gebhart/patrepeval huggingface dataset:
In-Depth Characterization of Prebiotic Galacto-oligosaccharides by a Combination of Analytical Techniques (2009)

A commercial prebiotic galacto-oligosaccharide mixture (Vivinal GOS) was extensively characterized using a combination of analytical techniques. The different techniques were integrated to give complementary information on specific characteristics of the oligosaccharide mixture, ranging from global information on degree of polymerization (DP) to the identity and concentration of individual oligosaccharides. The coupling of high-performance anion-exchange chromatography (HPAEC) to mass spectrometry (MS) was determined to be especially suitable to assign the DP of individual oligosaccharides on the basis of their m/z values as well as their quantification using external standards. The combination of NMR spectroscopy and methylation analysis after isolation using size exclusion chromatography (SEC) and hydrophilic interaction liquid chromatography (HILIC) was used for identification. All DP2 compounds could be identified and quantified in this way as well as the main DP3 compounds.
Apoptotic pathways in pancreatic ductal adenocarcinoma (2008)

Pancreatic ductal adenocarcinoma (PDAC) is one of the most common causes of cancer related death. Despite the advances in understanding of the molecular pathogenesis, pancreatic cancer remains a major unsolved health problem. Overall, the 5-year survival rate is less than 5% demonstrating the insufficiency of current therapies. Most cytotoxic therapies induce apoptosis and PDAC cells have evolved a plethora of molecular mechanisms to assure survival. We will present anti-apoptotic strategies working at the level of the death receptors, the mitochondria or involving the caspase inhibitors of the IAP family. Furthermore, the survival function of the phosphotidylinositol-3' kinase (PI3K)/AKT- and NF-kappaB-pathways are illustrated. A detailed molecular knowledge of the anti-apoptotic mechanisms of PDAC cells will help to improve therapies for this dismal disease and therapeutic strategies targeting the programmed cell death machinery are in early preclinical and clinical development.
A NEW DEVICE: (2003)

Department of Plastic and Reconstructive Surgery, Nippon Medical School Hospital, Tokyo, Japan Correspondence to Dr. Chin, Department of Plastic and Reconstructive Surgery, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8603, Japan [email protected]
Isolation and Characterization of the Complete Complementary and Genomic DNA Sequences of Human Serum Amyloid P Component1 (1986)

Complementary and genomic DNA clones corresponding to the human serum amyloid P component (SAP) mRNA have been isolated and analyzed. The nucleotide sequences of the cDNA and the corresponding regions of the genomic SAP DNA reported here were identical, and revealed that after coding for a signal peptide of 19 amino acids and the first two amino acids of the mature SAP protein, there is one small intron of 115-base pairs (bp), followed by a nucleotide sequence coding for the remaining 202 amino acid residues. The SAP gene has an ATATAAA sequence 29-bp upstream from the cap site, but there is no CAAT box-like sequence. A possible polyadenylation signal sequence, ATTAAA, was found to be located 28-bp upstream from the polyadenylation site. A comparison of the genomic SAP DNA sequence with that of human C-reactive protein (CRP) revealed a striking overall homology which was not uniform: several highly conserved regions were bounded by non-homologous regions. This comparison provides further support for the hypothesis that SAP and CRP are products of a gene duplication event.
Recent advances of highly selective CDK4/6 inhibitors in breast cancer (2017)

Uncontrolled cell division is the hallmark of cancers. Full understanding of cell cycle regulation would contribute to promising cancer therapies. In particular, cyclin-dependent kinases 4/6 (CDK4/6), which are pivotal drivers of cell proliferation by combination with cyclin D, draw more and more attention. Subsequently, extensive studies were carried out to explore drugs inhibiting CDK4/6 and assess the efficacy and safety of these drugs in cancer, especially breast cancer. Due to the insuperable adverse events and the less activity observed in vivo, the drug development of the initial pan-CDK inhibitor flavopiridol was consequently discontinued, and then highly specific inhibitors were extensively researched and developed, including palbociclib (PD0332991), ribociclib (LEE011), and abemaciclib (LY2835219). Food and Drug Administration has approved palbociclib and ribociclib for the treatment of hormone receptor-positive, human epidermal growth factor receptor 2-negative advanced or metastatic breast cancer, and recent clinical trial data suggest that palbociclib significantly improved clinical outcome when combined with letrozole or fulvestrant. Besides, the favorable effects of abemaciclib on prolonging survival of breast cancer patients have also been observed in clinical trials both for single-agent and combination strategy. In this review, we outline the preclinical and clinical advancement of these three orally bioavailable and highly selective CDK4/6 inhibitors in breast cancer.
Understanding Arterial Pressure Waveforms (2003)

