gebhart/patrepeval huggingface dataset:
Store-Operated CRAC Channels Regulate Gene Expression and Proliferation in Neural Progenitor Cells (2014)

Calcium signals regulate many critical processes during vertebrate brain development including neurogenesis, neurotransmitter specification, and axonal outgrowth. However, the identity of the ion channels mediating Ca(2+) signaling in the developing nervous system is not well defined. Here, we report that embryonic and adult mouse neural stem/progenitor cells (NSCs/NPCs) exhibit store-operated Ca(2+) entry (SOCE) mediated by Ca(2+) release-activated Ca(2+) (CRAC) channels. SOCE in NPCs was blocked by the CRAC channel inhibitors La(3+), BTP2, and 2-APB and Western blots revealed the presence of the canonical CRAC channel proteins STIM1 and Orai1. Knock down of STIM1 or Orai1 significantly diminished SOCE in NPCs, and SOCE was lost in NPCs from transgenic mice lacking Orai1 or STIM1 and in knock-in mice expressing the loss-of-function Orai1 mutant, R93W. Therefore, STIM1 and Orai1 make essential contributions to SOCE in NPCs. SOCE in NPCs was activated by epidermal growth factor and acetylcholine, the latter occurring through muscarinic receptors. Activation of SOCE stimulated gene transcription through calcineurin/NFAT (nuclear factor of activated T cells) signaling through a mechanism consistent with local Ca(2+) signaling by Ca(2+) microdomains near CRAC channels. Importantly, suppression or deletion of STIM1 and Orai1 expression significantly attenuated proliferation of embryonic and adult NPCs cultured as neurospheres and, in vivo, in the subventricular zone of adult mice. These findings show that CRAC channels serve as a major route of Ca(2+) entry in NPCs and regulate key effector functions including gene expression and proliferation, indicating that CRAC channels are important regulators of mammalian neurogenesis.
P1‐040: Quantitative comparison of dense‐core amyloid plaque burdens in Alzheimer's disease patients and amyloid precursor protein transgenic mice (2015)

The role of amyloid plaques in Alzheimer's disease (AD) remains controversial. Transgenic mice expressing human amyloid precursor protein (APP) with AD-linked mutations provide a toolkit for studying the effects of amyloidosis. However, different lines of mice vary greatly in their extents of plaque deposition. We here provide the first direct quantitative comparison of plaque deposition in four lines of APP transgenic mice and human AD brain. Using stereology-based methods, we quantified the areal fraction occupied by Thioflavin S-positive (ThioS+) plaques in the cortex and hippocampus of mice throughout the lifespan, and compared these values with plaque burdens in the frontal, temporal and parietal cortices of subjects from the Nun Study who were clinically and pathologically diagnosed with AD. ThioS+ plaques were present in 3-month 5XFAD mice and in 8-month APPSwePS1ΔE9 mice, but first appeared between 10 and 13 months of age in Tg2576 mice, and between 12 and 14 months in rTg9191 mice, a recently-developed regulatable line expressing human APP695 with the Swedish and London mutations. At 21 months of age, cortical plaque burdens reached 4.93% + 0.40% (mean + S.E.M., N = 3 mice; applies to all reported plaque burdens in mice), 1.59% + 0.43%, and 0.36% + 0.04% in APPSwePS1ΔE9, Tg2576, and rTg9191 mice, respectively; in 5XFAD mice, plaque burdens had already reached 6.13% + 0.34% at 15 months, the oldest age studied in this line. Hippocampal plaque burdens at 21 months were 3.29% + 0.32%, 0.94% + 0.20%, and 0.35% + 0.12% in APPSwePS1ΔE9, Tg2576, and rTg9191 mice, respectively; hippocampal plaque burden was 4.46% + 0.27% in 15-month 5XFAD mice. In human AD cortex, the ThioS+ plaque burden was 0.17% + 0.06% (composite of cortical regions, mean +S.E.M., N = 6 subjects; range 0.07% - 0.37%). Plaque burdens in transgenic mice can range from levels approximating those measured in human AD brains to more than an order of magnitude higher than those levels. The quantitative relationships between amyloidosis in humans and animal models should be considered when selecting the transgenic line and age to use to address each specific research question.
Bioactive Cytidine Deaminase, an Inhibitor of Granulocyte‐Macrophage Colony‐Forming Cells, Is Massively Released in Fulminant Meningococcal Sepsis (2000)

