gebhart/patrepeval huggingface dataset:
Macroporous biodegradable natural/synthetic hybrid scaffolds as small intestine submucosa impregnated poly(D, L-lactide-co-glycolide) for tissue-engineered bone (2004)

Poly(D,L-lactide-co-glycolide) (PLGA), a biodegradable synthetic polymer, is widely used in a variety of tissue-engineered applications, including drug-delivery systems. However, the PLGA scaffolds, macroporous and three-dimensional structure, are difficult to cell attachment and in-growth due to surface hydrophobicity. In order to introduce in new bioactive functionality from porcine small intestine submucosa (SIS) as natural source for PLGA, we fabricated SIS-powder-impregnated PLGA (SIS/PLGA) hybrid scaffolds. Fabrication parameters, including ratios of SIS, PLGA and salt, were optimized to produce the desired macroporous foam. The scaffolds had a relatively homogeneous pore structure, good interconnected pores from the surface to core region and showed an average pore size in the range 69.23-105.82 microm and over 90% porosity. The SIS/PLGA scaffolds degraded with a rate depending on the contents of the SIS. After the fabrication of the SIS/PLGA hybrid scaffolds the wettability of the scaffold was greatly enhanced, resulting in uniform cell seeding and distribution. So, it was observed that BMSC attachment to the SIS/PLGA scaffolds increased gradually with increasing SIS contents. Scaffolds of PLGA alone and SIS/PLGA were implanted subcutaneously under dorsal skin of athymic nude mouse to observe the osteoconductivity. It was found from the result that the effects of the SIS/PLGA scaffolds on bone formation are stronger than control PLGA scaffolds. In summary, the SIS/PLGA scaffolds have osteoconductive effects to allow remodeling and replacement by osseous tissue.
Quantitative Assessment of the Human Gut Microbiome Using Multitag Pyrosequencing (2010)

Recent advances in molecular techniques have now made it possible to interrogate the human microbiome in depth to better understand the interactions with the host organism and its role in diseases. We now report the utility of Length Heterogeneity Polymerase Chain Reaction (LH-PCR) to survey samples and a proprietary Multitagged Pyrosequencing (MTPS) methodology to interrogate the gut microbiome in healthy and disease states. We present an overview of our studies demonstrating the application of these molecular-biology techniques to an example disease state such as Inflammatory Bowel Disease (IBD). The findings show that there is a core mucosal bacterial microbiome (i.e., a mucosal biofilm) that is distinct from the luminal microbiome in health, and that the mucosal microbiome appears to be dysbiotic in IBD. We propose that the mucosal microbiome forms a synergistic and stable interaction with the host immune system, while the lumen microbiome varies based on diet or other environmental factors. We define this composite ecosystem of the human microbiome and human host as the Human Metabiome.
Separation of Foreground Text from Complex Background in Color Document Images (2009)

Reading of the foreground text is difficult in documents having multi colored complex background. Automatic foreground text separation in such document images is very much essential for smooth reading of the document contents. In this paper we propose a hybrid approach which combines connected component analysis and an unsupervised thresholding for separation of text from the complex background. The proposed approach identifies the candidate text regions based on edge detection followed by a connected component analysis. Because of background complexity it is also possible that a non text region may be identified as a text region. To overcome this problem we extract texture features of connected components and analyze the feature values. Finally the threshold value for each detected text region is derived automatically from the data of corresponding image region to perform foreground separation. The proposed approach can handle document images with varying background of multiple colors. Also it can handle foreground text of any color, font and size. Experimental results show that the proposed algorithm detects on an average 97.8% of text regions in the source document. Readability of the extracted foreground text is illustrated through OCRing.
I-TASSER server: new development for protein structure and function predictions (2015)

