gebhart/patrepeval huggingface dataset:
17β-Estradiol Inhibits MMP-9 and SUR1/TrpM4 Expression and Activation and Thereby Attenuates BSCB Disruption/Hemorrhage After Spinal Cord Injury in Male Rats (2015)

Blood-spinal cord barrier (BSCB) disruption and progressive hemorrhage after spinal cord injury (SCI) lead to secondary injury and the subsequent apoptosis and/or necrosis of neuron and glia, causing permanent neurological deficits. In this study, we examined the effect of 17β-estradiol (E2) on BSCB breakdown and hemorrhage as well as subsequent inflammation after SCI. After a moderate contusion injury at the 9th thoracic segment of spinal cord, E2 (300 μg/kg) was administered by iv injection immediately after SCI, and the same dose of E2 was then administered 6 and 24 hours after injury. Our data show that E2 attenuated BSCB permeability and hemorrhage and reduced the infiltration of neutrophils and macorphages after SCI. Consistent with this finding, the expression of inflammatory mediators was significantly reduced by E2. Furthermore, E2 treatment significantly inhibited the expression of sulfonylurea receptor 1 and transient receptor potential melastatin 4 after injury, which are known to mediate hemorrhage at an early stage after SCI. Moreover, the expression and activation of matrix metalloprotease-9 after injury, which is known to disrupt BSCB, and the degradation of tight junction proteins, such as zona occludens-1 and occludin, were significantly inhibited by E2 treatment. Furthermore, the protective effects of E2 on BSCB disruption and functional improvement were abolished by an estrogen receptor antagonist, ICI 182780 (3 mg/kg). Thus, our study provides evidence that the neuroprotective effect of E2 after SCI is, in part, mediated by inhibiting BSCB disruption and hemorrhage through the down-regulation of sulfonylurea receptor 1/transient receptor potential melastatin 4 and matrix metalloprotease-9, which is dependent on estrogen receptor.
73‐2: A Wide View Glass‐less 3D Display with Head‐Tracking System for Horizontal and Vertical Directions (2016)

In this study, a glass‐less 3D display with a head‐tracking system for horizontal and vertical directions was developed. Based on the viewer's head position, the barrier pitch and the position of the barrier aperture were optimized. This resulted in the expansion of the 3D viewing zone in a vertical direction from the display surface to the distance of “320 – 1016 mm”, and in the horizontal direction from the center of the display at a “±267 mm” distance.
Integration of functional oxides on SOI for agile silicon photonics (2015)

Photonic devices enabling light modulation and switching are of major importance for modern telecommunication. Silicon-based electro-optic modulators are intensively investigated because of their direct compatibility to CMOS fabrication processes. However, the performances of Si based modulators are intrinsically limited, in terms of data transmission rate and energy consumption. To overcome this limitation, ferroelectric oxides with naturally strong electro-optical coefficients combined to small footprint could be ideal candidates for high-speed modulators. We have designed an integration scheme to implement these materials on SOI photonic platform, for 1.55 μm Datacom systems. Monolithic integration of ferroelectric oxides on SOI via SrTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> templates is presented. The devices are based on a horizontal (crystalline Si / ferroelectric oxide / amorphous Si) slot waveguide configuration.
Lipidomic profiling reveals age-dependent changes in complex plasma membrane lipids that regulate neural stem cell aging (2022)

Abstract The aging brain exhibits a decline in the regenerative populations of neural stem cells (NSCs), which may underlie age-associated defects in sensory and cognitive functions 1–6 . While mechanisms that restore old NSC function have started to be identified 7–23 , the role of lipids – especially complex lipids – in NSC aging remains largely unclear. Using lipidomic profiling by mass spectrometry, we identify age-related lipidomic signatures in young and old quiescent NSCs in vitro and in vivo . These analyses reveal drastic changes in several complex membrane lipid classes, including phospholipids and sphingolipids in old NSCs. Moreover, poly-unsaturated fatty acids (PUFAs) strikingly increase across complex lipid classes in quiescent NSCs during aging. Age-related changes in complex lipid levels and side chain composition are largely occurring in plasma membrane lipids, as revealed by lipidomic profiling of isolated plasma membrane vesicles. Experimentally, we find that aging is accompanied by modifications in plasma membrane biophysical properties, with a decrease in plasma membrane order in old quiescent NSCs in vitro and in vivo . To determine the functional role of plasma membrane lipids in aging NSCs, we performed genetic and supplementation studies. Knockout of Mboat2 , which encodes a phospholipid acyltransferase, exacerbates age-related lipidomic changes in old quiescent NSCs and impedes their ability to activate. As Mboat2 expression declines with age, Mboat2 deficiency may drive NSC decline during aging. Interestingly, supplementation of plasma membrane lipids derived from young NSCs boosts the ability of old quiescent NSCs to activate. Our work could lead to lipid-based strategies for restoring the regenerative potential of NSCs in old individuals, which has important implications for countering brain decline during aging.
Triclinic Fluid Order (2010)

