gebhart/patrepeval huggingface dataset:
3′ IsomiR Species and DNA Contamination Influence Reliable Quantification of MicroRNAs by Stem-Loop Quantitative PCR (2014)

MicroRNAs (miRNAs) are ∼20-24 nucleotide-long regulatory RNAs that have been proven to play important roles in many cellular processes. Since their discovery, a number of different techniques have been developed to detect and accurately quantify them. For individual mature miRNA measurements, quantitative stem-loop real-time PCR represents a widely used method. Although there are some data on optimization of this technique, there are still many factors that have not been investigated yet. In this study, we have thoroughly optimized this technique and pointed out several important factors that influence reliable quantification. First, we found that total RNA input can affect the measurements. Second, our data showed that carryover DNA contamination could also mislead the detection in a sequence-specific manner. Additionally, we provided evidence that different 3' isomiR species of a particular miRNA can be reverse transcribed and cross-detected even by specifically targeted assays. Besides these, we have investigated the measurement of reaction efficiencies from total RNA samples and the accuracy of simultaneous reverse transcription reactions for increasing reliability and cost effectiveness without the loss of sensitivity and specificity. In summary, we provide a detailed, refined protocol for reliable detection of microRNA species by quantitative stem-loop PCR.
ChemInform Abstract: C—H Bond Oxidation Initiated Pummerer‐ and Knoevenagel‐Type Reactions of Benzyl Sulfide and 1,3‐Dicarbonyl Compounds. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Slow-wave resonance in periodic stacks of anisotropic layers (2007)

We consider a Fabry-Perot resonance (a transmission band edge resonance) in periodic layered structures involving birefringent layers. In a previous publication [Phys. Rev. E 72, 036619 (2005)] we have shown that the presence of birefringent layers with misaligned in-plane anisotropy can dramatically enhance the performance of the photonic-crystal resonator. It allows us to reduce its size by an order of magnitude without compromising on its performance. The key characteristic of the enhanced slow-wave resonator is that the Bloch dispersion relation $\ensuremath{\omega}(k)$ of the periodic structure displays a degenerate photonic band edge, in the vicinity of which the dispersion curve can be approximated as $\mathrm{\ensuremath{\Delta}}\ensuremath{\omega}\ensuremath{\sim}(\mathrm{\ensuremath{\Delta}}k{)}^{4}$, rather than $\mathrm{\ensuremath{\Delta}}\ensuremath{\omega}\ensuremath{\sim}(\mathrm{\ensuremath{\Delta}}k{)}^{2}$. Such a situation can be realized in specially arranged stacks of misaligned anisotropic layers. On the down side, the presence of birefringent layers results in the slow-wave resonance being coupled only with one (elliptic) polarization component of the incident wave, while the other polarization component is reflected back to space. In this paper we show how a small modification of the periodic layered array can solve the above fundamental problem and provide a perfect impedance match regardless of the incident wave polarization, while preserving the giant slow-wave resonance characteristic of a degenerate photonic band edge. Both features are of critical importance for many practical applications, such as the enhancement of various light-matter interactions, light amplification and lasing, optical and microwave filters, antennas, etc.
A Quantitatively Controlled Method to Study Prospectively Interstitial Cystitis and Demonstrate the Efficacy of Pentosanpolysulfate (1993)

A randomized, prospective, double-blind, placebo-controlled study was conducted at 7 clinical centers on 148 patients. Patients received orally either 100 mg. pentosanpolysulfate (a synthetic polysaccharide) 3 times per day or a placebo. Of the patients on drug therapy 32% showed significant improvement compared to 16% of those on placebo (p = 0.01). This study provides a model to assess this disease quantitatively in a prospective manner using a method whereby the patients globally assess their symptoms as either worse or improved by 0, 25, 50, 75 or 100%. Patients on drug therapy also experienced a significant decrease in pain and urgency (p = 0.04 and 0.01) on analogue scales when compared to placebo and also more drug patients showed an average increase of more than 20 ml. in voided volume than did placebo patients (p = 0.02). All adverse effects were minor, with 7 in the drug group and 10 in the placebo group. The results support the concept that some patients with the interstitial cystitis syndrome may have abnormal bladder surface glycosaminoglycans.
Motion and communication co-optimization with path planning and online channel prediction (2016)