The I-TASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER) is an online resource for automated protein structure prediction and structure-based function annotation. In I-TASSER, structural templates are first recognized from the PDB using multiple threading alignment approaches. Full-length structure models are then constructed by iterative fragment assembly simulations. The functional insights are finally derived by matching the predicted structure models with known proteins in the function databases. Although the server has been widely used for various biological and biomedical investigations, numerous comments and suggestions have been reported from the user community. In this article, we summarize recent developments on the I-TASSER server, which were designed to address the requirements from the user community and to increase the accuracy of modeling predictions. Focuses have been made on the introduction of new methods for atomic-level structure refinement, local structure quality estimation and biological function annotations. We expect that these new developments will improve the quality of the I-TASSER server and further facilitate its use by the community for high-resolution structure and function prediction.
RNA-directed RNA polymerases from healthy and from virus-infected cucumber. (1986)

Much work has been done on the isolation, purification, and characterization of the RNA-directed RNA polymerase (EC 2.7.7.48) of cucumber mosaic virus (CMV)-infected cucumbers. Uninfected plants were reported to have no such enzyme, but we recently detected low levels of the activity in cucumber. Since tobacco and cowpea contain such an enzyme that is variably increased in amount by various virus (as well as viroid) infections, we assumed that this would also be the case upon CMV infection of cucumber. However, further purification and characterization of the RNA-directed RNA polymerases from healthy and from infected cucumber suggests that these are different enzymes. The presumed CMV replicase was obtained pure and consists of a major polypeptide of Mr 100,000 and minor components of Mr 110,000 and about 10,000. The Km is 5 microM ([3H]GTP) when tobacco mosaic virus RNA is used as template.
Struktur‐Wirkungs‐Beziehungen bei Analeptica vom Typ des Nicethamids, 3. Mitt. Synthese von Analogen des 6‐Methyl‐nicethamids (1975)

Abstract Als potentiell analeptisch wirksame Substanzen mit partiell fixierter funktioneller Gruppe werden strukturanaloge Amide, Imide und Lactame des 6‐Methyl‐nicethamids beschrieben.
Emerging optical code-division multiple access communication systems (1989)

All-optical systems, which perform signal processing functions optically so that the signal conversion from optical to electrical is done only when desired, are considered. Three such schemes are discussed, namely, fiber-optic code-division multiple-access (CDMA) systems, neuromorphic CDMA systems, and ultrashort-light-pulse CDMA systems. Fiber-optic CDMA systems in which incoherent optical signal processing techniques are used to establish optical CDMA systems are first examined. In particular, a novel class of sequences for incoherent fiber-optic CDMA systems, called optical orthogonal codes, are discussed. The codes are then applied to neuromorphic optical systems, and various applications of the networks are examined. Recent experiments that demonstrate the ability to encode and decode extremely fast, femtosecond optical pulses and that suggest the possibility of ultrahigh-speed CDMA systems based on ultrashort light pulses are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
74]Interaction between heat-stable enterotoxin and its receptor (guanylyl cyclase C): Influence of mutation at N-linked glycosylation sites on its ligand binding (2006)

Guanylyl cyclase (GC) C, identified from cDNA libraries of several mammalian small intestines, is a membrane-associated receptor for a heat-stable enterotoxin (STa) produced by enterotoxigenic Escherichia coli and an endogenous peptide, guanylin [1, 2]. The extracellular domain of guanylyl cyclase C, which includes the ligand-binding site, activates the cytoplasmic domain, catalyzing the conversion of GTP to cGMP as an intracellular signal. GC-C exhibits glyco-modifications and contains seven or eight potential N -glycosylation sites in the extracellular domain. To investigate the role of the N-glycosylation, each asparagine residue at the potential sites of porcine GC-C was converted to alanine by site-directed mutagenesis.
Semen preparation techniques for intrauterine insemination (2004)

There is insufficient evidence to recommend any specific preparation technique. Large high quality randomised controlled trials, comparing the effectiveness of a gradient and/ or a swim-up and/ or wash and centrifugation technique on clinical outcome are lacking. Further randomised trials are warranted. Results from studies comparing semen parameters may suggest a preference for gradient technique, but firm conclusions cannot be drawn and the limitations should be taken into consideration.
Chirality in Polar Mesogens: Reentrant Cholesteric and New Smectic Phases (1985)