Among the condensed phases, those of lowest point group symmetry are the triclinic crystals, which have only the identity element or the identity and inversion elements. Such low symmetry is stabilized by the specificity of molecular interaction, which is weakened with increasing disorder, so that known phases with fluid degrees of freedom are more symmetric. Here we report triclinic order, appearing as a broken symmetry in a single, isolated, fluid smectic liquid crystal layer freely suspended in air, showing that none of its principal dielectric axes lies either normal or parallel to the layer plane.
Tetrahydroisoquinoline CXCR4 Antagonists Adopt a Hybrid Binding Mode within the Peptide Subpocket of the CXCR4 Receptor (2018)

The rationale for the structural and mechanistic basis of a tetrahydroisoquinoline (THIQ) based series of CXCR4 antagonists is presented. Using the previously reported crystal structures which reveal two distinct binding sites of CXCR4 defined as the small molecule (IT1t or minor) binding pocket and peptide (CVX15 or major) binding pocket, we hypothesized our THIQ small molecule series could bind like either molecule in these respective receptor configurations (IT1t versus CVX15 based poses). To this end, a thorough investigation was performed through a combination of receptor mutation studies, medicinal chemistry, biological testing, conformational analysis, and flexible docking. Our findings showed that the CVX15 peptide-based CXCR4 receptor complexes (red pose) were consistently favored over the small molecule IT1t based CXCR4 receptor configurations (blue pose) to correctly explain the computational and mutational studies as well as key structural components of activity for these small molecules.
A divide and conquer approach for web services location allocation problem (2021)

The appropriate choice of locations for the deployment of web services is of significant importance. The placement of a web service closer to user centers minimizes the response time, however deployment cost may increase. The placement becomes more challenging when multiple web services are involved. In this paper, we address the problem of placing multiple web services with the aim of simultaneously minimizing conflicting objectives of total deployment cost and network latency. We solve the location allocation problem for each web service independently and combine the resulting solutions using a novel merge algorithm. We demonstrate through extensive experiments and simulations that the proposed approach is not only computationally efficient but also produces good quality solutions. Further, the proposed merge algorithm is generic and could be easily adapted to tackle any bi-objective optimization problem that can be decomposed into non-overlapping sub-problems.
Learning-In-The-Loop Optimization: End-To-End Control And Co-Design Of Soft Robots Through Learned Deep Latent Representations (2019)

Soft robots have continuum solid bodies that can deform in an infinite number of ways. Controlling soft robots is very challenging as there are no closed form solutions. We present a learning-in-the-loop co-optimization algorithm in which a latent state representation is learned as the robot figures out how to solve the task. Our solution marries hybrid particle-grid-based simulation with deep, variational convolutional autoencoder architectures that can capture salient features of robot dynamics with high efficacy. We demonstrate our dynamics-aware feature learning algorithm on both 2D and 3D soft robots, and show that it is more robust and faster converging than the dynamics-oblivious baseline. We validate the behavior of our algorithm with visualizations of the learned representation.
Stanford DRO Toolkit: Digital Reference Objects for Standardization of Radiomic Features (2020)

