gebhart/patrepeval huggingface dataset:
Constructing habitat for a sustainable native fisheries in the Sphinx Lake end pit lake system (2011)

Fisheries habitat and watershed integrity are highly valued resources in the subalpine natural subregion of west-central Alberta. Teck’s Luscar open pit coal mine has been in operation in this area since 1969, and 51-C6 pit was mined from 1992 to 1999. Accomplishing a sound development and reclamation plan to meet biodiversity objectives for 51-C6 pit included operational considerations such as surface water diversions and post-mining fisheries habitat development. The pit had to be mined and reclaimed such that the end pit and inlet/outlet streams would sustain in perpetuity the full range of habitat and watershed features needed to support native Athabasca Rainbow Trout (Oncorhynchus mykiss) and Bull Trout (Salvelinus confluentus). The five year post-reclamation fisheries habitat and population assessment indicates a surging Rainbow Trout population, high growth rates and enhanced habitat conditions as compared with the pre-mine cold-water, lotic system. This paper covers the process from environmental assessment through construction and reclamation to closure assessment, highlighting the challenges, uncertainties, and successes of Teck’s award-winning Sphinx Lake system within the context of biological diversity.
Viability of sub-0.4-nm diameter carbon nanotubes (2002)

Hartree-Fock (HF) and density functional theory calculations indicate that a (4,0) carbon nanotube (CNT) of sub-0.4-nm diameter is stable and its heat of formation is close to that of the stable ${\mathrm{C}}_{36}$ $({\mathrm{D}}_{6h}).$ Semiempirical molecular-orbital calculation shows that such narrow tubular structure is more stable than the corresponding opened fragment in the innermost zone of a large CNT. Simulated TEM images show that an extra-narrow CNT does not show the typical CNT image regardless of the microscopic resolution. In order to aid experimental identification, the Raman spectrum of the (4,0) CNT obtained from HF calculation shows ${A}_{1g}$ breathing modes in $489--725 {\mathrm{cm}}^{\ensuremath{-}1}.$
Probing the Ultrafast Solution Dynamics of a Cyanine Dye in an Organic Solvent Interfaced with Water (2009)

Dependence of ultrafast dynamics on the excited state evolution and ground state recovery of a cyanine dye (IR125) in dichloromethane (DCM) solvent interfaced with neat water is presented. We use degenerate pump-probe transient absorption spectroscopy to show that the excited-state dynamics of the dye molecule is strongly dependent on the position of the measurements from bulk DCM solution to the solution near the water layer. The decay component of the transient corresponding to the excited state lifetime increases from bulk DCM solution to its interface with water. Such results show that the effect of the presence of water layer over the dye solution in DCM extends several micrometers, indicating the surfactant nature of the IR125 molecules, and provides us a measure of the penetration of water into the DCM layer. The initial ultrafast decay component (coherent spike) directly correlates to the pulse-width of our near-transform limited pulses used in these experiments. This approach of measuring the excited state decay of a dye across an immiscible liquid interface can provide important characteristics of microtransport across such interfaces.
In Vitro Degradation of Poly(<scp>d</scp>,<scp>l</scp>-lactide-<i>co</i>-glycolide) Foams Processed with Supercritical Fluids (2015)

In the present study, we evaluated the degradation behavior of poly(d,l-lactide-co-glycolide) (PLGA) before and after foaming with supercritical CO2. Initial polymer samples, shaped as tablets, and foamed samples were immersed in a Sörensen buffer solution and maintained for 10 weeks at a constant temperature of 37 °C under mild stirring (50 rpm). The pH of the degradation environment was monitored, and the mass and structure modifications suffered by the samples at various stages of the study were determined. A comparison was performed between the in vitro behaviors of the PLGA samples before and after supercritical fluid processing. It was observed that the PLGA foams degrade slower than the PLGA tablets. These data are essential for evaluating the suitability of various processing methods in the design of biodegradable medical devices or implants with well-defined requirements regarding their stability and mechanical properties during specific applications.
Microseismic Mapping of Hydraulic Fractures Using Multi-Level Wireline Receivers (1995)