This paper considers the problem of optimally balancing motion energy and communication transmission energy of a mobile robot tasked with transmitting a given number of data bits to a remote station, while navigating to a pre-specified destination in a given amount of time. The problem is cast in the setting of optimal control, where the robot has to choose its path, acceleration, and transmission rate along the path so as to minimize its energy required for transmission and motion, while satisfying various power and communication constraints. We use realistic models for the robot's channel estimation, motion dynamics, and power and energy costs. The main contribution of the paper is to show how to co-optimize robot's path along with other communication and motion variables. Two versions of the problem are solved: the first is defined offline by assuming that all the channel measurements are taken before the robots starts moving, while in the second the channel estimation is updated while the robot is in motion, and hence it is solved online. In both cases we utilize an in-house algorithm that computes near-optimal solutions in little time, which enables its use in the online setting. The optimization strategy is described in detail and validated by simulation of realistic scenarios.
Sensory Characterization of Commercial Lager Beers and Their Correlations with Iso-&#945;-Acid Concentrations (2014)

A total of 40 commercial lager beers (6 dark, 28 pale and 6 alcohol free) were analysed by High-Performance Liquid Chromatography (HPLC) and evaluated by a descriptive sensorial panel. Discriminant Analysis was applied to 15 sensory descriptors to obtain a classification by types of beer. Cluster Analysis identified 4 clusters grouping the 15 sensory descriptors. The Correlation Matrix confirmed a correlation between them and the subsequent Principal Component Analysis. A stepwise discriminant analysis was used to eliminate the less significant descriptors, leading to 100% of the samples being correctly classified with a reduced number of variables (colour intensity, smell of caramel, smell of toasted, persistence and viscosity). The analysis of the correlations between iso-Î±-acid concentrations and sensory descriptors shows a good relationship with bitter taste. Thus, HPLC data can be used for predicting lager beer bitterness through the mathematical correlation developed in this paper.
SOME CHEMICAL AND BIOLOGICAL PROPERTIES OF 19-NOR-17?-ETHYNYLTESTOSTERONE (1958)

A brief chronological discussion of the chemistry of 19-nor steroids was presented and details concerning the syntheses of the progestationally active 19-nor-17alpha-ethinyltestosterone (Norlutin) and 19-nor-17alpha-methyltestosterone were given. The oral progestational activity of Norlutin and of the methyl ethyl and vinyl analogs in rabbits is approximately 5 times that of 17alpha-ethinyltestosterone. Norlutin is equally potent intramuscularly but is not active on direct application to the rabbit uterus. The reason for this lack of progestational activity by intrauterine administration is not known but it may be due to interference by contaminating estrogen. The oral estrogenic activity of Norlutin is relatively low. Norlutin is negligibly androgenic differing in this respect from the other 17-substituted derivatives studied. Norlutin is antigonadotropic. This property is shared by the 19-nor-17alpha-methyl ethyl and vinyl analogs and also by 17alpha-methyltestosterone but is obscured to varying degrees by the direct androgenic action of these compounds on the target organs. The possibility that suppression of pituitary secretion of gonadotropin by Norlutin may be due to contaminating 17alpha-ethinylestradiol 3-methyl ether or to the formation of 17alpha-ethinylestradiol from Norlutin in the intestinal tract is discussed. Norlutin and (to a lesser degree) 19-nor-17alpha-methyltestosterone exhibit an anabolic or anticatabolic action by counteracting loss in liver weight (and nitrogen) due to fasting. This effect while shown by 17alpha-ethinylestradiol 3-methyl ether is not due entirely to contamination of Norlutin by this estrogen. 17alpha-methyltestosterone is inactive in this test. Norlutin also accelerates slightly the restoration of liver mass following partial hepatectomy.
Molecular Recognition Remolds the Self-Assembly of Hydrogelators and Increases the Elasticity of the Hydrogel by 10<sup>6</sup>-Fold (2004)

