gebhart/patrepeval huggingface dataset:
Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers (2019)

Production of short-chain fatty acids (SCFAs), especially butyrate, in the gut microbiome is required for optimal health but is frequently limited by the lack of fermentable fiber in the diet. We attempted to increase butyrate production by supplementing the diets of 174 healthy young adults for 2 weeks with resistant starch from potatoes (RPS), resistant starch from maize (RMS), inulin from chicory root, or an accessible corn starch control. RPS resulted in the greatest increase in total SCFAs, including butyrate. Although the majority of microbiomes responded to RPS with increases in the relative abundance of bifidobacteria, those that responded with an increase in <i>Ruminococcus bromii</i> or <i>Clostridium chartatabidum</i> were more likely to yield higher butyrate concentrations, especially when their microbiota were replete with populations of the butyrate-producing species <i>Eubacterium rectale</i> RMS and inulin induced different changes in fecal communities, but they did not generate significant increases in fecal butyrate levels.<b>IMPORTANCE</b> These results reveal that not all fermentable fibers are equally capable of stimulating SCFA production, and they highlight the importance of the composition of an individual's microbiota in determining whether or not they respond to a specific dietary supplement. In particular, <i>R. bromii</i> or <i>C. chartatabidum</i> may be required for enhanced butyrate production in response to RS. Bifidobacteria, though proficient at degrading RS and inulin, may not contribute to the butyrogenic effect of those fermentable fibers in the short term.
Generation of Hierarchical Multiresolution Terrain Databases Using Wavelet Filtering (2000)

Chromosomal instability (CIN) is a hallmark of cancer that results from errors in chromosome segregation during mitosis. Targeting of CIN-associated vulnerabilities is an emerging therapeutic strategy in drug development. KIF18A, a mitotic kinesin, has been shown to play a role in maintaining bipolar spindle integrity and promotes viability of CIN cancer cells. To explore the potential of KIF18A, a series of inhibitors was identified. Optimization of an initial hit led to the discovery of analogues that could be used as chemical probes to interrogate the role of KIF18A inhibition. Compounds <b>23</b> and <b>24</b> caused significant mitotic arrest in vivo, which was sustained for 24 h. This would be followed by cell death either in mitosis or in the subsequent interphase. Furthermore, photoaffinity labeling experiments reveal that this series of inhibitors binds at the interface of KIF18A and tubulin. This study represents the first disclosure of KIF18A inhibitors with in vivo activity.
BMP2 Regulation of CXCL12 Cellular, Temporal, and Spatial Expression Is Essential During Fracture Repair (2015)

The cellular and humoral responses that orchestrate fracture healing are still elusive. Here we report that bone morphogenic protein 2 (BMP2)-dependent fracture healing occurs through a tight control of chemokine C-X-C motif-ligand-12 (CXCL12) cellular, spatial, and temporal expression. We found that the fracture repair process elicited an early site-specific response of CXCL12(+)-BMP2(+) endosteal cells and osteocytes that was not present in unfractured bones and gradually decreased as healing progressed. Absence of a full complement of BMP2 in mesenchyme osteoprogenitors (BMP2(cKO/+)) prevented healing and led to a dysregulated temporal and cellular upregulation of CXCL12 expression associated with a deranged angiogenic response. Healing was rescued when BMP2(cKO/+) mice were systemically treated with AMD3100, an antagonist of CXCR4 and agonist for CXCR7 both receptors for CXCL12. We further found that mesenchymal stromal cells (MSCs), capable of delivering BMP2 at the endosteal site, restored fracture healing when transplanted into BMP2(cKO/+) mice by rectifying the CXCL12 expression pattern. Our in vitro studies showed that in isolated endosteal cells, BMP2, while inducing osteoblastic differentiation, stimulated expression of pericyte markers that was coupled with a decrease in CXCL12. Furthermore, in isolated BMP2(cKO/cKO) endosteal cells, high expression levels of CXCL12 inhibited osteoblastic differentiation that was restored by AMD3100 treatment or coculture with BMP2-expressing MSCs that led to an upregulation of pericyte markers while decreasing platelet endothelial cell adhesion molecule (PECAM). Taken together, our studies show that following fracture, a CXCL12(+)-BMP2(+) perivascular cell population is recruited along the endosteum, then a timely increase of BMP2 leads to downregulation of CXCL12 that is essential to determine the fate of the CXCL12(+)-BMP2(+) to osteogenesis while departing their supportive role to angiogenesis. Our findings have far-reaching implications for understanding mechanisms regulating the selective recruitment of distinct cells into the repairing niches and the development of novel pharmacological (by targeting BMP2/CXCL12) and cellular (MSCs, endosteal cells) interventions to promote fracture healing.
Polyglutamine fibrillogenesis: The pathway unfolds (2002)

