gebhart/patrepeval huggingface dataset:
Precise and versatile microplate reader-based analyses of biosensor signals from arrayed microbial colonies (2023)

Genetically encoded fluorescent biosensors have emerged as a powerful tool to support phenotypic screenings of microbes. Optical analyses of fluorescent sensor signals from colonies grown on solid media can be challenging as imaging devices need to be equipped with appropriate filters matching the properties of fluorescent biosensors. Toward versatile fluorescence analyses of different types of biosensor signals derived from arrayed colonies, we investigate here the use of monochromator equipped microplate readers as an alternative to imaging approaches. Indeed, for analyses of the LacI-controlled expression of the reporter mCherry in <i>Corynebacterium glutamicum,</i> or promoter activity using GFP as reporter in <i>Saccharomyces cerevisiae</i>, an improved sensitivity and dynamic range was observed for a microplate reader-based analyses compared to their analyses via imaging. The microplate reader allowed us to capture signals of ratiometric fluorescent reporter proteins (FRPs) with a high sensitivity and thereby to further improve the analysis of internal pH via the pH-sensitive FRP mCherryEA in <i>Escherichia coli</i> colonies. Applicability of this novel technique was further demonstrated by assessing redox states in <i>C. glutamicum</i> colonies using the FRP Mrx1-roGFP2. By the use of a microplate reader, oxidative redox shifts were measured in a mutant strain lacking the non-enzymatic antioxidant mycothiol (MSH), indicating its major role for maintaining a reduced redox state also in colonies on agar plates. Taken together, analyses of biosensor signals from microbial colonies using a microplate reader allows comprehensive phenotypic screenings and thus facilitates further development of new strains for metabolic engineering and systems biology.
Ultra-deep next-generation sequencing of plasma cell-free (cf) DNA from patients with advanced cancers. (2016)

11537 Background: Plasma cfDNA offers an easily obtainable source of DNA for molecular analysis, which provides an attractive alternative to tumor tissue testing. Novel ultrasensitive multiplex technologies are needed for further implementation of cfDNA testing in personalized cancer therapy. Methods: We have developed an ultra-deep next-generation sequencing method for detection of somatic alterations in up to 62 common cancer related genes in plasma cfDNA. Each cfDNA fragment was uniquely barcoded and amplified prior to Illumina target enrichment workflow, followed by ultra-deep sequencing ( > 10,000X). Proprietary data processing and analysis tools were developed to enable sensitive detection of rare mutant molecules over high wild-type background (detection of 1 in 1,000 - 10,000 molecules). Results were compared to molecular profiling of archival primary or metastatic tumor tissue obtained at different points of clinical care from a CLIA-certified laboratory. Results: Plasma cfDNA was extracted from 61 patients with advanced cancers (colorectal, n = 16; non-small cell lung [NSCLC], n = 12; breast, n = 6; melanoma, n = 4; cholangiocarcinoma, n = 3; thyroid, n = 3; ovarian, n = 3; pancreatic, n = 3; appendiceal, n = 2; cervical, n = 2; glioma, n = 2; other, n = 6) and for the presence of alterations in up to 62 common cancer related genes. Ultra-deep sequencing of plasma cfDNA detected key driver molecular alterations reported from archival tumor tissue samples in 66% (41/62) cases and absolute agreement between utra-deep sequencing of plasma cfDNA and archival tumor tissue was reported 53% (33/62) cases. There were no disagreements in samples from patients with cholangiocarcinoma, cervical, ovarian and pancreatic cancer, while none of the plasma cfDNA samples from patients with glioma revealed molecular alterations detected in the tumor tissue. Conclusions: Detecting common oncogenic alterations using ultra-deep sequencing of plasma cfDNA is feasible and should be further investigated for testing in patients with advanced cancer.
Pyrosequencing of TPMT Alleles in a General Swedish Population and in Patients with Inflammatory Bowel Disease (2004)