Extracted from text ... REGISTRAR PRIZE 
40 
Understanding arterial pressure waveforms 
their relation to the cardiac cycle 
the difference in waveforms recorded from different body 
sites 
The arterial pulse is the result of a wave of vascular distention, 
initiated by the impact of the stroke volume ejected into 
a closed system with every heartbeat. The forward-propagating 
pressure wave has both a fast-moving (10m/sec) and slower 
(0, 5m/sec) component.5 The wave is reflected back mostly by 
the arteriole, which provides the majority of peripheral vascular 
resistance.6 Peak aortic blood flow acceleration produces 
the initial rise of the pressure pulse, whereas the ejection ..
MicroRNA functions in animal development and human disease (2005)

Five years into the 'small RNA revolution' it is hard not to share in the excitement about the rapidly unravelling biology of microRNAs. Since the discovery of the first microRNA gene, lin-4, in the nematode Caenorhabditis elegans, many more of these short regulatory RNA genes have been identified in flowering plants, worms, flies, fish, frogs and mammals. Currently, about 2% of the known human genes encode microRNAs. MicroRNAs are essential for development and this review will summarise our current knowledge of animal microRNA function. We will also discuss the emerging links of microRNA biology to stem cell research and human disease, in particular cancer.
Changes in Distance Running Mechanics Due to Systematic Variations in Running Style (1991)

There is little information on how a change in one feature of an individual’s running mechanics affects other aspects of running style. This study manipulated experimental conditions such that eight subjects ran with three different step lengths, three step widths, and three varying degrees of shoulder rotation. The effect of these changes on rearfoot pronation measures, step length, and step width were examined. Results showed that varying step length over a range of 18 cm and shoulder rotation over a range of 17° caused no significant differences in maximal pronation angle, total amount of pronation, or maximal pronation velocity. Varying step width from landing approximately 5 cm lateral to the midline to crossing over a midline by 2 cm increased the maximum pronation from 12.2 to 18.3°, the amount of pronation from 14.1 to 21.1°, and maximal pronation velocity from. 329°/s to 535°/s. It is suggested that runners with problems due to excessive pronation might try changing step width. Changes in step width and shoulder rotation had no significant effect on step length, and alterations to shoulder rotation did not affect step length or step width significantly. These results suggest that a runner attempts to maintain some aspects of running mechanics despite major alterations to other elements of running style.
Microgel Capsules Tailored by Droplet‐Based Microfluidics (2012)

Microgel capsules are micrometer-sized particles that consist of a cross-linked, solvent-swollen polymer network complexed with additives. These particles have various applications, such as drug delivery, catalysis, and analytics. To optimize the performance of microgel capsules, it is crucial to control their size, shape, and content of encapsulated additives with high precision. There are two classes of microgel-capsule structures. One class comprises bulk microcapsules that consist of a polymer network spanning the entire particle and entrapping the additive within its meshes. The other class comprises core-shell structures; in this case, the microgel polymer network just forms the shell of the particles, whereas their interior is hollow and hosts the encapsulated payload. Both types of structures can be produced with exquisite control by droplet-based microfluidic templating followed by subsequent droplet gelation. This article highlights some early and recent achievements in the use of this technique to tailor soft microgel capsules; it also discusses applications of these particles. A special focus is on the encapsulation of living cells, which are very sensitive and complex but also very useful additives for immobilization within microgel particles.
Proquinoid acceptors as building blocks for the design of efficient π-conjugated fluorophores with high electron affinity (2000)

