gebhart/patrepeval huggingface dataset:
Selective changes in laminin adhesion and alpha 6 beta 4 integrin regulation are associated with the initial steps in keratinocyte maturation. (1996)

In skin, the distribution of integrins is compartmentalized. Whereas the alpha 6 beta 4 integrin complex is polarized to the basal portion of proliferating cells in the basal layer juxtaposed to the basement membrane, alpha 3 beta 1 integrin receptors are localized on the cell surface surrounding basal and suprabasal cells, suggesting beta 1 integrins mediate both cell-matrix and cell-cell interactions. As initiation of maturation in skin is associated with the detachment of cells from the basement membrane, the early loss of alpha 6 beta 4, but not alpha 3 beta 1, integrin expression could be a determining factor in the transition from the proliferating to a differentiating keratinocyte. We have studied the regulation of adhesion potential and integrin expression during differentiation of mouse basal keratinocytes culture in 0.05 mM Ca2+ medium and induced to differentiate in 0.12 mM Ca2+ medium. Within 12-24 h after elevation of Ca2+, a selective loss of the alpha 6 beta 4 integrin complex is associated with the induction of the spinous cell marker keratin 1. This early differentiation phenotype coincides with loss of cell attachment mediated by alpha 6 beta 4 to laminins 1 and 5 but not a fibronectin or collagen IV. Selective loss of attachment to laminin is also detected in spinous cells isolated from newborn epidermis in vivo. The loss of alpha 6 and beta 4 protein expression is a consequence of transcriptional and posttranscriptional events, including reduction in mRNA transcripts, reduced synthesis of the alpha 6 protein, and enhanced processing of the alpha 6 and beta 4 chains as determined by Western blots and pulse-chase experiments in metabolically labeled keratinocytes. Selective processing of the beta 4 intracellular domain is detected before loss of beta 4 from the cell surface in basal keratinocytes, and this process is accelerated during differentiation. Whereas early keratinocyte maturation is linked to the selective loss of the alpha 6 beta 4 complex, loss of both beta 1 and beta 4 integrin mRNA and protein occurs as cells proceed to later stages in the differentiation program as induced by 0.5 mM Ca2+ or suspension culture. These conditions are characterized by accelerated expression of transglutaminase; reduced keratin 1 protein; loss of adhesion to fibronectin, laminin 1, laminin 5, and collagen IV; and rapid cell death. Contributing to the down-regulation of beta 1 integrins during terminal differentiation is a selective sensitivity of alpha 3 beta 1 but not alpha 6 beta 4 to down-regulation by transforming growth factors beta 1 and beta 2, factors that are also expressed differentially in normal skin. This study indicates that down-regulation of the alpha 6 beta 4 but not beta 1 integrins occurs during the initial steps of keratinocyte differentiation and is associated with detachment from the laminin matrix. Such changes could contribute an important signal to initiate the process of terminal keratinocyte differentiation.
Supplemental Figure Legends and Figures from Holo-Retinol–Binding Protein and Its Receptor STRA6 Drive Oncogenic Transformation (2023)

&lt;p&gt;Supplemental Figure legends and Figures Fig. S1: Levels of STRA6 and RBP in breast cancers Fig. S2: Effects of decreased STRA6 expression on oncogenic properties. Fig. S3: Immunoblots demonstrating variable RBP expression levels and effects on "wound healing". Fig. S4: Effects of decreased expression of RBP on oncogene expression.&lt;/p&gt;
Controlled quantum dot array segmentation via highly tunable interdot tunnel coupling (2022)

Recent demonstrations using electron spins stored in quantum dot array as qubits are promising for developing a scalable quantum computing platform. An ongoing effort is, therefore, aiming at the precise control of the quantum dot parameters in larger and larger arrays which represents a complex challenge. Partitioning of the system with the help of the inter-dot tunnel barriers can lead to a simplification for tuning and offers a protection against unwanted charge displacement. In a triple quantum dot system, we demonstrate a nanosecond control of the inter-dot tunnel rate permitting to reach the two extreme regimes, large GHz tunnel coupling, and sub-Hz isolation between adjacent dots. We use this development to isolate a subpart of the array in a metastable configuration while performing charge displacement and readout in the rest of the system. The degree of control over tunnel coupling achieved in a unit cell should motivate future protocol development for tuning, manipulation, and readout including this capability.
Joint Rain Detection and Removal from a Single Image with Contextualized Deep Networks (2019)