Next to wild type, the most frequent alleles in Sweden are TPMT*3A and TPMT*3C. A previously established phenotypic cutoff for distinguishing normal from intermediate metabolizers was confirmed. To identify the majority of cases (90%) with low or intermediate TPMT activity, it was sufficient to analyze individuals for only 3 of the 10 SNPs investigated. Nevertheless, this investigation indicates that other mutations might be of relevance for decreased enzymatic activity.
Multi-size circular shifting networks for decoders of structured LDPC codes (2007)

The need for circularly shifting an array of data is a distinguishing feature of decoders for structured low-density parity-check (LDPC) code, as a result of an efficient trade-off between performance and parallelisation of the elaborations, or throughput. Since the decoder must typically cope with blocks of data with different size, described is an efficient architecture of a reconfigurable multi-size circular shifting network, used to circularly shift an array with arbitrary size.
Cytosolic gangliosides of rat brain: Their fractionation into protein‐bound complexes of different ganglioside compositions (1984)

The sialic acid moiety of rat brain cytosolic gangliosides was radiolabeled by intracranial injection of N-(3H)acetylmannosamine. Upon ammonium sulphate fractionation, Sepharose 6B gel filtration, and hydroxylapatite-cellulose chromatography, ganglioside-bound radioactivity of brain cytosolic extract followed the behavior of protein and not that of purified gangliosides. This indicates that cytosolic gangliosides occur as ganglioside-protein complexes. By application of hydroxylapatite-cellulose column chromatography, fractions were obtained having different ganglioside composition. In particular, one fraction contained GM1, one GD1a, and one GT1b with a ganglioside homogeneity better than 95% in each fraction. This indicates the occurrence in brain cytosol of a GM1-protein complex, a GD1a-protein complex, and a GT1b-protein complex.
Nanometre-scale infrared chemical imaging (AFM-IR) of organic matter in ultra-carbonaceous Antarctic micrometeorites (UCAMMS) and future analyses of Hayabusa 2 samples. (2020)

Introduction: The chemical composition of organic matter (OM) in interplanetary samples (meteorites and micrometeorites) is suitably characterized by the distribution of the different chemical bonds using infrared (IR) vibrational spectroscopy (see e.g. [1]). Classical IR microscopy provides a global view of the dust grain chemical structure content but remains limited by the diffraction, with typical spot sizes sampling a few micrometers in the mid-IR range. This spatial resolution limitation is well above that of complementary techniques such as isotopic imaging with NanoSIMS or transmission electron or X-ray microscopy techniques. These techniques reveal mineralogical, chemical and isotopic heterogeneities at the sub-micron scale but do not give full access to the distribution of the various chemical bonds. The IR diffraction limitation can be circumvented by using AFM-IR microscopy. This technique opens a new window for studies of OM at ten to tens of nanometer scales and will be of importance for studies of the samples from carbonaceous asteroid Ryugu, returned by the Hayabusa 2 space probe in December 2020. AFM-IR is now a well-established microscopy technique in the vibrational field. It combines an atomic force microscope (AFM) and a tunable IR source to detect photo-thermal effect and access chemical information down to a nanoscale resolution [2]. This technique is now applied in a wide diversity of scientific fields [3], and was recently used to analyze extraterrestrial OM [4, 5]. We report here on recent results obtained on imaging two UltraCarbonaceous Antarctic MicroMeteorites (UCAMMs) using AFM-IR [5]. A small fraction of the Antarctic micrometeorites from the Concordia collection consists in UCAMMs, particles with extreme concentrations in OM, most of them exhibiting large deuterium excesses [6]. UCAMMs are also found in Japanese interplanetary dust collections [7-9]. These UCAMMs most likely originate from the surface of small icy bodies in the outer regions of the solar system [1,6,7,10]. The large OM fraction of UCAMMs (considerably higher than in the most carbon-rich meteorites) enables direct analyses without the pre-treatment generally applied to extract the OM from other meteoritic samples, and give access to unaltered chemical maps of the intimate association of minerals and organics.
Using Fabric Softeners, Drying and Ironing in Germany (2011)

