gebhart/patrepeval huggingface dataset:
The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation (2020)

Transcription factors (TFs) bind DNA sequence motif vocabularies in cis-regulatory elements (CREs) to modulate chromatin state and gene expression during cell state transitions. A quantitative understanding of how motif lexicons influence dynamic regulatory activity has been elusive due to the combinatorial nature of the cis-regulatory code. To address this, we undertook multi-omic data profiling of chromatin and expression dynamics across epidermal differentiation to identify 40,103 dynamic CREs associated with 3,609 dynamically expressed genes, then applied an interpretable deep learning framework to model the cis-regulatory logic of chromatin accessibility. This identified cooperative DNA sequence rules in dynamic CREs regulating synchronous gene modules with diverse roles in skin differentiation. Massively parallel reporter analysis validated temporal dynamics and cooperative cis-regulatory logic. Variants linked to human polygenic skin disease were enriched in these time-dependent combinatorial motif rules. This integrative approach reveals the combinatorial cis-regulatory lexicon of epidermal differentiation and represents a general framework for deciphering the organizational principles of the cis-regulatory code in dynamic gene regulation. HIGHLIGHTS An integrative multi-omic resource profiling chromatin and expression dynamics across keratinocyte differentiation Predictive deep learning models of chromatin dynamics reveal a high-resolution cis-regulatory DNA motif lexicon of epidermal differentiation Model interpretation enables discovery of combinatorial cis-regulatory logic of homotypic and heterotypic motif combinations Massively parallel reporter experiments validate temporal dynamics and cis-regulatory logic of the combinatorial motif lexicon
Testing for antibodies to AIDS‐associated retrovirus (HTLV‐III/LAV) by indirect fixed cell immunofluorescence: Specificity, sensitivity, and applications (1986)

Seropositivity to the AIDS-associated retrovirus, HTLV-III/LAV, has profound implications. Simple and reliable tests are needed to detect such antibodies. A rapid, sensitive indirect immunofluorescence assay (IFA) on acetone-fixed virus-producing CEM/LAV-N1 cells was adapted for detection of human antibodies to HTLV-III/LAV. Specific and nonspecific patterns of of immunofluorescent reactivity were easily distinguished, and results paralleled those obtained by Western blotting and radioimmunoprecipitation (RIP), indicating that there is no need to confirm IFA positivity. In contrast, the commercial enzyme-linked immunosorbent assay (ELISA) was less reliable. False positives occurred with sera from seven hemophiliacs that were negative on Western blots, and false-negative reactions were observed on two occasions. These involved low-titer AIDS-patients' sera that were positive on Western blots, and from one of which virus was successfully isolated. Our results emphasize the requirement for confirmatory assays when the ELISA test is used for primary screening of sera for antibodies to HTLV-III/LAV. The IFA method is especially well-suited to quantitative analysis of serum antibody levels. Our data suggest that serum antibody titers rise as disease progression occurs, ultimately falling as severe complications ensue. It is suggested that in laboratories where the demand for HTLV-III/LAV antibody testing is not excessive (1,000-2,000 sera/month), IFA could serve as the only serological assay for both screening and epidemiological purposes.
Aktiv in jedem Alter – Sport und Ernährung in den verschiedenen Lebensphasen: Senioren (2016)

Regelmäßige körperliche Aktivität ist bei Senioren und chronisch Kranken essenziell für die Prävention von Gebrechlichkeit und Stürzen. Die Herausforderung besteht darin, präzise zu definieren, welchen Umfang und welche Intensität die Aktivität haben sollte, um den Erhalt von Funktionalität und Gesundheit optimal zu fördern. Die meisten Daten zur körperlichen Aktivität von Senioren stammen aus Umfragen mit Selbstauskünften. Subjektive Daten sind jedoch wenig verlässlich. Eine Möglichkeit zur Erfassung objektiver Daten bieten sensorbasierte Messungen, die bei Senioren zu Hause eingesetzt werden und körperliche Aktivitäten quantifizieren. Diese Messungen bieten eine präzise Basis für die Entwicklung neuer Präventionsstrategien im häuslichen Umfeld. Ein erster Anwendungsbereich ist das Coaching von Senioren mithilfe von Tablet-PCs, über die maßgeschneiderte Übungsanleitungen und Empfehlungen zur körperlichen Aktivität vermittelt werden.
Unrolled Projected Gradient Descent for Multi-spectral Image Fusion (2019)