Addition of vancomycin (1, the receptor) to the supramolecular hydrogel of self-assembled pyrene-d-Ala-d-Ala (2, the ligand) increases the storage modulus of the hydrogel of 2 by about 106-fold. Rheology, microscopy, and spectroscopy investigations suggest that the two-dimensional polymers, formed by the ligand-receptor interaction between 1 and 2, and the self-dimerization of 1, are mainly responsible for the observed dramatic increase in elasticity.
Early Greek Knowledge of the West - Erik Wikén: Die Kunde der Hellenen von dem Lande und den Völkern der Apenninenhalbinsel bis 300 v. Chr. Pp. viii + 212; sketch-maps in text. Lund: Gleerup, 1937. Paper (1938)

Early Greek Knowledge of the West - Erik Wikén: Die Kunde der Hellenen von dem Lande und den Völkern der Apenninenhalbinsel bis 300 v. Chr. Pp. viii + 212; sketch-maps in text. Lund: Gleerup, 1937. Paper - Volume 52 Issue 1
Failures and Successes of Clinical Trials for Parkinson Disease Treatments (2005)

The Proceedings of the First International Symposium on Translational Clinical Research for Inherited and Orphan Retinal Diseases: Sponsored by the National Neurovision Research Institute Inc.: Clinical Trials: Clinical Trials in Other Neurological Diseases
A Workload-Driven Approach to Dynamic Data Balancing in MongoDB (2015)

With rapid growth of demand on Big Data storage, MongoDB has been a prevalent choice to store unstructured data in recent years. MongoDB evenly distributes data across shard servers to ensure that all the shard servers hold approximately same amount of data and the data access workload will be balanced across these servers. This approach, however, can hardly guarantee the performance of data access when there are hotspots in data because it supposes all the data will be accessed in same patterns. This paper puts forward a workload-driven approach to dynamic data balancing in MongoDB. In this approach, the workload will be monitored in real time by parsing and analyzing log of MongoDB in order to find the hotspots of data. Then, the heat of hotspots will be diffused across shard servers by dynamic data migration. After migration, the workload will be rebalanced across shard servers though data are probably not even distributed, and the performance of hotspots access will be improved. The evaluation of this approach has shown its effectiveness from three aspects, including the improvement of performance, the data migration and the improvement of utilization of CPU.
The functions of the carotid and aortic bodies (1940)

Abstract The carotid and aortic bodies are structures whose specialized function it is to respond to changes in the chemical composition of the arterial blood by setting up afferent impulses which enter the central nervous system with the glossopharyngeal and vagus nerves, respectively. The nerve impulses in question are stimulant to the medullary centers (respiratory, vasomotor, and, in the case of the carotid body of the dog, cardioinhibitory). The impulses from the stretch receptors of the carotid sinuses and aortic arch (carried by the same nerves) are inhibitory to these centers (except the cardioinhibitory, which is stimulated by them). The chemically sensitive receptors (chemoreceptors) can be stimulated by anoxemia, asphyxia, increased carbon dioxide tension, or increased hydrogenion concentration, or by a variety of drugs and poisons which have no common chemical or physiologic attribute although the list includes inhibitors of oxidations (cyanide, sulfide) and substances with nicotinic properties (nicotine, lobeline, coniine, and choline and its derivatives). Reflexes from these structures are responsible for much, if not all, of the stimulant effects of anoxia on respiration and circulation. They probably are not concerned in the normal control of respiration, the sensitivity of the chemoreceptors to carbon dioxide being much less than that of the centers unless the latter is depressed; in that event these reflexes become an important factor in maintaining respiration. An explanation that is in accord with existing information on the subject is that the chemoreceptors represent a survival in relatively undifferentiated form of a reflex mechanism originally developed for a water-breathing ancestral form. The ability of these structures to set up a strong reflex stimulation to respiration when exposed to an environment that would depress or paralyze nerve cells (severe anoxia, very high carbon dioxide tension or acidity, deep narcosis) is probably related to their primitive status and responsible for much, if not all, of their value to the organism.
Age dependent increase in the levels of osteopontin inhibits skeletal muscle regeneration (2012)

