two nested Expectation-Maximization (EM) algorithms. Under suitable sparsity assumptions on the innovations, we prove recovery guarantees and derive confidence bounds for the state estimates. We provide simulation studies as well as application to spike deconvolution from calcium imaging data which verify our theoretical results and show significant improvement over existing algorithms.
The Bit Interleaved Coded Modulation module for DVB-NGH: Enhanced features for mobile reception (2012)

This paper describes the main features of the DVB-NGH Bit-Interleaved Coded Modulation (BICM) module. This latter is derived from a sub-set of DVB-T2 BICM components with additional features intended to first lower receiver complexity and power consumption and then to increase receiver robustness over mobile reception. Therefore, the long code block size was removed, a different range of coding rates was chosen, non-uniform constellations were adopted in order to provide shaping gain, and the principle of signal space diversity was extended to four-dimensional rotated constellations. Moreover the structure of the time interleaver offers the possibility to significantly increase the interleaving depth, a feature required for mobility over terrestrial and satellite links.
Empirical Channel Model for Human Body Communication (2014)

In this letter, an empirical channel model for human body communication (HBC) is presented based upon impulse response. For a channel model over a wide range of frequencies between 5 and 80 MHz, the amplitude of an impulse response is modeled with a random variable at each sampling point; the random variable is found using empirically obtained impulse responses with respect to multiple subjects of 70 human subjects. This empirical channel model is obtained when a signal transmitter and receiver are located on opposite hands. However, it provides a practical way to estimate the performance of HBC systems within an environment of multiple users and various devices.
Examining the ecological validity of the Talent Development Environment Questionnaire (2012)

It is clear that high class expertise and effective practice exists within many talent development environments across the world. However, there is also a general consensus that widespread evidence-based policy and practice is lacking. As such, it is crucial to develop solutions which can facilitate effective dissemination of knowledge and promotion of evidence-based talent development systems. While the Talent Development Environment Questionnaire (Martindale et al., 2010 ) provides a method through which this could be facilitated, its ecological validity has remained untested. As such, this study aimed to investigate the real world applicability of the questionnaire through discriminant function analysis. Athletes across ten distinct regional squads and academies were identified and separated into two broad levels, 'higher quality' (n = 48) and 'lower quality' (n = 51) environments, based on their process quality and productivity. Results revealed that the Talent Development Environment Questionnaire was able to discriminate with 77.8% accuracy. Furthermore, in addition to the questionnaire as a whole, two individual features, 'quality preparation' (P < 0.01) and 'understanding the athlete' (P < 0.01), were found to be significant discriminators. In conclusion, the results indicate robust structural properties and sound ecological validity, allowing the questionnaire to be used with more confidence in applied and research settings.
Bidirectional cross talk between patient‐derived melanoma and cancer‐associated fibroblasts promotes invasion and proliferation (2016)

Tumor-stroma interactions are critical for epithelial-derived tumors, and among the stromal cell types, cancer-associated fibroblasts (CAFs) exhibit multiple functions that fuel growth, dissemination, and drug resistance. However, these interactions remain insufficiently characterized in non-epithelial tumors such as malignant melanoma. We generated monocultures of melanoma cells and matching CAFs from patients' metastatic lesions, distinguished by oncogenic drivers and immunoblotting of characteristic markers. RNA sequencing of CAFs revealed a homogenous epigenetic program that strongly resembled the signatures from epithelial cancers, including enrichment for an epithelial-to-mesenchymal transition (EMT). Melanoma CAFs in monoculture displayed robust invasive behavior while patient-derived melanoma monocultures showed very little invasiveness. Instead, melanoma cells showed increased invasion when co-cultured with CAFs. In turn, CAFs showed increased proliferation when exposed to melanoma conditioned media (CM), mediated in part by melanoma-secreted transforming growth factor-alpha that acted on CAFs via the epidermal growth factor receptor. This study provides evidence that bidirectional interactions between melanoma and CAFs regulate progression of metastatic melanoma.
Quantification of cytomegalovirus DNA in peripheral blood leukocytes by a branched-DNA signal amplification assay (1997)