In this paper, we consider the problem of fusing low spatial resolution multi-spectral (MS) aerial images with their associated high spatial resolution panchromatic image. To solve this problem, various methods have been proposed, using either model-based or model-agnostic algorithms such as deep learning techniques. In this paper, we aim to utilize more interpretable architectures to solve the MS fusion problem by integrating existing ideas from image processing with deep learning. In particular, we develop a signal processing-inspired learning solution, where we unroll the iterations of the projected gradient descent (PGD) algorithm, and each iteration contains a projection operation carried out by a deep convolutional neural network. We observe that our proposed method provides a new perspective on existing deep-learning solutions, and under certain circumstance it reduces to current black-box deep learning methods. Our extensive experimental results show significant improvements of the proposed approach over several baselines.
Generation of a planar offset curve based on minimum distance (2009)

A robust algorithm for removing both local and global self intersections in a planar offset curve is presented. Our scheme is based on the minimum distance from a point to an original parametric curve. The method consists of the following two steps: 1) in the 2D plane, generation of the field of minimum distance from a point to an original planar parametric curve, 2) in the field, extraction of the iso-curve, regarding the offset distance as the minimum distance. The iso-curve is the non-self-intersection offset curve. Therefore, the advantage of our method is that the planar offset curve does not need to be approximated by a rational curve; however, both local and global self-intersections in the offset curve can be directly and automatically eliminated.
Propagation of electrical tree structures in solid polymeric insulation (1997)

Two alternative theoretical approaches to electrical tree propagation exist. Stochastic models attribute tree structures to random probabilistic factors, whereas in the discharge-avalanche model mechanism-driven field fluctuations are responsible. Here we review the predictions of these approaches in the light of the available experimental evidence. It is shown that both models give the fractal structures and the form of structure distribution observed experimentally. The width of the distribution functions predicted are, however, less than those found experimentally. The quantitative formulation available to the physical model also enables it to reproduce several other features of tree propagation such as voltage dependence, growth laws, and discharge behavior patterns. This is not possible in the stochastic approach without mechanistic assumptions which are difficult to relate to the stochastic process. The connection between the discharge-avalanche model and deterministic chaos is explored. Experimental evidence is presented supporting the contention that the electrical treeing phenomenon is the result of a deterministic breakdown mechanism operating in a chaotic regime at fields lower than those required for runaway breakdown. Space-charge deposition and re-arrangement is proposed as the physical origin of the chaotic field fluctuations. Tree shapes are shown to be related to the variation in the fluctuation range available as the tree grows in accord with the predictions of the discharge-avalanche model.
Phosphate-binding capacities of calcium and aluminum formulations. (1998)

Calcium and aluminum phosphate binders are used to treat hyperphosphatemia which is responsible for the development of osteodystrophy commonly seen in patients with end-stage renal disease. The purpose of this study was to determine the phosphate binding capacities of several frequently used calcium and aluminum formulations. The effect of formulation types on phosphate binding was evaluated. Calcium and aluminum phosphate binders were administered to six healthy volunteers after phosphate load on separate study days. Total urine outflow was collected afterwards to determine the amount of phosphate recovered, which indicates the ability of the phosphate binder to reduce gastrointestinal phosphate absorption. The amounts of urinary phosphate recovered were different after administration of the phosphate binders. Calcium acetate resulted in the least amount of phosphate excreted. Calcium carbonate suspension, when compared with the tablet formulation, caused a smaller amount of phosphate excreted in the urine. Different phosphate binders formulations were found to have different phosphate binding capacities. Patients should therefore be closely monitored for efficacy after switching from one phosphate binder to another.
Calibration of Phone Likelihoods in Automatic Speech Recognition (2016)