Rain streaks, particularly in heavy rain, not only degrade visibility but also make many computer vision algorithms fail to function properly. In this paper, we address this visibility problem by focusing on single-image rain removal, even in the presence of dense rain streaks and rain-streak accumulation, which is visually similar to mist or fog. To achieve this, we introduce a new rain model and a deep learning architecture. Our rain model incorporates a binary rain map indicating rain-streak regions, and accommodates various shapes, directions, and sizes of overlapping rain streaks, as well as rain accumulation, to model heavy rain. Based on this model, we construct a multi-task deep network, which jointly learns three targets: the binary rain-streak map, rain streak layers, and clean background, which is our ultimate output. To generate features that can be invariant to rain steaks, we introduce a contextual dilated network, which is able to exploit regional contextual information. To handle various shapes and directions of overlapping rain streaks, our strategy is to utilize a recurrent process that progressively removes rain streaks. Our binary map provides a constraint and thus additional information to train our network. Extensive evaluation on real images, particularly in heavy rain, shows the effectiveness of our model and architecture.
Mechanosensitive control of plant growth: bearing the load, sensing, transducing, and responding (2015)

As land plants grow and develop, they encounter complex mechanical challenges, especially from winds and turgor pressure. Mechanosensitive control over growth and morphogenesis is an adaptive trait, reducing the risks of breakage or explosion. This control has been mostly studied through experiments with artificial mechanical loads, often focusing on cellular or molecular mechanotransduction pathway. However, some important aspects of mechanosensing are often neglected. (i) What are the mechanical characteristics of different loads and how are loads distributed within different organs? (ii) What is the relevant mechanical stimulus in the cell? Is it stress, strain, or energy? (iii) How do mechanosensing cells signal to meristematic cells? Without answers to these questions we cannot make progress analyzing the mechanobiological effects of plant size, plant shape, tissue distribution and stiffness, or the magnitude of stimuli. This situation is rapidly changing however, as systems mechanobiology is being developed, using specific biomechanical and/or mechanobiological models. These models are instrumental in comparing loads and responses between experiments and make it possible to quantitatively test biological hypotheses describing the mechanotransduction networks. This review is designed for a general plant science audience and aims to help biologists master the models they need for mechanobiological studies. Analysis and modeling is broken down into four steps looking at how the structure bears the load, how the distributed load is sensed, how the mechanical signal is transduced, and then how the plant responds through growth. Throughout, two examples of adaptive responses are used to illustrate this approach: the thigmorphogenetic syndrome of plant shoots bending and the mechanosensitive control of shoot apical meristem (SAM) morphogenesis. Overall this should provide a generic understanding of systems mechanobiology at work.
Nosocomial infection by Staphylococcus haemolyticus and typing methods for epidemiological study (1994)

A patient with chronic myelogenous leukemia became colonized with a Staphylococcus haemolyticus strain and experienced a septic episode caused by this strain during a cytostatic course. The strain was multiply resistant to antibiotics; the MIC and MBC of vancomycin were 2 and 4 mg/liter, and the MIC and MBC of teicoplanin were 4 and 16 mg/liter, respectively. We performed a surveillance study on the carriage of S. haemolyticus in medical and nursing staff of the hospital ward where the patient was treated. S. haemolyticus was isolated from 18 sites on 12 of the 39 people tested. A number of typing methods were performed in order to investigate the possible relationships among the isolates. Methods used were immunoblotting of staphylococcal peptides, plasmid analysis, restriction fragment length polymorphism of chromosomal DNA, and pulsed-field gel electrophoresis of total DNA. Compared with the immunoblotting technique, the molecular methods were more discriminative. The strain colonizing the patient showed a consistent pattern by all typing methods during isolation. When the immunoblot technique was used, similar patterns were found with isolates from hospital staff and isolates from unrelated sources. With the molecular techniques, no evidence of a local spread of the patient's strain was found. However, plasmid profiles and restriction fragment length polymorphism and pulsed-field gel electrophoresis patterns showed that S. haemolyticus isolates collected from hospital ward personnel were related, which was not the case with isolates collected from unrelated sources. Restriction fragment length polymorphism analysis was more discriminative when IS431 was used as a DNA probe instead of a probe based on the 16S rRNA gene. S. haemolyticus, as in this case, may develop resistance to vancomycin and teicoplanin. These antibiotics are considered the last-resort drugs for the therapy of nosocomial gram-positive infections. Thus, local spread of staphylococci resistant to these drugs is an important problem, which should be prevented by strict hygienic measures and antibiotic policy.
Introduction to Adaptive Optics (2000)

