gebhart/patrepeval huggingface dataset:
Studies on the human intestinal di-/tripeptide transporter HPT-1 as a potential carrier for orally administered drugs (1998)

The purpose of the present study was to isolate and characterize the human intestinal di-/tripeptide transporter HPT-1 and to establish functional assays using isolated HPT-1. In addition, molecular recognition between the immobilized artificial membranes and solute molecules was also investigated in this study. HPT-1 was isolated for the first time from Caco-2 cell membranes and human intestinal brush border membranes. An efficient two-step procedure has been developed to purify sufficient quantity of HPT-1 for functional assays. In the first step of purification, a lectin was selected to remove over 95% of contaminating proteins. The second step uses either IAM (immobilized artificial membrane) chromatography or immobilized monoclonal antibodies that block the transport function of HPT-1. Amino acid sequencing confirmed that the isolated protein was HPT-1. A model of the membrane topology of HPT-1 was proposed based on amino acid sequence analysis. The purified HPT-1 was functional after being reconstituted in liposomes. Moreover, HPT-1 isoforms have been identified in different human intestinal segments. This study establishes the foundation for future studies on substrate structural requirements of HPT-1. Molecular dynamics (MD) simulations have been used in this study to provide molecular insights into the interactions involved in solute partitioning into the IAM surface. It was observed during the MD simulations that IAM surfaces not only model all interactions involved in solute partitioning into phospholipid membranes, but are also flexible enough to form solute cavities. Inside the solute cavities in IAM surfaces, the solute molecules adopt specific orientations which are determined by interactions between the solutes and IAM phospholipids. Consequently, different solutes have different solvent accessible surface areas and contact with different parts of phospholipids. All these factors profoundly affect the overall interaction energy between the solutes and their boundary phospholipids, and regulate solute partitioning in fluid and immobilized membranes. This is the first study to demonstrate the importance of the unique microstructure of IAM surfaces, in addition to their bulk interfacial properties, in predicting drug-membrane interaction and drug transport across biological membranes.
Improvement of Biological Indicators by Uniformly Distributing Bacillus subtilis Spores in Monolayers To Evaluate Enhanced Spore Decontamination Technologies (2016)

Novel decontamination technologies, including cold low-pressure plasma and blue light (400 nm), are promising alternatives to conventional surface decontamination methods. However, the standardization of the assessment of such sterilization processes remains to be accomplished. Bacterial endospores of the genera Bacillus and Geobacillus are frequently used as biological indicators (BIs) of sterility. Ensuring standardized and reproducible BIs for reliable testing procedures is a significant problem in industrial settings. In this study, an electrically driven spray deposition device was developed, allowing fast, reproducible, and homogeneous preparation of Bacillus subtilis 168 spore monolayers on glass surfaces. A detailed description of the structural design as well as the operating principle of the spraying device is given. The reproducible formation of spore monolayers of up to 5 × 10(7) spores per sample was verified by scanning electron microscopy. Surface inactivation studies revealed that monolayered spores were inactivated by UV-C (254 nm), low-pressure argon plasma (500 W, 10 Pa, 100 standard cubic cm per min), and blue light (400 nm) significantly faster than multilayered spores were. We have thus succeeded in the uniform preparation of reproducible, highly concentrated spore monolayers with the potential to generate BIs for a variety of nonpenetrating surface decontamination techniques.
Levels of CEA and Ca 19 - 9 in the sera and peritoneal cavity in patients with gastric and pancreatic cancers (2012)

Levels of tumor markers in sera could signalize inoperability of tumor (Ca 19 - 9 in cases of pancreatic carcinoma); peritoneal levels could predict R1 resection especially in gastric cancer patients and risk of early peritoneal recurrence of the disease. Difference between the levels in the peritoneum and sera may signalize the route of dissemination (hematogenous and intraperitoneal).
A study on treeing breakdown and fractal characteristics according to method of acoustic emission detection in high polymer (2002)

