gebhart/patrepeval huggingface dataset:
Differential Regulation of Vitamin D Receptor and Its Ligand in Human Monocyte-Derived Dendritic Cells (2003)

The functions of dendritic cells (DCs) are tightly regulated such that protective immune responses are elicited and unwanted immune responses are prevented. 1 alpha 25-dihydroxyvitamin D(3) (1 alpha 25(OH)(2)D(3)) has been identified as a major factor that inhibits the differentiation and maturation of DCs, an effect dependent upon its binding to the nuclear vitamin D receptor (VDR). Physiological control of 1 alpha 25(OH)(2)D(3) levels is critically dependent upon 25-hydroxyvitamin D(3)-1 alpha-hydroxylase (1 alpha OHase), a mitochondrial cytochrome P450 enzyme that catalyzes the conversion of inactive precursor 25-hydroxyvitamin D(3) (25(OH)D(3)) to the active metabolite 1 alpha 25(OH)(2)D(3). Using a human monocyte-derived DC (moDC) model, we have examined the relationship between DC VDR expression and the impact of exposure to its ligand, 1 alpha 25(OH)(2)D(3). We show for the first time that moDCs are able to synthesize 1 alpha 25(OH)(2)D(3) in vitro as a consequence of increased 1 alpha OHase expression. Following terminal differentiation induced by a diverse set of maturation stimuli, there is marked transcriptional up-regulation of 1 alpha OHase leading to increased 1 alpha OHase enzyme activity. Consistent with this finding is the observation that the development and function of moDCs is inhibited at physiological concentrations of the inactive metabolite 25(OH)D(3). In contrast to 1 alpha OHase, VDR expression is down-regulated as monocytes differentiate into immature DCs. Addition of 1 alpha 25(OH)(2)D(3) to moDC cultures at different time points indicates that its inhibitory effects are greater in monocyte precursors than in immature DCs. In conclusion, differential regulation of endogenous 1 alpha 25(OH)(2)D(3) ligand and its nuclear receptor appear to be important regulators of DC biology and represent potential targets for the manipulation of DC function.
Glycopeptides as versatile tools for glycobiology (2006)

This review describes the recent advances in the field of glycopeptide and small glycoprotein synthesis. The strategies covered include chemical and chemoenzymatic synthesis, native chemical ligation (NCL), and expressed chemical ligation. The importance of glycopeptide synthesis is exemplified by giving the reader an overview of how versatile and important these well-defined glycopeptides are as tools in glycobiology.
Increased mRNA Expression of IL‐10 in Mononuclear Cells in Multiple Sclerosis and Optic Neuritis (1995)

The inflammatory nature of multiple sclerosis (MS) implicates the participation of immunoregulatory cytokines, including the Th2 related IL-10. We describe the use of in situ hybridization with cDNA oligonucleotide probes to detect and enumerate mononuclear cells (MNC) expressing mRNA for IL-10, which is known to down-regulate Th1 cell related cytokines such as interferon-gamma. Expression of IL-10 was studied in blood MNC of MS and blood and cerebrospinal fluid (CSF) MNC of optic neuritis (ON) patients without culture and after culture in the presence of myelin basic protein (MBP), the control antigen acetylcholine receptor (AChR), and without antigen. Numbers of IL-10 mRNA expressing MNC were elevated in the MS patients' blood both when enumerated without culture and after culture with MBP. Control patients with myasthenia gravis had elevated numbers of AChR-reactive IL-10 mRNA expressing cells, while numbers of MBP-reactive IL-10 positive cells did not differ from numbers registered in cells without antigen. Patients with ON, in many instances representing early MS, had IL-10 positive blood MNC that were elevated to the same extent as in clinically definite MS, and further increased in the CSF. ON patients examined within 1 month after onset had lower numbers of MBP induced IL-10 mRNA expressing blood MNC compared with patients examined later suggesting that IL-10 is related to the degree of inflammation and outcome in ON.
Sequence Divergence in the 3′‐Untranslated Region Has an Effect on the Subfunctionalization of Duplicate Genes (2012)