Abstract Hydraulic fracture diagnostic experiments are being conducted at the GRI/DOE Multi-Site (M-Site) located in the Piceance basin of Colorado. Tests described in this paper use s multi-level advanced-receiver system to bu¡!d on previous work that showed the advantages of using a single advanced receiver to monitor microseisms. The current test has a four-level receiver system monitoring four separate fracture experiments conducted over a one week period, and includes a velocity tomographic survey and detailed orientation survey. Hydraulic fractures were monitored from an offset well 210 ft away from the treatment well The results of these monitoring tests show a fracture developing asymmetrically with time, yielding a fracture-wing asymmetry of 2:1. The fracture initially grows within the pay zone to essentially its total length, and then begins to grow upward, and later in time grow downward. Comparison with fracture models gives only a partial agreement in the final size.
New functionalities of the 3.0 version of TFEL, MFront and MTest (2017)

International audience
Potential‐sensitive membrane association of a fluorescent dye (1987)

Unilamellar phosphatidylcholine/cholesterol (5:1, w/w) vesicles and the fluorescent dye safranine O mixed in appropriate ratios produced a membrane potential‐dependent enhancement of dye fluorescence. The fluorescence enhancement was shown to be dependent on the sign and magnitude of valinomycin‐induced potassium diffusion potentials. The enhancement and a blue‐shifted maximum (both of which also occur in ethanol vs aqueous solution) provided evidence that the enhanced fluorescence arises from an additional population of safranine O molecules which become associated with a hydrophobic region of the vesicular membrane. Consistent with this interpretation, the polarization of safranine O fluorescence was also found to increase in a potential‐dependent manner. A time‐dependent decay of the fluorescence enhancement — presumably due to decay of the membrane potential — was attributed to non‐specific ion leakage at valinomycin concentrations above 3 μM.
Bedside, Benchtop, and Bioengineering: Physicochemical Imaging Techniques in Biomineralization (2016)

The need to quantify physicochemical properties of mineralization spans many fields. Clinicians, mineralization researchers, and bone tissue bioengineers need to be able to measure the distribution, quantity, and the mechanical and chemical properties of mineralization within a wide variety of substrates from injured muscle to electrospun polymer scaffolds and everything in between. The techniques available to measure these properties are highly diverse in terms of their complexity and utility. Therefore it is of the utmost importance that those who intend to use them have a clear understanding of the advantages and disadvantages of each technique and its appropriateness to their specific application. This review provides all of this information for each technique and uses heterotopic ossification and engineered bone substitutes as examples to illustrate how these techniques have been applied. In addition, we provide novel data using advanced techniques to analyze human samples of combat related heterotopic ossification.
Proteomic Analysis of the Xanthan-Degrading Pathway of <i>Microbacterium</i> sp. XT11 (2019)

Xanthan, a highly stable polysaccharide which is not easily degraded by most microorganisms, contains a cellulosic backbone with trisaccharide side chains composed of mannosyl-glucuronyl-mannose attached α-1,3 to alternating glucosyl residues. Different digestion strategies were first applied to demonstrate the complexity about the proteomes of <i>Microbacterium</i> sp. XT11 in xanthan medium and glucose medium. Significantly up-regulated proteins induced by xanthan were screened out by the label-free quantitation of the proteomes of <i>Microbacterium</i> sp. XT11 in xanthan medium and glucose medium. Consequently, 2746 and 2878 proteins were identified in proteomes of <i>Microbacterium</i> sp. XT11 in xanthan medium and glucose medium individually, which represent 80.6 and 84.4% of total protein dataset predicted to be expressed by the gene. In the list of 430 induced proteins containing the proteins specifically expressed or up-regulated in xanthan medium, 19 proteins involved in carbohydrate-active enzymes database and 38 proteins annotated with transporter activity were critical in the degrading pathway of xanthan. Four CAZymes (GH3, GH38, GH9, and PL8) and one ABC transporter (LX1-1GL001097) were verified with quantitative real-time polymerase chain reaction. Four CAZymes (GH3, GH38, GH9, and PL8) were further verified with the enzyme assay. This study suggests a xanthan-degrading pathway in <i>Microbacterium</i> sp. XT11, and other potential xanthan degradation-related proteins still need further investigation.
Development of Nemo remotely operated underwater vehicle for the inspection of the Costa Concordia wreck (2015)