Abstract Several chiral polar mesogens are described. The existence of the reentrant cholesteric phase is discussed from a molecular structure point of view (chain length, central cores). Compound 1c (n = 3) provides the first example of a double reentrant sequence: K-SA-N*rc-SA-N*-I. In addition, we have obtained the chiral variant of some new smectic modifications: Sc2*, Sc*…
High-pressure sterilization : maximizing the benefits of adiabatic heating (2003)

Taking into account the importance of temperature and temperature control could make high-pressure sterilization economically more feasible.
Characterization of dextromethorphan O- and N-demethylation catalyzed by highly purified recombinant human CYP2D6. (2001)

The O-demethylation of dextromethorphan to dextrorphan in humans is catalyzed primarily by cytochrome P450 2D6 (CYP2D6). However, contrary to conventional wisdom, preparations of recombinant cytochrome P450 (P450) expressed from CYP2D6*1 cDNA also appear to produce significant amounts of 3-methoxymorphinan, the N-demethylated metabolite of dextromethorphan, when assayed in vitro. We hypothesized that both pathways were intrinsic to 2D6 and here further examine the kinetics of formation using a highly purified preparation of CYP2D6 in a reconstituted lipid system. Purified CYP2D6 protein with a measured molecular weight of 55772.0 (55769.6 Da predicted) was reconstituted into an active, lipid-vesicle environment with purified rat cytochrome P450 reductase before the addition of substrate and NADPH. Reaction kinetics were followed, and apparent Michaelis-Menten constants were determined for the appearance of each metabolite by high-pressure liquid chromatography, using both UV and fluorescence detection. In a 2-min assay, purified 2D6 catalyzed the formation of dextrorphan with an apparent K(m) value of 1.9 +/- 0.2 microM and a V(max) value of 8.5 +/- 0.2 nmol/nmol of P450/min and measured simultaneously the formation of 3-methoxymorphinan with an apparent K(m) value of 5000 +/- 700 microM and V(max) value of 176 +/- 12 nmol (nmol of P450)(-1) min(-1). These results indicate that at least two distinct binding orientations exist for dextromethorphan within the active site of CYP2D6.
Instrument techniques for rheometry (2005)

This article presents a review of some latest advances in rheology measuring techniques. Consideration is given to the modification and approaches in conventional measuring techniques and also to the development of specialty instruments. A number of sensing technologies such as nuclear-magnetic-resonance imaging and ultrasonic pulse Doppler mapping have recently been adopted to produce viscoelastic measurements for both Newtonian and non-Newtonian materials. The working principles of these technologies and their applications are described. Other recent developments in modifications of conventional rheometers for performance enhancement and for complex material characterizations have been thoroughly discussed. Some instrument designs and their special applications, such as interfacial rheometers, extensional rheometers, and high-pressure rheometers, have also been evaluated in detail.
Blood Cell Gene Expression Profiling in Subjects With Aggressive Periodontitis and Chronic Arthritis (2008)

Several genes upregulated in subjects with LAgP were related to immune responses including TLR2 and myomesin 2.
THE FUNCTION OF PHYTOCHROME IN THE NATURAL ENVIRONMENT—IV. LIGHT QUALITY AND PLANT DEVELOPMENT (1977)

Abstract— Studies of the effect of light quality on the growth of Cucurbita pepo L . and Chenopodium album L . showed that large changes in morphological development can be induced by altering the proportion of red and far‐red in the incident radiation. Although phytochrome photoequilibria established at the beginning of the dark period affected development, similar changes were achieved with long term and continuous irradiation. The change in the growth pattern of C. album (a common weed species in cultivated land) caused by simulated wheat canopy shade, appeared to involve a redirection of growth towards processes which would achieve greater height at the expense of lateral growth. The evidence presented supports the hypothesis that phytochrome may be involved in the detection of mutual shading and the modification of development in an appropriate manner.
<i>N</i>‐Acyl‐trihalogenacetaldimine als reaktive Zwischenstufen bei Eliminierungs‐Additions‐Reaktionen, III. Darstellung und Reaktionen der 1.2.2.2‐Tetrahalogen‐<i>N</i>‐acyl‐äthylamine (1966)