Cytidine deaminase (CDD) catalyzes the hydrolytic deamination of cytidine, which thereby is converted to uridine. CDD is found in serum and different tissues, with particularly high concentrations in polymorphonuclear neutrophils (PMN). We measured the CDD levels in plasma from patients with systemic meningococcal disease. Thirty-seven patients had significantly higher plasma levels of CDD than did 29 healthy control subjects (P=.0001). CDD levels in plasma or serum increased from a median of 96 ng/mL in healthy control subjects to medians of 168 ng/mL in patients without persistent shock (n=23; P=.001) and 422 ng/mL in patients with fulminant meningococcal septicemia (n=14; P=.0001). In most patients with fulminant septicemia, CDD levels in plasma increased during the first 3-53 h after the initiation of therapy (P=.003). CDD alone had no immediate harmful effect when injected into mice during a 4-day period. CDD may modulate the stimulatory effect of colony-stimulating factors on PMN in patients.
The Crustal Stress Field of Northern Chile (2021)

Earth and Space Science Open Archive This preprint has been submitted to and is under consideration at Geophysical Research Letters. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more about preprints preprintOpen AccessYou are viewing the latest version by default [v1]The Crustal Stress Field of Northern ChileAuthorsCarlosHerreraiDJohn FCassidyiDStan EDossoiDJanDettmerWasjaBlochiDChristianSippliDPabloSalazariDSee all authors Carlos HerreraiDCorresponding Author• Submitting AuthorUniversity of VictoriaiDhttps://orcid.org/0000-0002-1222-7742view email addressThe email was not providedcopy email addressJohn F CassidyiDNatural Resources CanadaiDhttps://orcid.org/0000-0002-9234-4884view email addressThe email was not providedcopy email addressStan E DossoiDUniversity of VictoriaiDhttps://orcid.org/0000-0003-2384-7370view email addressThe email was not providedcopy email addressJan DettmerUniversity of Calgaryview email addressThe email was not providedcopy email addressWasja BlochiDFreie Universität BerliniDhttps://orcid.org/0000-0002-0341-4925view email addressThe email was not providedcopy email addressChristian SippliDInstitute of Geophysucs, Czech Academy of SciencesiDhttps://orcid.org/0000-0003-4130-6340view email addressThe email was not providedcopy email addressPablo SalazariDUniversidad Catolica del NorteiDhttps://orcid.org/0000-0002-7496-705Xview email addressThe email was not providedcopy email address
THE EFFECTS OF SHORT TERM VIBRATION ON GRIP STRENGTH, SENSATION, AND CIRCULATION (1995)

Philadelphia College of Pharmacy & Science, Philadelphia, PA 19104 and Widener University, Institute for Physical Therapy Education, Chester, PA 19013.
Cell Adhesion onto Highly Curved Surfaces: One‐Step Immobilization of Human Erythrocyte Membranes on Silica Beads (2003)

This paper deals with single-step, orientation-selective immobilization of human erythrocyte membranes on bare silica beads with different topographies: 1) solid (nonporous) silica beads with a diameter of 3 microns and 2) porous silica beads with a diameter of 5 microns. Erythrocyte membranes were immobilized onto beads simply by incubation, without sonication or osmotic lysis. Membrane orientation before and after immobilization was identified with two immunofluorescence labels: 1) the extracellular part of glycophorin can be labeled with a first monoclonal antibody and a second polyclonal antibody with fluorescence dyes (outside label), while 2) the cytoplasmic domain of Band 3 can be recognized with a first monoclonal antibody and a second fluorescent polyclonal antibody (inside label). Adherent erythrocytes on the beads all ruptured, inverted the asymmetric orientation of the membrane, and selectively exposed their cytoplasmic domain. The surface topography did not influence the orientation or the amount of immobilized membrane. On the other hand, the fact that no adsorption or rupture of erythrocytes could be observed on planar quartz substrates suggests a significant influence of contact curvature on adhesion energy.
Cyanocarbazole Derivatives for High‐Performance Electroluminescent Devices (2004)