Quantification of cytomegalovirus (CMV) DNA in blood may aid in the identification of patients at highest risk for developing CMV disease, the evaluation of new therapeutics, and the prompt recognition of drug-resistant CMV strains. A branched-DNA (bDNA) assay was developed for the reliable quantification of CMV DNA in peripheral blood leukocytes. The bDNA assay allowed for the highly specific and reproducible quantification of CMV DNA in clinical specimens. Furthermore, the bDNA assay was at least as sensitive as culture techniques and displayed a nearly 3 log10 dynamic range in quantification. Changes in CMV DNA levels measured by the bDNA assay in a human immunodeficiency virus-positive patient undergoing therapy were consistent with CMV culture, antigen, and genotype results and correlated with disease progression and resistance markers. The bDNA assay for the quantification of CMV DNA may provide a useful tool that can be used to aid physicians in monitoring disease progression, evaluating therapeutic regimens, and recognizing viral resistance and drug failure.
<title>Electron Microscopy Of Atoms</title> (1977)

Paper not available for publication© (1977) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
RF Self-Interference Cancellation for Full-Duplex (2014)

This paper proposes two RF self-interference cancellation techniques. Their small form-factor enables full-duplex communication links for small -to-medium size portable devices and hence promotes the adoption of full-duplex in mass-market applications and next-generation standards, e.g. IEEE802.11 a
SAion - SEN's unique solution for 450mm ion implant (2014)

The SAion-450 is a leading-edge ion implanter developed for the upcoming 450mm wafer generation. The SAion-450 has extremely wide process coverage and productivity throughout both the medium current (MC) and high current (HC) process ranges. Although the area of a 450mm wafer is 2.25 times larger than that of a 300mm wafer, the SAion-450 can process typical MC recipes with higher productivity than the current 300mm MC implanter, the MC3-II/GP. Additionally, low energy (LE) productivity can be significantly enhanced with the addition of the LE beam line option. This can be easily installed (or removed) in a production fab. The SAion product line also includes a 300mm model. The SAion-300 is equipped with the same beamline as the SAion-450 in order to deliver the same process characteristics in 300mm fabs as in 450mm wafer lines. Thus, the SAion series can serve as a bridge tool to assure smooth wafer size transition from 300mm to 450mm.
Maximizing Stone Fragmentation Efficiency With Ultrasonic Probes: Impact of Probe Pressure and Rotation (2009)

Differences in probe manipulation impact stone fragmentation efficiency and procedural success.
Evaluation of laser dye mutagenicity using the ames/salmonella microsome test (1985)

Twenty-five laser dyes and four analogs were tested for mutagenicity in the Ames/Salmonella test. Seven dyes and two analogs gave positive mutagenic responses with bacterial strains TA1538 and TA98. Of two widely used families of laser dyes (coumarins and rhodamines), four coumarin samples, but none of the rhodamine samples, were mutagenic. All mutagenic compounds require enzyme activation for positive response except two terphenyl analogs, which are mutagenic with or without activation. Using high-performance liquid chromatography (HPLC), it was determined that five mutagenic dye samples had multiple components. The dyes themselves may not be the mutagenic agents in all cases (as with Nile Blue) but may contain impurities that are mutagenic. One dye, adicyanomethylene (DCM) (greater than or equal to 95% pure), was mutagenic at doses below 0.5 micrograms/plate on strains TA1538 and TA98. DCM also induced reversions in strains TA96, TA97, TA100, TA102, and TA104, although less efficiently. This study indicates the need for further toxicological testing of these types of compounds. The mutagenic components of these dye mixtures, whether it is the dye or a contaminant, presents a possible hazard to those handling them. Therefore, practices and procedures for the safe handling of specific dyes should be reviewed in light of these findings.
Early emergence of Yersinia pestis as a severe respiratory pathogen (2015)