Nine neurodegenerative diseases are caused by expanding CAG repeats coding for polyglutamine (polyGln) (1–4). These include Huntington's disease, dentatorubral and pallidoluysian atrophy, several forms of spino-cerebellar ataxia, and spinal and bulbar muscular atrophy. Within the central nervous system, each disease has a distinctive pattern of degeneration, with considerable overlap among the diseases (5, 6). The genes containing CAG repeats show no homology to each other outside of the glutamine repeats, and most are genes of unknown function. Thus, speculation concerning pathogenesis has focused on the polyGln expansion itself.
Biochemical and Pathogenic Properties of <i>Shewanella alga</i> and <i>Shewanella putrefaciens</i> (1998)

We characterized 49 strains of Shewanella spp. from clinical (n = 31) and nonhuman (n = 18) sources. Most Shewanella alga organisms (Gilardi biovar 2; Centers for Disease Control and Prevention [CDC] biotype 2) originated from clinical material (92%), failed to produce acid from carbohydrates other than D-ribose, and were biochemically and enzymatically fairly homogeneous. In contrast, Shewanella putrefaciens organisms (Gilardi biovars 1 and 3; CDC biotype 1) were more often associated with nonhuman sources (70%), were able to utilize a number of sugars (sucrose, L-arabinose, and maltose), and were found to exhibit wider variations in biochemical characteristics; three biotypes within S. putrefaciens were detected. Notable differences between the two species in enzymatic activity, determined with the API-ZYM system (bioMérieux, Hazelwood, Mo.), and cellular fatty acid profiles, determined by the MIDI system (Microbial ID Inc., Newark, Del.), were also detected. Pathogenicity studies of mice indicate that S. alga appears to be the more virulent species, possibly due to the production of a hemolytic substance.
Sound Propagation in Layered Media with a Rough Interface (1957)

When sound propagates in a fluid layer of suitable thickness, overlying a much thicker layer of greater density and sound velocity, the normal-mode propagation expected ideally [C. L. Pekeris, “Theory of propagation of explosive sound in the sea,” in Memoir 27 of the Geological Society of America (1948)] is a result of total internal reflection. Anything preventing such reflection, such as a rough interface, should cause attenuation of the sound. A qualitative explanation is that some diffusely reflected sound strikes the interface at less than critical angles and escapes. Such attenuations have been studied with the apparatus of the accompanying paper by Ryan, Eby, and Williams. Small solid spheres were spread on the rubber-water interface; the extra attenuation caused by them was measured in the water layer as a function of frequency, water depth, sphere size, and area density of spheres. This attenuation is roughly proportional to area density of spheres, and to their acoustic scattering cross sections, and varies additionally with sphere size, water depth, and frequency, Frequencies were 100–250 kc; sphere radii 0.07–0.23 cm; water depths 0.5–2.0 cm. Glass, lead, and steel spheres behaved alike. (Supported in part by the Office of Naval Research.)
Ridge Regression in Practice (1975)

Summary The use of biased estimation in data analysis and model building is discussed. A review of the theory of ridge regression and its relation to generalized inverse regression is presented along with the results of a simulation experiment and three examples of the use of ridge regression in practice. Comments on variable selection procedures, model validation, and ridge and generalized inverse regression computation procedures are included. The examples studied here show that when the predictor variables are highly correlated, ridge regression produces coefficients which predict and extrapolate better than least squares and is a safe procedure for selecting variables.
Macro- and Microemulsions (1985)