Abstract 3‐Cyano‐9‐diarylamino carbazoles have been synthesized. These new compounds emit in the blue to green region. Double‐layer electroluminescent devices using these compounds as the hole‐transport/emitting materials are highly efficient. Two of the compounds can be fabricated into single‐layer devices with good performance. Green‐ and blue‐emitting devices with good performance were also fabricated using one of the compounds as the hole‐injection layer.
Graphene-Wrapped Polyaniline Nanowire Arrays on Nitrogen-Doped Carbon Fabric as Novel Flexible Hybrid Electrode Materials for High-Performance Supercapacitor (2014)

We report the synthesis of reduced graphene oxide (RGO) sheet wrapped polyaniline (PANI) nanowire arrays grown on nitrogen-doped carbon fiber cloth (eCFC). The RGO coating layer is important to accommodate volume change and mechanical deformation of the coated PANI nanowires arrays during the long-term charge/discharge processes. The resulting hierarchical symmetric supercapacitor based on RGO/PANI/eCFC composites shows an enhanced capacitive behavior with a maximum energy density of 25.4 Wh kg(-1), a maximum power density of 92.2 kW kg(-1) and a specific capacitance of 1145 F g(-1), which is higher than that of PANI/eCFC (1050 F g(-1)) and GO/PANI/eCFC (940 F g(-1)). Moreover, the assembled supercapacitor exhibits excellent charge/discharge rates and a good cycling stability, retaining over 94% of its initial capacitance after 5000 cycles.
Interference Alignment and the Degrees of Freedom of Wireless $X$ Networks (2009)

We explore the degrees of freedom of M times N user wireless X networks, i.e., networks of M transmitters and N receivers where every transmitter has an independent message for every receiver. We derive a general outer bound on the degrees of freedom region of these networks. When all nodes have a single antenna and all channel coefficients vary in time or frequency, we show that the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">total</i> number of degrees of freedom of the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</i> network is equal to [(MN)/(M+N-1)] per orthogonal time and frequency dimension. Achievability is proved by constructing interference alignment schemes for X networks that can come arbitrarily close to the outer bound on degrees of freedom. For the case where either M=2 or N=2 we find that the degrees of freedom characterization also provides a capacity approximation that is accurate to within O(1) . For these cases the degrees of freedom outer bound is exactly achievable.
Systems-level analyses of protein-protein interaction network dysfunctions via epichaperomics identify cancer-specific mechanisms of stress adaptation (2023)

Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based 'omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks.
Fat Transplantation and Facial Contour (1998)

Injection of adipose tissue into corporal depressions to improve contour is not a new procedure. According to the literature, the grafted fat undergoes ischemia, producing a local inflammatory process and reabsorption of part of the injected volume, and the desired result is not achieved. Starting from the premise that vascular insufficiency occurs in the core of grafted tissue, leading to reabsorption, the authors of this paper studied the outcome of injection of small volumes of fat into facial depressions. The subjects, 16 patients with facial depressions (12 with Romberg's syndrome and 4 with lupus), were subjected to small volumes of adipose tissue grafting. Three to seven sessions of fat grafting were necessary to obtain a uniform facial contour. The interval between each procedure was 2–3 months. Ultrasonography and biopsies were performed. The cutaneous ultrasound demonstrated viable adipose tissue, confirming the pathological result.
Kinetics and Mechanism of Iron(III) Complexation by Ferric Binding Protein:  The Role of Phosphate (2004)

Iron transport across the periplasmic space to the cytoplasmic membrane of certain Gram-negative bacteria is mediated by a ferric binding protein (Fbp). This requires Fe(3+) loading of Fbp at the inner leaflet of the outer membrane. A synergistic anion is required for tight Fe(3+) sequestration by Fbp. Although phosphate fills this role in the protein isolated from bacterial cell lysates, nitrilotriacetate anion (NTA) can also satisfy this requirement in vitro. Here, we report the kinetics and mechanism of Fe(3+) loading of Fbp from Fe(NTA)(aq) in the presence of phosphate at pH 6.5. The reaction proceeds in four kinetically distinguishable steps to produce Fe(3+)Fbp(PO(4)) as a final product. The first three steps exhibit half-lives ranging from ca. 20 ms to 0.5 min, depending on the concentrations, and produce Fe(3+)Fbp(NTA) as an intermediate product of significant stability. The rate for the first step is accelerated with an increasing phosphate concentration, while that of the third step is retarded by phosphate. Conversion of Fe(3+)Fbp(NTA) to Fe(3+)Fbp(PO(4)) in the fourth step is a slow process (half-life approximately 2 h) and is facilitated by free phosphate. A mechanism for the Fe(3+)-loading process is proposed in which the synergistic anions, phosphate and NTA, play key roles. These data suggest that not only is a synergistic anion required for tight Fe(3+) sequestration by Fbp, but also the synergistic anion plays a critical role in the process of inserting Fe(3+) into the Fbp binding site.
Gel electrophoresis of nucleic acids: a practical approach (1982)

