gebhart/patrepeval huggingface dataset:
Delineation of the healthy rabbit kidney by immunohistochemistry – A technical note (2021)

Liver diseases pose a big global health problem and liver failure may result from viral infection, overnutrition or tumors. Studying pathologic liver tissue demands for accurate and specific histological stainings and immunohistochemical labellings, including chromogenic and fluorescent approaches. Moreover, a reliable set of healthy liver stainings and labellings are required, to provide a baseline or reference for the pathological situation. Here, we used the liver tissue of a healthy rabbit and compared different histological key steps, such as paraffin embedding after formalin fixation versus cryopreservation; or an antigen retrieval (AR) step in processing paraffin sections versus the same procedure without AR; or chromogenic with fluorescent detection system, respectively. Moreover, we provide images of serial sections, where we stained the same morphological structure with different markers, including collagen I, collagen III, fibronectin, α-SMA, elastin, protease-activated receptor-2 (PAR-2) which is an inflammation-related marker, ki67 for proliferating cells, and orcein (as negative control for pathological aberrations like Wilson disease). Differences between conditions were quantitatively assessed by measuring the colour intensity. Generally, we observed that cryosections exhibited a stronger signal intensity in immunohistochemically labelled sections than in paraffin sections; however, the strong staining got slurred, which sometimes hampered proper identification of morphological structures at higher magnifications. Moreover, there was a clear increase in signal intensity for paraffin sections when an AR step was performed compared to condition without AR. Results for mouse isotype staining as a negative control clearly supported those findings. Different stainings of the portal triad, the central vein and the bile ducts revealed a clear-cut distribution of extracellular matrix components, with prominent fibronectin and elastin around the lumen of the central vein as well as a patchy PAR-2 expression. As for the bile ducts, complete absence of α-SMA and PAR-2 was found at the margins, however, collagen I expression and elastin were positive and showed a strong signal. Like this, we provide useful and valuable reference images for researchers using the rabbit liver model. It may help to decide which of the immunohistochemical protocols are valuable to reach a certain aim and which protocols lead to the best visualization of the target structure.
Flavonoids from Sudanese <i>Albizia zygia</i> (Leguminosae, Subfamily Mimosoideae), a Plant with Antimalarial Potency (2011)

Three flavonoids were isolated for the first time from the Sudanese medicinal plants Albizia zygia. Compounds 1-3 were identified by interpretation of ESI mass data, (1)H, (13)C and 2D NMR as well as by comparison with published data as 4',7-dihydroxyflavanone (1) 3',4',7-trihydroxyflavone (2), 3-O-methylfisetin (3',4',7-trihydroxy-3-methoxyflavone, 3). All flavonoids were tested against Plasmodium falciparum, and only compound 2 showed high antimalarial activity (IC50 0.078 µg/ml).
Properties of12C resonances determined from the10B(3He,pααα) and11B(3He,dααα) reactions studied in complete kinematics (2012)

We have used the ${}^{10}$B(${}^{3}$He$,p\ensuremath{\alpha}$$\ensuremath{\alpha}$$\ensuremath{\alpha}$) reaction at 4.9 MeV and the ${}^{11}$B(${}^{3}$He$,d\ensuremath{\alpha}$$\ensuremath{\alpha}$$\ensuremath{\alpha}$) reaction at 8.5 MeV to determine the energy, width, and decay mechanism of resonances in ${}^{12}$C above the triple-$\ensuremath{\alpha}$ threshold up to 21 MeV in excitation energy. Comparison with various models has allowed us to estimate the degree of clustering of the states studied.
Genetics of Obesity: What have we Learned? (2011)