Yersinia pestis causes the fatal respiratory disease pneumonic plague. Y. pestis recently evolved from the gastrointestinal pathogen Y. pseudotuberculosis; however, it is not known at what point Y. pestis gained the ability to induce a fulminant pneumonia. Here we show that the acquisition of a single gene encoding the protease Pla was sufficient for the most ancestral, deeply rooted strains of Y. pestis to cause pneumonic plague, indicating that Y. pestis was primed to infect the lungs at a very early stage in its evolution. As Y. pestis further evolved, modern strains acquired a single amino-acid modification within Pla that optimizes protease activity. While this modification is unnecessary to cause pneumonic plague, the substitution is instead needed to efficiently induce the invasive infection associated with bubonic plague. These findings indicate that Y. pestis was capable of causing pneumonic plague before it evolved to optimally cause invasive infections in mammals.
Successful allogeneic bone marrow transplantation in juvenile CML: conditioning or graft-versus-leukaemia effect? (1993)

Allogeneic BMT is the treatment of choice for juvenile CML (JCML). This has been successful following conditioning with cyclophosphamide (120 mg/kg) and total body irradiation (TBI) (10-15.75 Gy). However, busulphan (16 mg/kg) and cyclophosphamide (200 mg/kg) (Bu/Cy) conditioning has been reported to be insufficient to eradicate the malignant clone in JCML. We report successful BMT and eradication of the disease at 18 months follow-up in a child 15 months old at presentation, who was conditioned with busulphan 20 mg/kg and cyclophosphamide 200 mg/kg, with the addition of splenic irradiation. Despite using higher than conventional doses of busulphan, pharmacokinetic analysis revealed very low busulphan peak levels and rapid excretion. As a possible consequence, only partial chimerism was achieved, but full engraftment ensued following the discontinuation of cyclosporin A, rebound donor lymphocytosis and the onset of acute GVHD. We suggest that host resistance to engraftment and tumour elimination was overcome by removing a suppressive effect on donor lymphocytes, allowing a graft-versus-leukaemia effect.
Role of Transforming Growth Factor-α and the Epidermal Growth Factor Receptor in Embryonic Rat Testis Development1 (2000)

Embryonic testis development requires the morphogenesis of cords and growth of all cell populations to allow organ formation. It is anticipated that coordination of the growth and differentiation of various cell types involves locally produced growth factors. The current study was an investigation of the hypothesis that transforming growth factor-alpha (TGF-alpha) is involved in regulating embryonic testis growth. TGF-alpha has previously been shown to function in the postnatal testis. TGF-alpha and other members of the epidermal growth factor (EGF) family act through the epidermal growth factor receptor (EGFR) to stimulate cell proliferation and tissue morphogenesis. To understand the potential actions of TGF-alpha in the embryonic testis, general cell proliferation was investigated. Characterization of cell proliferation in the rat testis throughout embryonic and postnatal development indicated that each cell type has a distinct pattern of proliferation. Germ cell growth was transiently suppressed around birth. Interstitial cell growth was high embryonically and decreased to low levels around birth. A low level of Sertoli cell proliferation was observed at the onset of testis cord formation. Sertoli cell proliferation in early embryonic development was low; the levels were high later in embryonic development and remained high until the onset of puberty. Both TGF-alpha and the EGFR were shown to be expressed in the embryonic and postnatal rat and mouse testis. Perturbation of TGF-alpha function using neutralizing antibodies to TGF-alpha on testis organ cultures dramatically inhibited the growth of both embryonic and neonatal testis. TGF-alpha antibodies had no effect on cord formation. The TGF-alpha antibody was found to be specific for TGF-alpha in Western blots when compared to EGF and heregulin. Testis growth was also inhibited by perturbation of EGFR signaling using an EGFR kinase inhibitor. Therefore, TGF-alpha appears to influence embryonic testis growth but not morphogenesis (i.e., cord formation). Treatment of embryonic testis organ cultures with exogenous TGF-alpha also perturbed development, leading to an increased proliferation of unorganized cells. Testis from EGFR and TGF-alpha knockout mice were analyzed for testis morphology. TGF-alpha knockout mice had no alterations in testis phenotype, while EGFR knockout mice had a transient decrease in the relative amount of interstitial cells before birth. Observations suggest that there may be alternate or compensatory factors that allow testis growth to occur in the apparent absence of TGF-alpha actions in the mutant mice. In summary, the results obtained suggest that TGF-alpha is an important factor in the regulation of embryonic testis growth, but other factors will also be involved in the process.
Release of Intracranial Pressure Leads to Improvement of Otoacoustic Emissions--A Case Report of a Kenyan Child with Complicated Tuberculous Meningitis (2013)

