gebhart/patrepeval huggingface dataset:
Differential Gene Expression of <i>TRPM1</i>, the Potential Cause of Congenital Stationary Night Blindness and Coat Spotting Patterns (<i>LP</i>) in the Appaloosa Horse (<i>Equus caballus</i>) (2008)

The appaloosa coat spotting pattern in horses is caused by a single incomplete dominant gene (LP). Homozygosity for LP (LP/LP) is directly associated with congenital stationary night blindness (CSNB) in Appaloosa horses. LP maps to a 6-cM region on ECA1. We investigated the relative expression of two functional candidate genes located in this LP candidate region (TRPM1 and OCA2), as well as three other linked loci (TJP1, MTMR10, and OTUD7A) by quantitative real-time RT-PCR. No large differences were found for expression levels of TJP1, MTMR10, OTUD7A, and OCA2. However, TRPM1 (Transient Receptor Potential Cation Channel, Subfamily M, Member 1) expression in the retina of homozygous appaloosa horses was 0.05% the level found in non-appaloosa horses (R = 0.0005). This constitutes a >1800-fold change (FC) decrease in TRPM1 gene expression in the retina (FC = -1870.637, P = 0.001) of CSNB-affected (LP/LP) horses. TRPM1 was also downregulated in LP/LP pigmented skin (R = 0.005, FC = -193.963, P = 0.001) and in LP/LP unpigmented skin (R = 0.003, FC = -288.686, P = 0.001) and was downregulated to a lesser extent in LP/lp unpigmented skin (R = 0.027, FC = -36.583, P = 0.001). TRP proteins are thought to have a role in controlling intracellular Ca(2+) concentration. Decreased expression of TRPM1 in the eye and the skin may alter bipolar cell signaling as well as melanocyte function, thus causing both CSNB and LP in horses.
Tailoring Plasmonic Metamaterials for DNA Molecular Logic Gates (2013)

Structural and functional information encoded in DNA combined with unique properties of nanomaterials could be of use for the construction of novel biocomputational circuits and intelligent biomedical nanodevices. However, at present their practical applications are still limited by either low reproducibility of fabrication, modest sensitivity, or complicated handling procedures. Here, we demonstrate the construction of label-free and switchable molecular logic gates that use specific conformation modulation of a guanine- and thymine- rich DNA, while the optical readout is enabled by the tunable alphabetical metamaterials, which serve as a substrate for surface enhanced Raman spectroscopy (MetaSERS). By computational and experimental investigations, we present a comprehensive solution to tailor the plasmonic responses of MetaSERS with respect to the metamaterial geometry, excitation energy, and polarization. Our tunable MetaSERS-based DNA logic is simple to operate, highly reproducible, and can be stimulated by ultra-low concentration of the external inputs, enabling an extremely sensitive detection of mercury ions.
A comparison of diamond growth rate using in-liquid and conventional plasma chemical vapor deposition methods (2009)

In order to make high-speed deposition of diamond effective, diamond growth rates for gas-phase microwave plasma chemical vapor deposition and in-liquid microwave plasma chemical vapor deposition are compared. A mixed gas of methane and hydrogen is used as the source gas for the gas-phase deposition, and a methanol solution of ethanol is used as the source liquid for the in-liquid deposition. The experimental system pressure is in the range of 60–150 kPa. While the growth rate of diamond increases as the pressure increases, the amount of input microwave energy per unit volume of diamond is 1 kW h/mm3 regardless of the method used. Since the in-liquid deposition method provides a superior cooling effect through the evaporation of the liquid itself, a higher electric input power can be applied to the electrodes under higher pressure environments. The growth rate of in-liquid microwave plasma chemical vapor deposition process is found to be greater than conventional gas-phase microwave plasma chemical vapor deposition process under the same pressure conditions.
The αvβ6 integrin regulates its own expression with cell crowding: Implications for tumour progression (2001)