In this paper we study the probabilistic properties of the posteriors in a speech recognition system that uses a deep neural network (DNN) for acoustic modeling. We do this by reducing Kaldi's DNN shared pdf-id posteriors to phone likelihoods, and using test set forced alignments to evaluate these using a calibration sensitive metric. Individual frame posteriors are in principle well-calibrated, because the DNN is trained using cross entropy as the objective function, which is a proper scoring rule. When entire phones are assessed, we observe that it is best to average the log likelihoods over the duration of the phone. Further scaling of the average log likelihoods by the logarithm of the duration slightly improves the calibration, and this improvement is retained when tested on independent test data.
Synthesis and Characterization of an Electroluminescent Polyester Containing the Ru(II) Complex (1997)

A new electroluminescent polyester based on an electrochemically stable polypyridylruthenium(II) complex was prepared by the step-growth polymerization method. The versatility of changing its solubility by changing counteranions makes it possible to prepare thin-film devices by either spin-coating or the self-assembly technique. Single-layer LEDs fabricated from this polymer by the spin-coating method showed bright orange-red emission with a maximum luminance level of 300 cd/m2. Self-assembled multilayers of this material exhibit external quantum efficiencies close to 1%.
Gamma-Ray Spectrum ofAc228 (1954)

The gamma radiation from a radioactively pure source of ${\mathrm{Ac}}^{228}$ has been studied using a NaI scintillation spectrometer. Gamma rays of 0.098, 0.127, 0.336, 0.410, 0.458, 0.907, 0.965, 1.587, 0.155, 0.220, 0.278, and 0.790 Mev are indicated, of which the last four are previously unreported. A double scintillation spectrometer is described which was used to investigate gamma-gamma coincidences. A decay scheme for ${\mathrm{Ac}}^{228}$ is suggested.
Primary Structure of Protein L10 from the Large Subunit ofEscherichia coliRibosomes (1976)

The complete primary structure of protein L10 from the large subunit of the Escherichia coli ribosome has been determined. L10 is composed of 165 residues and has the amino acid composition: Asp6, Asn3, Thr9, Ser6, Glu14, Gln4, Pro5, Gly9, Ala33, Val15, Met5, Ile5, Leu15, Tyr3, Phe6, His1, Lys12, Arg13 and Cys1. The molecular weight of L10 is 17 738. The amino acid sequence was determined by a combination of automated Edman degradation of the intact protein in a modified Beckman sequentor and sequencing peptides obtained from digestions with trypsin, themolysin, Staphylococcus aureus protease and chymotrypsin. Further information was obtained from cyanogen bromide fragments and peptides resulting from digestion with trypsin after protection of the epsilon-amino groups of the lysine residues with exo-cis-3,6-endoxo-delta4-tetrahydrophthalic anhydride (ETPA).
Why Teach Playwriting (1992)

The glomerular barriers to water and macromolecular movement were examined 2 and 24 h after the administration of a monoclonal antibody (mAb) specific to an antigen located on the epithelial slit diaphragm and the external aspect of the glomerular basement membrane. By micropuncture techniques 2 h after mAb administration, single-nephron GFR (SNGFR) and plasma flow were unchanged but the glomerular capillary hydrostatic pressure gradient and glomerular capillary hydrostatic pressure were increased and the glomerular ultrafiltration coefficient (LpA) decreased to values that were 50% of the normal control. There was no increase in urinary protein excretion at 2 h. However, at 24 h after mAb, nephron plasma flow (SNPF) and SNGFR increased and the glomerular ultrafiltration coefficient returned to values indistinguishable from the normal control. At 24 h, there was a marked increase in protein excretion. The administration of meclofenamate decreased values for SNGFR and SNPF to normal. Immunoglobulin G was exclusively bound to glomerular capillary walls in a linear or continuous fashion at 2 h, but in a discontinuous, granular pattern at 24 h. These studies suggest that after mAb, important limiting glomerular barriers for hydraulic conductivity and protein excretion reside on the epithelial aspect of the glomerular capillary basement membrane, specifically at the level of the slit diaphragm. Studies also suggest that alterations in glomerular capillary hydraulic conductivity can be effectively separated from increases in macromolecular permeability.
Estimation of the Quality Factor Using Peak Frequency Method in Polish Shale Gas Deposits (2017)