The association of aromatic electron donor groups with proquinoid acceptors leads to π-conjugated fluorophores combining tunable emission wavelength at constant geometry, high fluorescence efficiency and high electron affinity.
High-Avidity T Cells Are Preferentially Tolerized in the Tumor Microenvironment (2012)

One obstacle in eliciting potent antitumor immune responses is the induction of tolerance to tumor antigens. TCR(lo) mice bearing a TCR transgene specific for the melanoma antigen tyrosinase-related protein-2 (TRP-2, Dct) harbor T cells that maintain tumor antigen responsiveness but lack the ability to control melanoma outgrowth. We used this model to determine whether higher avidity T cells could control tumor growth without becoming tolerized. As a part of the current study, we developed a second TRP-2-specific TCR transgenic mouse line (TCR(hi)) that bears higher avidity T cells and spontaneously developed autoimmune depigmentation. In contrast to TCR(lo) T cells, which were ignorant of tumor-derived antigen, TCR(hi) T cells initially delayed subcutaneous B16 melanoma tumor growth. However, persistence in the tumor microenvironment resulted in reduced IFN-γ production and CD107a (Lamp1) mobilization, hallmarks of T-cell tolerization. IFN-γ expression by TCR(hi) T cells was critical for upregulation of MHC-I on tumor cells and control of tumor growth. Blockade of PD-1 signals prevented T-cell tolerization and restored tumor immunity. Depletion of tumor-associated dendritic cells (TADC) reduced tolerization of TCR(hi) T cells and enhanced their antitumor activity. In addition, TADCs tolerized TCR(hi) T cells but not TCR(lo) T cells in vitro. Our findings show that T-cell avidity is a critical determinant of not only tumor control but also susceptibility to tolerization in the tumor microenvironment. For this reason, care should be exercised when considering T-cell avidity in designing cancer immunotherapeutics.
Identification of a novel class of mammalian Fc γ receptor (1995)

A cDNA encoding an Ig receptor that conferred the ability to bind erythrocytes sensitized with IgG2, but not IgG1, was cloned by screening a cattle alveolar macrophage library, made in the vector pCDM8, expressed in COS-7 cells. A search of the PIR database indicated a greater level of similarity with human Fc alpha R than with any other FcR. The percentage of identical amino acids was 41% and nucleotides 56%. This high similarity is between the extracellular and transmembrane domains; the cytoplasmic tails are unrelated. Similarities with human Fc gamma RI, Fc gamma RII, Fc gamma RIII, Fc epsilon RI, or bovine Fc gamma RII were less than 28%. COS-7 cells transfected with the cloned plasmid bound erythrocytes specifically sensitized with IgG2 but not with IgG1. In tests with heat-aggregated bovine Igs, IgG2 purified from serum bound to transfected COS-7 cells but IgG1 from serum and IgA from tracheobronchial secretions did not. Human serum IgA also failed to bind to transfected COS-7 cells although it did bind to bovine neutrophils and monocytes. Only aggregated bovine IgG2 inhibited the binding of IgG2-sensitized erythrocytes to COS-7 cells transfected with the plasmid. These observations indicate that the FcR bound IgG2 specifically and was not a receptor for IgA. Thus, this receptor, which we have named bovine Fc gamma 2R, represents a novel class of mammalian Fc gamma R, the evolution of which is likely to have been influenced by the truncated hinge of the bovine IgG2 molecule. Analysis of genetic divergence of the genes encoding bovine and human Fc gamma R and Fc alpha R indicated that the novel bovine gene and the human Fc alpha R gene probably evolved from a common ancestor, which is not shared by other Fc gamma R.
Synthesis of Goethite by Separation of the Nucleation and Growth Processes of Ferrihydrite Nanoparticles Using Microfluidics (2009)

Microfluidic synthesis is used to form nanoparticles by separate nucleation and growth processes using two microreactors (see picture) operating under different temperature and flow conditions. Ferrihydrite nanoparticles precipitated in the first microreactor are aged under continuous flow in a second microtubular reactor, leading to goethite nanoparticles. TMAOH = tetramethylammonium hydroxide.
How genetics research in Parkinson's disease is enhancing understanding of the common idiopathic forms of the disease (2005)

