gebhart/patrepeval huggingface dataset:
Activation of RNA metabolism-related genes in mouse but not human tissues deficient in SMN (2005)

Mutations of the survival of motor neuron gene (SMN1) are responsible for spinal muscular atrophies (SMA), a frequent recessive autosomal motor neuron disease. SMN is involved in various processes including RNA metabolism. However, the molecular pathway linking marked deficiency of SMN to SMA phenotype remains unclear. Homozygous deletion of murine Smn exon 7 directed to neurons or skeletal muscle causes severe motor axonal or myofiber degeneration, respectively. With the use of cDNA microarrays, expression profiles of 8,400 genes were analyzed in skeletal muscle and spinal cord of muscular and neuronal mutants, respectively, and compared with age-matched controls. A high proportion of genes (20 of 429, 5%) was involved in pre-mRNA splicing, ribosomal RNA processing, or RNA decay, and 18 of them were upregulated in mutant tissues. By analyzing other neuromuscular disorders, we showed that most of them (14 of 18) were specific to the SMN defect. Quantitative PCR analysis of these transcripts showed that gene activation was an early adaptive response to the lack but not reduced amount of full-length SMN in mouse mutant tissues. In human SMA tissues, activation of this program was not observed, which could be ascribed to the reduction but not the absence of full-length SMN.
Effect of Immunization of Cats with <i>Isospora felis</i> and BCG on Immunity to Reexcretion of <i>Toxoplasma gondii</i> Oocysts* (1978)

The effect of pretreatment with Isospora felis and bacillus Calmette-Guérin (BCG) on the reexcretion of Toxoplasma gondii oocysts was studied in 16 coccidia-free cats. The following conclusions were drawn: (A) Chronically T. gondii-infected cats reexcreted T. gondii oocysts after superinfection with I. felis, and this reexcretion was prevented in cats infected with I. felis before T. gondii infection. (B) Administration of BCG before Toxoplasma infection had no apparent effect on the outcome of the infection.
Plant Growth Experiments Using a Red Laser Diode and Blue Light Emitting Diodes. (1996)

Growth experiments of Sprouting Radish were carried out for the first time by using a red laser diode (LD) and two blue light emitting diodes (LED) as the light source for the photosynthesis. The output power and the central wavelength of the LD are 5 mW and 670 nm, and those of the LED are 1.2 mW and 450 nm, respectively. The type of the LD is selected so that the central wavelength of the LD matches to the band center of the absorption spectrum of the plant. It is found that the plant under the artificial light grows similarly to that under sunlight.
IL‐33 promotes innate IFN‐γ production and modulates dendritic cell response in LCMV‐induced hepatitis in mice (2015)

Recent studies have revealed IL-33 as a key factor in promoting antiviral T-cell responses. However, it is less clear as to how IL-33 regulates innate immunity. In this study, we infected wild-type (WT) and IL-33(-/-) mice with lymphocytic choriomeningitis virus and demonstrated an essential role of infection-induced IL-33 expression for robust innate IFN-γ production in the liver. We first show that IL-33 deficiency resulted in a marked reduction in the number of IFN-γ(+) γδ T and NK cells, but an increase in that of IL-17(+) γδ T cells at 16 h postinfection. Recombinant IL-33 (rIL-33) treatment could reverse such deficiency via increasing IFN-γ-producing γδ T and NK cells, and inhibiting IL-17(+) γδ T cells. We also found that rIL-33-induced type 2 innate lymphoid cells were not involved in T-cell responses and liver injury, since the adoptive transfer of type 2 innate lymphoid cells neither affected the IFN-γ and TNF-α production in T cells, nor liver transferase levels in lymphocytic choriomeningitis virus infected mice. Interestingly, we found that while IL-33 was not required for costimulatory molecule expression, it was critical for DC proliferation and cytokine production. Together, this study highlights an essential role of IL-33 in regulating innate IFN-γ-production and DC function during viral hepatitis.
Local characterization of transmission properties of a two-dimensional photonic crystal (1997)

