gebhart/patrepeval huggingface dataset:
Bacteriorhodopsin is involved in halobacterial photoreception. (1993)

The bacterio-opsin gene was introduced into a "blind" Halobacterium salinarium mutant that (i) lacked all the four retinal proteins [bacteriorhodopsin (BR), halorhodopsin, and sensory rhodopsins (SRs) I and II] and the transducer protein for SRI and (ii) showed neither attractant response to long wavelength light nor repellent response to short wavelength light. The resulting transformed cells acquired the capability to sense light stimuli. The cells accumulated in a light spot, demonstrating the BR-mediated orientation in spatial light gradients. As in wild-type cells, a decrease in the intensity of long wavelength light caused a repellent response by inducing reversals of swimming direction, but, in contrast to wild-type cells, a decrease in the intensity of short wavelength light also repelled the cells. An increase in light intensity evoked an attractant response (i.e., a transient suppression of spontaneous reversals). Signal processing times and adaptation kinetics were similar to the SRI-mediated reactions. However, compared to SR-mediated photoresponses, higher light intensities were necessary to induce the BR-mediated responses. The light sensitivity of the transformant was increased by adding 1 mM cyanide and decreased by the addition of arginine, agents that respectively reduce and increase the light-independent generation of the electrochemical potential difference of H+ ions (delta mu H+). A decrease in irradiance to an intensity that was still high enough to saturate BR-initiated delta mu H+ changes failed to induce the repellent effect, but the addition of a protonophorous uncoupler sensitized the cell to these light stimuli. The BR D96N mutant (Asp-96 is replaced by Asn) with decreased proton pump activity showed strongly reduced BR-mediated responses. Azide, which increases this mutant's H+ pump efficiency, increased the photosensitivity of the mutant cells. Moreover, azide diminished (i) the membrane potential decreasing and (ii) repellent effects of blue light added to the orange background illumination in this mutant. We conclude that the BR-mediated photoreception is due to the light-dependent generation of delta mu H+. Our data are consistent with the assumption that the H. salinarium cell monitors the membrane energization level with a "protometer" system measuring total delta mu H+ changes or its electric potential difference component.
Photonic-crystal light-emitting diodes on p-type GaAs substrates for optical communications (2008)

Oxide-confined photonic-crystal (PhC) light-emitting diodes (LEDs) on p-type GaAs substrate in the 830 nm range are reported. The device consists of a bottom distributed Bragg reflector (DBR), quantum wells (QWs), and a top DBR, with a photonic-crystal structure formed within the n-type ohmic contact ring for light extraction. The etching depth of the PhC holes is 17-pair out of the 22-pair top DBR being etched off. The internally reflected spontaneous light emission can be extracted out of PhC holes because of lower reflectance within those areas. High-resolution micrographic imaging studies indicate that the device emits light mainly through the photonic-crystal holes and it is suitable for optical communications.
Measurement of the frequency response induced by electrostriction in optical fibers (1997)

Accurate measurements of the frequency response of the nonlinear refractive index induced by the combined effects of Kerr nonlinearity with electrostrictional excitation of acoustic waves in optical fibers are presented. A detailed experimental investigation of both standard (zero-dispersion wavelength,lambda(0) approximately 1.31microm) and dispersion-shifted (lambda(0)=1.55microm) single-mode fibers showed the presence of several resonant peaks induced by the electrostrictive nonlinearity in the fiber structure. This investigation has provided better insight into the frequency behavior of the electrostriction-induced acoustic waves in optical fibers.
Age-Related Increased Prevalence of Asthma and Nasal Polyps in Chronic Rhinosinusitis and Its Association with Altered IL-6 Trans-Signaling (2015)