Candidate gene and genome-wide association studies have led to the discovery of nine loci involved in Mendelian forms of obesity and 58 loci contributing to polygenic obesity. These loci explain a small fraction of the heritability for obesity and many genes remain to be discovered. However, efforts in obesity gene identification greatly modified our understanding of this disorder. In this review, we propose an overlook of major lessons learned from 15 years of research in the field of genetics and obesity. We comment on the existence of the genetic continuum between monogenic and polygenic forms of obesity that pinpoints the role of genes involved in the central regulation of food intake and genetic predisposition to obesity. We explain how the identification of novel obesity predisposing genes has clarified unsuspected biological pathways involved in the control of energy balance that have helped to understand past human history and to explore causality in epidemiology. We provide evidence that obesity predisposing genes interact with the environment and influence the response to treatment relevant to disease prediction.
Coats' disease of the retina (unilateral retinal telangiectasis) caused by somatic mutation in the NDP gene: a role for norrin in retinal angiogenesis (1999)

Coats' disease is characterized by abnormal retinal vascular development (so-called 'retinal telangiectasis') which results in massive intraretinal and subretinal lipid accumulation (exudative retinal detachment). The classical form of Coats' disease is almost invariably isolated, unilateral and seen in males. A female with a unilateral variant of Coats' disease gave birth to a son affected by Norrie disease. Both carried a missense mutation within the NDP gene on chromosome Xp11.2. Subsequently analysis of the retinas of nine enucleated eyes from males with Coats' disease demonstrated in one a somatic mutation in the NDP gene which was not present within non-retinal tissue. We suggest that Coats' telangiectasis is secondary to somatic mutation in the NDP gene which results in a deficiency of norrin (the protein product of the NDP gene) within the developing retina. This supports recent observations that the protein is critical for normal retinal vasculogenesis.
Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner (2005)

The functional interaction between the orphan nuclear receptors small heterodimer partner (SHP) and liver receptor homolog 1 (LRH-1), where SHP binds to LRH-1 and represses its constitutive transcriptional activity, is crucial for regulating genes involved in cholesterol homeostasis. Here, we report structural and biochemical analyses of the LRH-1/SHP interaction. The crystal structure and modeling studies of the LRH-1 ligand-binding domain bound to either of the two LXXLL-related motifs of SHP show that the receptor undergoes conformational changes to accommodate the SHP docking and reveal key residues that determine the potency and selectivity of SHP binding. Through a combination of mutagenesis and binding studies, we demonstrate that only the second SHP LXXLL motif is required for repressing LRH-1, and this motif displays a strong preference for binding to LRH-1 over the closely related receptor steroidogeneic factor 1 (SF-1). Structural comparisons indicate that this binding selectivity is determined by residues flanking the core LXXLL motifs. These results establish a structural model for understanding how SHP interacts with LRH-1 to regulate cholesterol homeostasis and provide new insights into how nuclear receptor/coregulator selectivity is achieved.
Prospective Controlled Animal Study on Biopsy Sampling with New Flexible Cryoprobes versus Forceps: Evaluation of Biopsy Size, Histological Quality and Bleeding Risk (2010)

Since cryobiopsy sampling is not associated with a higher bleeding risk compared with forceps biopsy, this new biopsy technique offers--in addition to a good specimen quality--a safe and valuable tool with the potential of improving the outcome of diagnostic endoscopy.
Cascadable, latching photonic switch with high optical gain by the monolithic integration of a vertical-cavity surface-emitting laser and a pn-pn photothyristor (1991)

The authors report the first demonstration of a cascadable, photonic switch based on the monolithic integration of a multi-quantum-well vertical-cavity surface-emitting laser (VCSEL) and a latching pn-pn photothyristor grown by low-pressure metalorganic vapor-phase epitaxy (LP-MOCVD). The VCSEL and pn-pn photothyristor structures can be independently optimized for optical switching, logic, and memory functions. Optical switching with high gain (30000), high contrast (30 dB), low switching power (11 nW), and latching memory have been demonstrated. The integrated pn-pn/VCSEL switch not only represents a volatile optical memory, but also can be used to implement a new class of optical logic gates with latching logic outputs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A fast-space-charge-wave electron beam duplexer (1963)