In this study, in order to observe treeing deterioration and tree shape in relation to fractal dimension, acoustic emission properties due to growth of tree in Polymer was investigated by using the measuring system of AE under AC voltage. The generated tree was photographed with a camera through a microscope. The obtained photograph was digitized by using a scanner and image processed with a personal computer. After that, the tree length was measured and then the fractal dimension of tree was calculated in using a scale covering method. And growing shape of tree was quantified in using fractal characteristics. To examine relation among growing shape of tree and characteristics of fractal in tree shape (tree type and bush type) was increased with increment of applied AC, AE pulse number and mean amplitude were increased along with near breakdown rather than tree initiation. While AE pulse number and mean amplitude were promoted, fractal was slowly increased with tree growth. Fractal dimension in accord to applied voltage was slowly increased, the results show that there is a relationship between characteristics of AE and fractal dimension.
Early Denervation and Later Reinnervation of the Heart Following Cardiac Transplantation: A Review (2016)

Although cardiac denervation occurs immediately after HTx, cardiac reinnervation is a variable phenomenon and is still
Crosswell electromagnetic tomography in steel-cased wells (1995)

Abstract The applicability of crosswell electromagnetic (EM) tomography is limited when the boreholes are steel cased. Steel casing is typically eight orders of magnitude more conductive than the formations around the borehole. Consequently, the high frequency signals which are needed to resolve the formation conductivity distribution in the interwell region cannot be radiated or received by antennas inside the casing. Introduction of small insulating gaps in the casing eliminates these problems by creating ports where signals can exit and enter the casing, making the casing an electric bipole antenna. The gapped casing can be operated in a shorted-port or open-port mode. In the shorted-port mode, the voltage is specified at a source port, and the current is measured at all the remaining shorted ports. In the open-port mode, the current is specified at a source port, and the voltage is measured at all the remaining open ports. For high-frequency shorted-port operation, the effective length of the casing bipole antenna is determined by the skin depth in the formations surrounding the casing. For high-frequency open-port operation, the effective length of the casing bipole antenna is determined by the casing gap interval, provided that it is less than the formation skin depth. The open-port mode is preferred.The interval between casing gaps is determined mainly by the well spacing. If the effective bipole length is proportional to the well spacing, the crosswell signal-to-noise ratio is approximately independent of the well spacing and the interwell resolution is approximately proportional to the well spacing at constant source input power. For large well spacings, gapped casing antennas outperform open-hole tools.Steel-cased wells completed or retrofitted with insulating gaps offer a stable, low-cost, permanent set of electrodes to implement long-term monitoring of petroleum reservoir fluid movements. Gapped casings offer a practical way to achieve high-frequency, wide-aperture EM tomographic datasets at large well spacings. Gapped casings can also be used for deep EM probing of the formations around a single well.
Numerical Prediction of Signal for Magnetic Flux Leakage Benchmark Task (2003)

Numerical results predicted by the finite element method based code are presented. The nonlinear magnetic time‐dependent benchmark problem proposed by the World Federation of Nondestructive Evaluation Centers, involves numerical prediction of normal (radial) component of the leaked field in the vicinity of two practically rectangular notches machined on a rotating steel pipe (with known nonlinear magnetic characteristic). One notch is located on external surface of pipe and other is on internal one, and both are oriented axially.
Smart Nanocomposite Polymer Membranes with On/Off Switching Control (2006)

Novel composite-gel membranes capable of regulating permeability in response to external temperature change are being explored. These membranes containing ordered nanochannels can act as “on−off” switches or “permeability valves”. The channels are designed to contain an ordered array of core−shell type magnetic polystyrene latex particles that can change their size in response to external stimuli. Expansion and contraction of the thin shell of magnetic latex particles affect the permeation pattern from the membrane “on” state to “off” state.
Reaktionen am (+)Z‐3,6‐Bis(aminooxymethyl)‐piperazin‐2,5‐dion, 2. Mitt.<sup>1</sup> Selektive Eliminations‐Additionsreaktionen (1979)