A Long Time Ago, in a Laboratory Far, Far, Really Far, Far Away Adaptive Optics Systems - Optics is Our Middle Name Speaking the Language - a Few Definitions Atmospheric Turbulence - Bad Air... Bad, Bad Air Laser Guide Stars - a Beacon in the Wilderness Systems -Putting it All Together Wavefront Sensors - the Eyes Deformable Mirrors - the Hands Control Computers and Reconstructors - the Brains.
Treatment with CD122 antibody durably reverses autoimmune skin disease in a mouse model of vitiligo (2017)

Abstract Vitiligo is a disfiguring autoimmune skin disease characterized by patchy depigmentation. Vitiligo affects approximately 1% of the population worldwide, and it is mediated by CD8+ T cells that kill melanocytes, the pigment producing cells in the skin. Like many autoimmune diseases, treatment options for vitiligo are limited, and depigmentation rapidly recurs after therapy is stopped. We hypothesized that tissue resident memory T cells (Trm) persisted in the skin to reactivate disease. We first confirmed the presence of melanocyte-specific cells with Trm phenotypes in biopsies from human patients and in a mouse model of vitiligo. Functional analysis of Trm cells in mice with vitiligo revealed that they can sense antigen in the skin as determined by Nur77-GFP reporting, as well as secrete cytokines and chemokines as determined by IFNγ, CXCL9 and CXCL10 reporting. Treatment with the S1P1 inhibitor FTY720 resulted in rapid repigmentation, yet preserved Trm. Treatment with a CD122 blocking antibody effectively depleted autoreactive Trm. Importantly, CD122 antibody was also able to durably reverse disease mice. We propose that depleting Trm by targeting the IL-15 axis may prove to be a highly effective and durable treatment for vitiligo and other autoimmune diseases.
Cholesteryl glucosides signal through the carbohydrate recognition domain of the macrophage inducible C-type lectin (mincle) (2021)

Cholesteryl α-d-glucosides (αGCs) are unique metabolic products of the cancer-causing human pathogen Helicobacter pylori. Via signalling through the Macrophage inducible C-type lectin (Mincle) and the induction of a pro-inflammatory response, they are thought to play a role in the development of gastric atrophy. Herein, we prepared the first library of steryl d-glucosides and determined that they preferentially signal through the carbohydrate recognition domain of human Mincle, rather than the amino acid consensus motif. Lipidated steryl d-glucosides exhibited enhanced Mincle agonist activity, with C18 cholesteryl 6-O-acyl-α-d-glucoside (2c) being the most potent activator of human monocytes. Despite exhibiting strong Mincle signalling, sito- (5b) and stigmasterol glycosides (6b) led to a poor inflammatory response in primary cells, suggesting that Mincle is a potential therapeutic target for preventing H. pylori-mediated inflammation and cancer.
S123 The effects of electronic cigarette flavourings on macrophage cytokine release and phagocytosis (2016)

