gebhart/patrepeval huggingface dataset:
High-Mobility Group Box Proteins Modulate Tumor Necrosis Factor-α Expression in Osteoclastogenesis via a Novel Deoxyribonucleic Acid Sequence (2008)

We have previously shown that mice lacking the TSH receptor (TSHR) exhibit osteoporosis due to enhanced osteoclast formation. The fact that this enhancement is not observed in double-null mice of TSHR and TNFalpha suggests that TNFalpha overexpression in osteoclast progenitors (macrophages) may be involved. It is unknown how TNFalpha expression is regulated in osteoclastogenesis. Here, we describe a receptor activator for nuclear factor-kappaB ligand (RANKL)-responsive sequence (CCG AGA CAG AGG TGT AGG GCC), spanning from -157 to -137 bp of the 5'-flanking region of the TNFalpha gene, which functions as a cis-acting regulatory element. We further show how RANKL treatment stimulates the high-mobility group box proteins (HMGB) HMGB1 and HMGB2 to bind the RANKL-responsive sequence and up-regulates TNFalpha transcription. Exogenous HMGB elicits the expression of cytokines, including TNFalpha, as well as osteoclast formation. Conversely, TSH inhibits the expression of HMGB and TNFalpha and the formation of osteoclasts. These results suggest that HMGB play a pivotal role in osteoclastogenesis. We also show a direct correlation between the expression of HMGB and TNFalpha and osteoclast formation in TSHR-null mice and TNFalpha-null mice. Taken together, we conclude that HMGB and TNFalpha play critical roles in the regulation of osteoclastogenesis and the remodeling of bone.
Putative Nanobacteria Represent Physiological Remnants and Culture By-Products of Normal Calcium Homeostasis (2009)

Putative living entities called nanobacteria (NB) are unusual for their small sizes (50-500 nm), pleomorphic nature, and accumulation of hydroxyapatite (HAP), and have been implicated in numerous diseases involving extraskeletal calcification. By adding precipitating ions to cell culture medium containing serum, mineral nanoparticles are generated that are morphologically and chemically identical to the so-called NB. These nanoparticles are shown here to be formed of amorphous mineral complexes containing calcium as well as other ions like carbonate, which then rapidly acquire phosphate, forming HAP. The main constituent proteins of serum-derived NB are albumin, fetuin-A, and apolipoprotein A1, but their involvement appears circumstantial since so-called NB from different body fluids harbor other proteins. Accordingly, by passage through various culture media, the protein composition of these particles can be modulated. Immunoblotting experiments reveal that antibodies deemed specific for NB react in fact with either albumin, fetuin-A, or both, indicating that previous studies using these reagents may have detected these serum proteins from the same as well as different species, with human tissue nanoparticles presumably absorbing bovine serum antigens from the culture medium. Both fetal bovine serum and human serum, used earlier by other investigators as sources of NB, paradoxically inhibit the formation of these entities, and this inhibition is trypsin-sensitive, indicating a role for proteins in this inhibitory process. Fetuin-A, and to a lesser degree albumin, inhibit nanoparticle formation, an inhibition that is overcome with time, ending with formation of the so-called NB. Together, these data demonstrate that NB are most likely formed by calcium or apatite crystallization inhibitors that are somehow overwhelmed by excess calcium or calcium phosphate found in culture medium or in body fluids, thereby becoming seeds for calcification. The structures described earlier as NB may thus represent remnants and by-products of physiological mechanisms used for calcium homeostasis, a concept which explains the vast body of NB literature as well as explains the true origin of NB as lifeless protein-mineralo entities with questionable role in pathogenesis.
Parameters favouring successful adult pig islet isolations for xenotransplantation in pig‐to‐primate models (2006)

Morphological screening of the pig pancreas before isolation, optimal blood exsanguination, WIT <10 min, and an endotoxin content <30 EU/mg in Liberase PI batches determine successful pig islet isolation for xenotransplantation in primates.
Molecular cloning and characterization of comC, a late competence gene of Bacillus subtilis (1989)

