gebhart/patrepeval huggingface dataset:
Thermodynamic parameters for DNA sequences with dangling ends (2000)

The thermodynamic contributions to duplex formation of all 32 possible single-nucleotide dangling ends on a Watson-Crick pair are reported. In most instances, dangling ends are stabilizing with free energy contributions ranging from +0.48 (GT(A)) to-0.96 kcal/mol (). In comparison, Watson-Crick nearest-neighbor increments range from -0. 58 (TA/AT) to -2.24 (GC/CG) kcal/mol. Hence, in some cases, a dangling end contributes as much to duplex stability as a Watson-Crick A-T base pair. The implications of these results for DNA probe design are discussed. Analysis of the sequence dependence of dangling-end stabilities show that the nature of the closing base pair largely determines the stabilization. For a given closing base pair, however, adenine dangling ends are always more or equally as stable as the other dangling nucleotides. Moreover, 5' dangling ends are more or equally as stabilizing as their 3' counterparts. Comparison of DNA with RNA dangling-end motifs shows that DNA motifs with 5' dangling ends contribute to stability equally or more than their RNA counterparts. Conversely, RNA 3' dangling ends contribute to stability equally or more than their DNA counterparts. This data set has been incorporated into a DNA secondary structure prediction algorithm (DNA MFOLD) (http://mfold2.wustl.edu/mfold/dna/for m1.cgi) as well as a DNA hybridization prediction algorithm (HYTHERtrade mark) (http://jsl1.chem.wayne.edu/Hyther/hythermenu .html).
Ultrafast response of monolayer molybdenum disulfide photodetectors (2015)

The strong light emission and absorption exhibited by single atomic layer transitional metal dichalcogenides in the visible to near-infrared wavelength range make them attractive for optoelectronic applications. In this work, using two-pulse photovoltage correlation technique, we show that monolayer molybdenum disulfide photodetector can have intrinsic response times as short as 3 ps implying photodetection bandwidths as wide as 300 GHz. The fast photodetector response is a result of the short electron-hole and exciton lifetimes in this material. Recombination of photoexcited carriers in most two-dimensional metal dichalcogenides is dominated by nonradiative processes, most notable among which is Auger scattering. The fast response time, and the ease of fabrication of these devices, make them interesting for low-cost ultrafast optical communication links.
C-Shaped Subwavelength Apertures for Silicon Photonics Applications (2010)

Optical transmission properties of C-shaped apertures in silver films on silicon are studied for subwavelength integrated photonic applications. The fundamental Fabry-Perot-like mode is recognized to attain the highest power throughput at the telecommunication wavelengths.
Modeling Corrosion Effects (2013)

This article describes how corrosion of steel reinforcement in concrete structures is one of the primary reasons for bridge deck deterioration, especially in regions where deicing salts are applied and in salt-laden coastal areas. Corrosion is mainly initiated by the diffusion of chlorides through concrete to the reinforcing bar depth. Epoxy-coated reinforcement (ECR) was introduced in the United States as a corrosion prevention method in the late 1970s. However, some agencies began observing premature corrosion-related deterioration in the mid-1980s. Specifications and fabrication methods have been adjusted, but ECR has continued to exhibit mixed results, with some applications performing very well and others experiencing limited corrosion resistance. The article discusses how it necessary to continue to examine the performance of ECR and to develop reliable methods for predicting the deterioration rate of structures containing ECR. This article will allow transportation system owners to anticipate repairs, rehabilitation, and replacement. This article focuses on the selection of suitable parameters for evaluating a bridge deck deterioration model based on the diffusion of chlorides to initiate corrosion and subsequent cracking and spalling for an existing deck constructed with ECR.
Homicidal Somnambulism: A Case Report (1994)

A case of a homicide and an attempted homicide during presumed sleepwalking is reported in which somnambulism was the legal defense and led to an acquittal. Other possible explanations including complex partial seizures, dissociative state, rapid eye movement sleep behavior disorder and volitional waking behavior are discussed. The evidence supporting the probability that this act occurred during an episode of somnambulism and sleep-related confusional arousal is reviewed and weighed. This evidence includes personal and family history of somnambulism and related disorders; neurological, psychiatric and psychological assessments; presence of possible precipitating factors; and polysomnographic data.
Experimental characterization of the MIMO wireless channel: data acquisition and analysis (2003)

