gebhart/patrepeval huggingface dataset:
Variation of Microfibril Angle, Density and Stiffness in Fifty Radiata Pine Trees (2001)

Sixty parent radiata pine trees were screened using SilviScan and 25 were selected for extremes of tracheid wall thickness and perimeter. For each of the 25 selected parents, eight 13-year-old half sib progeny were also characterised by tracheid wall thickness and perimeter. From these 200 progeny trees, 25 were selected to cover the ranges of tracheid wall thickness and perimeter. Two years later, a second set were selected from the remaining 175 progeny trees, firstly for tracheid length; and secondly for tracheid perimeter and wall thickness. Longitudinal stiffness of breast height samples from the 50 selected progeny trees, as measured by a sonic velocity technique, was strongly correlated with stiffness estimated by SilviScan, using a model based on densitometric and diffractometric data. Variation in density, MFA and MOE{SS} between the two sets of 25 trees were very different because of the different selection criteria. Age-age correlations were also sensitive to the selection criteria. Radial variation in MFA was strongly correlated with the absolute value of MFA near the pith, supporting the argument that selection for low MFA in very young trees would be an efficient means of improving wood quality.
P16INK4a is a tumor autoantigen in HR-HPV induced cancers (2005)

5140 The cellular tumor suppressor gene p16INK4a is over-expressed in a large number of high-risk human papilloma virus (HR-HPV) induced tumors, especially in cervical cancers. The massive over-expression results from a disrupted feed back mechanism of the Rb/E2F pathway induced by the HPV oncoprotein E7. In contrast, p16INK4a is expressed only in few normal cells, mainly terminally differentiated cells with low antigen presenting capacity. We could show previously, that T-cells from healthy donors can be stimulated to react against p16INK4a peptides presented by HLA-A2 positive cells. To further analyze if p16INK4a acts as a tumor autoantigen in cervical cancer, humoral and cellular immune responses against p16INK4a were monitored in cervical cancer patients. To measure humoral immune responses, sera derived from 70 cervical cancer patients were analyzed by western blotting. Using recombinant p16INK4a protein blotted on nylon membranes, five patients showed clear p16INK4a specific signals that could be blocked by serum pre-incubation with recombinant p16INK4a. For the analysis of cellular immune responses, infiltrating T-cells (TILs) were isolated from ten freshly resected cervical cancers or highly dysplastic lesions (CIN3) and tested for their reactivity against p16INK4a peptides. In two patients, TILs with a significant reactivity against the identical p16INK4a peptide that showed strong stimulation of the healthy donor T-cells were isolated from the respective lesions. These findings indicate that cervical carcinoma patients can develop humoral and cellular immune responses against the cellular tumor suppressor protein p16INK4a. P16INK4a can therefore be added to the group of over-expressed tumor autoantigens (like HER2/neu, hTERT, MUC1) and might be used as a novel target in immunotherapy of HR-HPV induced cancer.
The role of surface shear during accumulative roll bonding of an interstitial free steel (2004)

An interstitial free steel was severely plastically deformed in an accumulative roll bonding (ARB) experiment with 5 consecutive passes at 480degreesC with a nominal reduction of 50% per pass and an intermediate annealing treatment of 10 min. at 520degreesC. A total true strain was obtained of epsilon(nuM)=4.00 which corresponds to an accumulated reduction of 96.9%. The evolution of textures and microstructures was monitored by means of orientation microscopy. A lamellar microstructure, characteristic for severely rolled sheet material, was observed even after the highest strains. The average lamellar width was determined as a function of rolling strain. Under the given experimental limitations in terms of spatial resolution, no significant difference could be observed between the average lamellar width in the midsection and near the surface of the sheet. The texture analysis revealed a conventional cross-sectional gradient with plane strain rolling components in the midlayers and shear components in the subsurface area. Although these different strain modes did not affect the microstructure in terms of average lamellar spacing, an effect was observed on the average aspect ratio of the grains being much higher in the sheared (surface) than in the plane strain compressed areas (middle). The surface structure did not have an effect, though, on the bulk microstructural evolution in spite of the specific nature of the ARB process during which the surface layer of one pass reappears in the midsection of the next pass.
Microwave-assisted solid-state reactions involving metal powders and gases (1993)