Abstract Methoden zur Darstellung von 1.2.2.2‐Tetrahalogen‐ N ‐acyl‐äthylaminen werden beschrieben. Diese Verbindungen tauschen leicht das 1‐ständige Halogenatom gegen Nucleophile aus. Dabei ist die Reaktion mit Alkoholen von besonderem Interesse, da sie zum Schutz der Hydroxylgruppen des Serins, Threonins oder Cholesterins verwendet werden kann. Durch Behandeln mit Triäthylamin in Tetrahydrofuran sind aus den 1.2.2.2‐Tetrahalogen‐ N ‐acyl‐äthylaminen die freien N ‐Acyl‐trihalogenacetaldimine zugänglich. Die Reaktionen der Trifluor‐ und der Trichlor‐Verbindungen werden miteinander verglichen.
Bone marrow stromal cells use TGF-β to suppress allergic responses in a mouse model of ragweed-induced asthma (2010)

Bone marrow stromal cells [BMSCs; also known as mesenchymal stem cells (MSCs)] effectively suppress inflammatory responses in acute graft-versus-host disease in humans and in a number of disease models in mice. Many of the studies concluded that BMSC-driven immunomodulation is mediated by the suppression of proinflammatory Th1 responses while rebalancing the Th1/Th2 ratio toward Th2. In this study, using a ragweed induced mouse asthma model, we studied if BMSCs could be beneficial in an allergic, Th2-dominant environment. When BMSCs were injected i.v. at the time of the antigen challenge, they protected the animals from the majority of asthma-specific pathological changes, including inhibition of eosinophil infiltration and excess mucus production in the lung, decreased levels of Th2 cytokines (IL-4, IL-5, and IL-13) in bronchial lavage, and lowered serum levels of Th2 immunoglobulins (IgG1 and IgE). To explore the mechanism of the effect we used BMSCs isolated from a variety of knockout mice, performed in vivo blocking of cytokines and studied the effect of asthmatic serum and bronchoalveolar lavage from ragweed challenged animals on the BMSCs in vitro. Our results suggest that IL-4 and/or IL-13 activate the STAT6 pathway in the BMSCs resulting in an increase of their TGF-beta production, which seems to mediate the beneficial effect, either alone, or together with regulatory T cells, some of which might be recruited by the BMSCs. These data suggest that, in addition to focusing on graft-versus-host disease and autoimmune diseases, allergic conditions--specifically therapy resistant asthma--might also be a likely target of the recently discovered cellular therapy approach using BMSCs.
Genotypic and phenotypic characterization of garlic-fermenting lactic acid bacteria isolated from som-fak, a Thai low-salt fermented fish product (2002)

The present study indicates the role of fructans (garlic/inulin) as carbohydrate sources for LAB. Fructan fermenters may have several biotechnological applications, for example, as probiotics.
Skeletal muscle laminin and MDC1A: pathogenesis and treatment strategies (2011)

Laminin-211 is a cell-adhesion molecule that is strongly expressed in the basement membrane of skeletal muscle. By binding to the cell surface receptors dystroglycan and integrin α7β1, laminin-211 is believed to protect the muscle fiber from damage under the constant stress of contractions, and to influence signal transmission events. The importance of laminin-211 in skeletal muscle is evident from merosin-deficient congenital muscular dystrophy type 1A (MDC1A), in which absence of the α2 chain of laminin-211 leads to skeletal muscle dysfunction. MDC1A is the commonest form of congenital muscular dystrophy in the European population. Severe hypotonia, progressive muscle weakness and wasting, joint contractures and consequent impeded motion characterize this incurable disorder, which causes great difficulty in daily life and often leads to premature death. Mice with laminin α2 chain deficiency have analogous phenotypes, and are reliable models for studies of disease mechanisms and potential therapeutic approaches. In this review, we introduce laminin-211 and describe its structure, expression pattern in developing and adult muscle and its receptor interactions. We will also discuss the molecular pathogenesis of MDC1A and advances toward the development of treatment.
The Role of RASSF1A Methylation in Cancer (2007)