Abstract Die Acceptoreigenschaften von 3,6‐Dimethylen‐piperazin‐2,5‐dion (2) , dem Abbauprodukt von (+)‐ Z ‐3,6‐Bis(aminooxymethyl)‐piperazin‐2,5‐dion (1) sind pH abhängig: Reaktionen mit Nucleophilen bei pH unter 7 führen zu den Monoadditionsprodukten 3a, 3b und 5 , bei pH über 7 zu den Bisadditionsprodukten 4a, 4b, 6 und 8 . Die selben Additionsprodukte werden erhalten, wenn an Stelle von 2 dessen Vorstufe 1 eingesetzt wird. 4b und 6 sind außerdem durch Zweitaddition an 3b und 5 darstellbar.
Arthroscopic subacromial decompression: Results according to the degree of rotator cuff tear (1988)

We evaluated the results of arthroscopic subacromial decompression according to the degree of rotator cuff tear in 71 patients, available for follow-up for at least 1 year (average 19 months). Of the patients with stage II disease, 82% were satisfied regardless of whether they had no rotator cuff tear (nine of 11) or had a partial tear (28 of 34) of the rotator cuff. Of patients with stage III disease (complete rotator cuff tear), 88% (23 of 26) were satisfied. An acceptable objective UCLA shoulder rating greater than or equal to 28 points was seen in 82% (nine of 11) of the patients without a rotator cuff tear, 76% (26 of 34) with a partial tear, and 77% (20 of 26) with a complete tear. All four of the patients with complete tears less than 1 cm obtained excellent results. Three of the six failures were in patients with complete tears who had a narrowed acromial-humeral distance of less than 7 mm. The average UCLA pain score showed significant improvement from 2.8 (constant pain) to 8.6 (occasional pain) at 1-2 years postoperatively. The function, strength, and active forward flexion scores also increased at 1-2 years from their preoperative values. The overall patient satisfaction rate of 85% and the objective success rate of 77% are within the range of that seen with open rotator cuff repair.
Photomixing Experiments with a Ruby Optical Maser and a Traveling-Wave Microwave Phototube (1962)

A standard oxide-cathode S-band traveling-wave tube has been used as an improvised microwave phototube to study the coherent light output from a ruby optical maser (laser). The laser’s output consists of simultaneous, discrete optical components separated by the mode interval of 600 Mc/s between axial modes in the 12.5 cm laser rod. These components heterodyne in the TWT cathode to produce easily observed microwave outputs within the TWT bandwidth, corresponding to photobeats between third-through seventh-nearest-neighbor axial modes. This technique is a powerful tool for the study of optical masers, and also has important implications for communications via microwave-modulated light.
Midgap states and charge inhomogeneities in corrugated graphene (2007)

We study the changes induced by the effective gauge field due to ripples on the low energy electronic structure of graphene. We show that zero energy Landau levels will form, associated to the smooth deformation of the graphene layer, when the height corrugation, $h$, and the length of the ripple, $l$, are such that $h^2 / (l a) \gtrsim 1$, where $a$ is the lattice constant. The existence of localized levels gives rise to a large compressibility at zero energy, and to the enhancement of instabilities arising from electron-electron interactions including electronic phase separation. The combined effect of the ripples and an external magnetic field breaks the valley symmetry of graphene leading to the possibility of valley selection.
Iterative noise and channel estimation under the stochastic matching algorithm framework (1997)

In this letter, we introduce an unsupervised iterative algorithm to adapt HMMs trained using clean speech in order to recognize speech corrupted by an additive and a convolutional noise. Both types of noise are considered as stochastic processes that can be modeled using HMMs and can be estimated by applying Sankar's stochastic matching (SM) algorithm successively in the cepstral and in the linear spectral domain. These estimates are derived directly from the given test speech signal and the set of clean speech models, and lead to the estimation of a new set of HMMs that maximize the likelihood of the test signal.
Cancer Immunotherapy: Accomplishments to Date and Future Promise (2013)

