gebhart/patrepeval huggingface dataset:
A Digital Light Microscopic Method for Diatom Surveys Using Embedded Acid-Cleaned Samples (2022)

Diatom identification and counting by light microscopy of permanently embedded acid-cleaned silicate shells (frustules) is a fundamental method in ecological and water quality investigations. Here we present a new variant of this method based on “digital virtual slides”, and compare it to the traditional, non-digitized light microscopy workflow on freshwater samples. We analysed three replicate slides taken from six benthic samples using two methods: (1) working directly on a light microscope (the “traditional” counting method), and (2) preparing “virtual digital slides” by high-resolution slide scanning and subsequently identifying and labelling individual valves or frustules using a web browser-based image annotation platform (the digital method). Both methods led to comparable results in terms of species richness, diatom indices and diatom community composition. Although counting by digital microscopy was slightly more time consuming, our experience points out that the digital workflow can not only improve the transparency and reusability of diatom counts but it can also increase taxonomic precision. The introduced digital workflow can also be applied for taxonomic inter-expert calibration through the web, and for producing training image sets for deep-learning-based diatom identification, making it a promising and versatile alternative or extension to traditional light microscopic diatom analyses in the future.
PRNP 1368 polymorphism is not associated with sporadic Creutzfeldt‐Jakob disease in the Korean population (2008)

A significant difference of genotype and allele frequencies at PRNP 1368 was found between the normal Korean population and various European populations. In contrast to the results in the British and German populations, our study does not show a significant difference in genotype (P = 0.2763) and allele (P = 0.3750) frequencies of PRNP 1368 between sporadic CJD and normal controls.
Multiple prediction by wavefield extrapolation in common‐P domain (2008)

Wavefield extrapolation (WFE) multiple prediction typically operates in common shot domain, and is very effective to predict complex multiples such as diffracted multiples; however, it is a model‐based and relatively expensive approach. In this paper, we present a new WFE multiple prediction algorithm which operates in common‐P domain. This new algorithm is able to very efficiently predict source‐side multiples, and less model‐dependent; therefore enables its usage in the early stage of processing. In this paper, we first perform some analysis of two types of diffracted multiples : 1) source‐side diffracted multiples and 2) receiver‐side diffracted multiple. With the new insight of source‐side diffracted multiples, we have developed a new algorithm to predict source‐side multiples. This new algorithm for source‐side multiple prediction is a variant of WFE approach, but almost model independent. Testing on both synthetic and field data demonstrates the effectiveness of the new multiple prediction method.
Structure H clathrate hydrate equilibria of methane and adamantane (1992)

Abstract The first phase equilibrium data are presented for Structure H hydrates. The data represent the initial formation of these hydrates from methane, with adamantane— a previously determined Structure H former. Temperature and pressure conditions are consistent with hydrocarbon production/transportation/processing facilities. Structure H hydrates are shown to contain molecules indigenous to petroleum. which may not be present in natural gas.
The bandwidth heuristic search (1973)

Six conspecific yeast strains, representing an undescribed species, were isolated from rotten wood collected in different locations in Hungary and Germany and an additional one from fungal fruiting body in Taiwan. The seven strains share identical nucleotide sequences in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene. The Hungarian and Taiwanese isolates share identical internal transcribed spacer (ITS) sequences as well, while the two German isolates differ from them merely by three substitutions and four indels in this region. The investigated strains are very closely related to <i>Diddensiella santjacobensis</i>. Along their LSU D1/D2 domain they differ only by one substitution from the type strain of <i>D. santjacobensis</i>. However, in the ITS region of Hungarian and Taiwanese strains we detected 3.5 % divergence (nine substitutions and nine indels) between the undescribed species and <i>D. santjacobensis</i>, while the German strains differed by 13 substitutions and nine indels from <i>D. santjacobensis</i>. This ITS sequence divergence has raised the possibility that the strains investigated in this study may represent a different species from <i>D. santjacobensis</i>. This hypothesis was supported by comparisons of partial translation elongation factor 1-α (EF-1α) and cytochrome oxidase II (COX II) gene sequences. While no difference and 1-2 substitutions among the partial EF-1α and COX II gene sequences of the strains of the undescribed species, respectively, were detected; the undescribed species differ by about 4 % (36 substitutions) and 10 % (50-51 substitutions) from <i>D. santjacobensis</i> in these regions. Parsimony network analysis of the partial COX II gene sequences also separated the investigated strains from the type strain of <i>D. santjacobensis</i>. In this paper we propose <i>Diddensiella parasantjacobensis</i> f.a., sp. nov. (holotype: NCAIM Y.02121; isotypes: CBS 17819, DSM 114156) to accommodate the above-noted strains.
Inactivation of microorganisms by pulsed electric fields of different voltage waveforms (1994)