This paper reviews various aspects of macro- and microemulsions. The role of interfacial film of surfactants in the formation of these systems has been high-lighted. The formation of a surfactant film around droplets facilitates the emulsification process and also tends to minimize the coalescence of droplets. Macroemulsion stability in terms of short and long range interactions has been discussed. For surfactant stabilized macroemulsions, the energy barrier obtained experimentally is very high, which prevents the occurrence of flocculation in primary minimum. Several mechanisms of microemulsion formation have been described. Based on thermodynamic approach to these systems, it has been shown that interfacial tension between oil and water of the order of 10-3 dynes/cm is needed for spontaneous formation of microemulsions. The distinction between the cosolubilized and microemulsion systems has been emphasized.
ChemInform Abstract: Synthesis and NMR Investigation of 3,4‐Diazabicyclo[4.3.0]non‐2‐ene and N,N′‐Azo‐3‐azabicyclo[3.3.0]octane. X‐Ray Crystal Structure Analysis of a New Tetrazene Derivative. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Human T lymphocyte mitogenesis in response to the B oligomer of pertussis toxin is associated with an early elevation in cytosolic calcium concentrations (1987)

Pertussis toxin was found to serve as a mitogen in the human T lymphocyte, an effect which could be mimicked by its resolved binding component, the B oligomer. The mechanism of action of this component appeared to involve a rapid and sustained elevation of cytosolic calcium levels, as monitored by fura-2 fluorescence. The source of mobilized calcium was predominantly extracellular, suggesting that the binding of the B oligomer to the T cell plasma membrane in some way elicited calcium channel activation. Notably, the influx of calcium was not observed with cholera toxin, an AB toxin lacking mitogenic effects on the human T lymphocyte.
Active Site Residues of Human β-Glucuronidase (1999)

Human beta-glucuronidase (hGUSB) is a member of family 2 glycosylhydrolases that cleaves beta-D-glucuronic acid residues from the nonreducing termini of glycosaminoglycans. Amino acid sequence and structural homology of hGUSB and Escherichia coli beta-galactosidase active sites led us to propose that residues Glu(451), Glu(540), and Tyr(504) in hGUSB are involved in catalysis, Glu(451) being the acid-base residue and Glu(540) the nucleophile. To test this hypothesis, we introduced mutations in these residues and determined their effects on enzymes expressed in COS cells and GUSB-deficient fibroblasts. The extremely low activity in cells expressing Glu(451), Glu(540), and Tyr(504) hGUSBs supported their roles in catalysis. For kinetic analysis, wild type and mutant enzymes were produced in baculovirus and purified to homogeneity by affinity chromatography. The k(cat)/K(m) values (mM(-1).s(-1)) of the E540A, E451A, and Y504A enzymes were 34,000-, 9100-, and 830-fold lower than that of wild type hGUSB, respectively. High concentrations of azide stimulated the activity of the E451A mutant enzyme, supporting the role of Glu(451) as the acid-base catalyst. We conclude that, like their homologues in E. coli beta-galactosidase, Glu(540) is the nucleophilic residue, Glu(451) the acid-base catalyst, and Tyr(504) is also important for catalysis, although its role is unclear. All three residues are located in the active site cavity previously determined by structural analysis of hGUSB.
A New PCSK9 Gene Promoter Variant Affects Gene Expression and Causes Autosomal Dominant Hypercholesterolemia (2008)

PCSK9 is a rare cause of ADH in Spanish population and, up to what we know, none of the previously described mutations has been detected. We have identified a new mutation that could cause ADH by increasing the transcription of PCSK9.
Whisper‐to‐speech conversion using restricted Boltzmann machine arrays (2014)

Whispers are a natural vocal communication mechanism, in which vocal cords do not vibrate normally. Lack of glottal‐induced pitch leads to low energy, and an inherent noise‐like spectral distribution reduces intelligibility. Much research has been devoted to processing of whispers, including conversion of whispers to speech. Unfortunately, among several approaches, the best reconstructed speech to date still contains obviously artificial muffles and suffers from an unnatural prosody. To address these issues, the novel use of multiple restricted Boltzmann machines (RBMs) is reported as a statistical conversion model between whisper and speech spectral envelopes. Moreover, the accuracy of estimated pitch is improved using machine learning techniques for pitch estimation within only voiced (V) regions. Both objective and subjective evaluations show that this new method improves the quality of whisper‐reconstructed speech compared with the state‐of‐the‐art approaches.
Promoter hypomethylation and upregulation of trefoil factors in prostate cancer (2010)