We report that S100 proteins were reduced in patients with chronic rhinosinusitis (CRS). S100A8/9, which is important in epithelial barrier function, was particularly decreased in elderly patients with CRS. Epithelial expression of S100A8/9 is partly regulated by the IL-6 trans-signaling pathway. The goal of this study was to investigate whether or not age-related reduction of S100A8/9 in CRS is associated with blunting of IL-6 trans-signaling. The levels of IL-6, soluble IL-6 receptor (sIL-6R), soluble gp130 (sgp130), and S100A8/9 from control subjects (n = 10), and patients with CRS without nasal polyps (n = 13) and those with CRS with nasal polyps (CRSwNP) (n = 14), were measured by ELISA. Age-related differences in the level of each protein were investigated. Normal human bronchial epithelial cells were cultured in air-liquid interface and stimulated with IL-6/sIL-6R and tumor necrosis factor (TNF)-α with or without the addition of sgp130, a natural inhibitor of IL-6 trans-signaling. There was a significant age-related decline in S100A8/9 and an increase in sgp130 in nasal tissue samples from patients with CRSwNP, although there was no age-related difference in IL-6/sIL-6R production. Additionally, expression of the S100A8/9 gene and protein was increased significantly by IL-6/sIL-6R plus TNF-α in normal human bronchial epithelial cells. This increase was blocked by sgp130. These results suggest that increased sgp130 in older patients may inhibit IL-6 trans-signaling, impair barrier function, and decrease S1008/9 production in elderly patients with CRSwNP. Restoration of barrier function by targeting sgp130 may be a novel treatment strategy.
Successful Cap Rock Stress Testing With a Wireline Straddle Packer Tool Configured With an Innovative Controlled Pressure Bleedoff Design (2022)

Knowledge of the minimum principal stress in the overburden is highly valuable – and even required – for well design, drilling, completion, plug and abandonment, and reservoir injection planning optimization. Access to an effective methodology whereby the stress could in principle be reliably determined at multiple arbitrary depths along the wellbore throughout the overburden is thus highly beneficial to more reliably predict the in-situ stress state. Within the reservoir, such data have been successfully acquired using straddle packer wireline tools, the socalled microfrac test. However, shaly overburden and cap rock formations in particular have very low mobility, therefore the induced fracture bleeds off at an extremely low rate after shut-in. This lack of formation leak-off and fracture closure renders least principal stress analysis difficult without a controlled pressure release option including sufficient volume control. The recent deployment of new technology enables microfrac tests to be successfully applied to tight formations. A new flow-back option has been deployed and utilizes the injection pump in reverse mode as a fluid expander which moves fluid from high to low pressure. Fluid injected into the fracture flows back to the borehole at a controlled rate, enabling high quality tight formation stress testing. A description of the new method and the first field implementation, which turned out to be a success case where data were acquired at multiple depths in a well on the Norwegian Continental Shelf (NCS), is given. The subsequent application of the results in terms of constraining the minimum horizontal stress and pore pressure models for the well is presented, illustrating the value of the tool and the microfrac stress data.
<title>Thermal wave nondestructive testing (NDT) of ceramic coatings</title> (1995)

A description of preliminary experimental work, in which thickness of ceramic coatings is measured using pulse echo thermal wave imaging, is presented. The thermal wave measurement technique uses the time (relative to flash heating) at which the peak slope of the contrast curve occurs to determine the thickness of the coating layer, based on reflection of the thermal wave from the coating/substrate interface. Thermal wave thickness measurements are compared to measurements made (destructively) with a drill micrometer. Repeatability and precision of measurements are discussed.
Electric and magnetic response in a composite system of a dielectric photonic-crystal nanocavity and single metallic nanostructures (2013)

We demonstrate nanoscale interaction between dielectric and metallic nanocavities. The Q factor's change is affected by the location and the types of metallic nanocavities. These electric/magnetic local responses can be utilized for various photonic applications.
A graphical representation of glycan heterogeneity (2021)

A substantial shortcoming of large-scale datasets is often the inability to easily represent and visualize key features. This problem becomes acute when considering the increasing technical ability to profile large numbers of glycopeptides and glycans in recent studies. Here, we describe a simple, concise graphical representation intended to capture the microheterogeneity associated with glycan modification at specific sites. We illustrate this method by showing visual representations of the glycans and glycopeptides from a variety of species. The graphical representation presented allows one to easily discern the compositions of all glycans, similarities and differences of modifications found in different samples and, in the case of N-linked glycans, the initial steps in the biosynthetic pathway.
Inhomogeneity of viscous aqueous solutions (1995)