comC is a Bacillus subtilis gene required for the development of genetic competence. We have cloned a fragment from the B. subtilis chromosome that carries comC and contains all the information required to complement a Tn917lac insertion in comC. Genetic tests further localized comC to a 2.0-kilobase HindIII fragment. Northern (RNA) blotting experiments revealed that an 800-base-pair comC-specific transcript appeared at the time of transition from exponential to stationary phase during growth through the competence regimen. The DNA sequence of the comC region revealed two open reading frames (ORFs), transcribed in the same direction. The upstream ORF encoded a protein with apparent sequence similarity to the folC gene of Escherichia coli. Insertion of a chloramphenicol resistance determinant into this ORF and integration of the disrupted construct into the bacterial chromosome by replacement did not result in competence deficiency. The downstream ORF, which contained the Tn917lac insertion that resulted in a lack of competence, is therefore the comC gene. The predicted protein product of comC consisted of 248 amino acid residues and was quite hydrophobic. The comC gene product was not required for the expression of any other com genes tested, and this fact, together with the marked hydrophobicity of ComC, suggests that it may be a component of the DNA-processing apparatus of competent cells.
Biochemical characterization of human glutamate carboxypeptidase III (2006)

Human glutamate carboxypeptidase II (GCPII) is a transmembrane metallopeptidase found mainly in the brain, small intestine, and prostate. In the brain, it cleaves N-acetyl-L-aspartyl-glutamate, liberating free glutamate. Inhibition of GCPII has been shown to be neuroprotective in models of stroke and other neurodegenerations. In prostate, it is known as prostate-specific membrane antigen, a cancer marker. Recently, human glutamate carboxypeptidase III (GCPIII), a GCPII homolog with 67% amino acid identity, was cloned. While GCPII is recognized as an important pharmaceutical target, no biochemical study of human GCPIII is available at present. Here, we report the cloning, expression, and characterization of recombinant human GCPIII. We show that GCPIII lacks dipeptidylpeptidase IV-like activity, its activity is dependent on N-glycosylation, and it is effectively inhibited by several known inhibitors of GCPII. In comparison to GCPII, GCPIII has lower N-acetyl-L-aspartyl-glutamate-hydrolyzing activity, different pH and salt concentration dependence, and distinct substrate specificity, indicating that these homologs might play different biological roles. Based on a molecular model, we provide interpretation of the distinct substrate specificity of both enzymes, and examine the amino acid residues responsible for the differences by site-directed mutagenesis. These results may help to design potent and selective inhibitors of both enzymes.
NAI1 Gene Encodes a Basic-Helix-Loop-Helix–Type Putative Transcription Factor That Regulates the Formation of an Endoplasmic Reticulum–Derived Structure, the ER Body (2004)

Plant cells develop various types of endoplasmic reticulum (ER)-derived structures with specific functions. ER body, an ER-derived compartment in Arabidopsis thaliana, is a spindle-shaped structure. The NAI1 gene regulates the development of ER bodies because mutation of NAI1 abolishes the formation of ER bodies. To better understand the role of NAI1, we cloned the NAI1 gene using a positional cloning strategy. The nai1-1 mutant had a single nucleotide change at an intron acceptor site of At2g22770 (NAI1 gene). Because of this mutation, aberrant splicing of NAI1 mRNA occurs in the nai1-1 mutant. NAI1 encodes a transcription factor that has a basic-helix-loop-helix (bHLH) domain. Transient expression of NAI1 induced ER bodies in the nai1-1 mutant. Two-dimensional electrophoresis and RT-PCR analyses showed that a putative lectin was depressed at both the mRNA and protein levels in nai1 mutants, as was a beta-glucosidase (PYK10). Our results provide direct evidence that a bHLH protein plays a role in the formation of ER bodies.
Tyrosine kinase inhibitors. 2. Synthesis of 2,2'-dithiobis(1H-indole-3-alkanamides) and investigation of their inhibitory activity against epidermal growth factor receptor and pp60v-src protein tyrosine kinases (1994)

A series of amide analogues of the 2,2'-dithiobis(1H-indole-3-alkaonic acid) class of tyrosine kinase inhibitors have been prepared, by reaction of 1H-indole-3-alkanamides (8) with S2Cl2, and separation of the desired disulfides from the initial mixtures of mono-, di-, and trisulfides formed. These amides were evaluated in vitro against epidermal growth factor receptor and pp60v-src protein tyrosine kinases. Inhibitory activity against EGF receptor tyrosine kinase was chain-length dependent, with the propanamides being the most effective. Hydrogen bond donor capabilities in the amide function did not appear to be necessary, with an N-benzylamide being the most potent (IC50 = 0.85 microM). Further substitution on the benzyl ring did not increase potency, and substitution in the alpha-position of the propanamide side chain was acceptable. A water-soluble alpha-NH2 derivative showed good inhibitory activity toward the enzyme, was a potent inhibitor of cell growth in fibroblasts, and selectively inhibited intracellular tyrosine phosphorylation patterns. The nonreceptor kinase pp60v-src was in general much more sensitive than EGF receptor kinase to inhibition by these compounds, but with less pronounced structure-activity relationships.
Theoretical Basis of Indicator-Dilution Methods For Measuring Flow and Volume (1962)