Detailed performance assessment of space-time coding algorithms in realistic channels is critically dependent upon accurate knowledge of the wireless channel spatial characteristics. This paper presents an experimental measurement platform capable of providing the narrowband channel transfer matrix for wireless communications scenarios. The system is used to directly measure key multiple-input-multiple-output parameters in an indoor environment at 2.45 GHz. Linear antenna arrays of different sizes and construction with up to ten elements at transmit and receive are utilized in the measurement campaign. This data is analyzed to reveal channel properties such as transfer matrix element statistical distributions and temporal and spatial correlation. Additionally, the impact of parameters such as antenna element polarization, directivity, and array size on channel capacity are highlighted. The paper concludes with a discussion of the relationship between multipath richness and path loss, as well as their joint role in determining channel capacity.
XIAP protein is induced by placenta growth factor (PLGF) and decreased during preeclampsia in trophoblast cells (2014)

Increased trophoblast apoptosis has been implicated in pregnancies complicated by fetal growth restriction and preeclampsia (EC). We investigated placenta growth factor (PLGF) signaling during trophoblast apoptosis in culture and X-linked inhibitor of apoptosis protein (XIAP) and apoptosis inducible factor (AIF) in the preeclamptic placenta at term was determined. Primary trophoblasts were isolated and serum starved to induce apoptosis. Placenta growth factor was added and apoptosis markers were determined. Term preeclamptic placentae were homogenized and the levels of XIAP and XAF1 protein were assessed. In the absence of serum, primary cultures of term trophoblast showed a 5-fold increase in apoptosis as determined by annexin V binding. The increase in apoptosis induced by serum deprivation was caspase-independent and could be significantly reduced (p < 0.02) with the addition of 10 ng/ml rh PLGF to the media. In addition, PLGF mediated increased protein expression of the anti-apoptotic XIAP as well as decreased expression of the pro-apoptotic AIF in the primary trophoblast. In preeclamptic placenta, we determined the concomitant decrease in XIAP RNA as well as decreased expression of the phosphorylated XIAP protein. These results were coupled with increased levels of the pro-apoptotic protein XAF1. Our results suggest that PLGF protects trophoblast from caspase independent apoptosis in culture by increasing XIAP production and deceasing AIF. Also, our data suggests that decreased activation of XIAP and increased XAF1 could be factors associated with the increased placental apoptosis observed in the preeclamptic placenta at term.
Effect of hydroxy (HHO) gas addition on gasoline engine performance and emissions (2015)

The objective of this work was to construct a simple innovative HHO generation system and evaluate the effect of hydroxyl gas HHO addition, as an engine performance improver, into gasoline fuel on engine performance and emissions. HHO cell was designed, fabricated and optimized for maximum HHO gas productivity per input power. The optimized parameters were the number of neutral plates, distance between them and type and quantity of two catalysts of Potassium Hydroxide (KOH) and sodium hydroxide (NaOH). The performance of a Skoda Felicia 1.3 GLXi gasoline engine was evaluated with and without the optimized HHO cell. In addition, the CO, HC and NOx emissions were measured using TECNO TEST exhaust gas analyzer TE488. The results showed that the HHO gas maximum productivity of the cell was 18 L/h when using 2 neutrals plates with 1 mm distance and 6 g/L of KOH. The results also showed 10% increment in the gasoline engine thermal efficiency, 34% reduction in fuel consumption, 18% reduction in CO, 14% reduction in HC and 15% reduction in NOx.
Use of Fixatives to Accel erate Building Decontamination and Decommissioning (D&D) - 9047 (2009)