Abstract During the annually arranged Action Day Sustainable Washing on May 10 th , 5284 questionnaires about laundry treatment were collected from private people in Germany with the aim of obtaining information about consumer behaviour and attitudes towards sustainability. This is a non-representative census as only 15% of all respondents were male. Nevertheless, relative distribution and correlation provide a relevant insight into consumers’ behaviour towards washing, drying and ironing. The most important results of the analysis can be summed up as follows: – Nearly 50% of the respondents own a laundry-dryer. – Nearly one third of all respondents never use fabric softeners. The prevention of ecological damage was the reason for not using fabric softeners for 30% of the respondents. – About one fourth of all respondents always use fabric softeners, with younger people having a significantly higher attitude towards using them. – Under good weather conditions, about 90% of the respondents choose energy-saving alternatives to dry their laundry. – The average weekly time spent on ironing is about two hours on average of all respondents who gave information. The analysis shows that laundry treatment beyond the pure washing process is a multi-faceted process with several starting points of improvement in favour of sustainable handling.
Mutual antagonism between hepatitis B viral mRNA and host microRNA let-7 (2016)

The interplay between viral and host factors plays a major role in viral pathogenesis. Hepatitis B virus (HBV) infection is a global health problem that leads to liver cirrhosis and hepatocellular carcinoma (HCC). Although HBV proteins have been studied extensively about their implication in hepatocarcinogenesis, the molecular mechanisms of oncogenesis are still largely unknown. A recent concept in gene regulation, in which competitive endogenous RNAs compete for common microRNAs (miRNAs), suggests that mRNA targets are key elements in the regulation of miRNA availability. Here, we show that HBV mRNA in the preS2 region can be targeted by host miRNA let-7 g. This leads to the sequestration of let-7 g and inhibition of let-7 g function. The expression of HBV transcripts, including the preS2 region, de-repressed let-7 g targets, which may contribute to long-term oncogenesis. HBV transcript-expressing transgenic mice, but not non-targeted transcript-expressing mice, were more prone to chemically induced hepatoocarcinogenesis. Let-7 target protein expression was upregulated in human HCC tissues derived from HBV-infected patients. On the other hand, let-7 g inhibited HBV preS2 protein expression and viral products. These results suggest that the interplay between viral intermediate transcripts during HBV replication and host miRNAs is crucial to the pathogenesis of chronic viral infection.
Asymmetric Control in the Pictet–Spengler Reaction by Means of N‐Protected Amino Acids as Chiral Auxiliary Groups (1996)

Abstract Aromatic and aliphatic Schiff bases of tryptamine react with Fmoc‐ or phthaloyl‐protected amino acid chlorides to form N ‐acyliminium intermediates, which, in the presence of titanium alkoxides at room temperature, undergo Pictet–Spengler reactions to give tetrahydro‐β‐carbolines with diastereomeric ratios of up to 99:1. The chiral auxiliary can be removed from the Pictet–Spengler adducts by means of a simple reduction. To rationalize the observed stereoselectivity a transition‐state model is proposed in which the titanium atom coordinates both the carbonyl group of the N ‐acyliminium ion and the amino acid protecting group.
POPTARTS: A New Method to Determine Quantum Yields in a Molecular Beam (2022)

A new technique is reported to determine absolute photodissociation quantum yields, ϕ<sub>diss</sub>, in a molecular beam. The technique relies on a molecule having two available product channels, where a species in channel A can be converted photolytically to a species in channel B. The relative decrease in the species from channel A and the relative increase in species from B provide a direct measure of the relative product yield of each channel, with no external calibration required. In the event that only channels A and B exist, or at least dominate, then the sum rule ϕ<sub>A</sub> + ϕ<sub>B</sub> = 1 can be used to convert relative quantum yields into absolute yields. The technique is demonstrated using the well-understood and characterized photochemistry of HCHO. Formaldehyde photolysis at wavelengths near 310 nm produces either H + HCO (channel A) or H<sub>2</sub> + CO (channel B). HCO can then be photolyzed with high efficiency into H + CO. The product state distributions for HCO from channel A, CO from channel B, and CO from the secondary HCO photolysis event are all well-known; this is not a requirement but is utilized here to demonstrate the veracity of the technique. The zero-pressure quantum yields of HCO from HCHO photolysis via the 2<sup>3</sup>4<sup>1</sup> and 2<sup>1</sup>5<sup>1</sup> states of HCHO are determined to be 0.66 and 0.74, respectively, which are in excellent agreement with the established quantum yields at atmospheric pressure and support the conclusion that HCHO quantum yields at these photolysis energies are not pressure dependent.
Effect of Glucose and Adenosine Phosphates on Production of Extracellular Carbohydrases of Alternaria solani (1974)