The purpose here is to inquire into the justification of the use of the indicator-dilution principle for measurement of fluid flow and volume. What is the validity of the formal expressions? Upon what assumptions are they based? What are the effects of specified violations of these assumptions?
Wound Healing in the Cornea (2005)

A better understanding of the complete cascade of events involved in the corneal wound healing process and anomalies that lead to complications is critical to improve the efficacy and safety of refractive surgical procedures. Recent advances in understanding the biologic and molecular processes that contribute to the healing response bring hope that safe and effective pharmacologic modulators of the corneal wound healing response may soon be developed.
The Role of Secondary Interactions in Selective Electrostatic Multilayer Deposition (2000)

Electrostatic layer-by-layer thin films may be directed to specific regions of a surface based on electrostatics, secondary interactions, and steric repulsion. In this study, a series of polyamines ranging from hydrophobic polyallylammonium hydrochloride (PAH) to hydrophilic linear polyethyleneimine (LPEI) were coadsorbed with poly(acrylic acid) (PAA) onto patterned self-assembled monolayer (SAM) surfaces. When an acid (COOH) and oligoethylene glycol (EG) SAMs are used as the surface template, it was found that the region of preferred deposition for the more hydrophobic polyamine species was generally the EG region at pH 4.8, rather than the partially charged COOH region. The more hydrophilic LPEI species preferred adsorption on the COOH surface. It is proposed that PAH undergoes complexation with the EG surface based on hydrophobic and hydrogen bonding interactions at moderate pH. On the other hand, the LPEI backbone is hydrated and is thought to undergo large steric repulsion with the EG surface, thus resulting in deposition only on the COOH surface. The region of preferred adsorption also varied with pH, as the hydrogen-bonding interaction of PAA became important at low pH, and electrostatic interactions became the controlling element for selectivity at high pH, when all systems were highly charged. By tuning polyion−surface interactions, the region of polyion deposition can be carefully controlled on patterned chemical surfaces.
A parallel decoding scheme for turbo codes (2002)

The recursive computations in the MAP-based decoding of turbo codes usually introduce a significant amount of decoding delay. In this paper, we present a method for reducing the decoding delay by means of segmenting a block into several sub-blocks, which are partially overlapped. The proposed sub-block segmentation scheme allows for the parallel decoding of each component code by using several sub-block decoders. The number of steps for the recursive computations in each sub-block decoder is reduced to O(N/W), where W is the number of segmented sub-blocks. The decoding delay is approximately one-Wth that of a conventional MAP-based turbo-coding system. The cost paid is a slight degradation in bit error rate performance and a reasonable increase in hardware complexity.
Chemical Fixation of Carbon Dioxide by NaI/PPh3/PhOH (2003)

In the presence of catalytic amounts of sodium iodide, triphenylphosphine, and phenol, carbon dioxide can efficiently react with epoxides to give the corresponding five-membered cyclic carbonates in high yields. The mechanism of this reaction was disclosed by (31)P NMR spectroscopic data and deuterium labeling experiments.
Beam shaping to generate uniform laser light sheet and linear laser spots (2013)

Generation of “Laser Light Sheet” beams and linear laser spots characterized by uniform irradiance distribution is important in various laser techniques like Particle Image Velocimetry (PIV), Laser-Induced Fluorescence (LIF), hardening, annealing, cladding, uniform laser illumination of linear spatial light modulators. This task can be successfully solved with using refractive beam shaping optics of field mapping type in combination with additional optical components. Due to their unique features: low output divergence, high transmittance, flatness of output phase front and irradiance profile, as well as extended depth of field, the refractive field mappers provide freedom in further manipulation of intensity profile and shape of output beam. Typically design of refractive field mapping beam shapers has circular symmetry; therefore to create linear spot shapes it is suggested to apply anamorphic optical components like cylinder lenses, prism pairs, etc. The combined beam shaping systems allow achieving very high aspect ratio, up to 1:1000, of linear spots with simultaneous providing extended depth of field, i.e. it is possible to realize a “Laser Light Sheet” characterized by keeping uniform intensity of linear spot over extended distance along optical axis. This paper will describe some design basics of refractive beam shapers of the field mapping type and optical layouts for creating linear laser spots and “Laser Light Sheet”. Examples of real implementations will be presented as well.
Immunostimulatory Activity of Prothymosin‐Alpha in Senescencea (1991)