Summary In this study we estimate P- and S-waves attenuation quality factors using peak frequency method for the lower Silurian and Ordovician strata in north Poland. For the estimation of the quality factor we use dataset recorded by the downhole array during one of the first hydraulic fracturing experiment in Poland. We show that obtained results are consistent and the estimated quality factors for P- and S -waves have similar values within the uncertainty. We overcome the presence of the guided waves highly interfering and compromising the peak frequency method.
Mutations in the gene encoding neutrophil elastase in congenital and cyclic neutropenia (2000)

Congenital neutropenia and cyclic neutropenia are disorders of neutrophil production predisposing patients to recurrent bacterial infections. Recently the locus for autosomal dominant cyclic neutropenia was mapped to chromosome 19p13.3, and this disease is now attributable to mutations of the gene encoding neutrophil elastase (the ELA2 gene). The authors hypothesized that congenital neutropenia is also due to mutations of neutrophil elastase. Patients with congenital neutropenia, cyclic neutropenia, or Shwachman-Diamond syndrome were referred to the Severe Chronic Neutropenia International Registry. Referring physicians provided hematologic and clinical data. Mutational analysis was performed by sequencing polymerase chain reaction (PCR)-amplified genomic DNA for each of the 5 exons of the neutrophil ELA2 gene and 20 bases of the flanking regions. RNA from bone marrow mononuclear cells was used to determine if the affected patients expressed both the normal and the abnormal transcript. Twenty-two of 25 patients with congenital neutropenia had 18 different heterozygous mutations. Four of 4 patients with cyclic neutropenia and 0 of 3 patients with Shwachman-Diamond syndrome had mutations. For 5 patients with congenital neutropenia having mutations predicted to alter RNA splicing or transcript structure, reverse transcriptase-PCR showed expression of both normal and abnormal transcripts. In cyclic neutropenia, the mutations appeared to cluster near the active site of the molecule, whereas the opposite face was predominantly affected by the mutations found in congenital neutropenia. This study indicates that mutations of the gene encoding neutrophil elastase are probably the most common cause for severe congenital neutropenia as well as the cause for sporadic and autosomal dominant cyclic neutropenia.
Synthesis Imaging at Optical Wavelength with SIM (2004)

This presentation addresses synthesis imaging with the Space Interferometry Mission (SIM), and its likely future applications. These applications include imaging of crowded fields such as the cores of globular clusters and galaxy clusters. It may be possible to use image restoration in processing data from the SIM's interferometers.
DNA flow cytometry and prognostic factors in 1331 frozen breast cancer specimens (1988)

Breast cancer proliferative capacity as determined by the DNA thymidine labeling index, along with estrogen and progesterone receptor status, is highly predictive for risk of relapse and overall survival. Recently, DNA ploidy and proliferative capacity (S-phase fraction [SPF]) as determined by flow cytometry have also shown significant prognostic value. The authors have developed a technique which allows a 50 to 100 mg aliquot of the same frozen breast tumor specimen routinely employed in steroid receptor assays, to be assayed for both DNA ploidy and SPF by flow cytometry. Of the 1331 tumors examined, DNA histograms were evaluable for ploidy in 89% (1184) of specimens examined; 57% of these were aneuploid. Adapting a trapezoidal model to estimate SPF in both diploid and aneuploid tumors, the authors found 81% (1084) to be evaluable for SPF, with a median SPF of 5.8% for the entire population. The median SPF was significantly lower in diploid tumors (2.6%) than in aneuploid tumors (10.3%, P less than 0.0001). Both aneuploidy and high SPF were strongly associated with absence of steroid receptors. Aneuploid tumors showed more striking differences in the frequency of high S-phase values with respect to receptor status and age or menopausal status, whereas diploid but not aneuploid tumors showed lower SPF in node-negative versus node-positive patients. Because it is particularly important to identify the high-risk minority of node-negative patients, the authors examined the node-negative group separately. High SPF subgroups appeared in each category of receptor status and age or menopausal status within the node-negative group, suggesting that SPF will be an independent prognostic factor. With the DNA flow cytometric methods used here, it is now practical to determine ploidy and SPF for nearly every breast cancer patient. These factors, which show associations with established prognostic factors, such as receptor status can now be fully evaluated for their prognostic significance in broad patient populations.
CME stands for commercial medical education: and ACCME still won't address the issue (2015)

