gebhart/patrepeval huggingface dataset:
Expression and role of E- and P-cadherin adhesion molecules in embryonic histogenesis: I. Lung epithelial morphogenesis (1989)

The role of Ca2+-dependent cell-cell adhesion molecules, E- and P-cadherins, in the histogenesis of mouse embryonic lung was studied. All epithelial cells of the lung express both E- and P-cadherin at the early developmental stage. P-cadherin, however, gradually disappears during development, initially from the main bronchi and eventually from all epithelial cells. When a monoclonal antibody to E-cadherin (ECCD-1) was added to monolayer cultures of lung epithelial cells, it induced a partial disruption of their cell-cell adhesion, while a monoclonal antibody to P-cadherin (PCD-1) showed a subtle effect. A mixture of the two antibodies, however, displayed a synergistic effect. We then tested the effect of the antibodies on the morphogenesis of lung primordia using an organ culture system. In control media, the explants formed typical bronchial trees. In the presence of ECCD-1, the explants grew up at the same rate as in the control, but their morphogenesis was affected. The control explants formed round epithelial lobules with an open luminal space at the tips of the bronchial trees, whereas the lobules of explants incubated with ECCD-1 tended to be flat and devoid of the luminal space. PCD-1 showed a similar but very small effect. A mixture of the two antibodies, however, showed a stronger effect: the branching of epithelia was partially suppressed and the arrangement of epithelial cells was distorted in many places. These results suggest that E- and P-cadherin have a synergistic role in the organization of epithelial cells in lung morphogenesis.
Ultrafast carrier dynamics in a highly excited GaN epilayer (2001)

Femtosecond pump-probe transmission spectroscopy was performed at 10 K to study the nonequilibrium carrier dynamics in a GaN thin film for carrier densities ranging from $4\ifmmode\times\else\texttimes\fi{}{10}^{17}$ to ${10}^{19}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3}.$ Spectral hole burning was initially peaked roughly at the excitation energy for an estimated carrier density of $4\ifmmode\times\else\texttimes\fi{}{10}^{18}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3}$ and gradually redshifted during the excitation. Because of hot phonon effects, a very slow energy relaxation of the hot carriers at these densities was observed. The hot carriers were strongly confined in a nonthermal distribution and they relaxed collectively to the band edge for \ensuremath{\sim}1 ps. We observed remarkable persistence of the excitonic resonances in GaN at carrier densities well above the Mott density at early time delays, indicating that the excitons do not strongly couple to the nonthermal electron-hole plasma.
Polarisation-sensitive optical coherence tomography for material characterisation and testing (2005)

Optical Coherence Tomography (OCT) is an emerging technology for high-resolution non-contact imaging of semi-transparent structures. Originally developed for medical diagnostics, we extend the OCT-technique to problems posed in material testing and characterisation. Layer thickness and refractive indices as well as internal structures of polymer parts have been determined within this study. An extension of OCT, namely polarisation-sensitive OCT (PS-OCT) has been used to identify regions of increased anisotropy within injection-moulded plastic parts and to determine quantitatively internal strain within translucent materials in a non-destructive way.
Deterministic chaos: An introduction (1984)

A new edition of this well-established monograph, this volume provides a comprehensive overview over the still fascinating field of chaos research. The authors include recent developments such as systems with restricted degrees of freedom but put also a strong emphasis on the mathematical foundations. Partly illustrated in color, this fourth edition features new sections from applied nonlinear science, like control of chaos, synchronisation of nonlinear systems, and turbulence, as well as recent theoretical concepts like strange nonchaotic attractors, on-off intermittency and spatio-temporal chaotic motion
The Effects of Transcutaneous Electrical Stimulation during Wakefulness and Sleep in Patients with Obstructive Sleep Apnea (1992)