Mutations in these two genes, along with previously described Mendelian variants, are beginning to yield important information about loss of specific neuronal groups or to protein inclusion pathology. How this relates to sporadic Parkinson's disease, however, is not yet fully defined. There are clear phenotypic overlaps with genetic and sporadic Parkinson's disease, especially for the dominant genes, suggesting that common facets of pathogenesis may exist.
Detection of a Stable Intermediate in the Thermal Unfolding of a Cysteine-Free Form of Dihydrofolate Reductase from Escherichia Coli (1995)

The reversible temperature-induced unfolding of a cysteine-free mutant (C85S/C152E, des-Cys) of dihydrofolate reductase from Escherichia coli has been studied by absorbance and by both far- and near-ultraviolet circular dichroism spectroscopies. The non-coincidence of all three transition curves demonstrated the existence of a highly populated partially-folded form near 39 degrees C at pH 7.8. This intermediate retains substantial secondary structure and partially excludes one or more of the five tryptophans from solvent; however, the intermediate has lost specific tertiary packing around its aromatic residues. Increases in enthalpy, entropy, and heat capacity are observed for both the native/intermediate and intermediate/unfolded transitions; the majority of the changes in these parameters occurs in the first transition. These results suggest that the thermal unfolding reaction of des-Cys dihydrofolate reductase involves a stable intermediate whose properties resemble those of a molten globule.
Raman and IR Spectroscopy of Chemically Processed Single-Walled Carbon Nanotubes (2005)

IR and Raman spectroscopy has been used to study the evolution of the vibrational spectrum of bundled single-walled carbon nanotubes (SWNTs) during the purification process needed to remove metal catalyst and amorphous carbon present in arc-derived SWNT soot. We have carried out a systematic study to define the different outcomes stemming from the purification protocol (e.g., DO, DO/HCl, DO/HNO(3), H(2)O(2), H(2)O(2)/HCl), where dry oxidation (DO) or refluxing in H(2)O(2) was used in a first purification step to remove amorphous carbon. The second step involves acid reflux (HCl or HNO(3)) to remove the residual growth catalyst (Ni-Y). During strong chemical processing, it appears possible to create additional defects where carbon atoms are eliminated, the ring structure is now open, localized C=C bonds are created, and O-containing groups can be added to this defect to stabilize the structure. Evolution of SWNT skeletal disorder obtained via chemical processing was studied by Raman scattering. Higher intensity ratios of R- and G-band (I(R)/I(G)) are more typically found in SWNT materials with low D-band intensity and narrow G-band components. Using IR transmission through thin films of nanotubes, we can resolve the structure due to functional groups that were present in the starting material or added through chemical processing. After high-temperature vacuum annealing of the purified material at 1100 degrees C, IR spectroscopy shows that most of the added functional groups can be removed and that the structure that remains is assigned to the one- and two-phonon modes of SWNTs.
Hyaluronic Acid in End-Stage Renal Failure Treated by Haemodialysis: Clinical Correlates and Implications (1991)

Serum hyaluronic acid was measured in 176 adults and 15 children receiving regular dialysis therapy. Hyaluronic acid was elevated to greater than 80 micrograms/l in more than 90%, with median value 182 micrograms/l (range 39-898 micrograms/l). Concentrations did not correlate with serum creatinine, but showed a significant correlation with duration of dialysis and serum beta 2-microglobulin. Values greater than 400 micrograms/l were frequent in patients whose clinical condition deteriorated, but in others, hyaluronic acid remained stable over 4-15 months. Serum hyaluronic acid is mainly in a high-molecular-weight form, which in the presence of normal hepatic function suggests that there is a metabolic disorder involving connective tissue and/or vascular endothelium that increases with progressive loss of renal function. Hyaluronic acid may also be a biochemical marker of patients whose condition deteriorates despite renal replacement therapy.
Decomposing a scene into geometric and semantically consistent regions (2009)