Trefoil factors, mucin-associated peptides, are overexpressed in prostate cancer (PC). We hypothesized that promoter methylation contributes to the regulation of trefoil factors (TFF1, TFF2 and TFF3) in human prostate cells. Here we show hypomethylation of promoter regions of TFF1 and TFF3 in PC cell lines with significant TFF expression as compared to benign immortalized prostate cell lines and PC cell lines not expressing trefoil factor. The most striking difference was observed for CpG sites located close to the AUG start codon overlapping several putative binding sites for cellular transcription factors. TFF2 was hypermethylated and had no or very low expression in all prostate cell lines investigated. Treatment of methylated cell lines with 5-aza-2'-deoxycytidine restored TFF expression in cell lines not expressing TFF and increased expression significantly in low-expressing cell lines. In clinical samples, methylation of the promoter/enhancer regions of TFF1 and TFF3 was significantly lower in PC compared to benign prostatic hyperplasia. The present study shows an inverse relation between promoter methylation and expression of trefoil factors. Preliminary analysis on clinical samples suggests that this regulatory mechanism is responsible for the increased levels of TFF1 and TFF3 observed in PC. The overexpression and promoter hypomethylation of trefoil factors may serve as biomarkers in PC.
Performance analysis of permanent magnet brushless DC motor (1993)

The authors propose to reduce the torque ripple of brushless low power motor with neodymium-iron-boron (Nd-Fe-B) segmented magnets. They have voluntarily been chosen to have one slot per pole and per phase which is an unfavourable condition. Three techniques are studied. The first one consists in defining the influence of the winding. The second is a classical one. It is the skewing of the magnets or of the slots. The third is very original and consists in introducing a magnetic ring in the air-gap, this kind of ring, but not magnetic is generally recommended to maintain the magnets in case of high speed. This last technique is very interesting. It permits one to obtain a better torque quality with a small average value decrease. A finite elements method has been used to obtain these results.
Material - processing - quality relationships during the consolidation of out-of autoclave prepregs (2013)

Finally, I would like to thank the advisory
Oxidation of (±)-armepavine methiodide (1969)

The major product formed by oxidising (±)-armepavine methiodide with either silver nitrate or potassium ferricyanide is shown by chromatographic and spectroscopic comparisons with synthetic material to be 5,5′-bis-(1,2,3,4-tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-ylmethyl)-2,2′-dihydroxybiphenyl dimethiodide.
Sun protection policy in elementary schools in Hawaii. (2004)

Results of this study suggest the following: 1) school personnel in Hawaii are concerned about childhood sun exposure; 2) current school policies fail to address the issue; 3) most schools are receptive to developing sun protection policies and programs; and 4) students appear to be at high risk for sun exposure during school hours.
Stand-by power minimization through simultaneous threshold voltage selection and circuit sizing (1999)

We present a new approach for estimation and optimization of the average stand-by power dissipation in large MOS digital circuits. To overcome the complexity of state dependence in average leakage estimation, we introduce the concept of "dominant leakage states" and use state probabilities. Our method achieves speed-ups of 3 to 4 orders of magnitude over exhaustive SPICE simulations while maintaining accuracies within 9% of SPICE. This accurate estimation is used in a new sensitivity-based leakage and performance optimization approach for circuits using dual V t processes. In tests on a variety of industrial circuits, this approach was able to obtain 81-100% of the performance achievable with all low V t transistors, but with 1/3 to 1/6 the stand-by current.
Development of avian sarcoma and leukosis virus-based vector-packaging cell lines (1988)

We have constructed an avian leukosis virus derivative with a 5' deletion extending from within the tRNA primer binding site to a SacI site in the leader region. Our aim was to remove cis-acting replicative and/or encapsidation sequences and to use this derivative, RAV-1 psi-, to develop vector-packaging cell lines. We show that RAV-1 psi- can be stably expressed in the quail cell line QT6 and chicken embryo fibroblasts and that it is completely replication deficient in both cell types. Moreover, we have demonstrated that QT6-derived lines expressing RAV-1 psi- can efficiently package four structurally different replication-defective v-src expression vectors into infectious virus, with very low or undetectable helper virus release. These RAV-1 psi--expressing cell lines comprise the first prototype avian sarcoma and leukosis virus-based vector-packaging system. The construction of our vectors has also shown us that a sequence present within gag, thought to facilitate virus packaging, is not necessary for efficient vector expression and high virus production. We show that quantitation and characterization of replication-defective viruses can be achieved with a sensitive immunocytochemical procedure, presenting an alternative to internal selectable vector markers.
Contribution of Factor VIIIa A2 and A3-C1-C2 Subunits to the Affinity for Factor IXa in Factor Xase (2004)