Skeletal muscle regeneration following injury is accompanied by rapid infiltration of macrophages, which play a positive role in muscle repair. Increased chronic inflammation inhibits the regeneration of dystrophic muscle, but the properties of inflammatory cells are not well understood in the context of normal muscle aging. This work uncovers pronounced age-specific changes in the expression of osteopontin (OPN) in CD11b+ macrophages present in the injured old muscle as well as in the blood serum of old injured mice and in the basement membrane surrounding old injured muscle fibers. Furthermore, young CD11b+ macrophages enhance regenerative capacity of old muscle stem cells even when old myofibers and old sera are present; and neutralization of OPN similarly rejuvenates the myogenic responses of old satellite cells in vitro and notably, in vivo. This study highlights potential mechanisms by which age related inflammatory responses become counter-productive for muscle regeneration and suggests new strategies for enhancing muscle repair in the old.
System design principles combining sub-threshold circuit and architectures with energy scavenging mechanisms (2010)

Ultra low power (ULP) circuits and energy scavenging mechanisms, though conceptually appealing, have been mainly studied in isolation to date. In this paper, we observe energy harvesting prototypes to derive system-level models and to reveal practical issues specific to various types of energy harvesting systems. Our models predict how design decisions affect overall lifetime. We use our model to derive system driven principles for optimizing architecture, voltage selection, and sub-threshold circuit designs across different types of power harvesting systems.
Mesenchymal Stem Cells Acquire Characteristics of Cells in the Periodontal Ligament <i>in vitro</i> (2004)

Mesenchymal stem cells differentiate into multiple types of cells derived from mesenchyme. Periodontal ligament cells are primarily derived from mesenchyme; thus, we expected mesenchymal stem cells to differentiate into periodontal ligament. Using a combination of immunohistochemistry and in situ hybridization on co-cultures of mesenchymal stem cells and periodontal ligament, we observed a significant increase in mesenchymal stem cells' expression of osteocalcin and osteopontin and a significant decrease in expression of bone sialoprotein, characteristics of periodontal ligament in vivo. Increased osteopontin and osteocalcin and decreased bone sialoprotein expression was detected within 7 days and maintained through 21 days of co-culture. We conclude that contact or factors from periodontal ligament induced mesenchymal stem cells to obtain periodontal-ligament-like characteristics. Importantly, analysis of the data suggests the feasibility of utilizing mesenchymal stem cells in clinical applications for repairing and/or regenerating periodontal tissue.
Stress during Pregnancy and Offspring Pediatric Disease: A National Cohort Study (2011)

Maternal life stress during pregnancy may be a common risk factor for impaired child health. The results suggest new approaches to reduce childhood diseases.
Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitons (1999)

Four two-dimensional (2D) four-wave-mixing techniques that can be used to extract information about structure and coupling patterns of interacting chromophores are proposed. These techniques have close conceptual similarities with multiple-pulse NMR spectroscopies. Closed expressions for the signals are derived by solving the nonlinear exciton equations (NEE) which describe the dynamics of multiple excitations using the one-exciton Green function and the exciton–exciton scattering matrix. Possible applications include electronic spectroscopy of aggregates, e.g., photosynthetic antenna complexes, and infrared spectroscopy of localized vibrations (e.g., amid bands in polypeptides). Model calculations are presented for three-chromophore aggregates.
In0.53Ga0.47As <i>p</i>-<i>i</i>-<i>n</i> photodiodes with transparent cadmium tin oxide contacts (1992)

A new type of p-i-n In0.53Ga0.47As photodiode having an optically transparent composite top electrode consisting of a thin semitransparent metal layer and a transparent cadmium tin oxide (CTO) layer was investigated. The composite functions as the n or p contact, an optical window, and an antireflection coating. The transparent contact also prevents shadowing of the active layer by the top electrode, thus allowing greater collection of incident light. Since the CTO contact is nonalloyed, interdiffusion into the i-region is not relevant avoiding an increased dark current. The photodiodes exhibited leakage currents of ≤8 nA and some as low as 23 pA, with reverse breakdown voltages of ≥15–17 V. Responsivity was measured using a 1.55 μm InGaAsP diode laser focused onto an unpassivated 60 μm diam p-i-n photodiode and was ≥0.41 A/W. Photoresponse of the diodes to 3 ps pulses from a Nd:YLF laser (λ=1.047 μm) was 169 and 86 ps for the 60 and 9 μm diodes, respectively. The maximum frequency response of the 9 μm diode is packaging limited, and is expected to have an intrinsic response time of 20–30 ps.
Emerging role of non-coding RNA in neural plasticity, cognitive function, and neuropsychiatric disorders (2012)