Remotely operated underwater vehicles are mobile robots increasingly used in underwater applications; these devices are widely used and suitable for different scenarios, for example, for patrolling and monitoring and also for underwater interventions. In the last 30 years, the remotely operated underwater vehicles have become more and more advanced; at the same rate with the progressive technological development of these vehicles, the market of the specialized component industry is fast-increasing. Generally speaking, a remotely operated underwater vehicle allows to investigate areas inaccessible or too dangerous for human beings. The use of remotely operated underwater vehicles during a mission, with the related implication of support ships and specialized pilots, or the involvement of professional divers, is usually associated with high costs. The reduction of these costs is an important topic in the underwater robotic field and the easy piloting of these mobile robots is a crucial aspect in their development. This article describes Nemo remotely operated underwater vehicle, a remotely operated underwater vehicle prototype specifically designed for the exploration of the Costa Concordia wreck, Isola del Giglio, Italy. Nemo remotely operated underwater vehicle can be considered a mini-remotely operated underwater vehicle, that is, a remotely operated underwater vehicle with weight less than 25 kg and easily deployable from a small boat. This article describes the main characteristics of the vehicle: the onboard control logic and on the development of a user-friendly graphical user interface for underwater navigation able to take advantage of its high maneuverability. It is worth to note that the developed graphical user interface enables to operate the vehicle even to inexperienced pilots. Preliminary experimental data collected during navigation are provided.
Stimulation of epithelial membrane antigen expression by transforming growth factor-beta in normal and oncogene-transformed human mammary epithelial cells. (1989)

Transforming growth factor-beta (TGF beta) appears to play a role in regulating the expression of tissue-specific proteins in human mammary epithelial cells (HMEC), regardless of the state of malignant transformation. We demonstrated this by utilizing a series of normal, immortalized, and oncogene-transformed (SV40 T and v-Ha-ras) HMEC derived from one individual, and assaying for expression of a milk fat globule/epithelial membrane antigen (EMA) reactive with E29/EP1 monoclonal antibody. EMA was increased by TGF beta in all HMEC examined. This effect appeared to be dose-dependent between 5 and 15 ng/ml in the normal, immortalized, and v-Ha-ras-transformed cells but saturated at 5 ng/ml in the SV40 T-transformed cells. The SV40 T-transformed cells showed both enhanced basal expression of EMA and increased sensitivity to TGF beta stimulation of EMA expression. The degree of increase in EMA induced by TGF beta was proportional to the level of basal expression in each cell type and appeared to be unrelated to either the number of high affinity TGF beta receptors, or the relative sensitivity to growth inhibition by TGF beta. Therefore, the TGF beta effect on EMA appears to be modulated at a level beyond receptors in these cells. EMA expression was also stimulated by sodium butyrate and dexamethasone (both differentiating agents) in some of the HMEC. The effect of butyrate on EMA expression is consistent with previous findings in which butyrate selectively enhanced production of milk fat globule antigens in the breast tumor cell line MCF-7, ZR-75-1, MDA-MB-134, and MDA-MB-468 cells. The coupled effects of TGF beta and SV40 T-transformation in enhancing the expression of EMA, and the possible effect of SV40 T increasing the responsiveness to TGF beta, may provide a new model for the study of the effect of growth factors in regulating specific gene expression in human breast epithelial cells.
IR absorption spectra for isolated PFAS molecules using density functional theory (2021)

Calculations are presented of vibrational absorption spectra for isolated PFAS molecules using density function theory (DFT). These contaminants are among widely spread carcinogens in the environment of industrial countries. DFT calculated absorption spectra of isolated molecules represent quantitative estimates that can be correlated with additional information obtained from laboratory measurements. The DFT software GAUSSIAN was used for calculating the infrared (IR) spectra presented here. DFT calculated spectra can be used to construct templates, which are for spectral-feature comparison, and thus detection of spectral-signature features associated with target materials.
Whole genome sequencing data of Pakistani descent (2018)

A summary of functionally annotated variants in H2 genome. The Ensembl Variant Effect Predictor (VEP) tool was used to categorize total variants as synonymous, nonsynonymous, benign or damaging.
A sliding IF receiver for mm-wave WLANs in 65nm CMOS (2009)