Intracranial pressure usually is measured with invasive techniques. The usability of transient evoked otoacoustic emissions as non-invasive approach has been evaluated only once by Frank et al. This article presents the case of a Kenyan boy with tuberculous meningitis and an active malresorptive hydrocephalus. At this stage, the otoacoustic emissions did show very low correlations. After releasing pressure, the otoacoustic emissions improved significantly. This case report points out the possible usability of otoacoustic emissions in intracranial pressure monitoring.
Guayule and Russian Dandelion as Alternative Sources of Natural Rubber (2007)

Natural rubber, obtained almost exclusively from the Para rubber tree (Hevea brasiliensis), is a unique biopolymer of strategic importance that, in many of its most significant applications, cannot be replaced by synthetic rubber alternatives. Several pressing motives lead to the search for alternative sources of natural rubber. These include increased evidence of allergenic reactions to Hevea rubber, the danger that the fungal pathogen Microcyclus ulei, causative agent of South American Leaf Blight (SALB), might spread to Southeast Asia, which would severely disrupt rubber production, potential shortages of supply due to increasing demand and changes in land use, and a general trend towards the replacement of petroleum-derived chemicals with renewables. Two plant species have received considerable attention as potential alternative sources of natural rubber: the Mexican shrub Guayule (Parthenium argentatum Gray) and the Russian dandelion (Taraxacum koksaghyz). This review will summarize the current production methods and applications of natural rubber (dry rubber and latex), the threats to the production of natural rubber from the rubber tree, and describe the current knowledge of the production of natural rubber from guayule and Russian dandelion.
Improvement of L-phenylalanine production from glycerol by recombinant Escherichia coli strains: The role of extra copies of glpK, glpX, and tktA genes (2014)

Enhancing the gene copy numbers for glpX and tktA increased L-Phe productivity from glycerol without affecting growth rate. Engineering of glycerol metabolism towards L-Phe production in E. coli has to balance the pathways of gluconeogenesis, glycolysis, and PPP to improve the supply of the precursors, PEP and E4P.
Electromagnetic scattering by discrete random media: far field (2014)

By definition, a discrete random medium (DRM) is a scattering object in the form of an imaginary volume V populated by a large number N of particles in such a way that the spatial distribution of the particles throughout the volume is statistically uniform or quasi-uniform. Over time, particle positions and states change randomly, thereby resulting in random changes of the state ψ of the entire object (Section 10.4). Classical examples of a DRM are clouds and particle suspensions (Plates 1.1b—1.1d). In many cases a particulate surface (Plates 1.1e and 1.1f) can also be modeled as a DRM, since even minute changes of the source-of-light → object → detector configuration during the measurement are equivalent to multi-wavelength shifts in particle positions and, in essence, result in a stochastic scattering object. The volume packing density of a DRM can vary from almost zero for a cloud to more than 50% for a particulate surface.
An atomic frequency comb memory in rare-earth doped thin-film lithium niobate (2022)

We demonstrate compact chip-integrated atomic frequency comb storage in rare-earth doped thin-film lithium niobate. Our optical memory exhibits a broad storage bandwidth exceeding 100 MHz, and optical storage time of over 250 ns.
Entwicklung eines Bewertungssystems für Virtual Reality-Simulatoren in der Chirurgie (2011)

Zusammenfassung Chirurgische Fertigkeiten im Bereich der minimal invasiven Chirurgie können an Virtual Reality-Simulatoren geübt werden. Für ein zielgerichtetes Training ist die Bewertung der Übungsausführung wichtig. Deshalb werden neue Methoden zur Entwicklung eines Bewertungssystems für die automatisierte Beurteilung von Trainierenden eingeführt. Zwei Studien haben die Eignung des neuen Konzeptes gezeigt.
Overexpression of ribonucleotide reductase as a mechanism of resistance to 2,2-difluorodeoxycytidine in the human KB cancer cell line. (1999)