Processing foods with HV pulsed electric fields (PEF) is a new technology to inactivate microorganisms and denature enzymes with only a small increase in temperature. Introduction of this new technology will replace or complement conventional thermal processing methods. It will also provide consumers with safe, nutritious foods with fresh quality. For a given peak value of field intensity and amount of electric energy input, PEF inactivation of microorganisms is closely related to the waveform of applied pulses. Inactivation of microorganisms was studied with different waveshapes including exponential decay, oscillatory decay, square waves, and bipolar pulses. Microbial inactivation was tested in a parallel-plate static treatment chamber. Treatment field intensity ranged from 12 to 40 kV/cm while pulse length ranged from 30 to 180 /spl mu/s. From the microbial test results, bipolar square-wave pulses are the most efficient in terms of microbial inactivation for commercial PEF pasteurization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pilot-scale ozone/biological activated carbon treatment of reverse osmosis concentrate: potential for synergism between nitrate and contaminant removal and potable reuse (2020)

Reverse osmosis treatment for potable reuse can reduce the cost for removing nitrate and contaminants from wastewater prior to discharge.
Proteogenomic Analysis Reveals Unanticipated Adaptations of Colorectal Tumor Cells to Deficiencies in DNA Mismatch Repair (2013)

A growing body of genomic data on human cancers poses the critical question of how genomic variations translate to cancer phenotypes. We used standardized shotgun proteomics and targeted protein quantitation platforms to analyze a panel of 10 colon cancer cell lines differing by mutations in DNA mismatch repair (MMR) genes. In addition, we performed transcriptome sequencing (RNA-seq) to enable detection of protein sequence variants from the proteomic data. Biologic replicate cultures yielded highly consistent proteomic inventories with a cumulative total of 6,513 protein groups with a protein false discovery rate of 3.17% across all cell lines. Networks of coexpressed proteins with differential expression based on MMR status revealed impact on protein folding, turnover and transport, on cellular metabolism and on DNA and RNA synthesis and repair. Analysis of variant amino acid sequences suggested higher stability of proteins affected by naturally occurring germline polymorphisms than of proteins affected by somatic protein sequence changes. The data provide evidence for multisystem adaptation to MMR deficiency with a stress response that targets misfolded proteins for degradation through the ubiquitin-dependent proteasome pathway. Enrichment analysis suggested epithelial-to-mesenchymal transition in RKO cells, as evidenced by increased mobility and invasion properties compared with SW480. The observed proteomic profiles demonstrate previously unknown consequences of altered DNA repair and provide an expanded basis for mechanistic interpretation of MMR phenotypes.
Synthesis, Conformational Interconversion, and Photophysics of Tethered Porphyrin–Fullerene Dyads with Parachute Topology (2009)

The synthesis of a porphyrin-fullerene dyad with "parachute" topology is reported. To determine whether the dyad is "flexing" at room temperature, low-temperature NMR experiments were used. Computational modeling has shown the low-energy conformation of the dyad to be nonsymmetric. Although, (1)H NMR spectroscopy at room temperature is consistent with a molecule with C(2v) symmetry, the spectrum changes on lowering the temperature consistent with "windshield wiper"-like motion, in which the porphyrin moiety rotates from one side of the C(60) sphere to the other. Nanosecond and picosecond fluorescence lifetime experiments show two components contribute to the fluorescence decay, also consistent with the presence of more than one conformer.
Ultrasensitive Photodetectors Based on Island-Structured CH3NH3PbI3 Thin Films (2015)