We use a near-field scanning optical microscope to study optical transmission through a two-dimensional triangular photonic crystal. Spatial variations in the intensity of light coupled through the sample depend on the photon energy and the numerical aperture of the collection optics. We discuss the relationship between the observed dependence and the local structure of the optical modes in the crystal. Features in the data arising from modes with Fourier components inside and outside the first Brillouin zone can be distinguished by this technique.
A Feedback Control Approach to Organic Drug Infusions Using Electrochemical Measurement (2015)

This platform will contribute to high-performance TIVA application of intravenous propofol anesthesia.
High endothelial venules at the nexus of an IL-6/gp130/STAT3 axis controlling immune surveillance during fever (173.22) (2012)

Abstract Fever remains the least understood component of acute inflammation although it confers a survival benefit in endothermic and ectothermic vertebrates. Here we show that LPS- or turpentine-induced fever enhances immune surveillance by augmenting lymphocyte trafficking via high endothelial venules (HEV) in lymph nodes. We identified an autocrine feed-forward loop during the effector phase of fever in which IL-6 produced by HEV acts via the gp130 signal transducing subunit of the IL-6 receptor to enhance ICAM-1-dependent lymphocyte trafficking. Comparative analysis of the thermal response in gp130Y757F and gp130ΔSTAT mutant mice implicated STAT3/1 in the pathway downstream of fever that controls lymphocyte trafficking. An obligate role for STAT3 signaling was further delineated using Stat1-/- mice. While gp130-dependent MEK1-ERK1/2 signaling was not required for enhanced lymphocyte trafficking, ERK1/2 activation was necessary for the metalloproteinase-dependent shedding mechanism that restores endothelial ICAM-1 to homeostatic levels during the resolution phase of inflammation. Finally, thermally-induced lymphocyte trafficking across HEV lowered the threshold for antigen-driven priming of naïve T cells in lymph nodes. Taken together, these studies provide insight into a novel IL-6/gp130/STAT3 axis that acts as a highly integrated thermally-sensitive alert system to heighten immune surveillance during febrile responses.
Exome sequencing in an SCA14 family demonstrates its utility in diagnosing heterogeneous diseases (2012)

This work demonstrates the utility of exome sequencing to rapidly screen heterogeneous genetic disorders such as the ataxias. Exome sequencing is more comprehensive, faster, and significantly cheaper than conventional Sanger sequencing, and thus represents a superior diagnostic screening tool in clinical practice.
A review of the utility of obtaining repeated postoperative radiographs following single-level anterior cervical decompression, fusion, and plate placement (2008)

Pseudarthrosis and construct failure following single-level ACDFP occur rarely, and patients with new symptoms following surgery are as likely to have normal radiographic findings as they are to have abnormalities identified on their postoperative plain radiographs. Routinely obtaining postoperative radiographs at regular intervals in asymptomatic patients following single-level ACDFP does not appear to be warranted.
Abstract 2419: Lipid droplets promote glioblastoma cell growth through maintaining cholesterol homeostasis mediated by autophagy (2018)

Abstract Lipid droplets (LDs) have been studied as the major storage site of neutral lipids for decades, especially in the progression of metabolic diseases. Recently, the functions of LDs in cancers have begun to gain significant attention. Here, we provide evidence that LDs promote glioblastoma (GBM) cell growth through autophagy mediated maintenance of cholesterol homeostasis. Our data showed that LDs in tumor tissues from GBM patients are engulfed by autophagic vacuoles and lysosomes. Cellular cholesterol deprivation or removal of plasma membrane cholesterol by methyl-β-cyclodextrin (MβCD) activates autophagy to hydrolyze LDs to support GBM cell survival, whereas inhibition of autophagy blocks transportation of cholesterol to plasma membrane, leading to cell death. Fluorescence imaging reveals direct trafficking of LD-stored cholesterol to the plasma membrane through autophagic liberation. Our data demonstrate that LDs serve as cholesterol reservoir for GBM cell growth, suggesting that targeting LD-autophagy-cholesterol homeostasis metabolic pathway represents a potential means to treat GBM and other malignancies. Citation Format: Feng Geng, Xiang Cheng, Chunming Cheng, Arnab Chakravarti, Deliang Guo. Lipid droplets promote glioblastoma cell growth through maintaining cholesterol homeostasis mediated by autophagy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2419.
22 nm technology node active layer patterning for planar transistor devices (2009)

