gebhart/patrepeval huggingface dataset:
Development of Novel Nanobiosensor for Direct Measurement of the Oral Anticoagulant Agent: Dabigatran Etexilate (2018)

Abstract Dabigatran Etexilate is a new oral anticoagulant increasingly used for number of blood thrombosis conditions, prevention of strokes and systemic emboli among patients with atrial fibrillation. It provides safe and adequate anticoagulation for prevention and treatment of thrombus in several clinical settings. However, anticoagulation therapy can be associated with an increased risk of bleeding. There is a lack of specific laboratory tests to determine the level of this drug in blood. This is considered the most important obstacles of using this medication, particularly for patients with trauma, drug toxicity, in urgent need for surgical interventions or uncontrolled bleeding.The goal of this research project is to obtain and characterize DNA aptamers for Dabigatran Etexilate and to evaluate potential applications of these aptamers to develop low cost, sensitive, selective and user-friendly biosensors. In this work, we performed Systematic evolution of ligands by exponential enrichment (SELEX) to select specific DNA aptamers against dabigatran etexilate. Following multiple rounds of selection and enrichment with a randomized 60-mer DNA library, specific DNA aptamers for dabigatran were selected. We investigated the affinity and specificity of generated aptamers to the drug showing dissociation constants (Kd) ranging from 46.8- 208 nM. A preliminary application of one of the selected aptamers in an electrochemical nano-biosensor was successfully performed and showed high sensitivity and selectivity. This work represents novel work and clinically available. With further improvement of the assay and optimization, these aptamers are useful in developing Dabigatran Etexilate detection and analytical applications and with unique potentials of clinical uses in the near future. Disclosures No relevant conflicts of interest to declare.
Shelf-Life Enhancement of Donor Blood by He-Ne Laser Biostimulation (2015)

Shelf life of stored blood in a bank is an important parameter for the effective use of blood drawn from the donors. Several attempts have been made (such as antioxidant treatment and magnetic field intervention) to improve the above lifetime of 42 days. Here, we show that biostimulation by a He-Ne laser could enhance the shelf life to 63 days. The results are based on the fragility and conductivity measurement of red blood cells.
Postnatal Pancreas of Mice Contains Tripotent Progenitors Capable of Giving Rise to Duct, Acinar, and Endocrine Cells In Vitro (2015)

Postnatal pancreas is a potential source for progenitor cells to generate endocrine β-cells for treating type 1 diabetes. However, it remains unclear whether young (1-week-old) pancreas harbors multipotent progenitors capable of differentiating into duct, acinar, and endocrine cells. Laminin is an extracellular matrix (ECM) protein important for β-cells' survival and function. We established an artificial extracellular matrix (aECM) protein that contains the functional IKVAV (Ile-Lys-Val-Ala-Val) sequence derived from laminin (designated aECM-lam). Whether IKVAV is necessary for endocrine differentiation in vitro is unknown. To answer these questions, we cultured single cells from 1-week-old pancreas in semi-solid media supplemented with aECM-lam, aECM-scr (which contains a scrambled sequence instead of IKVAV), or Matrigel. We found that colonies were generated in all materials. Individual colonies were examined by microfluidic reverse transcription-polymerase chain reaction, immunostaining, and electron microscopy analyses. The majority of the colonies expressed markers for endocrine, acinar, and ductal lineages, demonstrating tri-lineage potential of individual colony-forming progenitors. Colonies grown in aECM-lam expressed higher levels of endocrine markers Insulin1, Insulin2, and Glucagon compared with those grown in aECM-scr and Matrigel, indicating that the IKVAV sequence enhances endocrine differentiation. In contrast, Matrigel was inhibitory for endocrine gene expression. Colonies grown in aECM-lam displayed the hallmarks of functional β-cells: mature insulin granules and glucose-stimulated insulin secretion. Colony-forming progenitors were enriched in the CD133(high) fraction and among 230 micro-manipulated single CD133(high) cells, four gave rise to colonies that expressed tri-lineage markers. We conclude that young postnatal pancreas contains multipotent progenitor cells and that aECM-lam promotes differentiation of β-like cells in vitro.
Chimeric CRISPR guides enhance Cas9 target specificity (2017)