Cancer remains a devastating disease as existing therapies are too often ineffective and toxicities remain unacceptably high. Immunotherapies for cancer offer the promise of the specificity and memory of the immune system against malignant cells to achieve durable cure with minimal toxicity. Beginning with the success of bone marrow transplantation for blood-borne cancers, and the more recent development of monoclonal antibody therapeutics for a variety of tumors, immunotherapies are already among the most successful class of treatments for cancer. Greater understanding of immunoregulatory mechanisms and improved techniques for immune cell manipulation and engineering have led to new immunomodulatory approaches and cell-based therapies for cancer that have generated great excitement within the biomedical community. As these technologies continue to improve, and as new approaches for harnessing the power and specificity of the immune system are developed, immunotherapies will play an increasingly important role in the treatment of cancer. Here, we review the history of immunotherapies for cancer and discuss existing and emerging immunotherapy technologies that hope to translate the promise of immunotherapy into clinical reality.
Synthesis of 2,3-Disubstituted Benzo[<i>b</i>]furans by the Palladium-Catalyzed Coupling of<i>o-</i>Iodoanisoles and Terminal Alkynes, Followed by Electrophilic Cyclization (2005)

[reaction: see text] 2,3-Disubstituted benzo[b]furans are readily prepared under very mild reaction conditions by the palladium/copper-catalyzed cross-coupling of various o-iodoanisoles and terminal alkynes, followed by electrophilic cyclization with I2, PhSeCl, or p-O2NC6H4SCl. Aryl- and vinylic-substituted alkynes undergo electrophilic cyclization in excellent yields. Biologically important furopyridines can be prepared by this approach in high yields.
Fatty acid regulates gene expression and growth of human prostate cancer PC-3 cells (2001)

It has been proposed that the omega-6 fatty acids increase the rate of tumor growth. Here we test that hypothesis in the PC-3 human prostate tumor. We found that the essential fatty acids, linoleic acid (LA) and arachidonic acid (AA), and the AA metabolite PGE(2) stimulate tumor growth while oleic acid (OA) and the omega-3 fatty acid, eicosapentaenoic acid (EPA) inhibited growth. In examining the role of AA in growth response, we extended our studies to analyze changes in early gene expression induced by AA. We demonstrate that c-fos expression is increased within minutes of addition in a dose-dependent manner. Moreover, the immediate early gene cox-2 is also increased in the presence of AA in a dose-dependent manner, while the constitutive cox-1 message was not increased. Three hours after exposure to AA, the synthesis of PGE(2) via COX-2 was also increased. Previous studies have demonstrated that AA was primarily delivered by low density lipoprotein (LDL) via its receptor (LDLr). Since it is known that hepatomas, acute myelogenous leukemia and colorectal tumors lack normal cholesterol feedback, we examined the role of the LDLr in growth regulation of the PC-3 prostate cancer cells. Analysis of ldlr mRNA expression and LDLr function demonstrated that human PC-3 prostate cancer cells lack normal feedback regulation. While exogenous LDL caused a significant stimulation of cell growth and PGE(2) synthesis, no change was seen in regulation of the LDLr by LDL. Taken together, these data show that normal cholesterol feedback of ldlr message and protein is lost in prostate cancer. These data suggest that unregulated over-expression of LDLr in tumor cells would permit increased availability of AA, which induces immediate early genes c-fos and cox-2 within minutes of uptake.
Extraordinarily slow nuclear spin relaxation in frozen laser-polarized<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mrow><mml:mi mathvariant="normal">Xe</mml:mi></mml:mrow><mml:mprescripts/><mml:mrow/><mml:mrow><mml:mn>129</mml:mn></mml:mrow><mml:mrow/><mml:mrow/></mml:mmultiscripts></mml:mrow></mml:math> (1993)

We studied the very slow nuclear spin-lattice relaxation of solid $^{129}\mathrm{Xe}$ as a function of temperature and magnetic field using laser-polarized nuclei. Relaxation times in excess of 500 h were measured. We present evidence for a new relaxation mechanism which results from a Raman spin-phonon scattering process involving the spin-rotation interaction. We also establish the existence of cross relaxation between $^{129}\mathrm{Xe}$ and the other magnetic isotope $^{131}\mathrm{Xe}$ and demonstrate that laser-polarized $^{129}\mathrm{Xe}$ can be used to cross polarize other nuclei that are present in the lattice.
Detecting Stealthy False Data Injection Using Machine Learning in Smart Grid (2014)