The Office of Decontamination and Decommissioning (D&D) and Facility Engineering is developing the D&D Toolbox to reduce risk and technical uncertainty in the Department’s cleanup programs and projects. The D&D Toolbox Project uses an integrated systems approach to develop an innovative suite of D&D technologies that can be readily used across the DOE complex to reduce technical risks, improve safety, and limit uncertainty within D&D operations. In support of the D&D Toolbox the Oak Ridge National Laboratory (ORNL) has identified the highest risk facilities at Oak Ridge and the associated technical risk or technology issues.
Functional outcome following thalamic haemorrhage: Relationship between motor and cognitive functions and ADL (1997)

Twenty-two patients with thalamic haemorrhage were examined to investigate the relationship between motor and cognitive function, and activities of daily living (ADL). Patients with unilateral spatial neglect had lower ADL scores on admission than patients without unilateral spatial neglect (Mean: 17.0 and 24.6, respectively; F = 4.38, df = 1, p < 0.05). Unilateral spatial neglect related to feeding, bowel control and transfer in Barthel index on admission. Patients with aphasia on admission had lower ADL at discharge than patients without aphasia on admission (Mean: 57.0 and 84.7, respectively; F = 7.70, df = 1, p < 0.05). Aphasia related to the bathing, toilet, stair climbing, dressing, and ambulation in Barthel index on discharge. There was a significant difference between the severity of paresis in upper and lower limb on admission and ADL at discharge. The two-way repeated measures ANOVA showed a significant difference between severity of paresis in lower limb and ADL improvement. It can be suggested that the most important predictor of outcome was paresis in lower limb, and not aphasia or unilateral spatial neglect.
Identification of Lynch Syndrome Among Patients With Colorectal Cancer (2020)

Lynch syndrome is the most common form of hereditary colorectal cancer (CRC) and is caused by germline mutations in DNA mismatch repair (MMR) genes. Identification of gene carriers currently relies on germline analysis in patients with MMR-deficient tumors, but criteria to select individuals in whom tumor MMR testing should be performed are unclear.
Magnetic field measurement by NMR imaging (1984)

Measurement of magnetic field distributions is performed using a method based on the nuclear magnetic resonance (NMR) technique of Fourier imaging. By selecting objects which limit the spatial distribution of the NMR-observable nuclei, images can be obtained which allow easy interpretation of the magnetic field distribution and facilitate rapid shimming of magnets. Results are presented showing the effect of a shim coil set of a superconducting solenoid magnet of the type use for NMR imaging. The application of this type of measurement to the rapid shimming of similar magnet designs is analysed. The effects of steel plates close to the magnet are also observed.
Establishment of In Vivo Brain Imaging Method in Conscious Mice (2010)

To our knowledge, this is the first study to report quantitative kinetic analysis of rCMRglu in mice that have been conscious throughout PET. This investigation will open avenues for research into in vivo functional brain molecular imaging in both normal and genetically manipulated mice.
Unified Creeping Model Identifying the Critical State of Granular Material (2022)

Abstract We propose a state evolution model to study the creep of a granular packing both below and beyond the yield stress. Three types of creeping curves are observed under both static and dynamic loading conditions. The experiments are analyzed using the proposed model which introduces characteristic strain to account for the influences of historic strain on current state. A criterion to identify the stability of a granular system is obtained based on the proposed model. Two key factors dominating the stability of the granular system are recognized, the shear wave velocity and critical velocity. Our laboratory experiments in combination with the proposed criterion offers a physical explanation for intrinsic triggering mechanism of system evolution from stable to fluidic state: decrease in wave velocity or/and critical velocity.
A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles (2008)

We discovered a new small non-coding RNA (sRNA) gene, vrrA of Vibrio cholerae O1 strain A1552. A vrrA mutant overproduces OmpA porin, and we demonstrate that the 140 nt VrrA RNA represses ompA translation by base-pairing with the 5' region of the mRNA. The RNA chaperone Hfq is not stringently required for VrrA action, but expression of the vrrA gene requires the membrane stress sigma factor, sigma(E), suggesting that VrrA acts on ompA in response to periplasmic protein folding stress. We also observed that OmpA levels inversely correlated with the number of outer membrane vesicles (OMVs), and that VrrA increased OMV production comparable to loss of OmpA. VrrA is the first sRNA known to control OMV formation. Moreover, a vrrA mutant showed a fivefold increased ability to colonize the intestines of infant mice as compared with the wild type. There was increased expression of the main colonization factor of V. cholerae, the toxin co-regulated pili, in the vrrA mutant as monitored by immunoblot detection of the TcpA protein. VrrA overproduction caused a distinct reduction in the TcpA protein level. Our findings suggest that VrrA contributes to bacterial fitness in certain stressful environments, and modulates infection of the host intestinal tract.
Colorectal cancer screening in the UK: Joint Position Statement by the British Society of Gastroenterology, the Royal College of Physicians, and the Association of Coloproctology of Great Britain and Ireland (2000)