<h3>Background</h3> Electronic cigarettes (e-cigarettes) are marketed as an alternative to tobacco cigarettes, but little is known regarding their biological effects. Studies to date have produced varying results, reflecting varying chemical compositions of different e-liquids. Chronic tobacco smoking is known to alter macrophage function, resulting in impaired bacterial phagocytosis and increased release of cytokines including TNFα, CXCL8 and IL-6. To date, there is little understanding of the effects of e-cigarettes on human macrophages. It was hypothesised that e-cigarettes would produce effects on macrophage function comparable to those of tobacco cigarettes. <h3>Methods</h3> Six e-liquids were investigated: tobacco-flavoured e-liquid (± nicotine), banoffee-pie-flavoured e-liquid (± nicotine), e-liquid vehicle (propylene glycol + vegetable glycerine) and nicotine-vehicle solution. Effects of e-cigarette vapour extracts (e-CVEs) were compared with cigarette smoke extract (CSE) from a tobacco cigarette. Monocyte-derived macrophages (MDMs) from healthy subjects (n = 6) were cultured for 24 h with e-CVEs or CSE then incubated for 4h with <i>Streptococcus pneumoniae</i> or <i>Haemophilus influenzae</i>. Cell viability was determined and phagocytosis was quantified using fluorimetry. Release of TNFα, CXCL8 and IL-6 was measured by ELISA. Expression of macrophage receptor with collagenous structure (MARCO) and toll-like receptors (TLRs) 2 and 4 was measured by flow cytometry. <h3>Results</h3> Neither CSE nor any of the e-CVEs had any significant effect on cell viability. In addition, none of the exposures produced any significant effect on phagocytosis, though higher concentrations of CSE displayed a trend towards reduced phagocytosis. CSE significantly reduced TNFα release (by approximately 70%; p &lt; 0.05). Tobacco- and banoffee pie-flavoured e-CVEs also caused significant reductions in TNFα release (by 30–50%; p &lt; 0.05), while nicotine and the e-liquid vehicle had no effect. Minimal effects were observed on CXCL8 and IL-6 release (0–30% reduction; p &gt; 0.05) with CSE and e-CVEs. Expression of MARCO and TLR4 were unaffected by all cell treatments. TLR2 expression appeared to be slightly increased by e-CVEs, but was not statistically significant. <h3>Conclusion</h3> Effects of e-CVEs on MDMs differed from those of CSE. E-liquid flavourings appeared to be responsible for changes in MDM function, while the e-liquid vehicle and nicotine solution had minimal effects. More research is needed to improve understanding of the biological effects of e-cigarette flavourings.
Time progression and depth dependence of high frequency AIBS in ex-vivo porcine corneas (2010)

Background, Motive & Objective: Ex-vivo corneal tissue is prone to edema (swelling from fluid intake), an important concern for transporting this tissue for transplantation. Edema is also an issue for all ex-vivo cornea experiments. While gross changes in thickness are easy to determine, subtle structural changes can also occur and may impact suitability for transplant. This investigation proposes to use high-frequency apparent integrated backscatter (AIBS) to monitor these subtle changes as ex-vivo corneal tissue is exposed to edema inhibiting fluid. Statement of Contribution/Methods: Within a couple days of sacrifice, whole porcine eye globes were embedded in gelatin up to the corneal/scleral junction. Specimens were imaged with a confocal scanning acoustic microscope using a single element ultrasonic transducer (53 MHz center frequency, 31 MHz bandwidth, 1.67 f#). A solution of 25% glycerol and 10% dextran-40 was used to stabilize corneal hydration and couple the ultrasound into the tissue. Images were captured about every ten minutes for over 5 hours after fluid introduction. Laterally averaged AIBS was calculated over bandwidth with respect to a reference spectrum of a reflected signal from a fused silica optical flat. While some gross measures of corneal backscatter have been previously reported, this is the first detailed experiment exploring time progression and depth dependence and therefore examining subtle changes that are occurring. Results: In the epithelium AIBS increased from -31 to -29 dB after the first 11 minutes. It then decreased gradually over the next 108 minutes to -34 dB. Over the final 205 minutes it stabilized at -33 dB. In the anterior stroma AIBS gradually increased from an initial value of -56 to -50 dB over 119 minutes. It stabilized at -50 dB during the remaining 205 minutes. At mid stroma it gradually increased from an initial value of -59 to -55 dB over the first 119 minutes and then stabilized at about -55 dB for the remaining time. In posterior stroma it changed little, varying somewhat between -62 and -60 dB. Initial corneal thickness was 0.942 mm which decreased to 0.920 mm by 140 minutes, remained stable at this thickness for 119 minutes and then gradually increased to 0.936 mm during the last 64 minutes. As a control we observed that other ex-vivo porcine tissues such as oral mucosa do not undergo edema and have stable AIBS. Discussion and Conclusions: Systematic changes in AIBS of ex-vivo porcine cornea were measured as functions of both time and depth and shown to be sensitive to changes in corneal tissue. Previous research on edema and corneal backscatter postulated that an AIBS increase might be caused by disruption of the orderly spatial arrangement of fibrillar collagen. These more detailed results indicate that this relationship is more complicated than can be explained by edema alone. For example, AIBS in the anterior stroma increases with decreasing fluid content as indicated by corneal thinning. Also, at times AIBS in anterior stroma and epithelium move in opposite directions.
Relaxation in two dimensions and the ‘‘sinh-Poisson’’ equation (1992)