Production of carbohydrases by Alternaria solani is inhibited by glucose under low growth conditions. In an enriched medium, glucose has little effect on the production of polygalacturonase and cellulase while it still suppresses production of beta-glucosidase. Low levels of all three enzymes were produced in the absence of their respective substrates. Such regulation has been found with many organisms. However, far greater production of these carbohydrases occurred with additions of adenosine phosphates to the growth media. Highest stimulation of enzyme production was by adenosine 5'-phosphate. Adenosine 5'-triphosphate and cyclic 3', 5'-adenosine monophosphate gave lesser amounts. Starvation appears to induce production of extracellular carbohydrases and adenosine 5'-phosphate may have a role in the starvation process.
Laboratory manual to accompany "introduction to the science of chemistry" (1955)

ADVERTISEMENT RETURN TO ISSUEPREVBook and Media Revie...Book and Media ReviewNEXTLaboratory manual to accompany "introduction to the science of chemistry"Cite this: J. Chem. Educ. 1955, 32, 4, 220Publication Date (Print):April 1, 1955Publication History Received3 August 2009Published online1 April 1955Published inissue 1 April 1955https://doi.org/10.1021/ed032p220.4RIGHTS & PERMISSIONSArticle Views93Altmetric-Citations-LEARN 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 InReddit PDF (945 KB) Get e-Alerts Get e-Alerts
Relation between flow cytometric DNA distribution and pathology in human bladder cancer. A report on 69 cases (1984)

High-resolution flow cytometric measurements of cellular DNA content have been performed in 69 patients with transitional cell carcinomas of the urinary bladder. By selective sampling of cells at cystoscopy, mapping of the whole bladder could easily be performed, including the tumor as well as different areas of the surrounding normal-appearing mucosa. The cell-cycle distribution showed an increasing fraction of cells with S- and G2-phase content parallel to the World Health Organization (WHO) grade of the tumors, ranging from 1.7% S-phase cells in normal subjects to nearly 20% in tumors of WHO grade 3. WHO grade 2 tumors could be divided into two populations: (1) diploid, with a cell-cycle distribution similar to grade 1 tumors and low frequency of infiltration; and (2) aneuploid, with a high rate of infiltration and high fractions of S- and G2-phase cells. Furthermore, the aneuploid tumors could be subdivided into two main classes, one hypertriploid with high frequency of involvement of the surrounding normal appearing mucosa; and one hypotetraploid, with less frequency of such involvement and infiltration. It is concluded that by selective sampling and mapping of the bladder mucosa using flow cytometry, subclassification of this type of tumor can be performed rapidly, giving a reliable measure of the involvement of the bladder in the neoplastic disease and a biologic subclassification based on the type of DNA aberrations.
Back Cover: Modeling magnetism of hexagonal Fe monolayers on 4d substrates (Phys. Status Solidi B 10/2011) (2011)

The article by Al-Zubi et al. (pp. 2242–2247) investigates the potential of modeling magnetic structures of an Fe monolayer on a highly spin-polarizable substrate on the basis of classical spin Hamiltonians whose materials specification is obtained by mapping total energies of ab-initio calculations for different spin-structures to interaction parameters. The cover images show two double-rowwise antiferromagnetic states that are superpositions of two spin-spirals with wavevectors ±Q, so-called 2Q-states. With respect to spin-spirals with a single wavevector, −Q or +Q, the two alternative superpositions gain a different amount of energy by interaction with the substrate. For the state created by Q in Γ−M direction, theory predicts that the inhomogeneous magnetization (shown by the green arrows) of the substrate stabilizes this magnetic structure as ground state for an Fe monolayer on Rh(111).
Comparison of Three Different Optical Coherence Tomography Models for Total Macular Thickness Measurements in Healthy Controls (2009)