Colorectal (large bowel) cancer is the second commonest cause of cancer related death in the western world and there are more than 30 000 new cases per annum in the UK with an average five year survival of 40%.1-3 Symptoms of colorectal cancer include change in bowel habit, rectal bleeding, anaemia, and abdominal pain but patients with colorectal cancer often have no symptoms until the cancer is advanced. Ninety per cent of cases are currently not diagnosed until the cancer has penetrated through the bowel wall or spread to lymph nodes or elsewhere (Dukes' stages B–D).4 Such cases have a much worse chance of surviving five years (64%, 38%, and 3%, respectively for Dukes' B, C, and D) than patients who present with cancer confined to the bowel wall (Dukes' A) who have approximately 83% chance of surviving five years. Because so many patients with colorectal cancer do not develop symptoms until their cancer is advanced, detection of a greater proportion of cases at an earlier stage can only be achieved by screening of asymptomatic individuals.

It is thought that 70–90% of cases of colorectal cancer arise from premalignant (adenomatous) polyps.5 They often have a stalk which consists of healthy tissue and allows them to be removed simply and completely by endoscopic snaring. This polyp to cancer sequence adds a strong intellectual argument in support of screening for colon cancer as it provides an opportunity not only to achieve early diagnosis (for example of Dukes' stage A carcinomas) but actually to prevent cancer development by removal of premalignant polyps.

There is evidence that approximately 10% of colorectal cancers are due to genetic causes but that about 90% of the cause is accounted for by environmental factors, particularly diet.6 The dietary factors involved are not fully understood …
Factors Affecting Photopolymerization Stress in Dental Composites (2008)

Polymerization stress development results from the complex interplay of volumetric shrinkage, reaction kinetics, and viscoelastic properties. The objective of this study was to examine the relationships among volumetric shrinkage, degree of conversion, rate of polymerization (RP(max)), and stress development for 2 model bis-GMA-based composites. Three irradiances were used--220, 400, or 600 mW/cm(2)--with exposure times adjusted to deliver the same radiant energy. Volumetric shrinkage was determined with a mercury dilatometer, degree of conversion and RP(max) by differential scanning calorimetry (DSC), and polymerization stress with a low-compliance device (Sakaguchi et al., 2004b). Results indicated that polymerization reaction rate and shrinkage were not correlated. Irradiance was directly related to polymerization reaction rate and to stress development. The group with the highest stress/degree of conversion exhibited the lowest RP(max), so it can be assumed, within the limitations of this study, that the conversion was most closely related to stress development.
Directly modulated high power semiconductor optical amplifier (2018)

High power Semiconductor Optical Amplifiers (SOA) are used in optical systems such as Mode Locked Lasers (MLL) as gain medium, or in Master Oscillator Power Amplifiers (MOPA) when they are monolithically integrated with a DFB Laser. In both applications, the optical power at the input of the SOA is rather large (from 1 to few 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> of mW) leading to gain saturation in the device. We present here an experimental study of the harmonic regime for a saturated high power SOA. The electro-optic parameters are measured and a model is proposed in two configurations: when the modulation is applied at the input or at the output of a two section high power SOA.
Isolation and characterization of a trisialoganglioside from mouse brain, containing 9-O-acetyl-N-acetylneuraminic acid. (1980)

