gebhart/patrepeval huggingface dataset:
The role of target accessibility for antisense inhibition. (2002)

It appears that the application of antisense nucleic acids to drug development and gene function analysis are now established fields, and success in the use of antisense molecules has increased over recent years through modulating chemical and biological properties of oligonucleotides via the specific chemistry employed in their construction. In contrast, the targets of antisense nucleic acids are unchangeable RNA molecules, each with a defined strcuture. The local properties of the target represent a major limitation of the effectiveness of complementary nucleic acid inhibitors, and as such the search for appropriate local target sites for the invasion of an antisense strand is the focus of current research. Here, recent developments in the study of target structures and their accessibility for antisense nucleic acids, as well as concepts for their analysis, will be summarized.
A Complementary Palette of NanoCluster Beacons (2014)

NanoCluster Beacons (NCBs), which use few-atom DNA-templated silver clusters as reporters, are a type of activatable molecular probes that are low-cost and easy to prepare. While NCBs provide a high fluorescence enhancement ratio upon activation, their activation colors are currently limited. Here we report a simple method to design NCBs with complementary emission colors, creating a set of multicolor probes for homogeneous, separation-free detection. By systematically altering the position and the number of cytosines in the cluster-nucleation sequence, we have tuned the activation colors of NCBs to green (C8-8, 460 nm/555 nm); yellow (C5-5, 525 nm/585 nm); red (C3-4, 580 nm/635 nm); and near-infrared (C3-3, 645 nm/695 nm). At the same NCB concentration, the activated yellow NCB (C5-5) was found to be 1.3 times brighter than the traditional red NCB (C3-4). Three of the four colors (green, yellow, and red) were relatively spectrally pure. We also found that subtle changes in the linker sequence (down to the single-nucleotide level) could significantly alter the emission spectrum pattern of an NCB. When the length of linker sequences was increased, the emission peaks were found to migrate in a periodic fashion, suggesting short-range interactions between silver clusters and nucleobases. Size exclusion chromatography results indicated that the activated NCBs are more compact than their native duplex forms. Our findings demonstrate the unique photophysical properties and environmental sensitivities of few-atom DNA-templated silver clusters, which are not seen before in common organic dyes or luminescent crystals.
Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroni (2002)

Quinoprotein alcohol dehydrogenases are redox enzymes that participate in distinctive catabolic pathways that enable bacteria to grow on various alcohols as the sole source of carbon and energy. The x-ray structure of the quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni has been determined at 1.44 A resolution. It comprises two domains. The N-terminal domain has a beta-propeller fold and binds one pyrroloquinoline quinone cofactor and one calcium ion in the active site. A tetrahydrofuran-2-carboxylic acid molecule is present in the substrate-binding cleft. The position of this oxidation product provides valuable information on the amino acid residues involved in the reaction mechanism and their function. The C-terminal domain is an alpha-helical type I cytochrome c with His(608) and Met(647) as heme-iron ligands. This is the first reported structure of an electron transfer system between a quinoprotein alcohol dehydrogenase and cytochrome c. The shortest distance between pyrroloquinoline quinone and heme c is 12.9 A, one of the longest physiological edge-to-edge distances yet determined between two redox centers. A highly unusual disulfide bond between two adjacent cysteines bridges the redox centers. It appears essential for electron transfer. A water channel delineates a possible pathway for proton transfer from the active site to the solvent.
Improved Glucose Disappearance Following Repeated Glucose Administration: Serum Insulin, Growth Hormone and Free Fatty Acid Levels During the Staub-Traugott Effect (1969)

The Staub-Traugott effect, the phenomenon of improved tolerance to repeated glucose administration, was investigated in fifteen healthy volunteers. Two glucose loads were administered intravenously forty-six minutes apart. Blood samples were taken periodically after each glucose infusion. The second glucose load was given immediately after the first sampling period. The glucose disappearance rate (K) improved after the second infusion from 2.04 ± 0.23 to 2.87 ±0.16 (p &amp;lt; 0.001). Serum immunoreactive insulin levels rose promptly after the glucose infusions, but while a decrease was noted following the first peak, the levels remained persistently elevated after the second glucose load. Growth hormone levels decreased and were slightly lower yet six to nine minutes after completion of the infusions. A striking reduction of free fatty acid levels followed the first glucose load; values fell to 50 per cent of the fasting levels prior to, and decreased even further following, the second infusion. Thus, the improved K of the second glucose tolerance test was associated with already diminished serum free fatty acid levels.
Packets-to-Prediction: An Unobtrusive Mechanism for Identifying Coarse-Grained Sleep Patterns with WiFi MAC Layer Traffic (2023)