ABSTRACT Recent studies demonstrated that sequence divergence in both transcriptional regulatory region and coding region contributes to the subfunctionalization of duplicate gene. However, whether sequence divergence in the 3′‐untranslated region (3′‐ UTR ) has an impact on the subfunctionalization of duplicate genes remains unclear. Here, we identified two diverging duplicate vsx1 (visual system homeobox‐1) loci in goldfish, named vsx1 A 1 and vsx1 A 2. Phylogenetic analysis suggests that vsx1 A 1 and vsx1 A 2 may arise from a duplication of vsx1 after the separation of goldfish and zebrafish. Sequence comparison revealed that divergence in both transcriptional and translational regulatory regions is higher than divergence in the introns. vsx1 A 2 expresses during blastula and gastrula stages and in adult retina but silences from segmentation stage to hatching stage, vsx1 A 1 starts expression from segmentation onward. Comparing to that zebrafish vsx1 expresses in all the developmental stages and in the adult retina, it appears that goldfish vsx1 A 1 and vsx1 A 2 are under going to share the functions of ancestral vsx1 . The different but overlapping temporal expression patterns of vsx1 A 1 and vsx1 A 2 suggest that sequence divergence in the promoter region of duplicate vsx1 is not sufficient for partitioning the functions of ancestral vsx1 . By comparing vsx1 A 1 and vsx1 A 2 3′‐ UTR ‐linked green fluorescent protein gene expression patterns, we demonstrated that the 3′‐ UTR of vsx1 A1 remains but the 3′‐ UTR of vsx1 A 2 has lost the capability of mediating bipolar cell specific expression during retina development. These results indicate that sequence divergence in the 3′‐ UTR s has a clear effect on subfunctionalization of the duplicate genes. J. Exp. Zool. (Mol. Dev. Evol.) 318B:531–544, 2012. © 2012 Wiley Periodicals, Inc.
Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A·A, C·C, G·G, and T·T Mismatches (1999)

Thermodynamic measurements are reported for 51 DNA duplexes with A.A, C.C, G.G, and T.T single mismatches in all possible Watson-Crick contexts. These measurements were used to test the applicability of the nearest-neighbor model and to calculate the 16 unique nearest-neighbor parameters for the 4 single like with like base mismatches next to a Watson-Crick pair. The observed trend in stabilities of mismatches at 37 degrees C is G.G > T.T approximately A.A > C.C. The observed stability trend for the closing Watson-Crick pair on the 5' side of the mismatch is G.C >/= C.G >/= A.T >/= T.A. The mismatch contribution to duplex stability ranges from -2.22 kcal/mol for GGC.GGC to +2.66 kcal/mol for ACT.ACT. The mismatch nearest-neighbor parameters predict the measured thermodynamics with average deviations of DeltaG degrees 37 = 3.3%, DeltaH degrees = 7. 4%, DeltaS degrees = 8.1%, and TM = 1.1 degrees C. The imino proton region of 1-D NMR spectra shows that G.G and T.T mismatches form hydrogen-bonded structures that vary depending on the Watson-Crick context. The data reported here combined with our previous work provide for the first time a complete set of thermodynamic parameters for molecular recognition of DNA by DNA with or without single internal mismatches. The results are useful for primer design and understanding the mechanism of triplet repeat diseases.
A general co-expression network-based approach to gene expression analysis: comparison and applications (2010)

We demonstrated that our novel approach is very effective in discovering the modular structures in microarray data, both for genes and for samples. As the method is essentially parameter-free, it may be applied to large data sets where the number of clusters is difficult to estimate. The method is also very general and can be applied to other types of data. A MATLAB implementation of our algorithm can be downloaded from http://cs.utsa.edu/~jruan/Software.html.
Design and Implementation of the TRIPS Primary Memory System (2006)

In this paper, we describe the design and implementation of the primary memory system of the TRIPS processor. To match the aggressive execution bandwidth and support high levels of memory parallelism, the primary memory system is completely partitioned into four banks, can support up to 256 in-flight memory instructions, aggressive reordering of in-flight loads and stores, up to four loads and stores every cycle and up to 64 outstanding cache misses to sixteen different cache lines. The design was implemented using IBM 130 nm ASIC technology and occupies 21% of the processor area. We describe in detail the microarchitecture of the memory system, detailed design of two of the most complex and interesting components -the LSQ and the MHU -and discuss the rationale behind some of the design decisions. Our design experience suggests that the complexity of the partitioned memory system is comparable to less aggressive centralized implementations.
Randomized Controlled Trial of the Effect of Bifidobacteria-Fermented Milk on Ulcerative Colitis (2003)