As the semiconductor device size shrinks without concomitant increase of the numerical aperture (NA=1.35) or index of the immersion fluid from 32 nm technology node, 22 nm patterning technology presents challenges in resolution as well as process window. Therefore, aggressive Resolution Enhancement Technique (RET), Design for Manufacturability (DFM) and layer specific lithographic process development are strongly required. In order to achieve successful patterning, co-optimization of the design, RET and lithographic process becomes essential at the 22 nm technology node. In this paper, we demonstrate the patterning of the active layer for 22 nm planar transistor device and discuss achievements and challenges in 22 nm lithographic printing. Key issues identified include printing tight pitches and 2-D features simultaneously without sacrificing the cell size, while maintaining large process window. As the poly-gate pitch is tightened, the need for improved corner rounding performance is required inorder to ensure proper gate length across the entire gate width. Utilizing water immersion at NA=1.2 and 1.35, we will demonstrate patterning of the active layer in a 22 nm technology node SRAM of a bit-cell having a size of 0.1 &mu;m<sup>2</sup> and smaller while providing large process window for other features across the chip. It is shown that highly layer-specific and design-aware RET and lithographic process developments are critical for the success of 22 nm node technology.
Delineation of Skin Strata in Reflectance Confocal Microscopy Images using Recurrent Convolutional Networks with Toeplitz Attention (2017)

Reflectance confocal microscopy (RCM) is an effective, non-invasive pre-screening tool for skin cancer diagnosis, but it requires extensive training and experience to assess accurately. There are few quantitative tools available to standardize image acquisition and analysis, and the ones that are available are not interpretable. In this study, we use a recurrent neural network with attention on convolutional network features. We apply it to delineate skin strata in vertically-oriented stacks of transverse RCM image slices in an interpretable manner. We introduce a new attention mechanism called Toeplitz attention, which constrains the attention map to have a Toeplitz structure. Testing our model on an expert labeled dataset of 504 RCM stacks, we achieve 88.17% image-wise classification accuracy, which is the current state-of-art.
Defining the hypoxic target volume based on positron emission tomography for image guided radiotherapy – the influence of the choice of the reference region and conversion function (2017)

A non-linear conversion function between uptake and oxygen partial pressure for <sup>18</sup>F-FMISO-PET could be applied to <sup>18</sup>F-HX4 images to delineate hypoxic sub-volumes of similar size, shape, and relative location as based directly on the uptake. In order to apply the model for e.g., dose-painting, new parameters need to be derived for the accurate calculation of dose-modifying factors for this tracer.
Dlaczego potrzebujemy nowej kombinacji leków ukierunkowanych molekularnie — enkorafenibu z binimetynibem — w zaawansowanym czerniaku z mutacją BRAF? (2018)

Dlaczego potrzebujemy nowej kombinacji lekw ukierunkowanych molekularnie -enkorafenibu z binimetynibem -w zaawansowanym czerniaku z mutacj BRAF
Dynamic control of directional asymmetry observed in ultrafast laser direct writing (2012)

A liquid crystal spatial light modulator (SLM) is used to control the focal symmetry and the associated directional “quill” effect encountered when using a femtosecond laser for direct laser writing of fused silica. Applying a blazed grating to the SLM effectively introduces pulse front tilt to the fabrication beam and a spatiotemporal asymmetry at the focus. As a result different fabricated features are generated when moving the substrate in opposite directions relative to the tilt. It is additionally shown that inhomogeneous pupil illumination can cause similar directionality in the fabrication via a spatial asymmetry in the focus.
A sparse image method for BEM capacitance extraction (1996)

Boundary element methods (BEM) are often used for complex 3-D capacitance extraction because of their efficiency, ease of data preparation, and automatic handling of open regions. BEM capacitance extraction, however, yields a dense set of linear equations that makes solving via direct matrix methods such as Gaussian elimination prohibitive for large problem sizes. Although iterative, multipole-accelerated techniques have produced dramatic improvements in BEM capacitance extraction, accurate sparse approximations of the electrostatic potential matrix are still desirable for the following reasons. First, the corresponding capacitance models are sufficient for a large number of analysis and design applications. Moreover, even when the utmost accuracy is required, sparse approximations can be used to precondition iterative solution methods.
Impaired Cerebellar Development and Function in Mice Lacking CAPS2, a Protein Involved in Neurotrophin Release (2007)