Oligonucleotide-guided nucleases (OGNs) have enabled rapid advances in precision genome engineering. Though much effort has gone into characterizing and mitigating mismatch tolerance for the most widely adopted OGN, Streptococcus pyogenes Cas9 (SpCas9), potential off-target interactions may still limit applications where on-target specificity is critical. Here we present a new axis to control mismatch sensitivity along the recognition-conferring spacer sequence of SpCas9’s guide RNA (gRNA). We introduce mismatch-evading loweredthermostability guides (melt-guides) and exhibit how nucleotide-type substitutions in the spacer can reduce cleavage of sequences mismatched by as few as a single base pair. Cotransfecting melt-guides into human cell culture with an exonuclease involved in DNA repair, we observe indel formation on a standard genomic target at approximately 70% the rate of canonical gRNA and undetectable on off-target data.
Acoustic system for material transport (1984)

An object within a chamber is acoustically moved by applying wavelengths of different modes to the chamber to move the object between pressure wells formed by the modes. In one system, the object is placed in one end of the chamber while a resonant mode, applied along the length of the chamber, produces a pressure well at the location. The frequency is then switched to a second mode that produces a pressure well at the center of the chamber, to draw the object. When the object reaches the second pressure well and is still traveling towards the second end of the chamber, the acoustic frequency is again shifted to a third mode (which may equal the first model) that has a pressure well in the second end portion of the chamber, to draw the object. A heat source may be located near the second end of the chamber to heat the sample, and after the sample is heated it can be cooled by moving it in a corresponding manner back to the first end of the chamber. The transducers for levitating and moving the object may be all located at the cool first end of the chamber.
Monitoring dynamic alterations in calcium homeostasis by <i>T</i><sub>1</sub>‐weighted and <i>T</i><sub>1</sub>‐mapping cardiac manganese‐enhanced MRI in a murine myocardial infarction model (2008)

Manganese has been used as a T(1)-weighted MRI contrast agent in a variety of applications. Because manganese ions (Mn(2+)) enter viable myocardial cells via voltage-gated Ca(2+) channels, manganese-enhanced MRI is sensitive to the viability and inotropic state of the heart. In spite of the established importance of Ca(2+) regulation in the heart both before and after myocardial injury, monitoring strategies to assess Ca(2+) homeostasis in affected cardiac tissues are limited. This study implements a T(1)-mapping method to obtain quantitative information both dynamically and over a range of MnCl(2) infusion doses. To optimize the current Mn(2+) infusion protocols, we performed both dose-dependent and temporal washout studies. A non-linear relationship between infused MnCl(2) solution dose and increase in left ventricular wall relaxation rate (DeltaR(1)) was observed. Control mice also exhibited significant Mn(2+) clearance over time, with a decrease in DeltaR(1) of approximately 50% occurring in just 2.5 h. The complicated efflux time dependence possibly suggests multiple efflux mechanisms. With the use of the measured relationship between infused Mn(2+) dose, DeltaR(1), and inductively coupled plasma mass spectrometry data analysis provided a means of estimating the absolute heart Mn concentration in vivo. We show that this technique has the sensitivity to observe or monitor potential alterations in Ca(2+) handling in vivo because of the physiological remodeling after myocardial infarction. Left ventricular free wall DeltaR(1) values were significantly lower (P = 0.005) in the adjacent zone, surrounding the injured myocardial tissue, than in healthy tissue. This inferred reduction in Mn concentration can be used to estimate potentially salvageable myocardium in vivo for future treatment or evaluation of disease progression.
Lithium Ion Aqueous Cells. (1995)

Abstract : Lithium ion aqueous cells were investigated using lithium intercalating compounds as anodes and cathodes. The aqueous electrolyte consisted of 4 to 5 molar solutions of either lithium perchlorate or lithium nitrate which contained lithium hydroxide in millimolar amounts to make the solutions slightly basic with a pH of about 8.5. Several electrode combinations were evaluated using lithium intercalating compounds such as lithium cobalt oxide and lithium manganese oxide as cathodes and lithium vanadium oxide, lithium manganese oxide, titanium disulfide, and molybdenum dioxide as the anodes. The cell employing manganese oxide as both the anode and cathode exhibited good charge-discharge characteristics with an open circuit potential of about one volt. jg
Surface-Enhanced Raman Gene Probe for HIV Detection (1998)