This paper presents a fully integrated receiver for mm-wave WLANs comprising LNA, RF mixer, quadrature IF mixers, local oscillator plus output stage for characterization, in 65 nm CMOS. The IF frequency set to 1/3 the RF frequency slides according to the received frequency. The architecture choice allows running the quadrature VCO around 20 GHz. A Phase Noise of -115 dBc/Hz @ 10 MHz offset from an equivalent LO at RF carrier is achieved with 36 mW power consumption and 12.5% frequency tuning range. The design of building blocks is discussed in details. Implemented prototypes use low-power digital devices and other measured performances are: 28 dB peak gain, 9 dB noise figure, 5 GHz RF bandwidth, -26 dBm 1-dB compression point, Gt 60 dB IRR. Total Power consumption is 80 mW from 1.5 V supply.
&lt;title&gt;Corneal modeling using conic section fits of PAR corneal topography system measurements&lt;/title&gt; (2001)

The purpose of this study was to measure the average shape and variability of human corneas and to develop a tool for analyzing, height, curvature, and aberrations based on a conic section model. Fresh Eye Bank Eyes were placed in Dextran until the corneal thickness reached a physiological value. The eyes were placed in a custom made holder and measured using an intraoperative PAR Corneal Topography System (CTS) mounted on an operation microscope. Topography was measured before and after removal of the epithelium. A series of MATLAB functions were written to analyze the raw-z (height) data in polar coordinates. The functions fit conic sections to the PAR CTS data along hemi-meridians at 5 degree(s) intervals. The conic shape factor and apical radius were used to calculate and display the curvature. The dependence of these parameters with meridional position was examined.
Analysis and design of an omni-directional antenna with enhanced E-plane directivity using cylindrical EBG surfaces (2006)

In this paper, a new method is presented for increasing the E-plane directivity of single dipole antennas by incorporating cylindrical metallo-dielectric electromagnetic bandgap (CMEBG) surfaces. Initially, the proposed structure is analysed for infinite CMEBG array length which is centre-fed by a simple radiating source using 3D full-wave simulation techniques. The analysis yields insight for the design and realisation of an omni-directional H-plane CMEGB antenna with enhanced E-plane directivity. The use of aperture arrays is employed to achieve significantly smaller unit cell. A comparative study between aperture and conducting CMEBG arrays illustrates what are the advantages and disadvantages of each structure. The cylindrical MEBG arrays behave as partially reflecting surfaces (PRSs) forming a cylindrical resonant cavity. A balanced dipole antenna is used as the feeder at the centre of the cavity. The directivity enhancement is demonstrated with simulated and measured results for an antenna prototype operating at about 2.4 GHz. A maximum directivity improvement of about four times is achieved.
Data from An Autocrine Loop between TGF-β1 and the Transcription Factor Brachyury Controls the Transition of Human Carcinoma Cells into a Mesenchymal Phenotype (2023)

&lt;div&gt;Abstract&lt;p&gt;The epithelial–mesenchymal transition (EMT) is a process associated with the metastasis of solid tumors as well as with the acquisition of resistance to standard anticancer modalities. A major initiator of EMT in carcinoma cells is TGF-β, which has been shown to induce the expression of several transcription factors ultimately responsible for initiating and maintaining the EMT program. We have previously identified Brachyury, a T-box transcription factor, as an inducer of mesenchymal features in human carcinoma cells. In this study, a potential link between Brachyury and TGF-β signaling has been investigated. The results show for the first time that Brachyury expression is enhanced during TGF-β1–induced EMT in various human cancer cell lines, and that a positive feedback loop is established between Brachyury and TGF-β1 in mesenchymal-like tumor cells. In this context, Brachyury overexpression is shown to promote upregulation of TGF-β1 at the mRNA and protein levels, an effect mediated by activation of the TGF-β1 promoter in the presence of high levels of Brachyury. Furthermore, inhibition of TGF-β1 signaling by a small-molecule inhibitor of TGF-β receptor type I decreases Brachyury expression, induces a mesenchymal-to-epithelial transition, and renders cancer cells more susceptible to chemotherapy. This study thus has implications for the future development of clinical trials using TGF-β inhibitors in combination with other anticancer agents. &lt;i&gt;Mol Cancer Ther; 12(9); 1805–15. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Pulsed EPR spectrometer (1987)