High-level, or holistic, scene understanding involves reasoning about objects, regions, and the 3D relationships between them. This requires a representation above the level of pixels that can be endowed with high-level attributes such as class of object/region, its orientation, and (rough 3D) location within the scene. Towards this goal, we propose a region-based model which combines appearance and scene geometry to automatically decompose a scene into semantically meaningful regions. Our model is defined in terms of a unified energy function over scene appearance and structure. We show how this energy function can be learned from data and present an efficient inference technique that makes use of multiple over-segmentations of the image to propose moves in the energy-space. We show, experimentally, that our method achieves state-of-the-art performance on the tasks of both multi-class image segmentation and geometric reasoning. Finally, by understanding region classes and geometry, we show how our model can be used as the basis for 3D reconstruction of the scene.
The role of the PI3K‐AKT kinase pathway in T‐cell development beyond the β checkpoint (2008)

The PI3K-AKT pathway can mediate diverse biological responses and is crucial for optimal immune responses and lymphocyte development. Deletion of PI3K subunits or AKT leads to blockage of T-cell development at the TCR-beta checkpoint. Studies with over-expression of constitutively activated AKT have implicated this pathway in anti-apoptosis of developing thymocytes and in development of regulatory T cells. However, the role of endogenous PI3K-AKT in T-cell development beyond the TCR-beta checkpoint remains unclear. Here, we inhibited the endogenous PI3K-AKT pathway in thymocytes after double negative stages by expressing the negative regulator, PTEN. These mice exhibit normal early T-cell development, but the transition from intermediate single positive to double positive (DP) thymocytes is inhibited, leading to a significantly decreased number of DP, single positive thymocytes and peripheral T cells. Proliferation of peripheral T cells is reduced but apoptosis of DP cells and subsequent T-cell maturation, including regulatory T cells, are normal. AKT phosphorylation can be readily observed in most WT T-cell compartments but not DP thymocytes in response to TCR activation. Thus, the PI3K-AKT pathway is crucial for the transition of intermediate single positive to DP thymocytes but is dispensable for apoptosis and maturation of developing thymocytes.
Device application and structure observation for hemispherical-grained Si (1992)

A polycrystalline-silicon surface with hemispherical grains (HSG) is deposited by low-pressure chemical vapor deposition at 590 °C. At the temperature, 590 °C, the structure of the Si film just after deposition is amorphous, but crystallization of the amorphous Si occurs to produce HSG-Si during annealing after deposition. The HSG-Si is formed by the nuclei generation on the clean amorphous-Si surface and by the crystalline growth during annealing. The surface area of the HSG-Si film is about twice as large as Si films deposited at other temperatures. By applying the HSG-Si film as the storage electrode for a 64-M-bit dynamic random access memories (DRAM) stacked-capacitor with a SiO2/Si3N4 dielectric film, a capacitance of twice the value is obtained. The increase of the capacitance makes it possible to reduce the DRAM cell area, even by using a relatively thick dielectric film for higher reliability.
misshapen encodes a protein kinase involved in cell shape control in Drosophila (1997)

We have identified a novel protein kinase encoded by the misshapen gene, which is required for the normal shape and orientation of Drosophila photoreceptor cells. misshapen is also expressed in the embryonic mesoderm, pole plasm and other sites of cell shape change or movement. We propose that msn may act in a signal transduction pathway leading to cytoskeletal re-arrangements.
Effects of rabeprazole, 20 mg, or esomeprazole, 20 mg, on 24‐h intragastric pH and serum gastrin in healthy subjects (2002)

In this clinical pharmacology study, rabeprazole 20 mg daily was more effective than esomeprazole 20 mg daily in increasing intragastric pH and maintaining pH > 3 and > 4. On day 5, mean pH AUC was higher after esomeprazole than rabeprazole.
Imaging with a 16 000-element 2-D array (1999)

Imaging with acoustical lenses in the low MHz frequency range using fully populated 2-D arrays offers the potential for high-resolution, real-time, 3D volume imaging, together with low power and low cost. A 2-D composite-piezoelectric receiver array bonded directly to a large custom-integrated circuit is the enabling technology for a new implementation of the original acoustical imaging paradigm. This 128×128 (16&amp;lt;th&amp;gt;384 total) element transducer hybrid array (THA) uses massively parallel, on-chip signal processing and is intended for medical and underwater imaging applications. The system under development, which is the acoustical analog of a video camera, will be discussed in this paper.