This paper will describe a device capable of interacting with the fast space charge wave of an electron beam, utilizing a conventional helix. Complete energy interchange occurs for two coupled positive energy modes if the propagation characteristics of the two waves are identical over the band and the Kompfner dip length is independent of frequency. In this device the Kompfner dip condition is satisfied for operation over an octave bandwidth. Experimental evidence of this type of operation has been obtained on both C and S-band versions. The device has a number of interesting applications. One of these, a duplexer, has been designed to operate at 10 kw peak power, 200 watts of average power, and protects the receiver against signal power greater than 10 mw. The operating characteristics of this device will be described.
Synthesis and characterization of polyamides containing arylene sulfide‐sulfone groups (1993)

Abstract Polyamides containing arylene sulfide as well as arylene sulfide‐sulfone linkages were prepared from bis(4‐phenylthio)dibenzoyl chloride (BPCl), 4,4′‐[sulfonylbis(4‐phenylthio)]dibenzoyl chloride (SPCl) and aromatic diamines both by solution and interfacial polymerization techniques. In the solution polymerization the effect of two different acid acceptors, lithium chloride and triethylamine, on inherent viscosity of the polyamides was studied. The effect of aromatic sulfone ether diamines and conventional aromatic diamines on viscosity and thermal properties of polyamides was also investigated. The polyamides prepared were characterized by IR, 1 H NMR, elemental analysis, solution viscosity, thermogravi‐metry, differential scanning calorimetry and X‐ray diffraction. Thermal and physical properties of polyamides prepared from BPCl and SPCl were compared.
An infrared spectroscopic study of Li2B4O7 (2001)

The temperature evolution of the infrared powder spectra of lithium tetraborate Li2B4O7 has been measured in the infrared region 50-1600 cm-1 and over a temperature range between 20 K and 680 K. In contrast to the sharp B-O bands, the Li-related bands in the region between 300 cm-1 and 510 cm-1 are rather broad even at 20 K. With increasing temperature these bands show a stronger thermal response than in the higher-frequency region: the bands at 350 cm-1 and 424 cm-1 shift significantly in frequency and become very broad above 500 K. The 508 cm-1 band appears to split into two individual bands near 500 K. The broadening of the Li-related bands is probably due to the thermally induced Li disorder. The temperature dependence of the B-O bending and stretching vibrations does not show clear evidence of structural phase transitions in Li2B4O7 occurring in the temperature range between 20 K and 680 K.
Nanofluidic Immobilization and Growth Detection of Escherichia coli in a Chip for Antibiotic Susceptibility Testing (2020)

Infections with antimicrobial resistant bacteria are a rising threat for global healthcare as more and more antibiotics lose their effectiveness against bacterial pathogens. To guarantee the long-term effectiveness of broad-spectrum antibiotics, they may only be prescribed when inevitably required. In order to make a reliable assessment of which antibiotics are effective, rapid point-of-care tests are needed. This can be achieved with fast phenotypic microfluidic tests, which can cope with low bacterial concentrations and work label-free. Here, we present a novel optofluidic chip with a cross-flow immobilization principle using a regular array of nanogaps to concentrate bacteria and detect their growth label-free under the influence of antibiotics. The interferometric measuring principle enabled the detection of the growth of <i>Escherichia coli</i> in under 4 h with a sample volume of 187.2 µL and a doubling time of 79 min. In proof-of-concept experiments, we could show that the method can distinguish between bacterial growth and its inhibition by antibiotics. The results indicate that the nanofluidic chip approach provides a very promising concept for future rapid and label-free antimicrobial susceptibility tests.
Astronaut Maneuvering-Unit Voice Controller (1969)

An experimental voice controller to be used in conjunction with an astronaut maneuvering unit has been developed by RCA Advanced Technology under the sponsorship of the Air Force Aero Propulsion Laboratory and the Air Force Avionics Laboratory. The voice controller will permit the spaceman to move about freely outside his space capsule merely by speaking commands into his helmet microphone. The experimental unit recognizes 13 command words in continuous speech, in real time, including such combinations as “roll right” and “pitch up.” The command vocabulary was chosen so that no two words differ only by a single phoneme. This was done to ensure that confusion between command words would not occur and so that the equipment could be simplified to the point where it could be built small enough to be included in the backpack of the astronaut. The experimental model is about the size of a suitcase, weighs 25 lb, and consumes 46 W. However, the experimental unit incorporates design principles necessary to construct a space unit that is less than 100 in.3 in volume, weighs less than 5 lb, and consumes less than 10 W.
Optical signatures of Dirac nodal lines in NbAs 2 (2018)