CH3NH3PbI3 perovskite-based optoelectronics have attracted intense research interests recently because of their easy fabrication process and high power conversion efficiency. Herein, we report a novel photodetector based on unique CH3NH3PbI3 perovskite films with island-structured morphology. The light-induced electronic properties of the photodetectors were investigated and compared to those devices based on conventional compact CH3NH3PbI3 films. The island-structured CH3NH3PbI3 photodetectors exhibited a rapid response speed (<50 ms), good stability at a temperature of up to 100 °C, a large photocurrent to dark current ratio (Ilight/Idark > 1 × 10(4) under an incident light of ∼6.59 mW/cm(2), and Ilight/Idark > 1 × 10(2) under low incident light ∼0.018 mW/cm(2)), and excellent reproducibility. Especially, the performance of the island-structured devices markedly exceed that of the conventional compact CH3NH3PbI3 thin-film devices. These excellent performances render the island-structured device to be potentially applicable for a wide range of optoelectronics.
Methods for increased sensitivity and scope in automatic segmentation and detection of lung nodules in CT images (2015)

We propose two methods for lung segmentation and nodule detection in the initial stage. The lung segmentation method is based on a combination of masks, flood fill algorithm, and morphological closing operation. The nodule detection method is based on a multi-level thresholding process combined with various feature extraction techniques. The methods are evaluated with the new Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) dataset, which increases the number of tested cases, and thus the confidence, reliability and robustness of the results as compared to previously reported research. We aimed at detecting all nodule challenges present in the LIDC-IDRI (nodules<3 mm and nodules with 3–30 mm diametric size). Statistically, we have detected 3058 nodules in the initial stage (including solid, non-or part-solid, juxta-vascular, juxta-plural, and well-circumscribed nodules). To the best of our knowledge and given the results presented in other previous works (for the final stage), our results indicate that we can detect more nodules in the initial stage than ever reported, and that we can handle all types of nodule challenges in LIDC-IDRI. Specifically, we have achieved a sensitivity of 85% on the complete LIDC-IDRI dataset. On the smaller dataset of 60 CT scans with 315 nodules, we detected 301 nodules and achieved a sensitivity of 95.5%.
Light Harvesting Dynamics in Gloeobacter Rhodopsin (GR) (2014)

GR is directly shown by ultrafast pump-probe measurements to bind the carotenoid Salinixanthin, which acts as an efficient light harvesting antenna. Along with Xanthorhodopsin, This proves light harvesting to be a prevalent strategy in retinal proteins.
Segmented simultaneous multi‐slice diffusion‐weighted imaging with navigated 3D rigid motion correction (2021)

This work demonstrates the feasibility of retrospective 3D rigid motion correction from shot navigators for segmented SMS DWI.
Deep learning for tactile understanding from visual and haptic data (2016)

Robots which interact with the physical world will benefit from a fine-grained tactile understanding of objects and surfaces. Additionally, for certain tasks, robots may need to know the haptic properties of an object before touching it. To enable better tactile understanding for robots, we propose a method of classifying surfaces with haptic adjectives (e.g., compressible or smooth) from both visual and physical interaction data. Humans typically combine visual predictions and feedback from physical interactions to accurately predict haptic properties and interact with the world. Inspired by this cognitive pattern, we propose and explore a purely visual haptic prediction model. Purely visual models enable a robot to “feel” without physical interaction. Furthermore, we demonstrate that using both visual and physical interaction signals together yields more accurate haptic classification. Our models take advantage of recent advances in deep neural networks by employing a unified approach to learning features for physical interaction and visual observations. Even though we employ little domain specific knowledge, our model still achieves better results than methods based on hand-designed features.
Antibacterial properties of glycosylated surfaces: variation of the glucosidal moiety and fatty acid conformation of grafted microbial glycolipids (2020)

Glycosylated surfaces can display antimicrobial properties.
Precipitation of Proteins in Supercritical Carbon Dioxide (1996)