Several institutions have developed image feature extraction software to compute quantitative descriptors of medical images for radiomics analyses. With radiomics increasingly proposed for use in research and clinical contexts, new techniques are necessary for standardizing and replicating radiomics findings across software implementations. We have developed a software toolkit for the creation of 3D digital reference objects with customizable size, shape, intensity, texture, and margin sharpness values. Using user-supplied input parameters, these objects are defined mathematically as continuous functions, discretized, and then saved as DICOM objects. Here, we present the definition of these objects, parameterized derivations of a subset of their radiomics values, computer code for object generation, example use cases, and a user-downloadable sample collection used for the examples cited in this paper.
Inhibition of SGLT-2 rescues bone marrow cell traffic for vascular repair. Role of glucose control and ketogenesis (2021)

The mechanisms whereby sodium-glucose cotransporter-2 inhibitors (SGLT2i) improve cardiovascular outcomes in people with diabetes are incompletely understood. Recent studies show that SGLT2i may increase the levels of circulating cells with vascular regenerative capacity, at least in part by lowering glycemia. Here, we used mice with streptozotocin-induced diabetes treated with the SGLT2i dapagliflozin at a dose that reduced glucose levels by ~20%. Dapagliflozin improved the diabetes-associated defect of hematopoietic stem cell mobilization after stimulation with G-CSF. Dapagliflozin rescued the traffic of bone marrow (BM)-derived cells to injured carotid arteries and improved endothelial healing in diabetic mice. Defective homing of CD49d&lt;sup&gt;+&lt;/sup&gt; granulocytes was causally linked with impaired endothelial repair and was reversed by dapagliflozin. The effects of dapagliflozin were mimicked by a similar extent of glucose reduction achieved with insulin therapy, and by a ketone drink that artificially elevated β-hydroxybutyrate. Inhibition of endothelial repair by resident cells using the CXCR4 antagonist AMD3100 did not abolish the vascular effect of dapagliflozin, indirectly supporting that endothelial healing by dapagliflozin was mediated by recruitment of circulating cells. In summary, we show that dapagliflozin improved the traffic of BM-derived hematopoietic cells to the site of vascular injury, providing a hitherto unappreciated mechanism of vascular protection.
A new stochastic image model based on Markov random fields and its application to texture modeling (2011)

Stochastic image modeling based on conventional Markov random fields is extensively discussed in the literature. A new stochastic image model based on Markov random fields is introduced in this paper which overcomes the shortcomings of the conventional models easing the computation of the joint density function of images. As an application, this model is used to generate texture patterns. The lower computational complexity and easily controllable parameters of the model makes it a more useful model as compared to the conventional Markov random field-based models.
Olfactory receptor accessory proteins play crucial roles in receptor function and gene choice (2017)

Each of the olfactory sensory neurons (OSNs) chooses to express a single G protein-coupled olfactory receptor (OR) from a pool of hundreds. Here, we show the receptor transporting protein (RTP) family members play a dual role in both normal OR trafficking and determining OR gene choice probabilities. <i>Rtp1</i> and <i>Rtp2</i> double knockout mice (RTP1,2DKO) show OR trafficking defects and decreased OSN activation. Surprisingly, we discovered a small subset of the ORs are expressed in larger numbers of OSNs despite the presence of fewer total OSNs in RTP1,2DKO. Unlike typical ORs, some overrepresented ORs show robust cell surface expression in heterologous cells without the co-expression of RTPs. We present a model in which developing OSNs exhibit unstable OR expression until they choose to express an OR that exits the ER or undergo cell death. Our study sheds light on the new link between OR protein trafficking and OR transcriptional regulation.
Collective cell migration of fibroblasts is affected by horizontal vibration of the cell culture dish (2020)

Regulating the collective migration of cells is an important issue in bioengineering. Enhancing or suppressing cell migration and controlling the migration direction is useful for various physiological phenomena such as wound healing. Several methods of migration regulation based on different mechanical stimuli have been reported. While vibrational stimuli, such as sound waves, show promise for regulating migration, the effect of the vibration direction on collective cell migration has not been studied in depth. Therefore, we fabricated a vibrating system that can apply horizontal vibration to a cell culture dish. Here, we evaluated the effect of the vibration direction on the collective migration of fibroblasts in a wound model comprising two culture areas separated by a gap. Results showed that the vibration direction affects the cell migration distance: vibration orthogonal to the gap enhances the collective cell migration distance while vibration parallel to the gap suppresses it. Results also showed that conditions leading to enhanced migration distance were also associated with elevated glucose consumption. Furthermore, under conditions promoting cell migration, the cell nuclei become elongated and oriented orthogonal to the gap. In contrast, under conditions that reduce the migration distance, cell nuclei were oriented to the direction parallel to the gap.
Synthesis, Photophysics, and Electrochemistry of Tetra(2‐thienyl)ethylene (TTE) Derivatives (2013)