Using polarized optical and magneto-optical spectroscopy, we have demonstrated universal aspects of electrodynamics associated with Dirac nodal lines that are found in several classes of unconventional intermetallic compounds. We investigated anisotropic electrodynamics of [Formula: see text] where the spin-orbit coupling (SOC) triggers energy gaps along the nodal lines. These gaps manifest as sharp steps in the optical conductivity spectra [Formula: see text] This behavior is followed by the linear power-law scaling of [Formula: see text] at higher frequencies, consistent with our theoretical analysis for dispersive Dirac nodal lines. Magneto-optics data affirm the dominant role of nodal lines in the electrodynamics of [Formula: see text].
Abstract P-4: Robust Method for Background Subtraction in Serial X-ray Diffraction Data (2021)

Background: Membrane receptors play an important role in signal transduction across the cell membrane in all living organisms. Their structural studies have been enabled by multiple technological breakthroughs in their heterologous expression, stabilization, crystallization, and crystallographic data collection as well as in cryogenic electron microscopy (cryoEM). During the last decade, serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has enabled structure determination of previously inaccessible proteins, including several G-protein-coupled receptors (GPCR), that produce only micrometer-sized crystals, thus paving the way towards understanding their activation mechanism and rational drug discovery. In addition to experimental difficulties, membrane protein structure determination is also often accompanied by data processing challenges. In particular, the lipidic cubic phase that serves as a carrier for membrane protein microcrystals, as well as various XFEL beam-shaping devices may generate substantial background scattering that could complicate the structure factor extraction from the diffraction images. Methods: In this work, we tested an adaptation of the denoising algorithm via matrix decomposition to XFEL-SFX data. We benchmarked its performance using high-background data from PAL-XFEL and established its applicability to serial crystallography image denoising, as well as compared it to the CrystFEL-based image denoising algorithm. Results: We find that, although the decomposition-based image denoising does not outperform CrystFEL median subtraction, it performs better than the integration without any additional subtraction. We find the non-negative matrix factorization performing better than more traditional singular-value decomposition methods, both in terms of visual interpretability and final data quality. Conclusion: We hope that this work will draw attention to background subtraction methods in structural biology, and will pave the way towards processing of most challenging datasets in structural biology, in particularly, those collected from membrane proteins.
Neuraminidase Reversal of Resistance to Lysis of Herpes Simplex Virus-Infected Cells by Antibody and Complement (1976)

The susceptibility to lysis by antibody and complement was examined in four human cell lines. The cells were infected with herpes simplex virus type 1 and lysis was assessed by the 51Cr release test by using antibodies to herpes simplex virus and guinea pig serum as a source of complement. The four cell lines were found to differ in their susceptibility to lysis, although virus replication was readily demonstrated in the different cell lines. By indirect immunofluorescence, no differences in the expression of virus antigens at the surface of the cells could be found between the different cell lines. Treatment of cells with neuraminidase markedly enhanced the sensitivity of the cells which were relatively insensitive to lysis. The enhancement of susceptibiltiy to lysis by neuraminidase occurred if cells were treated before reaction of the cells with antibody and if the cells were reacted with antibody before treatment with the enzyme. No enhancement was observed when cells were reacted with antibody and complement before neuraminidase treatment. Neuraminidase treatment did not seem to enhance appreciably the quantity of antibody which reacted at the cell surface. The observations suggest that surface properties of certain cells render the cells resistant to lysis by antibody and complement and that the resistance to lysis can be abrogated by treating the cells with neuraminidase.
Protein Interactions between CD2 and Lck Are Required for the Lipid Raft Distribution of CD2 (2008)