Aging power industries, together with the increase in demand from industrial and residential customers, are the main incentive for policy makers to define a road map to the next-generation power system called the smart grid. In the smart grid, the overall monitoring costs will be decreased, but at the same time, the risk of cyber attacks might be increased. Recently, a new type of attacks (called the stealth attack) has been introduced, which cannot be detected by the traditional bad data detection using state estimation. In this paper, we show how normal operations of power networks can be statistically distinguished from the case under stealthy attacks. We propose two machine-learning-based techniques for stealthy attack detection. The first method utilizes supervised learning over labeled data and trains a distributed support vector machine (SVM). The design of the distributed SVM is based on the alternating direction method of multipliers, which offers provable optimality and convergence rate. The second method requires no training data and detects the deviation in measurements. In both methods, principal component analysis is used to reduce the dimensionality of the data to be processed, which leads to lower computation complexities. The results of the proposed detection methods on IEEE standard test systems demonstrate the effectiveness of both schemes.
Knowledge-Based Speech Enhancement (2005)

Speech is a fundamental means of human communication. In the last several decades, much effort has been devoted to the efficient transmission and storage of speech signals. With advances in technology making mobile communication ubiquitous, communications anywhere has become a reality. The freedom and flexibility offered by mobile technology brings with it new challenges, one of which is robustness to acoustic background noise. Speech enhancement systems form a vital front-end for mobile telephony in noisy environments such as in cars, cafeterias, subway stations, etc., in hearing aids, and to improve the performance of speech recognition systems. In this thesis, which consists of four research articles, we discuss both single and multi-microphone approaches to speech enhancement. The main contribution of this thesis is a framework to exploit available prior knowledge about both speech and noise. The physiology of speech production places a constraint on the possible shapes of the speech spectral envelope, and this information s captured using codebooks of speech linear predictive (LP) coefficients obtained from a large training database. Similarly, information about commonly occurring noise types is captured using a set of noise codebooks, which can be combined with sound environment classi¯cation to treat different environments differently. In paper A, we introduce maximum-likelihood estimation of the speech and noise LP parameters using the codebooks. The codebooks capture only the spectral shape. The speech and noise gain factors are obtained through a frame-by-frame optimization, providing good performance in practical nonstationary noise environments. The estimated parameters are subsequently used in a Wiener filter. Paper B describes Bayesian minimum mean squared error estimation of the speech and noise LP parameters and functions there-of, while retaining the in- stantaneous gain computation. Both memoryless and memory-based estimators are derived. While papers A and B describe single-channel techniques, paper C describes a multi-channel Bayesian speech enhancement approach, where, in addition to temporal processing, the spatial diversity provided by multiple microphones s also exploited. In paper D, we introduce a multi-channel noise reduction technique motivated by blind source separation (BSS) concepts. In contrast to standard BSS approaches, we use the knowledge that one of the signals is speech and that the other is noise, and exploit their different characteristics.
Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome (2020)

Mechanistic insights into the role of the human microbiome in the predisposition to and treatment of disease are limited by the lack of methods to precisely add or remove microbial strains or genes from complex communities. Here, we demonstrate that engineered bacteriophage M13 can be used to deliver DNA to Escherichia coli within the mouse gastrointestinal (GI) tract. Delivery of a programmable exogenous CRISPR-Cas9 system enabled the strain-specific depletion of fluorescently marked isogenic strains during competitive colonization and genomic deletions that encompass the target gene in mice colonized with a single strain. Multiple mechanisms enabled E. coli to escape targeting, including loss of the CRISPR array or even the entire CRISPR-Cas9 system. These results provide a robust and experimentally tractable platform for microbiome editing, a foundation for the refinement of this approach to increase targeting efficiency, and a proof-of-concept for the extension to other phage-bacterial pairs of interest.