A good night's sleep is of the utmost importance for the seamless execution of our cognitive capabilities. Unfortunately, the research shows that one-third of the US adult population is severely sleep deprived. With college students as our focused group, we devised a contactless, unobtrusive mechanism to detect sleep patterns, which, contrary to existing sensor-based solutions, does not require the subject to put on any sensors on the body or buy expensive sleep sensing equipment. We named this mechanism Packets-to-Predictions(P2P) because we leverage the WiFi MAC layer traffic collected in the home and university environments to predict "sleep" and "awake" periods. We first manually established that extracting such patterns is feasible, and then, we trained various machine learning models to identify these patterns automatically. We trained six machine learning models-K nearest neighbors, logistic regression, random forest classifier, support vector classifier, gradient boosting classifier, and multilayer perceptron. K nearest neighbors gave the best performance with 87% train accuracy and 83% test accuracy.
Nonlinearity Attack Against the Kirchhoff–Law–Johnson-Noise (KLJN) Secure Key Exchange Protocol (2021)

This paper introduces a new attack against the Kirchhoff–Law–Johnson-Noise (KLJN) secure key exchange scheme. The attack is based on the nonlinearity of the noise generators. We explore the effect of total distortion ([Formula: see text]) at the second order ([Formula: see text]), third order ([Formula: see text]) and a combination of the second and third orders ([Formula: see text]) on the security of the KLJN scheme. It is demonstrated that as little as 1% results in a notable power flow along the information channel, which leads to a significant information leak. We also show that decreasing the effective temperature (that is, the wire voltage) and, in this way reducing nonlinearity, results in the KLJN scheme approaching perfect security.
A Normative Analytic Framework for Development of Practice Guidelines for Specific Clinical Populations (1997)

Development of guideline recommendations based on decision models provides a normative approach for evaluating the need for and the cost-effectiveness of site-specific guidelines that have been tailored to specific practice settings. Such site-specific guidelines can improve substantially the expected health benefit and the economic efficiency of practice guidelines.
Persistent RNA virus infection is short-lived at the single-cell level but leaves transcriptomic footprints (2021)

Several RNA viruses can establish life-long persistent infection in mammalian hosts, but the fate of individual virus-infected cells remains undefined. Here we used Cre recombinase-encoding lymphocytic choriomeningitis virus to establish persistent infection in fluorescent cell fate reporter mice. Virus-infected hepatocytes underwent spontaneous noncytolytic viral clearance independently of type I or type II interferon signaling or adaptive immunity. Viral clearance was accompanied by persistent transcriptomic footprints related to proliferation and extracellular matrix remodeling, immune responses, and metabolism. Substantial overlap with persistent epigenetic alterations in HCV-cured patients suggested a universal RNA virus-induced transcriptomic footprint. Cell-intrinsic clearance occurred in cell culture, too, with sequential infection, reinfection cycles separated by a period of relative refractoriness to infection. Our study reveals that systemic persistence of a prototypic noncytolytic RNA virus depends on continuous spread and reinfection. Yet undefined cell-intrinsic mechanisms prevent viral persistence at the single-cell level but give way to profound transcriptomic alterations in virus-cleared cells.
A general-purpose machine learning framework for predicting properties of inorganic materials (2016)

Abstract A very active area of materials research is to devise methods that use machine learning to automatically extract predictive models from existing materials data. While prior examples have demonstrated successful models for some applications, many more applications exist where machine learning can make a strong impact. To enable faster development of machine-learning-based models for such applications, we have created a framework capable of being applied to a broad range of materials data. Our method works by using a chemically diverse list of attributes, which we demonstrate are suitable for describing a wide variety of properties, and a novel method for partitioning the data set into groups of similar materials to boost the predictive accuracy. In this manuscript, we demonstrate how this new method can be used to predict diverse properties of crystalline and amorphous materials, such as band gap energy and glass-forming ability.
The sugar chain structures of ABO blood group active glycoproteins obtained from human erythrocyte membrane. (1978)