Ca2+-dependent activator protein for secretion 2 (CAPS2/CADPS2) is a secretory granule-associated protein that is abundant at the parallel fiber terminals of granule cells in the mouse cerebellum and is involved in the release of neurotrophin-3 (NT-3) and brain-derived neurotrophic factor (BDNF), both of which are required for cerebellar development. The human homolog gene on chromosome 7 is located within susceptibility locus 1 of autism, a disease characterized by several cerebellar morphological abnormalities. Here we report that CAPS2 knock-out mice are deficient in the release of NT-3 and BDNF, and they consequently exhibit suppressed phosphorylation of Trk receptors in the cerebellum; these mice exhibit pronounced impairments in cerebellar development and functions, including neuronal survival, differentiation and migration of postmitotic granule cells, dendritogenesis of Purkinje cells, lobulation between lobules VI and VII, structure and vesicular distribution of parallel fiber-Purkinje cell synapses, paired-pulse facilitation at parallel fiber-Purkinje cell synapses, rotarod motor coordination, and eye movement plasticity in optokinetic training. Increased granule cell death of the external granular layer was noted in lobules VI-VII and IX, in which high BDNF and NT-3 levels are specifically localized during cerebellar development. Therefore, the deficiency of CAPS2 indicates that CAPS2-mediated neurotrophin release is indispensable for normal cerebellar development and functions, including neuronal differentiation and survival, morphogenesis, synaptic function, and motor learning/control. The possible involvement of the CAPS2 gene in the cerebellar deficits of autistic patients is discussed.
Table S1 from Functional Properties of &lt;i&gt;KIT&lt;/i&gt; Mutations Are Associated with Differential Clinical Outcomes and Response to Targeted Therapeutics in CBF Acute Myeloid Leukemia (2023)

&lt;p&gt;Supplementary Table 1. Clinical and biologic characteristics of CBF patients treated on COG AAML0531 stratified by KIT mutational status.&lt;/p&gt;
Strain Gage Rosettes: Selection, Application and Data Reduction (2012)

This chapter contains sections titled: Introduction Errors, Corrections, and Limitations for Rosettes Applications of Gages to Load Cells References
Cancer stem cells (2016)

Cancer stem cells (CSCs) are a class of pluripotent cells that have been observed in most types of solid and hematologic cancers. CSCs have been shown in numerous cancer models to be involved in tumor development, cell proliferation, and metastatic dissemination, while possessing a capacity for sustained self-renewal. CSCs, which typically represent a small proportion of total cells of a given tumor, also exhibit resistance to chemotherapy and radiotherapy. Indeed, exposure to these treatments may promote "stemness" in nonstem cancer cells, which may explain why successful therapeutic reduction of tumor bulk will often fail to produce clinical improvement. Acquisition of stemness involves epithelial-mesenchymal transition (EMT), in which epithelial cells are transformed into a mesenchymal phenotype characterized by increased capacities for migration, invasiveness, and resistance to apoptosis. EMT may also contribute to metastasis by driving dissemination of mesenchymal CSCs to distant locations, whereupon the CSCs revert to an epithelial phenotype to support metastatic tumor growth. Several different approaches to treatment aimed at overcoming the intrinsic resistance of CSCs to conventional therapies are currently being developed. These include agents targeting tumorigenic pathways, such as JAK2/STAT3 and PI3K/mTOR, and immunotherapies, including vaccines and natural killer cells employed to induce a T cell response.
Prevention by the cannabinoid antagonist, SR141716A, of cannabinoid‐mediated blockade of long‐term potentiation in the rat hippocampal slice (1995)

Incubation of rat hippocampal slices in the presence of the synthetic cannabinoid (-)-11-OH-delta 8-dimethylheptyl tetrahydrocannabinol (HU-210) (100 nM) prevented the induction of long-term potentiation (LTP). Slices co-incubated with both HU-210 (100 nM) and the cannabinoid antagonist, SR141716A (100 nM), exhibited tetanically induced LTP, comparable to control slices. Intriguingly, coincubation with HU-210 and SR141716A prevented the induction of the early, short-term phase of LTP.
Whole-genome sequencing of human Pegivirus variant from an Egyptian patient co-infected with hepatitis C virus: a case report (2019)