Brownian principles for homogeneous media fail to explain the effect of viscous cosolvents on reaction rates. We examined the possibility that solvent viscosity in the microenvironment of a probe ${\mathrm{\ensuremath{\eta}}}^{\mathrm{*}}$ (microviscosity) differs from the bulk viscosity \ensuremath{\eta} (macroviscosity). ${\mathrm{\ensuremath{\eta}}}^{\mathrm{*}}$ was derived from the diffusion constant D of water tracers, measured in the presence of viscous cosolvents. We found that (a) ${\mathrm{\ensuremath{\eta}}}^{\mathrm{*}}$\ensuremath{\propto}${\mathrm{\ensuremath{\eta}}}^{\mathrm{\ensuremath{\alpha}}}$, where 0\ensuremath{\le}\ensuremath{\alpha}\ensuremath{\le}1, and (b) the temperature dependence of D is insensitive to the presence of these cosolvents. We propose that viscous aqueous solutions have an inhomogeneous microstructure with waterlike domains.
Enantiomeric resolution and modeling of DL‐alanine‐DL‐tryptophan dipeptide on amylose stationary phase (2018)

Abstract The enantiomeric resolution of DL‐alanine‐DL‐tryptophan dipeptide is described on amylose stationary phase. The eluent used was CH 3 OH─CH 3 COONH 4 (10mM)─CH 3 CN (50: 40, 10) at 0.8‐mL/min flow, 230‐nm detection, 25‐minute run time, and 25°C ± 1°C temperature. The chiral phase was amylose [AmyCoat RP (15 cm × 0.46 cm × 5 micron)]. The magnitudes of the retention factors (k) were 2.71, 3.52, 5.11, and 7.75. The magnitudes of separation factor (α) were 1.19, 1.57, and 1.51 while the resolution factors (Rs) were 3.25, 14.84, and 15.76. The limits of detection and quantitation were of 2.5 to 5.4 and 12.8 to 27.5 μg/mL. The enantiomeric resolution is controlled by hydrogen, hydrophobic, π‐π, steric, etc interactions. The elution order of the enantiomer was supported by the modeling data. The described method is fast, reproducible, precise, and selective, which can be used successfully for evaluating the enantiomers of the reported dipeptide.
ChemInform Abstract: Zeolites as Catalysts for the Synthesis of Fine Chemicals (2011)

Abstract Review: 260 refs.
High prevalence of actionable germline variants in unselected endometrial cancer (EC) patients. (2021)