A new ganglioside, containing an alkali-labile linkage, was extracted from mouse brain and purified.It represents 5.2% of total lipid-bound sialic acid in the tissue and was obtained in pure form with a yield of about 50%.It contains sphingosine, glucose, galactose, N-acetylgalactosamine, and sialic acid in the molar ratio 1/1/2/1/3 and, upon exhaustive neuraminidase treatment, gives the monosialoganglioside GMl.Partial acid hydrolysis, methylation analysis, gas-liquid chromatography-mass spectrometry, and chromium trioxide oxidation studies showed its basic neutral glycosphingolipid core to be ganglio-N-tetraose ceramide, Gall 3GalNAcl + 4 G d l -+ 4Glcl + 1'ceramide.T w o of the three sialic acid residues are Nacetylneuraminic acid and one, as shown by gas-liquid chromatography-mass spectrometry (GLC-MS), is 9-0- acetyl-N-acetylneuraminic acid, which contains the alkali-labile linkage.9-0-Acetyl-N-acetylneuraminic acid is a-ketosidically linked to position 8 of the N-acetylneuraminic acid residue bound to position 3 of the internal galactose.The third N-acetylneuraminic acid residue is linked to position 3 of the external galactose.The complete structure of the studied ganglioside is as follows: NeuAca2 * 3 G a l B l j 3GalNAcBl+ 4(9-0-Ac-NeuAca2 --* bNeuAca2 4 3)Gal/31+ 4GlcBl--., 1'-Nacylsphingosine, and it can be considered as a derivative of the trisialoganglioside G;Tlb.
Gas-assisted focused electron beam and ion beam processing and fabrication (2008)

Beams of electrons and ions are now fairly routinely focused to dimensions in the nanometer range. Since the beams can be used to locally alter material at the point where they are incident on a surface, they represent direct nanofabrication tools. The authors will focus here on direct fabrication rather than lithography, which is indirect in that it uses the intermediary of resist. In the case of both ions and electrons, material addition or removal can be achieved using precursor gases. In addition ions can also alter material by sputtering (milling), by damage, or by implantation. Many material removal and deposition processes employing precursor gases have been developed for numerous practical applications, such as mask repair, circuit restructuring and repair, and sample sectioning. The authors will also discuss structures that are made for research purposes or for demonstration of the processing capabilities. In many cases the minimum dimensions at which these processes can be realized are considerably larger than the beam diameters. The atomic level mechanisms responsible for the precursor gas activation have not been studied in detail in many cases. The authors will review the state of the art and level of understanding of direct ion and electron beam fabrication and point out some of the unsolved problems.
The Evolution of LTE towards IMT-Advanced (2009)

This paper provides a high-level overview of some technology components currently considered for the evolution of LTE, referred to as LTE-Advanced. First, a brief overview of LTE and some of its technologies are given and then the IMT-Advanced requirements are discussed. One of the targets with the evolution of LTE is to reach or seven surpass these requirements. The technology components considered for LTE-Advanced include extended spectrum flexibility to support up to 100MHz bandwidth, enhanced multi-antenna solutions with up to eight layer transmission in the downlink and up to four layer transmission in the uplink, coordinated multi-point transmission/reception, and the use of advanced repeaters/relaying.
Asymmetric Intermediate Reflector for N-I-P Multi-Junction Thin Film Silicon Solar Cells (2009)

We investigate n-i-p/n-i-p micromorph tandem cells deposited at process temperature below 200°C in order to be compatible with low Tg (&lt;180°C) plastic substrates. In this configuration, the thick microcrystalline cell is grown first and tends to smoothen the initial substrate texture. Hence, the amorphous cell is grown on an almost flat surface that yields low current density. To prevent this effect and to obtain a proper current matching, an asymmetric intermediate reflector, creating a structure favourable for a-Si:H cell, is developed and incorporated into the cells. The effective optical thickness of the amorphous intrinsic layer can be increased by a factor of more than three. Hence, the light induced degradation is reduced below 10% for 180 nm amorphous layer whereas the degradation for cells without intermediate reflector is between 15-20%, because 300 nm amorphous top cell is required for matching. We present a-Si:H/a-Si:H micromorph tandem cells with 10.1 % stable efficiency after 1000h light soaking and triple junction a-Si:H/a-Si:H/μc-Si:H solar cell with initial efficiency of 10.4%.