We report a new variant of HPgV in a patient suffering from hepatitis C viral infection.
Supplementary Table 1 from Tumor Subtype-Specific Cancer–Testis Antigens as Potential Biomarkers and Immunotherapeutic Targets for Cancers (2023)

&lt;p&gt;XLSX file - 14K, Supplemental Table S1. CT genes used in this study.&lt;/p&gt;
Studies of protein–nucleic acid interactions by photon correlation spectroscopy. I. tRNA–BSA interactions at low ionic strength (1980)

Photon correlation measurements of tRNA–BSA association in 1 mM sodium cacodylate buffer are reported. In terms of the overall geometry of the reactants (tRNA and BSA) and their aggregates as well as the reaction rate constants, we have confirmed that, in tRNA–BSA solutions, the tRNA–BSA aggregates in the presence of an excess of BSA are twice as big as those in an excess of tRNA. Furthermore, the experimentally estimated association rate constant is two orders of magnitude lower than the one calculated for a diffusion controlled reaction without taking into account electrostatic interactions in solution. Thus, it is important to include long-range repulsive electrostatic interactions which tend to slow down the reaction markedly.
Vortex circulation and polarity patterns in closely packed cap arrays (2016)

We studied curvature-driven modifications to the magnetostatic coupling of vortex circulation and polarity in soft-magnetic closely packed cap arrays. A phase diagram for the magnetic remanent/transition states at room temperature as a function of diameter and thickness was assembled. For specimens with vortex remanent state (40 nm-thick Permalloy on 330 nm spherical nanoparticles), both vortex circulation and polarity were visualized. Intercap coupling upon vortex nucleation leads to the formation of vortex circulation patterns in closely packed arrays. The remanent circulation pattern can be tailored choosing the direction of the applied magnetic field with respect to the symmetry axis of the hexagonal array. An even and random distribution of vortex polarity indicates the absence of any circulation-polarity coupling.
Clinical evaluation of the arched blade for cataract surgery (2006)

Editor, We read with interest the article by Kojima et al. (2005) on corneal phacoemulsification incision with an innovative arched blade. Postoperative wound integrity, optical and refractive outcomes are the major study parameters. Nevertheless, one of the potential untoward complications pertaining to this new wound construction technique deserves further discussion. As pointed out by authors, the main surgical benefits of this arched corneal wound stem from tight apposition between the wound slips, less distortion by the phaco tip and better self-sealing of the wound (Kojima et al. 2005). However, overly extreme tightness of the arched corneal wound, paradoxically, can lead to dreadful postoperative corneal wound thermal injury or burn. Even in conventional corneal phacoemulsification wound construction, thermal wound injury is an under-reported complication and can happen with experienced surgeons (Chang et al. 2002). Corneal wound thermal injury could result in severe wound gapping, wound leakage, endophthalmitis, persistent fistula formation and high postoperative astigmatism, requiring corrective refractive surgery or even penetrating keratoplasty (Chang et al. 2002; Sippel & Pineda 2002). Lack of effective irrigation and aspiration fluid flow with impaired heat dissipation around the phaco tip is believed to be the cause of unexpected thermal wound injury (Ernest et al. 2001; Chang et al. 2002). In the face of a tight corneal wound such as the proposed arched wound, the excessive encroachment of the wound may produce undue irrigation-sleeve compression, precluding the normal fluid flux cooling mechanism (Chang et al. 2002). Interestingly, most phaco wound burns cluster in those with dense cataracts as higher phaco energy is usually needed in the face of a hard nucleus (Chang et al. 2002). Kojima et al. (2005) did not report any problem with wound integrity after phacoemulsification. We would like to learn from the authors whether they consider the incidence of phaco wound burn would be unusually high in the event of a tight arched corneal incision if the same technique were to be used in patients with dense cataracts.
Initial experience with percutaneous edge-to-edge transcatheter mitral valve repair in a tertiary medical center in Taiwan (2017)

Trans-catheter edge-to-edge mitral valve repairs are safe and effective in Asians with symptomatic SMR, regarding the improvements of clinical symptoms and exercise capacities. MitraClips is also associated with reverse remodeling of pulmonary hypertension and left ventricular size in patients with SMR.