Upper airway (UA) collapse in obstructive sleep apnea (OSA) is considered in part to result from the decrease in UA dilator muscle tone that occurs during sleep. We hypothesized that augmentation of UA muscle function by transcutaneous electrical stimulation (TES) might function to enlarge UA size during wakefulness and/or prevent UA collapse during sleep in patients with OSA. Eight male patients with OSA were studied both awake and asleep, with TES administered to the submental region in two patients and to both the submental and subhyoid regions in six patients. Fast-CT scans obtained at FRC and end-inspiration (VTei) demonstrated increased UA size with tidal breathing, p less than or equal to 0.05. The active generation of -10 cm H2O pressure at FRC substantially decreased UA size, p less than or equal to 0.001. However, no changes in UA size were detected at either FRC or VTei with TES applied at 50 and 100% of the maximal tolerated intensity. The collapsibility of the UA in response to the generation of -10 cm H2O pressure was also unchanged by TES. In contrast to the lack of effect of TES on UA size, voluntary protrusion of the tongue increased cross-sectional area (CSA) of the orohypopharyngeal (OHP) segment of the UA, p less than 0.05, and to a lesser extent the CSA of the distal velopharyngeal segment, p = 0.06. When applied during sleep, TES failed to prevent or improve either sleep-disordered breathing or sleep architecture.(ABSTRACT TRUNCATED AT 250 WORDS)
Proceedings of the Fourth ACM International Multimedia Conference, Multimedia '96 (1996)

Third hepatectomy is safe and provides an additional benefit of survival similar to that of first and second liver resections. It is worthwhile when curative and integrated into an intended multimodal strategy of tumoral eradication.
Simulation of a quantum-dot flash memory (1998)

We present the simulation of a flash memory in which the floating gate is replaced by a silicon quantum dot. Unlike conventional flash memories, this device promises the advantage of self-limited direct charging of the floating gate with a low writing voltage, thus allowing one to overcome hot carrier degradation problems. Due to the small dimensions of this memory device, quantum effects are expected to play an important role. To estimate their magnitude, we compare a semiclassical simulation based on the solution of Poisson’s equation with a quantum computation solving the complete system of Schrödinger’s and Poisson’s equation. Despite the three-dimensional nature of the problem, a two-dimensional computational mesh proved to be sufficient to provide good agreement with experimental results, after three-dimensional corrections were included.
Epitope mapping of the 2009 pandemic and the A/Brisbane/59/2007 seasonal (H1N1) influenza virus haemagglutinins using mAbs and escape mutants (2014)

mAbs constitute an important biological tool for influenza virus haemagglutinin (HA) epitope mapping through the generation of escape mutants, which could provide insights into immune evasion mechanisms and may benefit the future development of vaccines. Several influenza A (H1N1) pandemic 2009 (pdm09) HA escape mutants have been recently described. However, the HA antigenic sites of the previous seasonal A/Brisbane/59/2007 (H1N1) (Bris07) virus remain poorly documented. Here, we produced mAbs against pdm09 and Bris07 HA proteins expressed in human HEK293 cells. Escape mutants were generated using mAbs that exhibited HA inhibition and neutralizing activities. The resulting epitope mapping of the pdm09 HA protein revealed 11 escape mutations including three that were previously described (G172E, N173D and K256E) and eight novel ones (T89R, F128L, G157E, K180E, A212E, R269K, N311T and G478E). Among the six HA mutations that were part of predicted antigenic sites (Ca1, Ca2, Cb, Sa or Sb), three (G172E, N173D and K180E) were within the Sa site. Eight escape mutations (H54N, N55D, N55K, L60H, N203D, A231T, V314I and K464E) were obtained for Bris07 HA, and all but one (N203D, Sb site) were outside the predicted antigenic sites. Our results suggest that the Sa antigenic site is immunodominant in pdm09 HA, whereas the N203D mutation (Sb site), present in three different Bris07 escape mutants, appears as the immunodominant epitope in that strain. The fact that some mutations were not part of predicted antigenic sites reinforces the necessity of further characterizing the HA of additional H1N1 strains.
How Well Does the Gleason Score Predict Prostate Cancer Death? A 20-Year Followup of a Population Based Cohort in Sweden (2006)

Although a high Gleason score is a determinant of prostate cancer death, its PPV is relatively low. Thus, further efforts in finding other or complementary indicators of prostate cancer outcome are needed.
DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma (2008)