Dr McMahon, who directs the US Accreditation Council for Continuing Medical Education (ACCME), criticises1 our article on how continuing medical education (CME) was used to sell hypoactive sexual desire disorder,2 stating that we ‘provide no supporting evidence’ for our claims that CME courses are an important marketing tool. Perhaps he missed the references in our article, but additional studies support our points.3–9

Dr McMahon also claims that industry supported only 11% of CME activities.1 ,10 However, ACCME doesn't count two forms of industry funding as commercial support. In 2011, ACCME stopped requiring reporting of in-kind support, defined as ‘nonmonetary resources provided by a commercial interest in support of a CME activity’. Examples include ‘equipment, supplies, and facilities’.11 In other words, industry can pay for meeting space, hotel rooms, audiovisual costs, food and other costs related to a CME event—but as long as the money is paid directly to a hotel, caterer and the like, none of the money is reported as commercial support.

Also, advertising …
Chemistry, biological activity, and uses of formamidine pesticides. (1976)

The formamidines, a relatively new group of acaricide-insecticides, are novel both in their range of biological activities and in their mode of action, which is presently unknown. This paper is a review of the historical development, properties, structures, uses, and chemistry of this group of pesticides, with particular emphasis on chlordimeform (Galecron or Fundal), N'-4-chloro-o-tolyl-N,N-dimethylformamidine, and amitraz, 1,3=di-(2,4-dimethylphenylimino)-2-methyl-2-azapropane. Their biological activity and uses are defined by their toxicity to spider mites, ticks, and certain insects, and they are particularly effective against juvenile and resistant forms of these organisms. A significant, but poorly understood feature of their field effectiveness is their breadth of toxic action which includes direct lethality, excitant-repellant behavioral effects, and chemosterilization. They are generally of low hazard for nontarget species with the significant exception of predaceous mites. Several aspects of the chemistry of these compounds are considered, including structure--activity relations, synthetic pathways, isomerism and configuration, and their chemical and environmental stability. A significant feature of the metabolism and toxicity of these agents is the possible activation of chlordimeform by N-demethylation in vivo. Strong evidence for this has been presented with the cattle tick, but recent results discussed here suggest that in other species, i.e., mice, German cockroaches or black cutworm eggs, N-demethylation is neither a strong activation nor a detoxication reaction.
Synthesis of 1,2,3-triazole-fused heterocycles viaPd-catalyzed cyclization of 5-iodotriazoles (2011)

A convenient approach toward polycyclic frameworks containing fused 1,2,3-triazoles is described. The synthesis consists of a Cu-catalyzed cycloaddition and an intramolecular Pd-catalyzed direct arylation or Heck reaction, and affords the products in good to excellent yields.
Congenital Lack of Olfactory Ability (1992)

Twenty-two patients, all of whom reported never having been able to smell anything, were studied to determine the particular features that distinguish individuals with congenital anosmia. The clinical evaluation on these patients included a thorough medical and chemosensory history, physical examination, nasal endoscopy, chemosensory testing, olfactory biopsies, and imaging studies. There was no evidence to indicate that these patients ever had a sense of smell. The results of olfactory testing suggested that these patients had an inability to detect both olfactory and trigeminal odorants; however, many of the patients in the group seemed to have a slight ability to perceive at least some component of trigeminal odorants. The olfactory epithelium, if it was present at all on biopsy, was abnormal in appearance.