Supercritical CO2 was used as an antisolvent to form protein particles that exhibited minimal loss of activity upon reconstitution. Organic protein solutions were sprayed under a variety of operating conditions into the supercritical fluid, causing precipitation of dry, microparticulate (1-5 microns) protein powders. Three proteins were studied: trypsin, lysozyme, and insulin. Amide I band Raman spectra were used to estimate the alpha-helix and beta-sheet structural contents of native and precipitate powders of each protein. Analysis of the Raman spectral revealed minimal (lysozyme), intermediate (trypsin), and appreciable (insulin) changes in secondary structure with respect to the commercial starting materials. The perturbations in secondary structure suggest that the most significant event during supercritical fluid-induced precipitation involved the formation of beta-sheet structures with concomitant decreases of alpha-helix. Amide I band Raman and Fourier-transform infrared (FTIR) spectra indicate that higher operating temperatures and pressures lead to more extensive beta-sheet-mediated intermolecular interactions in the precipitates. Raman and FTIR spectra of redissolved precipitates are similar to those of aqueous commercial proteins, indicating that conformational changes were reversible upon reconstitution. These results suggest that protein precipitation in supercritical fluids can be used to form particles suitable for controlled release, direct aerosol delivery to the lungs, and long-term storage at ambient conditions.
Plexiform‐like neurofibromas develop in the mouse by intraneural xenograft of an NF1 tumor‐derived Schwann cell line (2007)

Plexiform neurofibromas are peripheral nerve sheath tumors that arise frequently in neurofibromatosis type 1 (NF1) and have a risk of malignant progression. Past efforts to establish xenograft models for neurofibroma involved the implantation of tumor fragments or heterogeneous primary cultures, which rarely achieved significant tumor growth. We report a practical and reproducible animal model of plexiform-like neurofibroma by xenograft of an immortal human NF1 tumor-derived Schwann cell line into the peripheral nerve of scid mice. The S100 and p75 positive sNF94.3 cell line was shown to possess a normal karyotype and have apparent full-length neurofibromin by Western blot. These cells were shown to have a constitutional NF1 microdeletion and elevated Ras-GTP activity, however, suggesting loss of normal neurofibromin function. Localized intraneural injection of the cell line sNF94.3 produced consistent and slow growing tumors that infiltrated and disrupted the host nerve. The xenograft tumors resembled plexiform neurofibromas with a low rate of proliferation, abundant extracellular matrix (hypocellularity), basal laminae, high vascularity, and mast cell infiltration. The histologic features of the developed tumors were particularly consistent with those of human plexiform neurofibroma as well. Intraneural xenograft of sNF94.3 cells enables the precise initiation of intraneural, plexiform-like tumors and provides a highly reproducible model for the study of plexiform neurofibroma tumorigenesis. This model facilitates testing of potential therapeutic interventions, including angiogenesis inhibitors, in a relevant cellular environment.
Antagonist G-mediated targeting and cytotoxicity of liposomal doxorubicin in NCI-H82 variant small cell lung cancer (2004)

The aim of the present study was to characterize the interactions of antagonist G (H-Arg-D-Trp-N(me)Phe-D-Trp-Leu-Met-NH 2)-targeted sterically stabilized liposomes with the human variant small cell lung cancer (SCLC) H82 cell line and to evaluate the antiproliferative activity of encapsulated doxorubicin against this cell line. Variant SCLC tumors are known to be more resistant to chemotherapy than classic SCLC tumors. The cellular association of antagonist G-targeted (radiolabeled) liposomes was 20-30-fold higher than that of non-targeted liposomes. Our data suggest that a maximum of 12,000 antagonist G-targeted liposomes were internalized/cell during 1-h incubation at 37 masculine C. Confocal microscopy experiments using pyranine-containing liposomes further confirmed that receptor-mediated endocytosis occurred, specifically in the case of targeted liposomes. In any of the previously mentioned experiments, the binding and endocytosis of non-targeted liposomes have revealed to be negligible. The improved cellular association of antagonist G-targeted liposomes, relative to non-targeted liposomes, resulted in an enhanced nuclear delivery (evaluated by fluorimetry) and cytotoxicity of encapsulated doxorubicin for incubation periods as short as 2 h. For an incubation of 2 h, we report IC50 values for targeted and non-targeted liposomes containing doxorubicin of 5.7 +/- 3.7 and higher than 200 micro M doxorubicin, respectively. Based on the present data, we may infer that receptors for antagonist G were present in H82 tumor cells and could mediate the internalization of antagonist G-targeted liposomes and the intracellular delivery of their content. Antagonist G covalently coupled to liposomal drugs may be promising for the treatment of this aggressive and highly heterogeneous disease.
Different composition of the human and the mouse γδ T cell receptor explains different phenotypes of CD3γ and CD3δ immunodeficiencies (2007)