Abstract We have synthesized a series of tetra(2‐thienyl)ethylene (TTE) derivatives, selectively functionalized at the thiophene α positions, either by a coupling procedure or by direct electrophilic substitution of the TTE system. Optical spectroscopy revealed that TTE shows orange emission (470 nm) in a diluted 2‐MeTHF matrix at 77 K and blue (420 nm) aggregation‐induced emission (AIE) in the solid state. An exhaustive electrochemical study afforded a full rationalization of the electronic properties in terms of the HOMO and LUMO energy levels and gaps, as well as localization and features of the redox centers with respect to TTE functionalization.
Publisher’s Note: “Sample-detector coupling in atomic resolution magnetic resonance diffraction” [J. Appl. Phys. 92, 7345 (2002)] (2003)

First Page
Effects of ultrasound on unicellular algae (1976)

The effect of ultrasonic irradiation (up to 3W/cm2 and 1 MHz of frequency) on unicellular algae is experimentally studied. It is unambiguously shown that the damage of the cells and their breakage is to be related to cavitation. The dynamics of the breakage is examined from the point of view of practical application. Subject Classification: [43]80.40; [43]35.75.
Complex reinnervation pattern after unilateral renal denervation in rats (2016)

Renal denervation (DNX) is a treatment for resistant arterial hypertension. Efferent sympathetic nerves regrow, but reinnervation by renal afferent nerves has only recently been shown in the renal pelvis of rats after unilateral DNX. We examined intrarenal perivascular afferent and sympathetic efferent nerves after unilateral surgical DNX. Tyrosine hydroxylase (TH), CGRP, and smooth muscle actin were identified in kidney sections from 12 Sprague-Dawley rats, to distinguish afferents, efferents, and vasculature. DNX kidneys and nondenervated kidneys were examined 1, 4, and 12 wk after DNX. Tissue levels of CGRP and norepinephrine (NE) were measured with ELISA and mass spectrometry, respectively. DNX decreased TH and CGRP labeling by 90% and 95%, respectively (P < 0.05) within 1 wk. After 12 wk TH and CGRP labeling returned to baseline with a shift toward afferent innervation (P < 0.05). Nondenervated kidneys showed a doubling of both labels within 12 wk (P < 0.05). CGRP content decreased by 72% [3.2 ± 0.3 vs. 0.9 ± 0.2 ng/gkidney; P < 0.05] and NA by 78% [1.1 ± 0.1 vs. 0.2 ± 0.1 pmol/mgkidney; P < 0.05] 1 wk after DNX. After 12 wk, CGRP, but not NE, content in DNX kidneys was fully recovered, with no changes in the nondenervated kidneys. The use of phenol in the DNX procedure did not influence this result. We found morphological reinnervation and transmitter recovery of afferents within 12 wk after DNX. Despite morphological evidence of sympathetic regrowth, NE content did not fully recover. These results suggest a long-term net surplus of afferent influence on the DNX kidney may be contributing to the blood pressure lowering effect of DNX.
Interleukin-1β Suppresses Retinoid Transactivation of Two Hepatic Transporter Genes Involved in Bile Formation (2000)