The glycoproteins of human erythrocyte membrane have two groups of sugar chains with blood type ABH determinants, which are quite distinct in their molecular sizes. A neutral sugar chain and an acidic sugar chain, which belong to the small size group, were isolated from the glycoproteins obtained from the erythrocyte of blood type O individuals, and their structures were elucidated as Fucalpha1 leads to 2Galbeta1 leads to 3N-acetylgalactosaminitol and Fucalpha1 leads to 2Galbeta1 leads to 3(AcNeualpha2 leads to 6)N-acetylgalactosaminitol, respectively. The molecular weight of the large sugar chains with ABH determinants were estimated to be more than 4000. Both large and small neutral sugar chains of membrane glycoproteins obtained from blood type O erythrocyte could serve as acceptors of alpha-N-acetylgalactosaminyltransferases purified from milk of blood type A1 and A2 individuals, producing the same radioactive sugar chain distribution patterns. However, the acidic sugar chain with the H determinant could not serve as an acceptor of these enzymes.
Control of diesel engines (1998)

This article is intended to give control engineers an overview of models and controls of diesel engines. The main emphasis is on the engine's torque generation, including all necessary ancillary devices (turbocharger, injection-system, etc.), pollutant emission and model-based controls. The paper gives a brief introduction of the basic working principles and the salient features of diesel engines and their main differences to Otto (gasoline or spark-ignited) engines are shown. The most important control tasks are then identified and their implications on engine performance are analyzed. An overview of the current state-of-the-art in industrial diesel control applications is given. It also discusses models for the simulation of transient macroscopic effects, and how these models can be simplified to be useful for controller synthesis. Finally. an outlook on possible future control issues and their role in diesel engine evolution is presented.
Simulation of an Economic Policy on Second Life Using a Conjunctural Analysis Approach (2016)

Abstract. This paper intends to define an economic policy that does not compromise the coordination between the 4 main sectors of an economy: the real sector, the public sector, the exterior sector and the monetary sector. The subject is Second Life (SL) a totally virtual world that is starting to occupy a great economic place especially with e-commerce. For doing so, some data are arbitrarily chosen as done and projections are made from them. Data are expressed in billion of Linden dollars.
Abstract 16501: Intravenous Administration of Neonatal Mesenchymal Stem Cells Mediates Functional Recovery in a Renal Ischemia-reperfusion Injury Rodent Model (2020)

Introduction: The prevalence of acute kidney injury in cardiac surgery patients is up to 30%. However, treatments to facilitate kidney recovery are mainly limited to supportive care. In preclinical studies, stem cell therapy using adult Mesenchymal Stem Cells (aMSCs) has reduced kidney damage through the secretion of paracrine factors. Previously, we have established that our neonatal Mesenchymal Stem Cells (nMSCs) have a more potent anti-inflammatory and pro-angiogenic secretome profile than aMSCs. Hypothesis: Intravenous administration of nMSCs and their secretome (total conditioning media) will diminish kidney injury in a renal ischemia-reperfusion injury rodent model. Methods: Six to seven-week-old Brown-Norway rodents underwent bilateral renal clamping to induce 90-minute ischemia. After removal of the clamps and renal reperfusion, the rodents were injected with 100 uL of PlasmaLyte A (control; n=7), an nMSC suspension (10 million cells/kg; n=6), or a total conditioning media (TCM) suspension (10 mg/kg; n=6) via their lateral tail vein. Results: One day after nMSC and TCM treatment, both blood urea nitrogen (116.08 ± 12.02 vs 149.41 ± 9.26 mg/dL; *p=0.0434 and 111.34 ± 9.54 vs 149.41 ± 9.26 mg/dL; *p=0.0174, respectively) and blood creatinine (0.75 ± 0.074 vs 1.25 ± 0.18 mg/dL; **p=0.0028 and 0.76 ± 0.06 vs 1.25 ± 0.18 mg/dL; **p=0.0030, respectively) levels were significantly reduced compared to after PlasmaLyte A injection. Associated decreases in pro-apoptotic signaling molecules (CASP8, BAK, and BAD) and increases in anti-apoptotic signaling molecules (pAKT, SOD2, and BCL2) are being investigated. Conclusions: nMSC and TCM treatment via intravenous injection showed indications of a reduction in kidney injury. This therapy should be further investigated for use in select cardiac surgery patients.
Neutron soft error rate measurements in a 90-nm CMOS process and scaling trends in SRAM from 0.25-μm to 90-nm generation (2004)