Deletions on chromosome 8p are common in human tumors, suggesting that one or more tumor suppressor genes reside in this region. Deleted in Liver Cancer 1 (DLC1) encodes a Rho-GTPase activating protein and is a candidate 8p tumor suppressor. We show that DLC1 knockdown cooperates with Myc to promote hepatocellular carcinoma in mice, and that reintroduction of wild-type DLC1 into hepatoma cells with low DLC1 levels suppresses tumor growth in situ. Cells with reduced DLC1 protein contain increased GTP-bound RhoA, and enforced expression a constitutively activated RhoA allele mimics DLC1 loss in promoting hepatocellular carcinogenesis. Conversely, down-regulation of RhoA selectively inhibits tumor growth of hepatoma cells with disabled DLC1. Our data validate DLC1 as a potent tumor suppressor gene and suggest that its loss creates a dependence on the RhoA pathway that may be targeted therapeutically.
Influence of doping on the structural and optoelectronic properties of amorphous and microcrystalline silicon carbide (1992)

Amorphous and microcrystalline silicon carbide, undoped and doped, has attracted a great attention for its optical and electrical properties. The introduction of dopant atoms in the network of amorphous films permits the control of electrical properties but it gives rise to a decreasing of the optical gap. Microcrystalline SiC:H films seem to provide films having a wide range of electrical conductivities without drastic change in the optical gap. This paper presents the results of a detailed study on the effects of boron and phosphorus doping on structural, optical, and electrical properties of a-SiC:H and μc-SiC:H films. An optical gap as high as 2.1 eV, together with a conductivity of 10−3 Ω−1 cm−1, are shown by doped μc-SiC:H.
The science of virtual reality and virtual environments: a technical, scientific and engineering reference on virtual environments (1993)

*Virtual Environment Systems: An Introduction *The History of Virtual Environment Systems *Physiology and Perception in Virtual Environments *Virtual Environment Systems: Enabling Technology *Virtual Environment Systems: Software *The Realities of Virtual Reality *Applications of Virtual Environments *Concluding Remarks
Identification of Novel Human CTL Epitopes and Their Agonist Epitopes of Mesothelin (2005)

The identification of novel CTL agonist epitopes supports and extends observations that mesothelin is a potential target for immunotherapy of pancreatic and ovarian cancers, as well as mesotheliomas.
Listen, attend and spell: A neural network for large vocabulary conversational speech recognition (2016)

We present Listen, Attend and Spell (LAS), a neural speech recognizer that transcribes speech utterances directly to characters without pronunciation models, HMMs or other components of traditional speech recognizers. In LAS, the neural network architecture subsumes the acoustic, pronunciation and language models making it not only an end-to-end trained system but an end-to-end model. In contrast to DNN-HMM, CTC and most other models, LAS makes no independence assumptions about the probability distribution of the output character sequences given the acoustic sequence. Our system has two components: a listener and a speller. The listener is a pyramidal recurrent network encoder that accepts filter bank spectra as inputs. The speller is an attention-based recurrent network decoder that emits each character conditioned on all previous characters, and the entire acoustic sequence. On a Google voice search task, LAS achieves a WER of 14.1% without a dictionary or an external language model and 10.3% with language model rescoring over the top 32 beams. In comparison, the state-of-the-art CLDNN-HMM model achieves a WER of 8.0% on the same set.
Creation of Hybridomas from Mice Expressing Human Antibody by Introduction of a Human Chromosome (2006)

Monoclonal antibodies are not only used in human diagnostics, but also in human therapy. People cannnot be immunized in vivo with any kind of antigen, and many challenges have been done to obtain human monoclonal antibodies for therapeutic use. Transgenic approach is useful to generate highaffinity monoclonal antibodies. It is known that for each type of Ig chain kappa light chains, lambda light chains, and heavy chains there is a separate pool of gene segments from which a single polypeptide chain eventually synthesized. Each pool is on a three different chromosome and contains a large number of genes. But only a limited amount of DNA can be transferred using standard techniques. We have developed a novel procedure to introduce foreign genetic material into mice by using a chromosome itself as a vector. Human chromosome (hChr.) 14, 22, or hChr.2-derived fragment including Ig heavy, lambda or kappa genes was transferred into mouse ES cells via microcell-mediated chromosome transfer (MMCT). In this study we immunized the chimaeric mice containing hChr. 14-fragment by human serum albumin (HSA) and obtained a hybridoma expressing specific antibody to HSA comprised human μ chain . Furthermore we created the chimaeric mice containing two distinct human chromosomes in order to engineer mice that produce complete human antibody molecules, as an antibody molecule is composed of two identical light chains and two identical heavy chains.
Giant Birefringent Optics in Multilayer Polymer Mirrors (2000)