Cytokines have been implicated in the pathogenesis of inflammatory cholestasis. This is due to transcriptional down-regulation of hepatic transporters including the Na(+)/bile acid cotransporter, ntcp, and the multispecific organic anion exporter, mrp2. We have recently shown that ntcp suppression by lipopolysaccharide in vivo is caused by down-regulation of transactivators including the previously uncharacterized Footprint B-binding protein. Both the ntcp FpB element and the mrp2 promoter contain potential retinoid-response elements. We hypothesized that retinoic acid receptor (RAR) and retinoid X receptor (RXR) heterodimers would activate these two genes and that cytokines that reduce bile flow might do so by suppressing nuclear levels of these transactivators. Retinoid transactivation and interleukin-1beta down-regulation of the ntcp and mrp2 promoters were mapped to RXRalpha:RARalpha-response elements. Gel mobility shift assays demonstrated specific binding of RXRalpha:RARalpha heterodimers to the ntcp and mrp2 retinoid-response elements. The RXRalpha:RARalpha complex was down-regulated by IL-1beta in HepG2 cells. An unexpected finding was that an adjacent CAAT-enhancer-binding protein element was required for maximal transactivation of the ntcp promoter by RXRalpha:RARalpha. Taken together, these studies demonstrate regulation of two hepatobiliary transporter genes by RXRalpha:RARalpha and describe a mechanism which likely contributes to their down-regulation during inflammation.
Promoter CpG island methylation of RET predicts poor prognosis in stage II colorectal cancer patients (2014)

Improved prognostic stratification of patients with TNM stage II colorectal cancer (CRC) is desired, since 20-30% of high-risk stage II patients may die within five years of diagnosis. This study was conducted to investigate REarranged during Transfection (RET) gene promoter CpG island methylation as a possible prognostic marker for TNM stage II CRC patients. The utility of RET promoter CpG island methylation in tumors of stage II CRC patients as a prognostic biomarker for CRC related death was studied in three independent series (including 233, 231, and 294 TNM stage II patients, respectively) by using MSP and pyrosequencing. The prognostic value of RET promoter CpG island methylation was analyzed by using Cox regression analysis. In the first series, analyzed by MSP, CRC stage II patients (n = 233) with RET methylated tumors had a significantly worse overall survival as compared to those with unmethylated tumors (HRmultivariable = 2.51, 95%-CI: 1.42-4.43). Despite a significant prognostic effect of RET methylation in stage III patients of a second series, analyzed by MSP, the prognostic effect in stage II patients (n = 231) was not statistically significant (HRmultivariable = 1.16, 95%-CI 0.71-1.92). The third series (n = 294), analyzed by pyrosequencing, confirmed a statistically significant association between RET methylation and poor overall survival in stage II patients (HRmultivariable = 1.91, 95%-CI: 1.04-3.53). Our results show that RET promoter CpG island methylation, analyzed by two different techniques, is associated with a poor prognosis in stage II CRC in two independent series and a poor prognosis in stage III CRC in one series. RET methylation may serve as a useful and robust tool for clinical practice to identify high-risk stage II CRC patients with a poor prognosis. This merits further investigation.
Functional consequences of a germline mutation in the leucine‐rich repeat domain of NLRP3 identified in an atypical autoinflammatory disorder (2010)

This report is the first to describe a familial form of a cryopyrinopathy associated with a mutation outside of exon 3 of NLRP3. This finding, together with the known efficacy of anti-IL-1 treatments in these disorders, underlines the importance of screening all exons of NLRP3 in patients who present with atypical manifestations. In addition, the gain of function associated with this mutation in terms of activation of caspase 1 signaling was consistent with the observed inflammatory phenotype. Therefore, this study of the functional consequences of an LRR mutation sheds new light on the clinical relevance of in vitro assays.
Capacity limit of cognitive radio with dynamic frequency hopping under imperfect spectrum sensing (2012)

In this paper, we investigate the capacity limit of a single secondary user (SU) communication link in a cognitive radio system. An SU transmitter establishes the communication with its receiver by dynamically hopping in a frequency spectrum pool, and by sensing the spectrum to exploit the temporal communication opportunities. We characterize the performance of sensing by false-alarm and miss-detection probabilities. Firstly, focusing on a high channel input power region, we develop an upper bound on the SU capacity by assuming a Gaussian distributed output. A lower bound on the SU capacity is also derived using a Gaussian input. We then show that the lower bound closely approaches the upper bound at a high channel input power level. This means that the Gaussian input is nearly optimal in this case. Furthermore, we characterize the impact of primary user activities and sensing performance on the SU capacity by developing a closed-form tight approximation. Secondly, paying attention to a low channel input power region, we propose a genie-aided upper bound and a lower bound using the Gaussian input. By comparing these two bounds, a closed-form approximation to the capacity is developed and the near optimality of the Gaussian input is demonstrated. Finally, numerical results are provided to complement the theoretical discussion.