Expression of the growth-promoting integrin alphavbeta6 in colon cancer cells induces gelatinase B secretion and activation, the inhibition of which abolishes alphavbeta6-mediated tumour cell growth within a collagen matrix. Herein, we show that high cell density selectively enhances alphavbeta6 expression in a protein kinase C (PKC)-dependent manner in preference to other beta integrin subunits, resulting in a marked increase in gelatinase B secretion as cells reach confluence. Moreover, PKC activity increases with cell confluence, and the rise in PKC activity is much greater for alphavbeta6-expressing cells than for colon cancer cells which lack alphavbeta6. We propose a self-perpetuating system of colon cancer progression in which the integrin alphavbeta6 provides a means of sustaining tumour cell proliferation. In this model, alphavbeta6 regulates its own expression via a PKC-mediated signalling pathway as tumour cells become crowded and quiescent. The alphavbeta6-mediated induction of gelatinase B secretion facilitates peri-cellular matrix degradation, which helps overcome crowding and restores cell proliferation.
A Polymer Optoelectronic Interface Provides Visual Cues to a Blind Retina (2013)

A polymer bulk heterojunction structure utilized as an active photosensitive platform to evoke neuronal activity in a blind retina. The features of the elicited action potentials correlate with the optoelectronic properties of the polymer/electrolyte interface, and resembles the natural response of the retina to light. The polymer interface can be used as an optoelectronic epiretinal interface for retinal prosthesis with no requirement for external power sources or connection cables. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Screening, Characterization, and Cloning of the Gene for<i>N</i>-Carbamyl-<scp>D</scp>-Amino acid Amidohydrolase from Thermotolerant Soil Bacteria (1998)

For the production of D-amino acids, thermotolerant bacteria producing N-carbamyl-D-amino acid amidohydrolase were isolated from soil by enrichment culture at 45 degrees C with N-carbamyl-D-amino acids as the sole nitrogen source. The enzyme activities and substrate specificities of these strains were examined by the resting cells reaction. One of the enzymes, produced by Pseudomonas sp. strain KNK003A, was purified and characterized, and the amino acids of its N-terminal region were sequenced. A DNA fragment containing the gene for a thermostable N-carbamyl-D-amino acid amidohydrolase was then cloned into Escherichia coli. The gene encoded a peptide of 312 amino acids, with a calculated molecular weight of 35,000. The similarity of the deduced amino acid sequences of this enzyme and a related enzyme from a mesophile, Agrobacterium sp. strain KNK712, was 60%. A database was searched for similar sequences.
Antagonizing the corticotropin releasing hormone receptor 1 with antalarmin reduces the progression of endometriosis (2018)

Endometriosis is a disorder in which endometrial tissue is found outside the uterus causing pain, infertility and stress. Finding effective, non-hormonal and long-term treatments for endometriosis still remains one of the most significant challenges in the field. Corticotropin releasing hormone (CRH) is one of the main signaling peptides within the hypothalamic pituitary adrenal (HPA) axis released in response to stress. CRH can affect nervous and visceral tissues such as the uterus and gut via activation of two types of CRH receptors: CRHR1 and CRHR2. Our aim was to determine if blocking CRHR1 with antalarmin will reduce endometriosis progression. In experiment 1 we induced endometriosis in female rats by suturing uterine horn tissue next to the intestinal mesentery and allowed to progress for 7 days. We determined that after 7 days, there was a significant increase in CRHR1 within endometriotic vesicles as compared to normal uterus. In Experiment 2, we induced endometriosis and administered either antalarmin (20 mg/kg, i.p.) or vehicle during the first 7 days after surgery. A separate group of sham surgery rats served as non-endometriosis controls. Endometriosis was allowed to progress until 60 days after surgery, at which time rats were tested for anxiety behaviors. At the time of sacrifice, endometriotic vesicles, uterus and blood were collected. Treatment with antalarmin significantly reduced the size (67% decrease) and number (30% decrease) of endometriotic vesicles. Antalarmin also prevented the increase in CRH and CRHR1 mRNA within endometriotic vesicles but not of glucocorticoid receptor. Endometriosis did not change anxiety behaviors in the open field and zero-maze tests and prior antalarmin administration did not modify this. Our data provides the first in-vivo demonstration for use of CRHR1 antagonist for the treatment of endometriosis opening the possibility for further exploring CRH signaling as a treatment target for this debilitating disease.
<title>Image enhancement by nonlinear extrapolation in frequency space</title> (1994)