5577 Background: The use of upfront germline genetic testing for cancer patients to identify hereditary syndromes and to aid in treatment decision making has increased dramatically. Recent evidence suggests that such testing should be considered for all solid tumors. In EC, mismatch repair deficiency (MMRd) has emerged as an important molecular marker for treatment with checkpoint inhibitors. MMRd is the hallmark of Lynch syndrome (LS), the most common hereditary cause of EC. Therefore, identifying LS not only affords opportunities for cancer prevention but also for making treatment decisions for women who already have EC. Although tumor-based screening is highly effective, some LS diagnoses will be missed. Upfront multi-gene panel testing (MGPT) for EC has been evaluated as an alternative approach to identifying LS with the potential to simultaneously find actionable germline variants in other cancer susceptibility genes (CSGs). Our objective was to determine the frequency and types of actionable germline variants in a large, unselected group of women with EC. Methods: Prospective germline MGPT for 47 CSGs was performed for 961 unselected EC cases. Patients diagnosed from 2017-2020 were enrolled at nine different institutions. Clinicopathologic data were abstracted from patients’ records. Results: 101 likely pathogenic (LP) or pathogenic variants (PV) were identified in 98 women (10.2%). LP/PVs in LS genes were most common: 29 LS cases were identified (3.02%, 95% CI 2.1 - 4.3%). MGPT found 9 cases (one-third of LS cases) that were not identified by tumor screening: 6 were from institutions that do not perform tumor screening and 3 had normal immunohistochemistry. There were 72 LP/PVs found in 17 different CSGs. 21 patients (2.1%) had LP/PVs in high penetrance CSGs other than the LS genes, 19 of which were in genes associated with breast and/or ovarian cancer (4 in BRCA1, 6 in BRCA2, 6 in BRIP1, 2 in PALB2, 1 in RAD51C). BRCA1/2 PVs (1.04% of the study population, 95% CI 0.6 - 1.9%) were significantly more frequent in women with type II cancers than the rest of the cohort (P =.005, HR 2.00, 95% CI 1.16 - 4.75). 21 additional LP/PVs were found in moderate risk CSGs ( ATM, CHEK2, NBN, NF1). Conclusions: Upfront MGPT in an unselected EC population improved LS diagnosis and identified an additional 2% of patients with LP/PVs in highly penetrant CSGs. The enrichment of germline BRCA1/2 PVs in type II cancers is consistent with prior reports that non-endometrioid tumors are frequently deficient in homologous recombination. Germline BRCA mutation is a known predictive biomarker in ovarian cancer and an attractive therapeutic target in EC. Knowing germline status at the time of diagnosis facilitates further delineation of germline/phenotype associations, and it defines a genetic syndrome allowing for cancer prevention. Upfront MGPT in EC provides clinically impactful information and should be adopted into routine clinical care. Clinical trial information: NCT03460483.
3D Shape Estimation for Smooth Surfaces Using Double Mirror System (2021)

In this paper, a low cost, single camera, double mirror system that can be built in a desktop nail printer will be described. The usage of this system is to capture an image of a fingernail and to generate the 3D shape of the nail. The nail&#x2019;s depth map will be estimated from this rendered 3D nail shape. The paper will describe the camera calibration process and explain the calibration theory for this proposed system. Then a 3D reconstruction method will be introduced, as well. Experimental results will be shown in the paper, which illustrate the accuracy of the system to handle the rendering task.
Three-dimensional integration technology based on reconfigured wafer-to-wafer and multichip-to-wafer stacking using self-assembly method (2009)

We demonstrate two types of three-dimensional (3D) integration using chip self-assembly techniques with liquid surface tension. In reconfigured wafer-to-wafer 3D integration, many different sizes of chips having In/Au microbumps with/without TSV (through-silicon via) were temporarily placed by self-assembly on a reconfigured wafer in a back-to-face manner. The many chips can be then simultaneously transferred to an LSI wafer that is fully faced with the reconfigured wafer and has the same microbump array patterns to the self-assembled chips. On the other hand, in multichip-to-wafer 3D integration, Si chips having In/Au microbumps with sizes of 5 µm and 10 µm were directly self-assembled on another LSI wafer having the same In/Au microbumps in a face-to-face manner. After the self-assembly, these chips can be bonded at 200 °C without applying mechanical pressure. In both of the self-assembly-based 3D integration, the chips were precisely aligned and bonded to the LSI wafers through the microbump-to-microbump interconnection. We obtained good electrical characteristics using the microbump daisy chains formed between the self-assembled chips and the wafers.
60-GHz transceiver for high-speed wireless LAN system (2002)

We have developed a 60-GHz Transceiver unit for high-capacity wireless LAN systems, employing state-of-the-art MMIC technology. This prototype showed sufficiently good performance in an ethernet-compatible 10-Mbps random access CSMA/CD wireless system, and proved its potential usefulness in various commercial products.
The mechanism of thermal decomposition of trans-chloroethylbis(triethylphosphine)platinum(II) (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe mechanism of thermal decomposition of trans-chloroethylbis(triethylphosphine)platinum(II)Robert L. Brainard and George M. WhitesidesCite this: Organometallics 1985, 4, 9, 1550–1557Publication Date (Print):September 1, 1985Publication History Published online1 May 2002Published inissue 1 September 1985https://pubs.acs.org/doi/10.1021/om00128a012https://doi.org/10.1021/om00128a012research-articleACS PublicationsRequest reuse permissionsArticle Views169Altmetric-Citations32LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cerebrospinal fluid proteomics implicates the granin family in Parkinson’s disease (2020)