Long-time states of a turbulent, decaying, two-dimensional, Navier–Stokes flow are shown numerically to relax toward maximum-entropy configurations, as defined by the ‘‘sinh-Poisson’’ equation. The large-scale Reynolds number is about 14 000, the spatial resolution is (512)2, the boundary conditions are spatially periodic, and the evolution takes place over nearly 400 large-scale eddy-turnover times.
3935 A Study of Autonomous Mobile System in Outdoor Environment : Part 39 Hi-speed Remote Manual control in Autonomous Mobile Surveillance System (2005)

This paper describes the hi-speed remote manual control for the autonomous Mobile Surveillance System. In general, there are some problems for camera-based remote vehicle control, such as narrowness in camera view field, image time delay, and lack of distance information. To solve these problems, real-time environmental map made by the distance information from LRF and highly accurate position from the GPS/INS is used to compensate these problems. Experimental data reveals that the proposed method is valid and effective for hi-speed remote vehicle control.
Magnesium iron aluminum hydroxosalts and oxide catalysts for oxidative dehydrogenation of alkanes and alcohols (2008)

Methods are developed for the synthesis of precursors for oxide catalysts containing iron hydroxocarbonate and magnesium aluminum hydroxocarbonate with hydrotalcite-type layered structure and decavanadate and paramolybdate ions in anionic interlayers. These precursors are used to synthesize oxide catalysts for oxidative dehydrogenation of alcohols and alkanes with high selectivity and good yields of the desired product in conversion of ethane to ethylene and alcohols to carbonyl compounds.
A High-Speed Functional MicroCT Detector for Small Animal Studies (2006)

Dedicated MicroCT systems for noninvasive screening of small animals are now in routine use. However, speed of operation limits their use for functional studies. At Radiation Monitoring Devices (RMD), we are addressing this need by developing a digital X-ray detector that can simultaneously provide high speed, high sensitivity, and a large active imaging area. The system consists of a special high-speed CCD detector optically coupled to a scintillator. In its current configuration, the system provides an active area of 5 cmtimes5 cm, a spatial resolution of ~100 mum, and can operate at speeds of up to 225 frames per second. The system has been used to acquire volumetric CT data with 360 projections in ~12 seconds compared to several minutes needed for most commercial systems. This paper presents the design of various system components and performance characterization with CT reconstruction data from a mouse phantom
Selumetinib Plus Docetaxel Compared With Docetaxel Alone and Progression-Free Survival in Patients With KRAS-Mutant Advanced Non–Small Cell Lung Cancer (2017)

clinicaltrials.gov: NCT01933932.
Bztree: a high-performance latch-free range index for non-volatile memory (2018)

Storing a database (rows and indexes) entirely in non-volatile memory (NVM) potentially enables both high performance and fast recovery. To fully exploit parallelism on modern CPUs, modern main-memory databases use latch-free (lock-free) index structures, e.g. Bw-tree or skip lists. To achieve high performance NVM-resident indexes also need to be latch-free. This paper describes the design of the BzTree, a latch-free B-tree index designed for NVM. The BzTree uses a persistent multi-word compare-and-swap operation (PMwCAS) as a core building block, enabling an index design that has several important advantages compared with competing index structures such as the Bw-tree. First, the BzTree is latch-free yet simple to implement. Second, the BzTree is fast - showing up to 2x higher throughput than the Bw-tree in our experiments. Third, the BzTree does not require any special-purpose recovery code. Recovery is near-instantaneous and only involves rolling back (or forward) any PMwCAS operations that were in-flight during failure. Our end-to-end recovery experiments of BzTree report an average recovery time of 145 μs. Finally, the same BzTree implementation runs seamlessly on both volatile RAM and NVM, which greatly reduces the cost of code maintenance.
Selective oxidation of uronic acids into aldaric acids over gold catalyst (2015)

Uronic acids available from hemicelluloses were oxidized into aldaric acids, valuable building block chemicals. Au/Al<sub>2</sub>O<sub>3</sub> oxidized glucuronic and galacturonic acids quantitatively to the corresponding glucaric and galactaric acids at mild conditions.