The high dielectric loss tangents of metal powders at 2450 MHz have been utilised to facilitate the syntheses of a range of metal chlorides, oxochlorides, bromides and nitrides by direct combination of metals with gases.
Weight Change and Risk of Developing Type 2 Diabetes (2005)

A low initial BMI does not ameliorate the increase in risk of type 2 diabetes with weight gain. Avoidance of weight gain, even among lean individuals, is important to reduce the risk of this disease.
Evaluation of Toxic Agent Effects on Lung Cells by Fiber Evanescent Wave Spectroscopy (2005)

Biochemical changes in living cells are detected using a fiber probe system composed of a single chalcogenide fiber acting as both the sensor and transmission line for infrared optical signals. The signal is collected via evanescent wave absorption along the tapered sensing zone of the fiber. We spectroscopically monitored the effects of the surfactant Triton X-100, which serves as a toxic agent simulant on a transformed human lung carcinoma type II epithelial cell line (A549). We observe spectral changes between 2800-3000 cm(-1) in four absorptions bands, which are assigned to hydrocarbon vibrations of methylene and methyl groups in membrane lipids. Comparison of fiber and transmission spectra shows that the present technique allows one to locally probe the cell plasma membrane in the lipid spectral region. These optical responses are correlated with cellular metabolic activity measurements and LDH (lactate dehydrogenase) release assays that indicate a loss of cellular function and membrane integrity as would be expected in response to the membrane solubilizing Triton. The spectroscopic technique shows a significantly greater detection resolution in time and concentration.
High-Energy Tibial Plateau Fractures (2006)

The severity of a tibial plateau fracture and the complexity of its treatment depend on the energy imparted to the limb. Low-energy injuries typically cause unilateral depression-type fractures, whereas high-energy injuries can lead to comminuted fractures with significant osseous, soft-tissue, and neurovascular injury. Evaluation includes appropriate radiographs and careful clinical assessment of the soft-tissue envelope. Treatment is directed at safeguarding tissue vascularity and emphasizes restoration of joint congruity and the mechanical axis of the limb. Temporary joint-spanning external fixation facilitates soft-tissue recovery, whereas minimally invasive techniques and anatomically contoured plates can limit damage to the soft tissues and provide stable fixation. Alternatively, the use of limited internal fixation and definitive external fixation can minimize soft-tissue disruption, avoid complications, and allow fracture union. Complications, including infection, loss of fixation, and malalignment, are best avoided by following these biologically respectful treatment principles.
A novel a-Si:H AMOLED pixel circuit based on short-term stress stability of a-Si:H TFTs (2005)

This letter presents a novel pixel circuit for hydrogenated amorphous silicon (a-Si:H) active matrix organic light-emitting diode displays employing the short-term stress stability characteristics of a-Si:H thin film transistors (TFTs). The pixel circuit uses a programming TFT that is under stress during the programming cycle and unstressed during the drive cycle. The threshold voltage shift (V/sub T/-shift) of the TFT under these conditions is negligible. The programming TFT in turn regulates the current of the drive TFT, and the pixel current therefore becomes independent of the threshold voltage of the drive TFT.
Thermodynamics of Sequence-Specific Binding of PNA to DNA (2000)

For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes) and sequence specificity of binding (singly mismatched duplexes) using mainly absorption hypochromicity melting curves and isothermal titration calorimetry. For perfectly sequence-matched duplexes of varying lengths (6-20 bp), the average free energy of binding (DeltaG degrees ) was determined to be -6.5+/-0.3 kJ mol(-1) bp(-1), corresponding to a microscopic binding constant of about 14 M(-1) bp(-1). A variety of single mismatches were introduced in 9- and 12-mer PNA-DNA duplexes. Melting temperatures (T(m)) of 9- and 12-mer PNA-DNA duplexes with a single mismatch dropped typically 15-20 degrees C relative to that of the perfectly matched sequence with a corresponding free energy penalty of about 15 kJ mol(-1) bp(-1). The average cost of a single mismatch is therefore estimated to be on the order of or larger than the gain of two matched base pairs, resulting in an apparent binding constant of only 0.02 M(-1) per mismatch. The impact of a mismatch was found to be dependent on the neighboring base pairs. To a first approximation, increasing the stability of the surrounding region, i.e., the distribution of A.T and G.C base pairs, decreases the effect of the introduced mismatch.
Wavelets and filter banks: theory and design (1992)