&lt;i&gt;Background/Aims:&lt;/i&gt; Conventional time domain optical coherence tomography (OCT) has become an important diagnostic tool to measure retinal thickness in clinical routine. Recently, different models of high-speed, high-resolution frequency domain OCTs have been introduced by various manufacturers. The purpose of this study was to compare 3 commercially available OCT models for retinal thickness measurements in healthy controls. &lt;i&gt;Methods:&lt;/i&gt; OCT scans were performed on 28 healthy eyes with the RTVue-100 FD-OCT (Optovue Inc., USA), the Cirrus™ HD-OCT (Carl Zeiss Meditec Inc., USA) and the Stratus OCT 3000 (Carl Zeiss Meditec Inc.). Retinal thickness values were calculated and compared between OCT models. &lt;i&gt;Results:&lt;/i&gt; Differences in mean retinal thickness measurements between OCT models were statistically significant. Mean retinal thickness measurement with Cirrus OCT, RTVue OCT and with Stratus OCT was 300, 265 and 257 μm, respectively. &lt;i&gt;Conclusion:&lt;/i&gt; Measurements with different OCT models lead to significantly different retinal thickness values.
Abstract 15023: Minimum Electrode Spatial Resolution for Arrhythmia Rotor Detection and Localization (2022)

Introduction: Efficacy of electrotherapy or ablation therapy for treatment of arrhythmias is dependent on accurate detection of arrhythmia focal or reentrant drivers. However, success rates have been inconsistent, with frequent arrhythmia recurrence. A likely reason is the limited current spatial resolution of mapping devices, which averages 4 mm. The goal of this study was to determine the minimum spatial resolution necessary to identify and localize arrhythmia reentrant drivers (rotors). Methods: We conducted dual-sided (epicardial and endocardial) optical mapping studies in 12 donor human right ventricular wedge preparations subjected to arrhythmia induction protocol (S1S1 restitution and/or 50Hz burst pacing). The resulting arrhythmia data (0.7mm spatial resolution) was down sampled to different spatial resolutions (1.4-7mm) and up sampled back to full resolution. Rotors were tracked for each sub-resolution and compared to the rotors in the original data. Further comparisons were made according to arrhythmia type, sex, anatomical region, and mapped surface. Results: Rotor detection accuracy for currently used mapping devices was found to be 57±4%. Localization accuracy was 61±7%. For the current average spatial resolution, clinical rotor detection and localization accuracies can be expected to fall within a confidence interval of 47-67% and 46-75%, respectively. For the spatial resolutions tested, detection accuracy was above 80% only for a resolution of 1.4 mm, while localization accuracy reached that value at 2.1 mm. Moreover, the arrhythmia type affected detection and localization accuracies, which decreased consistently with loss of spatial resolution for unstable arrhythmias and had steadier values for stable arrhythmias. When comparing mapped surfaces, rotor incidence was higher in the endocardium, likely due to the presence of adipose tissue on the epicardial surface. Differences in sex and anatomical region had no statistically significant impact. Conclusions: The spatial resolution of current devices is insufficient to map rotors accurately, especially for unstable arrhythmias. For both detection and localization accuracies to be above 80%, a resolution of at least 1.4 mm is required.
Embedded DRAM for a reconfigurable array (2003)

A field-programmable gate array, coupled with an on-chip 2 Mb DRAM bank has been designed, to aid in the study of the tradeoffs involved in the design of embedded DRAM for FPGAs. The memory can be used both as configuration storage, enabling reconfiguration in under 5 /spl mu/s, and application data memory, providing application logic executing on the array with up to 2 GB/sec data bandwidth. The variable latency of the DRAM is hidden from the logic by a stall mechanism and an SRAM-like interface.