The γδ T cell receptor for antigen (TCR) comprises the clonotypic TCRγδ, the CD3 (CD3γe and/or CD3δe), and the ζζ dimers. γδ T cells do not develop in CD3γ-deficient mice, whereas human patients lacking CD3γ have abundant peripheral blood γδ T cells expressing high γδ TCR levels. In an attempt to identify the molecular basis for these discordant phenotypes, we determined the stoichiometries of mouse and human γδ TCRs using blue native polyacrylamide gel electrophoresis and anti-TCR–specific antibodies. The γδ TCR isolated in digitonin from primary and cultured human γδ T cells includes CD3δ, with a TCRγδCD3e2δγζ2 stoichiometry. In CD3γ-deficient patients, this may allow substitution of CD3γ by the CD3δ chain and thereby support γδ T cell development. In contrast, the mouse γδ TCR does not incorporate CD3δ and has a TCRγδCD3e2γ2ζ2 stoichiometry. CD3γ-deficient mice exhibit a block in γδ T cell development. A human, but not a mouse, CD3δ transgene rescues γδ T cell development in mice lacking both mouse CD3δ and CD3γ chains. This suggests important structural and/or functional differences between human and mouse CD3δ chains during γδ T cell development. Collectively, our results indicate that the different γδ T cell phenotypes between CD3γ-deficient humans and mice can be explained by differences in their γδ TCR composition.
Frequency- and time-domain FEM models of EMG: capacitive effects and aspects of dispersion (2002)

Electromyography (EMG) simulations have traditionally been based on purely resistive models, in which capacitive effects are assumed to be negligible. Recent experimental studies suggest these assumptions may not be valid for muscle tissue. Furthermore, both muscle conductivity and permittivity are frequency-dependent (dispersive). In this paper, frequency-domain and time-domain finite-element models are used to examine the impact of capacitive effects and dispersion on the surface potential of a volume conductor. The results indicate that the effect of muscle capacitance and dispersion varies dramatically. Choosing low conductivity and high permittivity values in the range of experimentally reported data for muscle can cause displacement currents that are larger than conduction currents with corresponding reduction in surface potential of up to 50% at 100 Hz. Conductivity and permittivity values lying toward the middle of the reported range yield results which do not differ notably from purely resistive models. Also, excluding dispersion can also cause large error-up to 75% in the high frequency range of the EMG. It is clear that there is a need to establish accurate values of both conductivity and permittivity for human muscle tissue in vivo in order to quantify the influence of capacitance and dispersion on the EMG signal.
[Combined use of low-frequency ultrasound and photodynamic therapy in the prevention of postoperative pleural empyema]. (2001)

Results of surgical treatment of 20 patients with malignant lung tumors operated in N.N. Burdenko faculty surgical clinic were analyzed. The authors have developed the method of prophylaxis of acute postoperative pleural empyemas patented in Russian Federation. This method is: after main stage of operation (lob- or pneumonectomy) pleural cavity in filled with antiseptic solutions (furacillin 1:5000, 0.02% chlorgexidin). 5 ml of photosense (sulfured ftalocyanin of aluminium) were injected in pleural cavity, after it pleural cavity is treated by low-frequency ultrasound. After it the antiseptic is removed and pleural cavity is irradiated by red light with use of KAMIN-VIDEO lamp. In all the 20 operated patients who had undergone sanation of pleural cavity by low-frequency ultrasound and it irradiation by KAMIN-VIDEO lamp the postoperative period was uncomplicated.
Quadrature chaos shift keying (2002)

In this paper we propose a multilevel version of the differential chaos shift keying (DCSK) scheme exhibiting the same bit error rate performance as DCSK but double data rate and spectral efficiency.