We report, for the first time, the use of surface-enhanced Raman (SERS)-active labels for primers used in polymerase chain reaction amplification of specific target DNA sequences. This method has the potential for combining the spectral selectivity and high sensitivity of the SERS technique with the inherent molecular specificity offered by DNA sequence hybridization. The effectiveness of the detection scheme is demonstrated using the gag gene sequence of the human immunodeficiency virus. The potential use of multiple probes for simultaneous detection of multiple biological targets is discussed.
Low RBM3 protein expression correlates with tumour progression and poor prognosis in malignant melanoma: An analysis of 215 cases from the Malmö Diet and Cancer Study (2011)

In line with previous in vitro data, we here show that RBM3 is down-regulated in metastatic melanoma and high nuclear RBM3 expression in the primary tumour is an independent marker of a prolonged OS. The potential utility of RBM3 in treatment stratification of patients with melanoma should be pursued in future studies.
Different query verification approaches used to test entity SQL (2008)

Testing a query language is a complex and challenging task. A tester must determine the representative subset of queries which must be tested from an infinite set of valid queries. Once the representative set of queries is determined, they then face the task of verifying the results returned when the queries are executed.
Theory and Measurement of PMD in spun fibers (2004)

In this paper we focus under a theoretical point of view on spun fibers and in particular we analyze how periodic or constant spin profiles affect the PMD properties of a fiber. Moreover, we introduce a measurement technique based on polarization sensitive reflectometry that allows to control the quality of the spin process.
An unambiguous and practical synthesis of Oroxylin A: a commonly misidentified flavone (2019)

Oroxylin A, a major flavonoid in the extracts of <i>Oroxylum indicum</i> as well as <i>Scutellaria baicalensis</i> possesses useful medicinal properties. Many of the published routes claiming the synthesis of Oroxylin A (<b>1</b>) have in fact led to a regioisomer Negletein that was misinterpreted as Oroxylin A. In the present work, we describe a novel, straight-forward and scalable semi-synthetic approach for rapid access to the title compound, the structure of which is unambiguously secured by NMR and X-ray crystallographic analysis of a derivative. This work also encompasses the synthesis of a glycosylated derivative of Oroxylin A <i>viz</i> OAGME (<b>2</b>), which has marked pharmacological importance.
Optimal parking in group elevator control (2004)

We consider the problem of optimally parking empty cars in an elevator group so as to anticipate and intercept the arrival of new passengers and minimize their waiting times. Two solutions are proposed, for the down-peak and up-peak traffic patterns. We demonstrate that matching the distribution of free cars to the arrival distribution of passengers is sufficient to produce savings of up to 80% in down-peak traffic. Since this approach Is not useful for the much harder case of up-peak traffic, we propose a solution based on the representation of the elevator system as a Markov decision process (MDP) model with relatively few aggregated states, and determination of the optimal parking policy by means of dynamic programming on the MDP model.
TED (2019)

Artificial intelligence systems are being increasingly deployed due to their potential to increase the efficiency, scale, consistency, fairness, and accuracy of decisions. However, as many of these systems are opaque in their operation, there is a growing demand for such systems to provide explanations for their decisions. Conventional approaches to this problem attempt to expose or discover the inner workings of a machine learning model with the hope that the resulting explanations will be meaningful to the consumer. In contrast, this paper suggests a new approach to this problem. It introduces a simple, practical framework, called Teaching Explanations for Decisions (TED), that provides meaningful explanations that match the mental model of the consumer. We illustrate the generality and effectiveness of this approach with two different examples, resulting in highly accurate explanations with no loss of prediction accuracy for these two examples.
Demonstration of Turbulence Resiliency in a Mode-, Polarization-, and Wavelength-Multiplexed Free-Space Optical Link Using Pilot-Assisted Optoelectronic Beam Mixing (2022)