Tumour suppressor gene inactivation is critical to the pathogenesis of cancers; such loss of function may be mediated by irreversible processes such as gene deletion or mutation. Alternatively tumour suppressor genes may be inactivated via epigenetic processes a reversible mechanism that promises to be more amenable to treatment by therapeutic agents. The CpG dinucleotide is under-represented in the genome, but it is found in clusters within the promoters of some genes, and methylation of these CpG islands play a critical role in the control of gene expression. Inhibitors of the DNA methyltransferases DNMT1 and DNMT3b have been used in a clinical setting, these nucleotide analogues lack specificity but the side effects of low dose treatments were minimal and in 2004 Vidaza (5-azacitidine) was licensed for use in myelodysplastic syndrome. Methylation inhibitors are also entering trials in conjunction with another class of epigenetic modifiers, the histone deacetylase inhibitors and this epigenetic double bullet offers hope of improved treatment regimes. Recently there has been a plethora of reports demonstrating epigenetic inactivation of genes that play important roles in development of cancer, including Ras-association domain family of genes. Epigenetic inactivation of RASSF1A (Ras-association domain family 1, isoform A) is one of the most common molecular changes in cancer. Hypermethylation of the RASSF1A promoter CpG island silences expression of the gene in many cancers including lung, breast, prostate, glioma, neuroblastoma and kidney cancer. Several recent studies have illustrated the diagnostic and prognostic potential of RASSF1A methylation. This presents RASSF1A methylation as an attractive biomarker for early cancer detection which, for most cancers, results in improved clinical outcome. DNA methylation analysis is applicable to a range of body fluids including serum, urine, bronchioalveolar lavage and sputum. The ease with which these body fluids can be acquired negates the need for invasive procedures to obtain biopsy material. This review will discuss the feasibility of using RASSF1A methylation as a diagnostic and prognostic marker in cancer management.
A rate control algorithm for the H.264 encoder (2003)

intended for video transmission in all areas where bandwidth or storage capacity is limited (e.g. video telephony or video conferencing over mobile channels and devices). Since its main applications concern video communication over time-varying bandwidth channels, the bit rate has to be controlled with scalable algorithms that can be implemented on low resource devices. The paper describes a rate control algorithm that needs reduced memory area and complexity compared to other ones. The number of coded bits for each frame can be accurately predicted through the percentage of null quantized coefficients. It is possible to reduce the hardware requirements of the original technique through a parametric model: in this way coefficient statistics storage is not needed and the whole rate control algorithm becomes more suitable for low-resource devices. I.
Relative tissue expression of homologous torsinB correlates with the neuronal specific importance of DYT1 dystonia-associated torsinA (2009)

A three base-pair deletion in the widely expressed TOR1A gene causes the childhood onset, neurological disease of DYT1 dystonia. Mouse Tor1a gene knockout also specifically affects the developing nervous system. However, in both cases, the basis of neuronal tissue specificity is unknown. TorsinA is one of four predicted mammalian torsin ATPases associated with assorted cellular activities (AAA+) proteins, raising the possibility that expression of a functionally homologous torsin compensates for torsinA loss in non-neuronal tissues. We find that all four mammalian torsins are endoplasmic reticulum resident glycoproteins. TorsinA, torsinB and torsin2 are all present in large M(r) complexes, which suggests that each assembles into an oligomeric AAA+ enzyme. Introducing a mutation (WB(EQ)) that typically stabilizes AAA+ proteins in a substrate-bound state causes torsinA and torsinB to associate with a shared nuclear envelope (NE) binding partner and this NE localization requires the torsinA interacting protein, lamina associated polypeptide 1. Although torsin proteins are widely expressed in the adult mouse, we identified that embryonic neuronal tissues contain relatively low torsinB levels. Therefore, our results reveal that torsinB expression inversely correlates with the cell and developmental requirement for torsinA. In conclusion, multiple cell types appear to utilize torsin AAA+ proteins and differential expression of torsinB may contribute to both the neuronal specific importance of torsinA and the symptom specificity of DYT1 dystonia.