The neutron soft error rate (SER) dependency on voltage and area was measured for a state-of-the-art 90-nm CMOS technology. The SER increased by 18% for a 10% reduction in voltage, and scaled linearly with diode area. The measured SER per bit of SRAMs in 0.25 /spl mu/m, 0.18 /spl mu/m, 0.13 /spl mu/m, and 90 nm showed an increase of 8% per generation.
Improving Performance and Availability of Services Hosted on IaaS Clouds with Structural Constraint-Aware Virtual Machine Placement (2011)

The increasing popularity of modern virtualization-based datacenters continues to motivate both industry and academia to provide answers to a large variety of new and challenging questions. In this paper we aim to answer focusing on one such question: how to improve performance and availability of services hosted on IaaS clouds. Our system, structural constraint-aware virtual machine placement (SCAVP), supports three types of constraints: demand, communication and availability. We formulate SCAVP as an optimization problem and show its hardness. We design a hierarchical placement approach with four approximation algorithms that efficiently solves the SCAVP problem for large problem sizes. We provide a formal model for the application (to better understand structural constraints) and the datacenter (to effectively capture capabilities), and use the two models as inputs to the placement problem. We evaluate SCAVP in a simulated environment to illustrate the efficiency and importance of the proposed approach.
Handlebars for the Yamahas: The struggle toward more intuitive programming of FM synthesizers (1986)

One currently popular technique for synthesis of musical sounds employs audio-rate frequency modulation (FM). Although this technique was first suggested in the 1970s [Chowning, J. Audio Eng. Soc. 21, 526–534 (1973)], it is still somewhat difficult to control. The specification of a particular tone color in terms of traditional Fourier amplitudes remains problematic, especially for time-varying spectra because the relative amplitudes of all the components are governed by Bessel functions. Conversely, the natures of the spectra resulting from various configurations of carriers, modulators, and modulators of modulators are not intuitively obvious. Preliminary work on a Fourier-to-Bessel mapping program which is intended to simplify FM implementations of specific spectra will be reported.
Edge-controlled growth and kinetics of single-crystal graphene domains by chemical vapor deposition (2013)

The controlled growth of large-area, high-quality, single-crystal graphene is highly desired for applications in electronics and optoelectronics; however, the production of this material remains challenging because the atomistic mechanism that governs graphene growth is not well understood. The edges of graphene, which are the sites at which carbon accumulates in the two-dimensional honeycomb lattice, influence many properties, including the electronic properties and chemical reactivity of graphene, and they are expected to significantly influence its growth. We demonstrate the growth of single-crystal graphene domains with controlled edges that range from zigzag to armchair orientations via growth-etching-regrowth in a chemical vapor deposition process. We have observed that both the growth and the etching rates of a single-crystal graphene domain increase linearly with the slanted angle of its edges from 0° to ∼19° and that the rates for an armchair edge are faster than those for a zigzag edge. Such edge-structure-dependent growth/etching kinetics of graphene can be well explained at the atomic level based on the concentrations of the kinks on various edges and allow the evolution and control of the edge and morphology in single-crystal graphene following the classical kinetic Wulff construction theory. Using these findings, we propose several strategies for the fabrication of wafer-sized, high-quality, single-crystal graphene.
<title>Optical music recognition using skeleton structure and neural network</title> (2002)