Supplementation with the BFM product was successful in maintaining remission and had possible preventive effects on the relapse of ulcerative colitis.
Polyubiquitination by HECT E3s and the Determinants of Chain Type Specificity (2009)

Polyubiquitination can mediate several different biochemical functions, determined in part by which lysine of ubiquitin is used to link the polyubiquitin chain. Among the HECT domain ubiquitin ligases, some, such as human E6AP, preferentially catalyze the formation of K48-linked polyubiquitin chains, while others, including Saccharomyces cerevisiae Rsp5 and human Itch, preferentially catalyze the formation of K63-linked chains. The features of HECT E3s that determine their chain type specificities have not been identified. We show here that chain type specificity is a function solely of the Rsp5 HECT domain, that the identity of the cooperating E2 protein does not influence the chain type specificity, that single chains produced by Rsp5 contain between 12 and 30 ubiquitin moieties, and that the determinants of chain type specificity are located within the last 60 amino acids of the C lobe of the HECT domain. Our results are also consistent with a simple sequential-addition mechanism for polyubiquitination by Rsp5, rather than a mechanism involving the formation of either E2- or E3-linked polyubiquitin chain transfers.
Cortical Neurogenesis in Adult Rats After Transient Middle Cerebral Artery Occlusion (2001)

This study suggests that new neurons can be generated in the cerebral cortex of adult rats after transient focal cerebral ischemia. Cortical neurogenesis may be a potential pathway for brain repair after stroke.
Ice valve for a mini/micro flow channel (2003)

We have developed a new ice valve to close or open liquid flow in a mini/micro channel. Unlike the traditionally used valve, no moving elements are needed in this normally open system. By freezing the working fluid running inside the channel using a thermoelectric cooling device (TECD), the flow can be blocked due to ice formation. If switching the TECD to heating, the frozen liquid becomes thawed and flow in the channel resumes its running state again. Several experiments were carried out to characterize the working performance of the ice valve for a micro tube. A theoretical model was established to analyze the time response constant of the ice valve. Without any leakage, being very clean, and easily controllable through electricity, this ice valve may find significant applications in microfluidics or nanofluidics.
Histology and Cytochemistry of Human Skin (1964)

The skin of the face is much more abundantly supplied with cholinesterase-containing nerves than skin elsewhere on the body. All the hair follicles on the chin and jowl have such specialized end-organs. The eccrine sweat glands on the face have nerves around the duct as well as around the secretory coil. Those around the duct are probably sensory afferent. With the exception of the external genitalia, the face has more cholinesterase-containing nerves than the skin elsewhere on the body. Also, the tactile end-organs around the hair follicles there are more numerous and better differentiated than elsewhere.
Rates of OH radical reactions. XII. The reactions of OH with cC3H6, cC5H10, and cC7H14. Correlation of hydroxyl rate constants with bond dissociation energies (1985)

Abstract Absolute rate constants for H‐atom abstraction by OH radicals from cyclopropane, cyclopentane, and cycloheptane have been determined in the gas phase at 298 K. Hydroxyl radicals were generated by flash photolysis of H 2 O vapor in the vacuum UV, and monitored by time‐resolved resonance absorption at 308.2 nm [OH( A 2 Σ + → X 2 Π)]. The rate constants in units of cm 3 mol −1 s −1 at the 95% confidence limits were as follows: k ( c C 3 H 6 ) = (3.74 ± 0.83) × 10 10 , k ( c C 5 H 10 ) = (3.12 ± 0.23) × 10 12 , k ( c C 7 H 14 ) = (7.88 ± 1.38) × 10 12 . A linear correlation was found to exist between the logarithm of the rate constant per CH bond and the corresponding bond dissociation energy for several classes of organic compounds with equivalent CH bonds. The correlation favors a value of D( c C 3 H 5 –H) = (101 ± 2) kcal mol −1 .
Immunization against chlamydial genital infection in guinea pigs with UV-inactivated and viable chlamydiae administered by different routes (1990)