In this study, human oropharyngeal epidermoid carcinoma KB cells that were resistant to 2,2-difluorodeoxycytidine (dFdCyd) were selected and designated the KB-Gem clone. The KB parental cell line IC50 was 0.3 microM dFdCyd, as compared with the KB-Gem clone IC50 of 32 microM dFdCyd. The KB-Gem clone demonstrated overexpression of ribonucleotide reductase (RR) M2 subunit mRNA (9-fold) and overexpression of M2 protein (2-fold); RR activity was 2.3-fold higher than the KB parental cell line. Both the dATP and dCTP pools of the KB-Gem clone increased 2-fold over the parental cell line, with no change in the dGTP and dTTP pools. Reverse transcriptase-PCR was used to clone the cDNA of deoxycytidine kinase (DCK). Resulting sequences revealed two silent mutations in the KB-Gem clone. The amino acid sequence of the DCK protein and mRNA expression remained unchanged. The KB-Gem clone's DCK enzyme activity was 56% of that of the parental cell line. After the endogenous dNTPs were removed with a G-25 column, no difference was evident between the enzyme activities of the KB-Gem clone and parental cells. Thus, contrary to previous hypotheses, DCK deficiency does not play the primary role in the resistance mechanism of dFdCyd, accepting a secondary role to the overexpression of the target gene, RR, and pool expansion.
Widespread occurrence of lysine methylation in Plasmodium falciparum proteins at asexual blood stages (2016)

Post-transcriptional and post-translational modifications play a major role in Plasmodium life cycle regulation. Lysine methylation of histone proteins is well documented in several organisms, however in recent years lysine methylation of proteins outside histone code is emerging out as an important post-translational modification (PTM). In the present study we have performed global analysis of lysine methylation of proteins in asexual blood stages of Plasmodium falciparum development. We immunoprecipitated stage specific Plasmodium lysates using anti-methyl lysine specific antibodies that immunostained the asexual blood stage parasites. Using liquid chromatography and tandem mass spectrometry analysis, 570 lysine methylated proteins at three different blood stages were identified. Analysis of the peptide sequences identified 605 methylated sites within 422 proteins. Functional classification of the methylated proteins revealed that the proteins are mainly involved in nucleotide metabolic processes, chromatin organization, transport, homeostatic processes and protein folding. The motif analysis of the methylated lysine peptides reveals novel motifs. Many of the identified lysine methylated proteins are also interacting partners/substrates of PfSET domain proteins as revealed by STRING database analysis. Our findings suggest that the protein methylation at lysine residues is widespread in Plasmodium and plays an important regulatory role in diverse set of the parasite pathways.
Near‐infrared Raman spectroscopy for gastric precancer diagnosis (2009)

Abstract Raman spectroscopy is a molecular vibrational spectroscopic technique that is capable of optically probing the biomolecular changes associated with neoplastic transformation. The purpose of this study was to apply near‐infrared (NIR) Raman spectroscopy for differentiating dysplasia from normal gastric mucosa tissue. A total of 65 gastric mucosa tissues (44 normal and 21 dysplasia) were obtained from 35 patients who underwent endoscopy investigation or gastrectomy operation for this study. A rapid NIR Raman system was utilized for tissue Raman spectroscopic measurements at 785‐nm laser excitation. High‐quality Raman spectra in the range of 800–1800 cm −1 can be acquired from gastric mucosa tissue within 5 s. Raman spectra showed significant differences between normal and dysplastic tissue, particularly in the spectral ranges of 850–1150, 1200–1500 and 1600–1750 cm −1 , which contained signals related to proteins, nucleic acids and lipids. The diagnostic decision algorithm based on the combination of Raman peak intensity ratios of I 875 /I 1450 and I 1208 /I 1655 and the logistic regression analysis yielded a diagnostic sensitivity of 90.5% and specificity of 90.9% for identification of gastric dysplasia tissue. This work demonstrates that NIR Raman spectroscopy in conjunction with intensity ratio algorithms has the potential for the noninvasive diagnosis and detection of precancer in the stomach at the molecular level. Copyright © 2009 John Wiley &amp; Sons, Ltd.