In this paper, our experiment consists of three steps to recognize printed music. The first step is the pre-processing stage: finding threshold for binary images, identifying staff-line parts, and removing them. The second step is the recognition stage. We first classify notes and other symbols by their sizes and characteristics. The skeleton structure analysis is used for recognizing music notes due to their complex combination of piano scores and the back-propagation and projection profile method are used for other symbols after their normalizing. The last step is the review stage. In which we investigate their syntactic validity and correct unrecognized or misconceived symbols.
Impact of Pre-Analytical Variables on Cancer Targeted Gene Sequencing Efficiency (2015)

Tumor specimens are often preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks, the most common clinical source for DNA sequencing. Herein, we evaluated the effect of pre-sequencing parameters to guide proper sample selection for targeted gene sequencing. Data from 113 FFPE lung tumor specimens were collected, and targeted gene sequencing was performed. Libraries were constructed using custom probes and were paired-end sequenced on a next generation sequencing platform. A PCR-based quality control (QC) assay was utilized to determine DNA quality, and a ratio was generated in comparison to control DNA. We observed that FFPE storage time, PCR/QC ratio, and DNA input in the library preparation were significantly correlated to most parameters of sequencing efficiency including depth of coverage, alignment rate, insert size, and read quality. A combined score using the three parameters was generated and proved highly accurate to predict sequencing metrics. We also showed wide read count variability within the genome, with worse coverage in regions of low GC content like in KRAS. Sample quality and GC content had independent effects on sequencing depth, and the worst results were observed in regions of low GC content in samples with poor quality. Our data confirm that FFPE samples are a reliable source for targeted gene sequencing in cancer, provided adequate sample quality controls are exercised. Tissue quality should be routinely assessed for pre-analytical factors, and sequencing depth may be limited in genomic regions of low GC content if suboptimal samples are utilized.
Temporal Decreases in Sperm Motility: Which Patients Should Have Motility Checked at Both 1 and 2 Hours After Collection? (2008)

A decrease in sperm motility, and thus total motile sperm count (TMSC), over a period of hours might have clinical implications in counseling couples considering intrauterine insemination (IUI), in vitro fertilization (IVF), and intracytoplasmic sperm injection (ICSI). The objective of this study was to identify patients with decreases in sperm motility from 1 to 2 hours after collection and examine predictive relationships with semen analysis parameters. Between 2001 and 2005, 2313 semen samples were analyzed. Sperm motility was evaluated at both 1 and 2 hours after time of collection. Relevant seminal parameters were compared between patients, with a decrease in 1-hour to 2-hour motility (n = 384) compared with those that showed no change (n = 1929). The same analysis was performed in a subset of patients with a TMSC between 10 and 40 million. In the total patient population, only 16% (384/2313) demonstrated a decrease in 1-hour to 2-hour motility. In patients displaying a decrease in the 1-2-hour motility, sperm concentration (33.5 vs 79 million/mL, P < .0001) and percent normal morphology (7% vs 8%, P < .0001) were significantly lower. Additionally, a significantly higher incidence of 1-2-hour motility decrease was seen in patients with midpiece anomalies (33.3% vs 15.9%, P = .01). Within the subpopulation of 10-40 million TMSC, the only statistically significant difference was in patients with midpiece anomalies (80.0% vs 28.2%, P = .02) who demonstrated a higher incidence of the 1-2-hour motility decrease. Overall, patients with a TMSC between 10 and 40 million showed a significantly higher incidence of 1-2-hour motility decrease compared with the rest of the patient population (29.0% vs 14.6%, P < .0001). Because decreases in 1-2-hour sperm motility affect only a small portion of patients, it is not necessary to check 2-hour motility on all patients. However, because patients with a TMSC between 10 and 40 million were significantly more likely to show a decrease in sperm motility-a decrease that could have possible clinical implications in couples deciding between IUI, IVF, or ICSI--checking 2-hour sperm motility should be considered in this population.
An investigation of a user-operated mass calibration package (1988)

Reported here are the results of two round-robin mass measurement programs.
LIVER TRANSPLANTATION IN PRIMARY BILIARY CIRRHOSIS - EXPERIENCE OF A SINGLE CENTRE. (2000)

Garcia, Raquel L.1; Garcia, Christian E.1; Gunson, Bridget; Neuberger, James M.1 Author Information