Gel electrophoresis of RNA, D.Grierson gel electrophoresis of DNA, P.G.Sealey pulsed field gel electrophoresis, R.Anand the electrophoresis of synthetic oligonucleotides, J.W.Efcavitch two-dimensional gel electrophoresis of nucleic acids, R de Wachter et al gel retardation of nucletic acid-protein interactions, M.M.Garner the analysis of sequence-specific DNA-binding proteins in cell extracts, G.H.Goodwin electrophoresis of nucleosomes, R.H.Nicholas gel electrophoresis of ribonuceotides, A.E.Dahlberg and P.J.Grabowski.
Lossless image compression using pixel reordering (2004)

Lossless image compression techniques typically consider images to be a sequence of pixels in row major order. The processing of each pixel consists of two separate operations. The first step forms a prediction as to the numeric value of the next pixel. Typical predictors involve a linear combination of neighboring pixel values, possibly in conjunction with an edge detection heuristic. In the second step, the difference between that prediction and the actual value of the next pixel is coded. In high-performance mechanisms such as JPEG-LS, the error differential is coded in a conditioning context established by a possibly-different set of neighboring pixels. A per-context arithmetic, minimum-redundancy, or Rice coder completes the processing of each pixel.In this paper we explore pixel reordering as a way of reducing the start-up (or learning) cost associated with each context. By permuting the prediction errors into an order that reflects the assessed volatility of the conditioning context, we are able to use a single coding context, with the changing probability estimates captured by local adaptation in the coder. In this sense, our proposal has elements in common with the Burrows-Wheeler text compression mechanism. The result is a lossless compression implementation that achieves excellent compression rates.
FGF21 counteracts alcohol intoxication by activating the noradrenergic nervous system (2023)

Animals that consume fermenting fruit and nectar are at risk of exposure to ethanol and the detrimental effects of inebriation. In this report, we show that the hormone FGF21, which is strongly induced by ethanol in murine and human liver, stimulates arousal from intoxication without changing ethanol catabolism. Mice lacking FGF21 take longer than wild-type littermates to recover their righting reflex and balance following ethanol exposure. Conversely, pharmacologic FGF21 administration reduces the time needed for mice to recover from ethanol-induced unconsciousness and ataxia. FGF21 did not counteract sedation caused by ketamine, diazepam, or pentobarbital, indicating specificity for ethanol. FGF21 mediates its anti-intoxicant effects by directly activating noradrenergic neurons in the locus coeruleus region, which regulates arousal and alertness. These results suggest that this FGF21 liver-brain pathway evolved to protect against ethanol-induced intoxication and that it might be targeted pharmaceutically for treating acute alcohol poisoning.
New virus‐specific T‐helper epitopes of foot‐and‐mouth disease viral VP1 protein (1993)

Immunogenicity studies of synthetic peptides from different regions of VP1 protein of foot-and-mouth disease virus strain A22 revealed the following active fragments: 39-61, 50-69, 135-159, 175-189, 170-189 and 197-213. Testing of virus neutralizing antibody production in rabbits primed by peptides and then inoculated by the virus showed that only peptides 135-159 and 170-189 were able to induce the functional T-cell helper activity. Localization of virus-specific T-cell recognition sites in sequences 135-159 and 170-189 was confirmed in in vitro recognition experiments of the virus by peptide activated mice lymphocytes.
Blind Men and the Elephant: Detecting Evolving Groups In Social News (2013)