A pulsed EPR spectrometer is described. This spectrometer is designed for the study of relaxation times of dilute solutions of samples in common solvents as a function of temperature both above and below room temperature. Resolution of pulse widths and spacings is 1 ns. Both continuous wave (cw) and pulsed electron spin-echo studies can be done on the same sample on the same spectrometer. Details of component choices and timing synchronization are provided. Phase alternation sequences for eliminating unwanted echoes are described. Examples of performance of the spectrometer are presented.
Two-phase cooperative jamming and beamforming for physical layer secrecy (2015)

The broadcast nature of wireless communications makes the propagation medium vulnerable to security attacks such as eavesdropping and jamming from adversarial or unauthorized users. Applying physical layer secrecy approaches will enable the exchange of confidential messages over a wireless medium in the presence of unauthorized eavesdroppers, without using any secret keys. However, physical layer security approaches are typically feasible only when the source-eavesdropper channel is weaker than the source-destination channel. Cooperative jamming can be used to overcome this challenge and increase the secrecy rate. In this paper, the security of two-phase relaying system with multiple intermediate nodes and in the presence of an eavesdropper is investigated. To enhance the system secrecy rate, a joint cooperative beamforming and jamming combined with relay and jammer selections is proposed. In phase I, the source node broadcasts a signal to relays while three intermediate nodes (which act as jammers) help the source node by transmitting random jamming signals to confuse the eavesdropper. Since the friendly (cooperative) jammers create interference for both the intended relays and the eavesdropper, optimal beamforming is applied such that no interference is caused at two preselected desired relays (that are going to receive the confidential massage in phase I). In phase II, two preselected relays transmit the source message with beamforming coefficients such that the received signal at the eavesdropper is completely nulled out. Our goal in this paper is to minimize the received SNR at the eavesdropper while increasing it at the destination as much as possible by applying different methods such as cooperative beamforming, cooperative jamming and relay selection. To avoid operational complexity, we consider the minimum number of intermediate nodes that are necessary without losing the performance. Numerical results demonstrate the advantage of our proposed scheme compared with the scheme with no cooperative jamming.
ChemInform Abstract: Bora‐Aromatic Systems. Part 12. Thermal Generation and Transformation of the Borepin Ring System: A Paradigm of Pericyclic Processes. (1990)

Abstract The synthesis of the borepin ring system, e.g. (IV), resulting from interaction of an alkyne with the highly reactive borole ring such as (I) and the occurrence of an unusual sequence of skeletal rearrangements is well known.
Luteinizing Hormone and Follicle-Stimulating Hormone Exhibit Different Secretion Patterns from Cultured Madin-Darby Canine Kidney Cells (2004)

LH, FSH, and chorionic gonadotropin (CG) are comprised of a common alpha subunit and a hormone-specific beta subunit. Using Madin-Darby canine kidney (MDCK) epithelial cells to examine the polarized secretion of human CG/LH, we previously reported that CG and LH were detected in the apical and basolateral compartments, respectively, and the carboxyl terminal end of the CGbeta subunit contains a strong apical signal. Here we show that the carboxyl seven amino acids in the LHbeta subunit contribute to the basolateral secretion of LH, and an LH chimera bearing the CGbeta apical signal is redirected from the basolateral to the apical compartments. Because LH and FSH are synthesized in the same cell, we also compared the secretion polarity of LH with FSH. MDCK cells expressing the FSH dimer displayed an almost equal distribution of protein into the apical and basolateral compartments. Given that the LHbeta and CGbeta carboxy terminal sequences, which differ from that in the FSHbeta subunit, occupy a pivotal role in their polarized behavior, the results support the hypothesis that pituitary exit of LH and FSH occur via different secretion pathways, and are released spatially from the pituitary via different circulatory routes.
An adaptation layer for real-time interoperability between legacy 100MbE and 40Gb/s (and beyond) optical label switched networks (2011)

We present a method, scalable to 1Tb/s transmission systems, of performing electronic lookup on asynchronous 40Gb/s burst mode channels to facilitate real-time end-to-end interoperability between legacy 100MbE networks and 40Gb/s optical label switched networks.