The wavelet transform is compared with the more classical short-time Fourier transform approach to signal analysis. Then the relations between wavelets, filter banks, and multiresolution signal processing are explored. A brief review is given of perfect reconstruction filter banks, which can be used both for computing the discrete wavelet transform, and for deriving continuous wavelet bases, provided that the filters meet a constraint known as regularity. Given a low-pass filter, necessary and sufficient conditions for the existence of a complementary high-pass filter that will permit perfect reconstruction are derived. The perfect reconstruction condition is posed as a Bezout identity, and it is shown how it is possible to find all higher-degree complementary filters based on an analogy with the theory of Diophantine equations. An alternative approach based on the theory of continued fractions is also given. These results are used to design highly regular filter banks, which generate biorthogonal continuous wavelet bases with symmetries.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Neuroprotective Strategies for the Treatment of Inherited Photoreceptor Degeneration (2012)

Photoreceptor degeneration is the hallmark of several groups of inherited neurodegenerative diseases causing blindness in humans. These diseases are a major cause of visual handicap and to date no satisfactory treatment is available. Here, we briefly review different approaches for the treatment of photoreceptor degeneration, to then focus on neuroprotection. Up to date, translation of experimental neuroprotection into a clinical setting has faced major obstacles, which are in part due to an incomplete understanding of the regulation of pro-survival as well as neurodegenerative mechanisms. Previous approaches were often based on the hypothesis that photoreceptor cell death was governed by a single, apoptotic cell death mechanism. This perception has turned out too simple as recent work has demonstrated that photoreceptor cell death is governed by non-apoptotic mechanisms as well. Moreover, there is evidence, that several different destructive processes are executed in parallel. Briefly reviewing the complexity of degenerative mechanisms, this review discusses relevant pathways, options to target signaling cascades, final common denominators of cell death, and the interplay of events executing cell death. In particular, we focus on cGMP-signaling, epigenetic and proteolytic processes and the corresponding enzymatic activities that were recently shown to be causally related to retinal degeneration. Finally, we illustrate how a better understanding of destructive mechanisms may enable identification and validation of novel targets for neuroprotection, and allow development of next generation neuroprotective treatments as well as combination therapy.
High-efficiency native-oxide-passivated high-index-contrast ridge waveguide lasers (2006)

A GaAs-based high-index-contrast ridge waveguide laser is fabricated using a self-aligned process of deep dry etching plus oxygen-enhanced wet thermal oxidation of low Al-content AlGaAs. Lasers operating at λ=813 nm (CW, 300 K) with external differential quantum efficiencies as high as 78% are demonstrated, indicating effective passivation of the directly-oxidised etched active region sidewall surface.
Anticardiolipin antibodies recognize beta 2-glycoprotein I structure altered by interacting with an oxygen modified solid phase surface. (1994)

Anticardiolipin antibodies (aCL) derived from the sera of individuals exhibiting the antiphospholipid syndrome (APS) directly bind to beta 2-glycoprotein I (beta 2-GPI), which is adsorbed to an oxidized polystyrene surface. Oxygen atoms were introduced on a polystyrene surface by irradiation with electron or gamma-ray radiation. X-ray photoelectron spectroscopy revealed the irradiated surfaces were oxidized to generate C-O and C = O moieties. aCL derived from either APS patients or (NZW x BXSB)F1 mice bound to beta 2-GPI coated on the irradiated plates, depending on the radiation dose. Antibody binding to beta 2-GPI on the irradiated plates was competitively inhibited by simultaneous addition of cardiolipin (CL)-coated latex beads mixed together with beta 2-GPI but were unaffected by addition of excess beta 2-GPI, CL micelles, or CL-coated latex beads alone. There was a high correlation between binding values of aCL in sera from 40 APS patients obtained by the anti-beta 2-GPI enzyme-linked immunosorbent assay (ELISA) using the irradiated plates and those by the beta 2-GPI-dependent aCL ELISA. Therefore, aCL have specificity for an epitope on beta 2-GPI. This epitope is expressed by a conformational change occurring when beta 2-GPI interacts with an oxygen-substituted solid phase surface.
Therapeutic implications of down-regulation of cyclophilin D in bipolar disorder (2010)