Multilayer mirrors that maintain or increase their reflectivity with increasing incidence angle can be constructed using polymers that exhibit large birefringence in their indices of refraction. The most important feature of these multilayer interference stacks is the index difference in the thickness direction ( z axis) relative to the in-plane directions of the film. This z -axis refractive index difference provides a variable that determines the existence and value of the Brewster's angle at layer interfaces, and it controls both the interfacial Fresnel reflection coefficient and the phase relations that determine the optics of multilayer stacks. These films can yield optical results that are difficult or impossible to achieve with conventional multilayer optical designs. The materials and processes necessary to fabricate such films are amenable to large-scale manufacturing.
Cooperation between Matrix Metalloproteinasesand the Plasminogen Activator-Plasmin Systemin Tumor Progression (1996)

Several classes of extracellular matrix (ECM)-degrading proteases have been shown to play an important role in tumor invasion and metastasis. Among them, the matrix metalloproteinases (MMPs) and the plasminogen activator (PA)-plasmin system have been the focus of numerous studies. However, few of those have examined the interaction of these two classes of proteases during tumor progression and their specific roles in this complex process have remained unclear. In this article, comparative information on the structure, function, and regulation of these two classes of proteases is reviewed and their interaction on various levels is discussed. This review shows that MMPs and the PA-plasmin system closely cooperate to achieve optimal degradation of the ECM during the invasive and metastatic process.
Motor skill learning and performance: a review of influential factors (2009)

All factors reviewed in this article appear to have both informational and motivational influences on learning. The findings seem to reflect general learning principles and are assumed to have relatively broad applicability. Therefore, the consideration of these factors in designing procedures for medical training has the potential to enhance the effectiveness and efficiency of training.
The homologous recombination system of phage lambda. Pairing activities of beta protein. (1986)

The red genes of phage lambda specify two proteins, exonuclease and beta protein, which are essential for its general genetic recombination in recA- cells. These proteins seem to occur in vivo as an equimolar complex. In addition, beta protein forms a complex with another polypeptide, probably of phage origin, of Mr 70,000. The 70-kDa protein appears to be neither a precursor nor an aggregated form of either exonuclease or beta protein, since antibodies directed against the latter two proteins failed to react with 70-kDa protein on Ouchterlony double diffusion analysis. beta protein promotes Mg2+-dependent renaturation of complementary strands (Kmiec, E., and Holloman, W. K. (1981) J. Biol. Chem. 256, 12636-12639). To look for other pairing activities of beta protein, we developed methods of purification to free it of associated exonuclease. Exonuclease-free beta protein appeared unable to cause the pairing of a single strand with duplex DNA; however, like Escherichia coli single strand binding protein (SSB), beta protein stimulated formation of joint molecules by recA protein from linear duplex DNA and homologous circular single strands. Like recA protein, but unlike SSB, beta protein promoted the joining of the complementary single-stranded ends of phage lambda DNA. beta protein specifically protected single-stranded DNA from digestion by pancreatic DNase. The half-time for renaturation catalyzed by beta protein was independent of DNA concentration, unlike renaturation promoted by SSB and spontaneous renaturation, which are second order reactions. Thus, beta protein resembles recA protein in its ability to bring single-stranded DNA molecules together and resembles SSB in its ability to reduce secondary structure in single-stranded DNA.
Bio-heat transfer model of deep brain stimulation-induced temperature changes (2006)