Non-coding RNAs (ncRNAs) have emerged as critical regulators of transcription, epigenetic processes, and gene silencing, which make them ideal candidates for insight into molecular evolution and a better understanding of the molecular pathways of neuropsychiatric disease. Here, we provide an overview of the current state of knowledge regarding various classes of ncRNAs and their role in neural plasticity and cognitive function, and highlight the potential contribution they may make to the development of a variety of neuropsychiatric disorders, including schizophrenia, addiction, and fear-related anxiety disorders.
Development of a hybrid hands-off human computer interface based on electromyogram signals and eye-gaze tracking (2005)

A hybrid hands-off human computer interface that uses infrared video eye gaze tracking (EGT) and electromyogram (EMG) signals is introduced. This system combines the advantages of both sub-systems, providing quick cursor displacement In long excursions and steady, accurate movement in small position adjustments. The hybrid system also provides a reliable clicking mechanism. The evaluation protocol used to test the system is described and the results for the hybrid, an EMG Only interface, and the standard hand-held mouse are described and compared. These results show that the hybrid system is, in an average, faster than the EMG-only system by a factor of 2 or more.
Prognostic Role of <i>KRAS</i> and <i>BRAF</i> in Stage II and III Resected Colon Cancer: Results of the Translational Study on the PETACC-3, EORTC 40993, SAKK 60-00 Trial (2009)

In stage II-III colon cancer, the KRAS mutation status does not have major prognostic value. BRAF is prognostic for OS in MS-L/S tumors.
DNA Cleavage via Superoxide Anion Formed in Photoinduced Electron Transfer from NADH to γ-Cyclodextrin-Bicapped C<sub>60</sub> in an Oxygen-Saturated Aqueous Solution (2002)

γ-Cyclodextrin-bicapped C60 (C60/γ-CyD) shows an efficient DNA cleaving-activity in the presence of NADH (β-nicotinamide adenine dinucleotide, reduced form) in an O2-saturated aqueous solution under visible-light irradiation. No DNA cleavage has been observed without NADH under experimental conditions that are otherwise the same, although singlet oxygen (1O2) has been detected by the ESR spin-trapping of the C60/γ-CyD-O2 system. This indicates that neither triplet excited state of C60/γ-CyD (3C60*/γ-CyD) nor 1O2 produced via an energy transfer from 3C60*/γ-CyD to O2 is an actual reactive species, which is responsible for the DNA damage under the present experimental conditions. In the presence of NADH, photoinduced electron transfer from NADH to 3C60*/γ-CyD occurs to yield two equivalents of the radical anion (C60•-/γ-CyD), which exhibits its characteristic NIR band at 1080 nm. The dynamics of the photoinduced electron transfer have been examined by monitoring the decay of triplet−triplet absorption band at 740 nm and concomitant rise of the NIR absorption band at 1080 nm due to C60•-/γ-CyD with use of the laser flash photolysis for the C60/γ-CyD-NADH system. In the presence of O2, C60•-/γ-CyD disappears via the electron transfer to O2 and an electron transfer from NADH to 1O2 to produced O2•-. The formation of O2•- has been confirmed by the spin trap with DEPMPO (5-diethoxyphosphoryl-5-methyl-1-pyrroline-N-oxide), which is an efficient O2•--trapping agent. The reorganization energy for the reduction of O2 to O2•- is evaluated as 43.4 kcal mol-1, which agrees with the literature value determined directly for the self-exchange between 36O2•- and 32O2. This indicates that the electron transfer from C60•-/γ-CyD to O2 proceeds via an outer-sphere pathway. The O2•- thus produced gives H2O2, ultimately yielding hydroxyl radical, which is shown to be an actual DNA-cleaving reagent.