We previously reported that neuron-specific mutant Polg1 (mitochondrial DNA polymerase) transgenic (Tg) mice exhibited bipolar disorder (BD)-like phenotypes such as periodic activity change and altered circadian rhythm. In this study, we re-evaluated two datasets resulting from DNA microarray analysis to estimate a biological pathway associated with the disorder. The gene lists were derived from the comparison between post-mortem brains of BD patients and control subjects, and from the comparison between the brains of Tg and wild-type mice. Gene ontology analysis showed that 16 categories overlapped in the altered gene expression profiles of BD patients and the mouse model. In the brains of Tg mice, 33 genes showed similar changes in the frontal cortex and hippocampus compared to wild-type mice. Among the 33 genes, SFPQ and PPIF were differentially expressed in post-mortem brains of BD patients compared to control subjects. The only gene consistently down-regulated in both patients and the mouse model was PPIF, which encodes cyclophilin D (CypD), a component of the mitochondrial permeability transition pore. A blood-brain barrier-permeable CypD inhibitor significantly improved the abnormal behaviour of Tg mice at 40 mg/kg.d. These findings collectively suggest that CypD is a promising target for a new drug for BD.
l-Arginine enhances aerobic exercise capacity in association with augmented nitric oxide production (2001)

We tested whether supplementation with L-arginine can augment aerobic capacity, particularly in conditions where endothelium-derived nitric oxide (EDNO) activity is reduced. Eight-week-old wild-type (E(+)) and apolipoprotein E-deficient mice (E(-)) were divided into six groups; two groups (LE(+) and LE(-)) were given L-arginine (6% in drinking water), two were given D-arginine (DE(+) and DE(-)), and two control groups (NE(+) and NE(-)) received no arginine supplementation. At 12-16 wk of age, the mice were treadmill tested, and urine was collected after exercise for determination of EDNO production. NE(-) mice demonstrated a reduced aerobic capacity compared with NE(+) controls [maximal oxygen uptake (VO(2 max)) of NE(-) = 110 +/- 2 (SE) vs. NE(+) = 122 +/- 3 ml O(2). min(-1). kg(-1), P < 0.001]. This decline in aerobic capacity was associated with a diminished postexercise urinary nitrate excretion. Mice given L-arginine demonstrated an increase in postexercise urinary nitrate excretion and aerobic capacity in both groups (VO(2 max) of LE(-) = 120 +/- 1 ml O(2). min(-1). kg(-1), P < 0.05 vs. NE(-); VO(2 max) of LE(+) = 133 +/- 4 ml O(2). min(-1). kg(-1), P < 0.01 vs. NE(+)). Mice administered D-arginine demonstrated an intermediate increase in aerobic capacity in both groups. We conclude that administration of L-arginine restores exercise-induced EDNO synthesis and normalizes aerobic capacity in hypercholesterolemic mice. In normal mice, L-arginine enhances exercise-induced EDNO synthesis and aerobic capacity.
Regulation of plasmid R1 replication: PcnB and RNase E expedite the decay of the antisense RNA, CopA (1997)

The replication frequency of plasmid R1 is controlled by an unstable antisense RNA, CopA, which, by binding to its complementary target, blocks translation of the replication rate-limiting protein RepA. Since the degree of inhibition is directly correlated with the intracellular concentration of CopA, factors affecting CopA turnover can also alter plasmid copy number. We show here that PcnB (PAPl-a poly(A)polymerase of Escherichia coli) is such a factor. Previous studies have shown that the copy number of ColE1 is decreased in pcnB mutant strains because the stability of the RNase E processed form of RNAI, the antisense RNA regulator of ColE1 replication, is increased. We find that, analogously, the twofold reduction in R1 copy number caused by a pcnB lesion is associated with a corresponding increase in the stability of the RNase E-generated 3' cleavage product of CopA. These results suggest that CopA decay is initiated by RNase E cleavage and that PcnB is involved in the subsequent rapid decay of the 3' CopA stem-loop segment. We also find that, as predicted, under conditions in which CopA synthesis is unaffected, pcnB mutation reduces RepA translation and increases CopA stability to the same extent.
Application of Probabilistic Fracture Mechanics to Prognosis of Aircraft Engine Components (2006)