Female guinea pigs were immunized with viable or UV light-inactivated chlamydiae (agent of guinea pig inclusion conjunctivitis), belonging to the species Chlamydia psittaci, by intravenous, subcutaneous, oral, or ocular routes. All animals were then inoculated vaginally with viable chlamydiae to determine the extent of protection against challenge infection induced by the various regimens. The course of genital infection was significantly reduced in intensity in all groups of animals except the unimmunized controls and those animals immunized orally with inactivated antigen. Guinea pigs immunized with viable antigen were more likely to develop resistance to challenge infection and, in general, had a significantly greater degree of protection than animals immunized with inactivated antigen. No one route seemed superior in producing a protective response. Animals in all groups demonstrating protection developed serum and secretion immunoglobulin G antibody responses to chlamydiae. Lymphocyte proliferative reactions to chlamydial antigen were variable among groups. Immunoblot analysis of serum and secretions indicated a wide range of antibody specificities, but most protected animals produced antibodies to the major outer membrane protein, lipopolysaccharide, and the 61-kilodalton protein. No definitive associations could be made between the increased ability of immunization with viable organisms to produce resistance to challenge infection and a particular immune parameter. These data indicate that viable chlamydiae given by various routes are able to induce a strong immune response which can provide resistance against reinfection in some cases or at least reduce the degree of infection to a greater degree than inactivated antigen. However, complete resistance to genital tract infection may be difficult to obtain and alternate immunizations strategies may have to be developed.
Strand displacement amplification—an isothermal,in vitroDNA amplification technique (1992)

Strand Displacement Amplification (SDA) is an isothermal, in vitro nucleic acid amplification technique based upon the ability of HincII to nick the unmodified strand of a hemiphosphorothioate form of its recognition site, and the ability of exonuclease deficient klenow (exo- klenow) to extend the 3'-end at the nick and displace the downstream DNA strand. Exponential amplification results from coupling sense and antisense reactions in which strands displaced from a sense reaction serve as target for an antisense reaction and vice versa. In the original design (G. T. Walker, M. C. Little, J. G. Nadeau and D. D. Shank (1992) Proc. Natl. Acad. Sci 89, 392-396), the target DNA sample is first cleaved with a restriction enzyme(s) in order to generate a double-stranded target fragment with defined 5'- and 3'-ends that can then undergo SDA. Although effective, target generation by restriction enzyme cleavage presents a number of practical limitations. We report a new target generation scheme that eliminates the requirement for restriction enzyme cleavage of the target sample prior to amplification. The method exploits the strand displacement activity of exo- klenow to generate target DNA copies with defined 5'- and 3'-ends. The new target generation process occurs at a single temperature (after initial heat denaturation of the double-stranded DNA). The target copies generated by this process are then amplified directly by SDA. The new protocol improves overall amplification efficiency. Amplification efficiency is also enhanced by improved reaction conditions that reduce nonspecific binding of SDA primers. Greater than 10(7)-fold amplification of a genomic sequence from Mycobacterium tuberculosis is achieved in 2 hours at 37 degrees C even in the presence of as much as 10 micrograms of human DNA per 50 microL reaction. The new target generation scheme can also be applied to techniques separate from SDA as a means of conveniently producing double-stranded fragments with 5'- and 3'-sequences modified as desired.
Repeat subtraction-mediated sequence capture from a complex genome (2010)

Sequence capture technologies, pioneered in mammalian genomes, enable the resequencing of targeted genomic regions. Most capture protocols require blocking DNA, the production of which in large quantities can prove challenging. A blocker-free, two-stage capture protocol was developed using NimbleGen arrays. The first capture depletes the library of repetitive sequences, while the second enriches for target loci. This strategy was used to resequence non-repetitive portions of an approximately 2.2 Mb chromosomal interval and a set of 43 genes dispersed in the 2.3 Gb maize genome. This approach achieved approximately 1800-3000-fold enrichment and 80-98% coverage of targeted bases. More than 2500 SNPs were identified in target genes. Low rates of false-positive SNP predictions were obtained, even in the presence of captured paralogous sequences. Importantly, it was possible to recover novel sequences from non-reference alleles. The ability to design novel repeat-subtraction and target capture arrays makes this technology accessible in any species.
0.1‐T human fat/water separation by SIDAC (1987)

High-resolution human fat/water separated images were obtained in 17 min at a static magnetic field strength as low as 0.1 T. The sequence used was based on SIDAC (spectroscopic imaging by dephasing amplitude changing), which employs a stepwise changing dephase gradient for the separation of spectral and spatial information of magnetic spins.
Transformation of Bacillus thuringiensis protoplasts by plasmid deoxyribonucleic acid (1981)