We experimentally demonstrate turbulence-resilient free-space optical (FSO) coherent communications with multiple multiplexed data channels in different orthogonal domains, including mode, polarization, and wavelength. The turbulence resiliency is enabled by utilizing pilot-assisted optoelectronic mixing of the received beams, wherein one pilot is being mixed with its corresponding beam. By transmitting additional continuous-wave (CW) pilot tones, whose frequencies are offset from the data-carrying beams, and mixing all pilot tones and beams in a single free-space-coupled photodetector (PD) at the receiver, the turbulence-induced modal coupling could be efficiently suppressed. The paper first discusses an experimental demonstration of a turbulence-resilient mode-division-multiplexed (MDM) FSO communication link using two orbital angular momentum (OAM) beams. Each OAM beam carries an independent 2-Gbit/s quadrature-phase-shift-keying (QPSK) data channel. Experimental results indicate that (i) the channel crosstalk under both the weaker and stronger turbulence distortions are measured to be lower than ∼−25.7 dB, (ii) the turbulence-induced OAM modal coupling could be effectively suppressed for the emulated 15 random turbulence realizations, and (iii) the error-vector magnitudes (EVM) of the multiplexed QPSK data channels are measured to be lower than by 17.4% and 19.8% under the relatively weaker and stronger turbulence effects, respectively. The paper subsequently describes an experimental demonstration of a turbulence-resilient FSO link with eight 0.5-Gbit/s QPSK data channels multiplexing two OAM beams ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">l</i> = +1 & <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">l</i> = −2), two polarizations, and two wavelengths. The measured bit-error rates (BERs) of all data channels under turbulence effects are below the 7% forward-error-correction (FEC) limit, with power penalties less than ∼3.7 dB.
Prenatal Equol Treatment: Does Not Alter Newborn Genital Development but Alters Depressive‐like Behaviors in Pre‐pubertal Offspring. (2009)

In this study we examined equol, the intestinal metabolite of daidzein, and its effects on genital morphology and subsequent postnatal behavior. Pregnant rats were divided into six treatment groups before subcutaneous injection treatments: 1) Non‐injected Controls, 2) dimethyl sulfoxide (DMSO)‐injected controls, 3) Equol at 10.5 mg/Kg (in DMSO), 4) Equol at 21.0 mg/Kg (in DMSO), 5) Equol at 63.0 mg/Kg (in DMSO), and 6) Flutamide (90 mg/Kg, androgen‐receptor blocker). The mothers received daily treatment injections from gestational days 14‐20. After birth, body weight and anogenital distance (AGD) were measured and sex determined. Some of the pups and mothers (a subset at birth) were sacrificed and trunk blood collected for determining isoflavone and 5alpha‐dihydrotestosterone (5alpha‐DHT) levels. The remainder of the pups developed postnatally until day 29 where animals underwent analysis via the Porsolt forced swim test to determine depressive‐like behaviors. In summary, equol exposure during late pregnancy 1) does not alter 5alpha‐DHT levels in the males or females or alter male external genital development, 2) the high equol dosed mothers weighed the least before and after birth and their offspring also weighed the least at birth, and 3) after birth the high dosed equol treated animals that gained the most weight postnatally displayed the least depressive‐like behaviors. (USDA 2004‐01811)
The sialidase NEU1 directly interacts with the juxtamembranous segment of the cytoplasmic domain of mucin-1 to inhibit downstream PI3K-Akt signaling (2021)

The extracellular domain (ED) of the membrane-spanning sialoglycoprotein, mucin-1 (MUC1), is an in vivo substrate for the lysosomal sialidase, neuraminidase-1 (NEU1). Engagement of the MUC1-ED by its cognate ligand, Pseudomonas aeruginosa-expressed flagellin, increases NEU1-MUC1 association and NEU1-mediated MUC1-ED desialylation to unmask cryptic binding sites for its ligand. However, the mechanism(s) through which intracellular NEU1 might physically interact with its surface-expressed MUC1-ED substrate are unclear. Using reciprocal coimmunoprecipitation and in vitro binding assays in a human airway epithelial cell system, we show here that NEU1 associates with the MUC1-cytoplasmic domain (CD) but not with the MUC1-ED. Prior pharmacologic inhibition of the NEU1 catalytic activity using the NEU1-selective sialidase inhibitor, C9-butyl amide-2-deoxy-2,3-dehydro-N-acetylneuraminic acid, did not diminish NEU1-MUC1-CD association. In addition, glutathione-S-transferase (GST) pull-down assays using the deletion mutants of the MUC1-CD mapped the NEU1-binding site to the membrane-proximal 36 aa of the MUC1-CD. In a cell-free system, we found that the purified NEU1 interacted with the immobilized GST-MUC1-CD and the purified MUC1-CD associated with the immobilized 6XHis-NEU1, indicating that the NEU1-MUC1-CD interaction was direct and independent of its chaperone protein, protective protein/cathepsin A. However, the NEU1-MUC1-CD interaction was not required for the NEU1-mediated MUC1-ED desialylation. Finally, we demonstrated that overexpression of either WT NEU1 or a catalytically dead NEU1 G68V mutant diminished the association of the established MUC1-CD binding partner, PI3K, to MUC1-CD and reduced downstream Akt kinase phosphorylation. These results indicate that NEU1 associates with the juxtamembranous region of the MUC1-CD to inhibit PI3K-Akt signaling independent of NEU1 catalytic activity.
Generalized binary noise stimulation enables time-efficient identification of input-output brain network dynamics (2016)