It is generally accepted that traditional logistics functions including periodic nondestructive inspections and planned maintenance increase the reliability and readiness of turbine engines. Nevertheless, further significant enhancements in reliability and readiness are believed to be possible through the implementation of a prognosis system based on online monitoring and interpretation of critical engine operating parameters and conditions to diagnose potential problems and forecast readiness. An approach is presented for improving probabilistic life prediction estimates through the application of prognosis methods. Actual F-16/F100 usage data from flight data recorders were interfaced with a probabilistic life prediction code to quantify the influence of usage on the probability of fracture of an idealized titanium compressor disk. For the example cases considered, it is shown that usage variability leads to about 6 × × variability in life and from 10 × × to 100 × variability in the probability of fracture. The results suggest that variability in usage could provide a basis for selectively extending the life of aircraft engines.
Tumor-infiltrating lymphocytes are a marker for microsatellite instability in colorectal carcinoma (2001)

The presence of MSI defines a subset of colorectal carcinomas with special molecular etiology and characteristic clinical, pathologic features, inclusive of increased survival. The authors conclude that quantification of TILs may provide a simple, single criterion for choosing which colorectal carcinomas are candidates for MSI testing.
Supramolecular Photonic Therapeutic Agents (2005)

A new approach to achieving selectivity for photodynamic therapy based upon the reversible off/on switching of the key therapeutic property (singlet oxygen generation) of a supramolecular photonic therapeutic agent (SPTA) in response to an external stimulus in the surrounding microenvironment is described. A series of SPTA analogues with pH responsive receptors of varying pKa are presented, in which the generation of singlet oxygen is shown to be dependent upon a proton source. For example, systems have been constructed such that the excited state energy of the photosensitizer can be decayed by a rapid photoinduced electron transfer (PET) mechanism, resulting in virtually no singlet oxygen being generated, but when the amine receptor is protonated the PET mechanism does not operate and singlet oxygen is produced. In vitro efficacy demonstrated that the SPTA derivatives can be activated within cells and one analogue is measured to have an EC50 value of 5.8 nM when assayed in the MRC5 cell line.
The DeoR-type transcriptional regulator SugR acts as a repressor for genes encoding the phosphoenolpyruvate:sugar phosphotransferase system (PTS) in Corynebacterium glutamicum (2007)

In C. glutamicum ATCC 13032 the DeoR-type regulator SugR acts as a pleiotropic transcriptional repressor of all described PTS genes. Thus, in contrast to most DeoR-type repressors described, SugR is able to act also on the transcription of the distantly located genes ptsG and ptsS of C. glutamicum. Transcriptional repression of the fructose-PTS gene cluster is observed during growth on acetate and transcription is derepressed in the presence of the PTS sugars glucose and fructose. This derepression of the fructose-PTS gene cluster is mainly modulated by the negative effector F-1-P, but reduced sensitivity to the other effectors, F-1,6-P or G-6-P might cause differential transcriptional regulation of genes of the general part of the PTS (ptsI, ptsH) and associated genes encoding sugar-specific functions (ptsF, ptsG, ptsS).
Visual robot navigation using flat earth obstacle projection (2002)

Autonomous robot navigation requires the solution of several problems like obstacle avoidance and road following. Traditionally, the problem of obstacle avoidance has been solved by using range information acquired through some form of range measurements like laser range cameras or vision based range estimation. This paper presents a novel approach for obstacle avoidance which does not require true range measurement. Obstacle information is acquired using a single color camera. Detected obstacles are projected into 3D grid derived from the camera geometry and a locally flat earth model for the terrain. A weighted polar histogram technique is used to generate the vehicle steering angle based on the current grid information.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>