Contributions of factor (F) VIIIa subunits to cofactor association with FIXa were evaluated. Steady-state fluorescence resonance energy transfer using an acrylodan-labeled A3-C1-C2 subunit and fluorescein-Phe-Phe-Arg-FIXa yielded K(d) values of 52 +/- 10 and 197 +/- 55 nM in the presence and absence of phospholipid vesicles, respectively. A3-C1-C2 was an effective competitor of FVIIIa binding to FIXa as judged by inhibition of FXa generation performed in the absence of vesicles (K(i) approximately 1.6K(d) for FVIIIa-FIXa). However, the capacity for A3-C1-C2 to inhibit FVIIIa-dependent FXa generation in the presence of phospholipid was poor with a K(i) values (approximately 400 nM) that were approximately 100-fold greater than the K(d) for FVIIIa-FIXa interaction (4.2 +/- 0.6 nM). These results indicated that a significant component of the interprotein affinity is contributed by FVIIIa subunits other than A3-C1-C2 in the membrane-dependent complex. The isolated A2 subunit of FVIIIa interacts weakly with FIXa, and recent modeling studies have implicated a number of residues that potentially contact the FIXa protease domain (Bajaj et al. (2001) J. Biol. Chem. 276, 16302-16309). Site-directed mutagenesis of candidate residues in the A2 domain was performed, and recombinant proteins were stably expressed and purified. Functional affinity determinations demonstrated that one mutant, FVIII/Asp712Ala exhibited an 8-fold increased K(d) (35 +/- 1.5 nM) relative to wild-type suggesting a contribution by this residue of approximately 10% of the FVIIIa-FIXa binding energy. Thus both A2 and A3-C1-C2 subunits contribute to the affinity of FVIIIa for FIXa in the membrane-dependent FXase.
An LLCL Power Filter for Single-Phase Grid-Tied Inverter (2011)

This paper presents a new topology of higher order power filter for grid-tied voltage-source inverters, named the LLCL filter, which inserts a small inductor in the branch loop of the capacitor in the traditional LCL filter to compose a series resonant circuit at the switching frequency. Particularly, it can attenuate the switching-frequency current ripple components much better than an LCL filter, leading to a decrease in the total inductance and volume. Furthermore, by decreasing the inductance of a grid-side inductor, it raises the characteristic resonance frequency, which is beneficial to the inverter system control. The parameter design criteria of the proposed LLCL filter is also introduced. The comparative analysis and discussions regarding the traditional LCL filter and the proposed LLCL filter have been presented and evaluated through experiment on a 1.8-kW-single-phase grid-tied inverter prototype.
Exploiting interframe redundancies in the lossless compression of 3D medical images (2002)

Summary form only given. An evaluation is made of different approaches to removing interframe redundancies. The test images we used are the MRI and CT images available from the Visual Human Project. Firstly, we found that linear predictive techniques are not able to provide any compression improvement. Even an optimal linear predictor (least-squares optimization), which holds pixels from the current and the previous frames, does not outperform the very simple 2D lossless JPEG predictor number 7. However nonlinear techniques, such as context-modeling do yield better results. In a simple experiment, lossless JPEG was estimated to code intraframe prediction errors using an interframe context. The context for coding the current pixel is formed by the magnitude of the prediction error of the corresponding pixel in the previous frame. Note that this prediction error comes from the intraframe prediction step in the previous frame. Using this interframe context-modeling approach, a reduction of the bit rate of up to 1 bit per pixel is obtainable. It is obvious that the context serves as an edge-detector, albeit a very simple and straightforward one. A new technique is proposed based on the 2D lossless image compressor JPEG-LS. The existing context-modeling scheme is extended to also catch the interframe redundancies. The interframe context is very similar to the abovementioned one, however the sign of the prediction error in the previous frame is also used.