Identification of input-output (IO) dynamics of brain networks in response to electrical stimulation is essential for devising closed-loop therapies for neurological disorders such as major depression. A critical component for accurate IO identification is the stimulation input design. The time available for open-loop stimulation to perform system identification is typically limited. While our prior design of a binary noise (BN) modulated input pattern satisfies the requirements for optimal identification and clinical safety, it does not incorporate any prior information about the underlying network. When the identification time is constrained, BN identification performance may be improved by incorporating such information. Here we design a generalized binary noise (GBN) modulated stimulation pattern that achieves time-efficient identification of IO dynamics by utilizing the time-constant information of the network. To test GBN's performance, we implemented a closed-loop controller within a clinical stimulation system. We used our closed-loop system to control mood symptoms in depression using simulated neural activity under linear network dynamics. With a short identification time (20 mins), the controller derived from GBN identification performed as well as an ideal controller that had full knowledge of the network model, and better than a controller derived from BN identification. Our results have important implications for optimal system identification and closed-loop control of brain network dynamics.
Coupled granular/continuous perpendicular recording media with soft magnetic underlayer (2002)

Fabrication, magnetic properties, and read/write characteristics of coupled granular/continuous (CGC) perpendicular media are described. The media consist of continuous Co/Pt multilayers, which have a strong in-plane exchange coupling, and a granular CoCrPt layer on top of a soft magnetic underlayer. These continuous and granular layers are magnetically coupled, thus the switching field distribution becomes effectively narrower. Recording measurements using a single-pole writer and a giant magnetoresistive reader show substantial improvement in the head output and resolution of the CGC medium, compared to the plain granular medium. Transition jitter and medium noise are reduced in the CGC media. As a result, the CGC media have 3–5 dB higher signal-to-noise ratio (SNR) and better thermal stability than the plain granular medium. The concept of CGC perpendicular media is a viable way to achieve both the thermal stability and medium SNR requirements for high-density recording.
Complex data analysis in high‐resolution SSFP fMRI (2007)

In transition-band steady-state free precession (SSFP) functional MRI (fMRI), functional contrast originates from a bulk frequency shift induced by a deoxygenated hemoglobin concentration change in the activated brain regions. This frequency shift causes a magnitude and/or phase-signal change depending on the off-resonance distribution of a voxel in the balanced-SSFP (bSSFP) profile. However, in early low-resolution studies, only the magnitude signal activations were shown. In this paper the task-correlated phase-signal change is presented in a high-resolution (1 x 1 x 1 mm3) study. To include this phase activation in a functional analysis, a new complex domain data analysis method is proposed. The results show statistically significant phase-signal changes in a large number of voxels comparable to that of the magnitude-activated voxels. The complex-data analysis method successfully includes these phase activations in the activation map and thus provides wider coverage compared to magnitude-data analysis results.
Automated, Certified Program-rewriting for Software Security Enforcement (2012)

Abstract : This project discovered and developed algorithms and tools for (1) automatically retrofitting binary legacy software with access controls, and (2) formally machine-certifying that the retrofitted software satisfies user-specified security policies. The research resulted in new software security systems for Java, ActionScript. and x86 native code that provably secure legacy code without any form of code-producer cooperation (e.g., source code or compiler support).