A procedure for creating images with higher resolution than the sampling rate would allow is described. The enhancement algorithm augments the frequency content of the image using shape-invariant properties of edges across scale by using a non-linearity that generates phase- coherent higher harmonics. The procedure utilizes the Laplacian pyramid image representation. Results are presented depicting the power-spectra augmentation and the visual enhancement of several images. Simplicity of computations and ease of implementation allow for real-time applications such as high-definition television.
Efficient and Robust Multicast Routing in Mobile Ad Hoc Networks (2005)

This paper argues that tree based protocols can have packet delivery ratios comparable to mesh based protocols if the tree construction algorithm can fix and detect broken links quickly, and at the same time have a much lower data packet overhead due to the absence of redundancy.We present such a protocol and call it robust multicasting in ad hoc networks using trees (ROMANT).ROMANT does not require a unicast routing protocol or the preassignment of cores to groups.We compare ROMANT with ODMRP and MAODV which are the state of the art in mesh based and tree based protocols respectively.The results from a wide range of scenarios of varying mobility, group members, number of senders, traffic load and number of multicast groups show that ROMANT attains a comparable or better packet delivery ratio than ODMRP and MAODV, and a much lower control overhead which is almost constant for a fixed number of groups, and varies sublinearly with increasing groups.
Progress in the crystal growth of Ce:LiSAF (1995)

The search for an efficient solid state laser with tunable emission in the ultraviolet wavelength region has resulted in the growth and development of cerium doped colquiriite crystals, such as LiCaAlF<SUB>6</SUB> (LiCAF) and LiSrAlF<SUB>6</SUB> (LiSAF). Results from preliminary research at Lawrence Livermore National Laboratory indicate that Ce:LiSAF is the preferred material of the colquiriite hosts, since it shows higher gains than Ce:LiCAF. Although the growth of chromium doped LiSAF has been developed to produce long boules of near-scatter-free material, the doping of LiSAF with cerium introduces different variables into the growth of high optical quality crystals. The main crystal growth issue for Ce:LiSAF is the charge compensation mandated by the substitution of the trivalent cerium ion for divalent strontium, which is located in the only site large enough to support the cerium ion. Initial growth runs produced opaque, heavily cracked crystals with less than 10 mm of cleaner, single crystal material. The addition of charge compensating ions into the starting charge and their effect in attaining higher doped and less-stressed material is discussed. The selection of growth parameters needed to produce higher-doped, near-scatter-free Ce:LiSAF will also be described.
Use of Microcontact Printing Methods to Direct Pattern Formation of Calcified Mesoporous Silicon (2002)

Silicon surfaces with nanoporous and bulk-Si domains are accessible by soft lithographic processes based on microcontact printing. The nanoporous areas can be further modified—also biochemically—by calcium phosphate deposition (see Figure for a patterned sample). Both nanoporous Si and the calcium phosphate-covered material are biocompatible and interesting for implants that release drugs over extended periods of time.
Contribution of trans-acting factor alleles to normal physiological variability: vitamin D receptor gene polymorphism and circulating osteocalcin. (1992)