A method has been developed to transform plasmid deoxyribonucleic acid into protoplasts of the insect pathogen Bacillus thuringiensis. Protoplasts were formed by treatment of cells with lysozyme. The efficiency of formation of protoplasts was affected by the strain, the media, and the cell density. Deoxyribonucleic acid uptake was induced by polyethylene glycol. Deoxyribonucleic acid from the Staphylococcus aureus plasmid pC194 was used for transformation. Although this plasmid could not be isolated as a stable extrachromosomal element, its chloramphenicol resistance was transferred to the recipient protoplasts. This was confirmed by assay for the enzyme chloramphenicol acetyltransferase, which confers resistance to chloramphenicol. This suggested that pC194 acts as an insertion element in B. thuringiensis.
Protective Effect of Bifidobacterium-Monoassociation against Lethal Activity of Escherichia coli (1982)

Germ-free ICR mice monoassociated with Bifidobacterium longum (GB mice) lived longer than non-treated germ-free (GF) mice after intragastric or intravenous (i.v.) administration of a high dose of viable E. coli, or i.v. injection of endotoxin. The number of viable E. coli and the endotoxin level in various organs at 24 hr post - injection were significantly lower in GB than GF mice. Antilethal activity was not elicited by the feeding of heat-killed B. longum. The antilethal effect was observed 3, but not less than 2, weeks after the association of B. longum. Furthermore, the effect was not observed when GF-athymic nude mice (BALB/c background) were used. After intragastric administration of a sublethal dose, the number of viable E. coliin organs of GB mice decreased to an undetectable level within 7 days, while the organisms were persistently isolated in GF mice. In both groups, many (109 v.c./g) E. coli persisted in the intestine. These results suggest that B. longum organisms monoassociated with GF mice generate systemic resistance to the invading E. coli, and increase the resistance to the lethal activity of endotoxin.
Method for Determining Frying Oil Degradation by Near-Infrared Spectroscopy (2006)

A rapid near-infrared (NIR) spectroscopic method for measuring degradation products in frying oils, including total polar materials (TPMs) and free fatty acids (FFAs), has been developed. Calibration models were developed using both forward stepwise multiple linear regression (FSMLR) and partial least-squares (PLS) regression techniques and then tested with two independent sets of validation samples. Derivative treatments had limited usefulness, especially in the longer (1100-2500 nm) wavelength region. When using a wavelength region of 700-1100 nm, PLS models gave improved results compared to FSMLR models. The best correlations (r) between the NIR and wet chemical methods for TPM and FFA were 0.983 and 0.943, respectively. In the longer wavelength region (1100-2500 nm), FSMLR models were as good or better than PLS models. The best correlations for TPM and FFA obtained in this region were 0.999 and 0.983, respectively.
Cloning and mRNA expression analysis of a novel human protooncogene, c-mer. (1994)

A human B-lymphoblastoid lambda gt11 expression library was screened using anti-phosphotyrosine antibodies yielding complementary DNAs encoding active tyrosine kinases. The resulting clones were used to obtain the sequence of a novel 984 amino acid transmembrane tyrosine kinase. Analysis of the complementary DNA revealed extracellular immunoglobulin and fibronectin type III domains and the unusual kinase signature sequence KWIAIES; all are characteristic of the axl family of tyrosine kinases. The novel tyrosine kinase was not expressed in normal B- and T-lymphocytes but, unlike axl, was expressed in numerous neoplastic B- and T-cell lines. Transcripts for the novel receptor-like tyrosine kinase were detected in normal peripheral blood monocytes and bone marrow. One alternatively spliced transcript was detected which contained an insert in the membrane proximal region that could encode for a truncated, soluble receptor. Sequence comparison shows that the kinase may be the human protooncogene for the recently isolated chicken retroviral oncogene v-ryk (recently renamed v-eyk), a truncated tyrosine kinase whose expression by retroviral infection produced sarcomas in chickens. The intracellular domain of the human kinase shows 83% similarity and 71% identity to v-ryk. Since the ryk designation has been used to name another tyrosine kinase and an analysis of RNA expression demonstrated that this novel human kinase is expressed in monocytes and tissues of epithelial and reproductive origin, we have designated our novel protooncogene c-mer.
Selective stimulation of parasympathetic nerve fibers to the human sinoatrial node. (1992)

Electrical stimulation of parasympathetic nerve fibers in a fat pad near the sinoatrial node increased atrial cycle length without affecting atrioventricular nodal conduction. This is the first study in which such nerve fibers that innervate the sinoatrial node have been selectively stimulated in humans.