We propose an automated and unsupervised methodology for a novel summarization of group behavior based on content preference. We show that graph theoretical community evolution (based on similarity of user preference for content) is effective in indexing these dynamics. Combined with text analysis that targets automatically-identified representative content for each community, our method produces a novel multi-layered representation of evolving group behavior. We demonstrate this methodology in the context of political discourse on a social news site with data that spans more than four years and find coexisting political leanings over extended periods and a disruptive external event that lead to a significant reorganization of existing patterns. Finally, where there exists no ground truth, we propose a new evaluation approach by using entropy measures as evidence of coherence along the evolution path of these groups. This methodology is valuable to designers and managers of online forums in need of granular analytics of user activity, as well as to researchers in social and political sciences who wish to extend their inquiries to large-scale data available on the web.
TABLE 1 from Optimizing Precision Medicine for Breast Cancer Brain Metastases with Functional Drug Response Assessment (2023)

&lt;p&gt;GSEA using the Hallmark gene sets comparing the paired brain metastases and primary breast tumors. Gene sets with FDR &lt; 0.05&lt;/p&gt;
The Abelson tyrosine kinase and the Nedd4-family ubiquitin ligase Suppressor of Deltex converge at the Notch PPxY motif to regulate endosomal trafficking and signaling (2020)

Abstract The conserved Notch signaling pathway coordinates diverse cellular processes during animal development. Unlike most cell surface receptors that use a cytoplasmic cascade to amplify and diversify signaling dynamics, Notch itself transduces external cues directly to the nucleus. How appropriate signaling dynamics and transcriptional responses are achieved with this pathway architecture remains unclear. Here, we report that the cytoplasmic tyrosine kinase Abelson (Abl) fine-tunes Notch signaling by regulating Notch endocytic trafficking. We show that Abl can directly phosphorylate a PPxY motif important for Nedd4-family ubiquitin-ligase-mediated transfer of Notch into degradative endosomal compartments. Consistent with this, loss of Abl or inhibition of its kinase activity results in aberrant endosomal accumulation of Notch, while mutation of the PPxY tyrosine renders Notch insensitive to such regulation. Phenotypic and genetic interaction studies in the wing, together with parallel assays in cultured cells, show that loss or gain of Abl activity can respectively increase or decrease Notch output. We propose that the Notch PPxY motif operates as a molecular hub that integrates multiple post-translational modifications to regulate Notch trafficking and fine-tune signaling output.
AOBO<sub>4</sub> Type Electrode Materials for Rechargeable Lithium Battery (1993)

Materialswith many vacancies or interstices in thcir structures have a possibility of apPlication as a cathode foHechargeable lithium battery This type of inorganic materials have layered structuresframework structuresand some
Energy Consumption of Next-Generation Optical-Wireless Converged Networks (2012)

We compare three different plausible architectures for next-generation optical-wireless convergence in energy conservation viewpoint. Our analysis provides insight into QoS rich optical-wireless converged network architectures that preserve energy efficiency.
Optical evidence for transient photoinduced magnetization inLa0.7Ca0.3MnO3 (2005)

Pump-probe Kerr spectroscopy reveals evidence for transient photoinduced magnetization (PIM) near ${T}_{c}$ in the colossally magnetoresistive manganite ${\mathrm{La}}_{0.7}{\mathrm{Ca}}_{0.3}\mathrm{Mn}{\mathrm{O}}_{3}$. For temperatures above ${T}_{c}$, the PIM signature reaches full strength at the field-driven magnetic phase transition, while below ${T}_{c}$ it exhibits a magnetic activation threshold of $\ensuremath{\sim}0.5\phantom{\rule{0.3em}{0ex}}\mathrm{T}$. We compare the temperature dependence of the effect with diffuse spin scattering previously measured with neutrons and discuss these findings in the context of phase separation near ${T}_{c}$.
A Direct RF-to-Information Converter for reception and wideband interferer detection employing pseudo-random LO modulation (2017)

The Direct RF-to-Information Converter (DRF2IC) unifies high sensitivity signal reception, narrowband spectrum sensing and energy-efficient wideband interferer detection into a fast-reconfigurable and easily scalable architecture. In reception mode, the DRF2IC RF front-end (RFFE) consumes 46.5mW and delivers 40MHz RF bandwidth, 41.5dB conversion gain, 3.6dB NF and -2dBm B1dB. 72dB out-of-channel blocker rejection is achieved in narrowband sensing mode. In compressed sensing wideband interferer detection mode, 66dB operational dynamic range, 40dB instantaneous dynamic range, 1.43GHz instantaneous bandwidth (IBW) is demonstrated and 6 interferers scattered over 1.26GHz are detected in 1.2uS consuming 58.5mW.