Osteocalcin, the most abundant noncollagenous protein in bone, is a marker of bone turnover in normal and disease states. Its synthesis is induced by calcitriol, the active hormonal form of vitamin D, through the vitamin D receptor and a specific vitamin D-responsive element in the osteocalcin gene promoter. Serum concentrations of osteocalcin are under strong genetic influence. To ascertain whether variability in circulating osteocalcin levels may reflect allelic variation in the vitamin D receptor gene, we have analyzed the relationship between frequent restriction fragment length polymorphisms (RFLPs, detected by endonucleases Bsm I, EcoRV, and Apa I) that define human vitamin D receptor alleles and serum osteocalcin in a cohort of normal subjects. In 91 Caucasian subjects, RFLPs in the vitamin D receptor gene predicted circulating osteocalcin levels (P less than 0.0001) independent of age or menopause effects. Since the osteocalcin gene and the vitamin D receptor gene are encoded on different chromosomes, the interaction between these two genes occurs in trans. Thus, common alleles of this trans-acting factor, the vitamin D receptor, are functionally different and contribute to "normal" physiological variability in osteocalcin levels. Preliminary analysis in monozygotic and dizygotic twin pairs indicates that the greater diversity in lumbar spine density between the dizygotic pairs can be explained by divergence in vitamin D receptor alleles. Variations in this receptor and other transacting factor genes may confound physiological studies of regulation of target genes and will need to be considered in future human and animal studies. This approach to genetic analysis provides a paradigm for the study of functional variation in trans-acting factors and the role such variation may play in the generation and evolution of physiological diversity.
Synthesizing cellular networks from evolved ribosome–mRNA pairs (2006)

We describe cellular engineering for the creation of multiple new cellular modules each composed of an orthogonal ribosome and orthogonal mRNA. These modules operate independently of the endogenous ribosome and mRNA. We discuss some of the applications of orthogonal pairs and highlight the expression of Boolean logic in gene regulation using multiple orthogonal pairs.
Supplemental Figures 1-6 from GSK3 Inhibition Drives Maturation of NK Cells and Enhances Their Antitumor Activity (2023)

<p>This supplementary file contains Supplemental Figures 1-6. Supplemental Figure 1 shows that 7-day ex vivo culture of NK cells with IL-15 and 5 μM CHIR99021 leads to an increase in the frequencies of NK cells with heterogeneous adaptive NK cell phenotypes (defined by expression of CD57, PLZF, SYK and FcεR1γ) relative to DMSO controls. Supplemental Figure 2 contains a detailed phenotypic characterization of receptor expression and cytotoxic granule component levels in sorted CD3-CD56dimCD57- and CD3-CD56dimCD57+ NK cells cultured for 7 days with IL-15 and either DMSO or 5 μM CHIR99021. Supplementary Figure 3 shows an analysis of NK cell phenotype, viability and proliferation after 7-day culture with IL-15 and either DMSO or CHIR99021 at several concentrations (1 μM, 3 μM and 5 μM). Supplemental Figure 4 shows an analysis of NK cell function (CD107a and IFN-γ) against K562 cells. NK cells were cultured for 7 days in IL-15 and either DMSO or 5 μM CHIR99021. Function was determined for individual CD3-CD56+ NK cell subsets gated on CD57 and NKG2C. Supplemental Figure 5 shows an analysis of NK cell function (CD107a and IFN-γ) against K562 cells. NK cells were cultured for 7 days in IL-15 and either DMSO or 5 μM CHIR99021. Function was determined for individual CD3-CD56+ NK cell subsets gated on CD57 and KIR. Supplemental Figure 6 shows the frequency of ex vivo expanded NK cells expressing CD57 and/or NKG2C 14 days after adoptive transfer into NSG mice.</p>
Atrial Defibrillation Thresholds of Electrode Configurations Available to an Atrioventricular Defibrillator (2001)

The atrial defibrillation threshold of CS-->SVC+Can is significantly lower than that of RV-->SVC+Can. In addition, the low atrial defibrillation threshold of RV+CS-->SVC+Can merits further investigation. Based on corroboration of low atrial defibrillation thresholds of CS-based configurations in humans, physicians might consider using CS leads with atrioventricular defibrillators.
Exploiting interference locality in coordinated multi-point transmission systems (2012)