Parkinson's disease, the most common age-related movement disorder, is a progressive neurodegenerative disease with unclear etiology. Better understanding of the underlying disease mechanism(s) is an urgent need for the development of disease-modifying therapeutics. Limited studies have been performed in large patient cohorts to identify protein alterations in cerebrospinal fluid (CSF), a proximal site to pathology. We set out to identify disease-relevant protein changes in CSF to gain insights into the etiology of Parkinson's disease and potentially assist in disease biomarker identification. In this study, we used liquid chromatography-tandem mass spectrometry in data-independent acquisition (DIA) mode to identify Parkinson's-relevant biomarkers in cerebrospinal fluid. We quantified 341 protein groups in two independent cohorts (n = 196) and a longitudinal cohort (n = 105 samples, representing 40 patients) consisting of Parkinson's disease and healthy control samples from three different sources. A first cohort of 53 Parkinson's disease and 72 control samples was analyzed, identifying 53 proteins with significant changes (p < 0.05) in Parkinson's disease relative to healthy control. We established a biomarker signature and multiple protein ratios that differentiate Parkinson's disease from healthy controls and validated these results in an independent cohort. The second cohort included 28 Parkinson's disease and 43 control samples. Independent analysis of these samples identified 41 proteins with significant changes. Evaluation of the overlapping changes between the two cohorts identified 13 proteins with consistent and significant changes (p < 0.05). Importantly, we found the extended granin family proteins as reduced in disease, suggesting a potential common mechanism for the biological reduction in monoamine neurotransmission in Parkinson's patients. Our study identifies several novel protein changes in Parkinson's disease cerebrospinal fluid that may be exploited for understanding etiology of disease and for biomarker development.
Special report: The AgAID AI institute for transforming workforce and decision support in agriculture (2022)

Tackling the grand challenges of 21st century agriculture (Ag) will require a fundamental shift in the way we envision the role of artificial intelligence (AI) technologies, and in the way we build agricultural AI systems. This shift is needed especially for complex, high-value agricultural ecosystems such as those in the Western U.S., where 300+ crops are grown. Farmers and policy makers in this region face variable profitability, major crop loss and poor crop quality owing to several challenges, including increased labor costs and shortages of skilled workers, weather and management uncertainties, and water scarcity. While AI is expected to be a significant tool for addressing these challenges, AI capabilities must be expanded and will need to account for human input and human behavior – calling for a strong AI-Ag coalition that also creates new opportunities to achieve sustained innovation. Accomplishing this goal goes well beyond the scope of any specific research project or disciplinary silo and requires a more holistic transdisciplinary effort in research, development, and training. To respond to this need, we initiated the AgAID Institute, a multi-institution, transdisciplinary National AI Research Institute that will build new public-private partnerships involving a diverse range of stakeholders in both agriculture and AI. The institute focuses its efforts on providing AI solutions to specialty crop agriculture where the challenges pertaining to water availability, climate variability and extreme weather, and labor shortages, are all significantly pronounced. Our approach to all AgAID Institute activities is being guided by three cross-cutting principles: (i) adoption as a first principle in AI design; (ii) adaptability to changing environments and scales, and (iii) amplification of human skills and machine efficiency. The AgAID Institute is conducting a range of activities including: using agricultural AI applications as testbeds for developing innovative AI technologies and workflows; laying the technological foundations for climate-smart agriculture; serving as a nexus for culturally inclusive collaborative and transdisciplinary learning and knowledge co-production; preparing the next generation workforce for careers at the intersection of Ag and AI technology; and facilitating technology adoption and transfer.