In T lymphocytes, lipid rafts are preferred sites for signal transduction initiation and amplification. Many cell membrane receptors, such as the TCR, coreceptors, and accessory molecules associate within these microdomains upon cell activation. However, it is still unclear in most cases whether these receptors interact with rafts through lipid-based amino acid modifications or whether raft insertion is driven by protein-protein interactions. In murine T cells, a significant fraction of CD2 associates with membrane lipid rafts. We have addressed the mechanisms that control the localization of rat CD2 at the plasma membrane, and its redistribution within lipid rafts induced upon activation. Following incubation of rat CD2-expressing cells with radioactive-labeled palmitic acid, or using CD2 mutants with Cys226 and Cys228 replaced by alanine residues, we found no evidence that rat CD2 was subjected to lipid modifications that could favor the translocation to lipid rafts, discarding palmitoylation as the principal mechanism for raft addressing. In contrast, using Jurkat cells expressing different CD2 and Lck mutants, we show that the association of CD2 with the rafts fully correlates with CD2 capacity to bind to Lck. As CD2 physically interacts with both Lck and Fyn, preferentially inside lipid rafts, and reflecting the increase of CD2 in lipid rafts following activation, CD2 can mediate the interaction between the two kinases and the consequent boost in kinase activity in lipid rafts.
Effective Drag Coefficient for Gas-Particle Flow in Shock Tubes (1970)

Effective drag coefficients for flows of suspensions of spherical glass particles in air were derived from simultaneous measurements of pressure and particle concentration in the flow behind weak shock waves. Average particle diameters were 29 and 62μm. The instantaneous concentration was determined by light scattering, and the results agree well with earlier shock-tube data based on streak records. They exhibit several unexpected features: the correlation between drag coefficient and Reynolds number is much steeper (∝ Re−1.7) than the generally used “standard” curve but approaches it at Reynolds numbers of several hundred; the correlation is independent of the particle concentration over the range of the experiments, that is, for particle-to-gas flow rate ratios between about 0.05 and 0.36; if the Reynolds number immediately behind the shock front is changed by varying the shock strength, the points move along the correlation, but if it is changed by changing the particle size, the entire correlation is shifted although to a smaller extent than would correspond to the direct effect of particle diameter on the Reynolds number. To account for the observations, a flow model is developed which allows for microscopic longitudinal and lateral perturbations of the particle motion that are the result of various causes, such as particle interactions with wakes of other particles, lateral forces caused by particle rotation, or electrostatic forces. Because of the nonlinearity of the equation of motion, the averaged particle motion is different from that of a particle without perturbations. The effective drag coefficient for the average particle motion is therefore different from the standard drag coefficient applied along the actual motion. With this model and plausible assumptions for the average lateral velocity component of the particle motion, all features of the experimental data can be qualitatively explained.
Diversity in treatment modalities of Stage II/III urothelial cancer in Japan: sub-analysis of the multi-institutional national database of the Japanese Urological Association (2016)

This study demonstrated the variety of treatments used for Japanese patients with Stage II/III urothelial cancer. Treatment standardization for these entities may be necessary.
Filter-Based Miniature Spectrometers: Spectrum Reconstruction Using Adaptive Regularization (2011)

Miniature spectrometers provide a cost and size advantage over traditional spectrometers. However, unlike traditional spectrometers in which appropriate dispersive optics and/or interferometric devices are well-developed, miniature spectrometers usually do not have ideal (or close to ideal) wavelength-specific filtering mechanism to resolve the power of the input spectrum at specified wavelengths. Hence, the raw outputs from the filtering mechanism may not be adequate to represent spectra of measured objects. The nonideal filtering mechanism makes reconstruction process necessary. In this work, the method of Tikhonov regularization for stabilizing the solution of inverse problems is applied to a prototype filter-based nano-optic spectrum sensor from nanoLambda. L-curve criterion and generalized cross validation (GCV) criterion for adaptively selecting the regularization parameter are examined. Satisfactory results are obtained by exploiting non-negative constraints on the reconstructed spectrum, with the regularization parameter being selected by the L-curve criterion. As a result, low-cost miniature spectrometer on-a-chip can be realized.