Coordinated Multi-Point (CoMP) transmission is emerging as a concept that can substantially suppress interference, thus improving the capacity of multi-cell wireless networks. However, existing CoMP techniques either require sharing of data and channel state information (CSI) for all links in the network, or have limited capability of interference suppression. In this paper, we propose distributed interference alignment and cancellation (DIAC) to overcome these limitations. DIAC builds on a key intuition of interference locality — since each link is interfered with a limited number of neighboring links, it is sufficient to coordinate with those strong interferers and ignore others, in order to bound the overhead in CoMP. DIAC realizes the localized coordination by integrating interference cancellation and distributed interference alignment, and can be applied to both the uplink and downlink of multi-cell wireless networks. We validate DIAC using both model-driven and trace-based simulation where the traces are collected by implementing a MIMO-OFDM channel estimator on a software radio platform. Our experiments show that DIAC can substantially improve the degrees of freedom in multi-cell wireless networks.
Design of Biomolecules for Nanoengineered Biomaterials for Regenerative Medicine (2011)

An important goal in the development of highly functional organic materials is to design self-assembling molecules that can reproducibly display chemical signals across length scales. Within the biomedical field, biomolecules are highly attractive candidates to serve as bioactive building blocks for the next generation of biomaterials. The peptide amphiphiles (PAs) developed by the Stupp Laboratory at Northwestern University generated a highly versatile self-assembly code to create well-defined bioactive nanofibers that have been proven to be very effective at signaling cells in vitro and in vivo. Here, we describe the basic steps necessary for synthesis and assembly of PA molecules into functional nanostructures.
Rapid assay of plutonium in soils by passive L x-ray counting (1992)

A technique has been developed to rapidly measure the presence of plutonium in soils, filters, smears, and glass waste forms by measuring the uranium L-shell x-ray emissions associated with the decay of plutonium. In addition, the technique can simultaneously acquire spectra of samples and automatically analyze them for the amount of americium, and gamma-ray emitting activation and fission products present. The samples are counted with a large area, thin-window, n-type Ge spectrometer which is equally efficient for the detection of low energy x-rays (>10 key), as well as high-energy gamma rays (>1 MeV). A 8192-channel analyzer is used to acquire the entire photon spectrum at one time. A dual-energy, time-tagged pulser, that is injected into the test input of the preamplifier to monitor the energy scale, detector resolution, and pulse pile-up will be installed in FY-92. The L x-ray portion of each spectrum is analyzed by a linear least-squares spectral fitting technique originally developed for the analysis of spectra from NaI(Tl) detectors. The gamma-ray portion of each spectrum is analyzed by a standard Ge gamma-ray analysis package. Detection limits (also referred to as lower limits of detection) for plutonium in contaminated soils that have been achieved by this technique are reported.
Calibrated breast density methods for full field digital mammography: A system for serial quality control and inter‐system generalization (2015)

A methodology for monitoring and maintaining serial calibration accuracy for breast density measurements was evaluated. Calibration datasets for a given unit can be translated forward in time with minimal phantom imaging effort. Similarly, cross-calibration is a method for generalizing calibration datasets across similar units without additional phantom imaging. This methodology will require further evaluation with mammograms for complete validation.
Reflective twisted nematic liquid crystal displays. II. Elimination of retardation film and rear polarizer (1997)

Reflective twisted nematic liquid crystal displays consisting of just one input polarizer, a liquid crystal cell, and a rear reflector are discussed. We first show that all such display modes reported in the literature can be depicted systematically in a series of parameter space diagrams. Then by making use of such diagrams as a guide, we show that other new high quality reflective display modes can be obtained. The three parameters that are varied are the input polarizer angle α, the liquid crystal twist angle φ, and the cell gap–liquid crystal birefringence product dΔn. A full numerical simulation which takes into account of the liquid crystal director deformation under the application of an electric field was used to optimize such displays. Experimental results agree well with the theoretical predictions.
Electrostatic-directed deposition of nanoparticles on a field generating substrate (2008)

We demonstrate a new assembly method to position metal nanoparticles delivered from the gas phase onto surfaces using the electrostatic force generated by biased p–n junction-patterned substrates. Aligned deposition patterns of metal nanoparticles were observed, and the patterning selectivity quantified. A simple model accounting for the generated electric field, and the electrostatic, van der Waals, and image forces, was used to explain the observed results. (Some figures in this article are in colour only in the electronic version)