There is a growing interest in the use of chronic deep brain stimulation (DBS) for the treatment of medically refractory movement disorders and other neurological and psychiatric conditions. Fundamental questions remain about the physiologic effects of DBS. Previous basic research studies have focused on the direct polarization of neuronal membranes by electrical stimulation. The goal of this paper is to provide information on the thermal effects of DBS using finite element models to investigate the magnitude and spatial distribution of DBS-induced temperature changes. The parameters investigated include stimulation waveform, lead selection, brain tissue electrical and thermal conductivities, blood perfusion, metabolic heat generation during the stimulation and lead thermal conductivity/heat dissipation through the electrode. Our results show that clinical DBS protocols will increase the temperature of surrounding tissue by up to 0.8 degrees C depending on stimulation/tissue parameters.
Material and device considerations for organic thin-film transistor sensors (2009)

The rapid development of the field of organic electronics has sparked great interest in the use of organic thin-film transistors (OTFTs) as low-cost electronic sensors. The direct coupling of the electronic and the sensor media to provide real time electrical output has already demonstrated high sensitivity to a variety of chemical species. The synthetic versatility of organic materials also provides endless routes to impart functionality for specifically targeted chemical interactions. Owing to their compatibility with flexible materials and simple fabrication methods, OTFTs are poised to have a tremendous impact on future portable detection technology. This article reviews recent progress made toward improved sensitivity, selectivity and stability of OTFT sensors through material and device engineering. Specific consideration is paid to the interaction of the electronic materials with the analytes as a means of providing insight into mechanistic principles as well as the future direction of OTFTs.
Highly Specific Affinities of Short Peptides against Synthetic Polymers (2007)

We investigated polymer-binding 7-mer peptides that recognize differences in the polymer stereoregularity of all-purpose poly(methyl methacrylate)s (PMMAs) with simple chemical structures. Quantitative surface plasmon resonance measurements detected association/dissociation processes of the peptides against PMMA film surfaces, followed by an estimation of kinetic parameters such as association/dissociation rate constants and affinity constants. Greater association and smaller dissociation constants of the peptides were observed against a target isotactic PMMA than the structurally similar reference syndiotactic PMMA, followed by greater affinity constants against the target. A c02 peptide composed of the Glu-Leu-Trp-Arg-Pro-Thr-Arg sequence showed the greatest affinity constant (2.8x10(5) M(-1)) for the target, which was 41-fold greater than that for the reference, thus demonstrating extremely high peptide specificities. The substitution of each amino acid of the c02 peptide to Ala (Ala scanning) clearly revealed the essential amino acids for the affinity constants; the essential order was Pro5>>Thr6>Arg7>Glu1>Arg4. In fact, the shorter 4-mer peptide composed of the C-terminal Arg-Pro-Thr-Arg sequence of the c02 peptide still demonstrated strong target specificity, although the N-terminal 4-mer peptide Glu-Leu-Trp-Arg completely lost its specificity. The possible conformations modeled with Molecular Mechanics supported the significance of the Arg-Pro-Thr-Arg sequence. The thermodynamic parameters of the c02 peptide suggested an induced fit mechanism for the specific affinity. The present affinity analyses of polymer-recognizing peptides revealed significant and general information that was essential for potential applications in peptidyl nanomaterials.
Scanningless depth-resolved microscopy (2005)

The ability to perform optical sectioning is one of the great advantages of laser-scanning microscopy. This introduces, however, a number of difficulties due to the scanning process, such as lower frame rates due to the serial acquisition process. Here we show that by introducing spatiotemporal pulse shaping techniques to multiphoton microscopy it is possible to obtain full-frame depth resolved imaging completely without scanning. Our method relies on temporal focusing of the illumination pulse. The pulsed excitation field is compressed as it propagates through the sample, reaching its shortest duration at the focal plane, before stretching again beyond it. This method is applied to obtain depth-resolved twophoton excitation fluorescence (TPEF) images of drosophila egg-chambers with nearly 105 effective pixels using a standard Ti:Sapphire laser oscillator.
Commentary The struggle to detect circulating DNA (2006)

In various diseases, such as cancer, autoimmune disease, sepsis or myocardial infarction, elevated levels of circulating DNA can be measured. However, its predictive value is under debate. Circulating DNA in plasma is protein-bound (nucleosomal) DNA. Quantification of circulating DNA can be performed by real-time quantitative PCR or immunological methods such as ELISA. The diagnostic value of both methods can be impaired by inappropriate handling of the samples. Assessment of circulating DNA in patients admitted to the intensive care unit offers a tool for predicting morbidity and mortality.