In this study we evaluated the immunorestorative activity of prothymosin-alpha (ProT-alpha) in senescence. Aged rats were repeatedly injected with ProT-alpha after antigen challenge. Both humoral and cell-mediated immune reactions were tested. The results show that ProT-alpha exerted a marked immunopotentiating effect in aged rats. Moreover, ProT-alpha induced enhancement of PFC response, and skin hypersensitivity reactions were more pronounced in senescent rats than in young adult controls. ProT-alpha treatment increased thymus and spleen weights in aged rats, and induced qualitative and quantitative improvements of the cellular make-up of the thymus and thymus-dependent areas of the spleen. The results imply that "restoring" thymus endocrine function by exogenous administration of ProT-alpha may improve immune system homeostasis in senescence.
Neuronal man : the biology of mind (1985)

World-famous neurobiologist Jean-Pierre Changeux here bridges inter-disciplinary boundaries to present an extraordinarily wide-ranging synthesis of current knowledge about the human brain. He presents his radical hypothesis that there is no 'mind' in man - nothing psychic - but only neurons, synapses, electricity and chemistry.
Biocompatible Solid-Phase Microextraction Coatings Based on Polyacrylonitrile and Solid-Phase Extraction Phases (2007)

The applications of solid-phase microextraction (SPME) are continuously expanding, and one of the most interesting current aspects consists of applying SPME for fast analysis of biological fluids. The goal of this study is to develop biocompatible SPME coatings that can be utilized for in vivo and in vitro extractions, in direct contact with a biological matrix such as blood or tissue. The biocompatibility of the proposed new coatings is confirmed by X-ray photoelectron spectroscopy, and their performance is tested by developing an SPME/HPLC method for analysis of verapamil, loperamide, diazepam, nordiazepam, and warfarin in buffer solutions and in human plasma. The coatings prove to be biocompatible by not adsorbing proteins and are successfully applied for fast drug analysis and assay of drug plasma protein binding.
Growth, carcass, and tenderness characteristics of virgin, spayed, and single-calf heifers. (1996)

Fifty-three Angus/Gelbvieh rotationally crossed heifers were slaughtered after 100 d on a high-concentrate diet. The average slaughter age for each of three different groups was 31, 33, or 35 mo, which falls within the USDA's 30- to 42-mo age range for animals producing "B" maturity carcasses. Each age group consisted of five or six heifers that had never been bred (virgin), six heifers ovariectomized at 1 yr of age (spayed), and six heifers that had weaned calves approximately 120 d postpartum (single-calf). Slaughter weight was higher (P < .05) for the virgin heifers but total weight gain in the feedlot was similar among the three groups. Single-calf heifers fed 100 d after weaning calves tended to be fatter than virgin or spayed heifers. Carcass maturity scores for the single-calf, virgin, and spayed heifers were different (P < .05); single-calf heifers produced carcasses that appeared older and spayed heifers produced carcasses that appeared younger. Maturity scores coupled with lighter and shorter metacarpal bone weights indicated single-calf heifers matured earlier (P < .05) than the other groups. Panel tenderness and Warner-Bratzler (WB) shear values of rib roasts from virgin, spayed, and single-calf heifers were determined. No differences among groups of heifers existed but scores within each group varied greatly. Marbling score was correlated (P < .05) with panel tenderness and shear force and the hydroxylysylpyridinium (HP) crosslink of muscle collagen was correlated (P < .05) with shear values. Because no significant (P < .05) correlation existed between HP in bone collagen or HP or WB shear values in muscle, we concluded that collagen maturation processes in muscle and bone occur independently. With the exception of differences in bone maturity scores, few meaningful differences in characteristics of virgin, spayed, and single-calf heifers existed, but these maturity differences could change carcass grade and influence value.
Expression of myosin isoenzymes in cardiac-muscle cells in culture (1984)

Myosin isoenzyme profiles of rat and chicken embryonic cardiac myocytes were studied during differentiation and growth in vitro by native-gel electrophoresis and assay of Ca2+-activated ATPase. The electrophoretic pattern of myosin extracted from 18-day-embryonic-rat myocytes after 7 days in culture exhibits three isoenzyme bands, V1, V2 and V3, of which the slow-migrating V3 is predominant. This resembles the isoenzyme profiles from 18-20-day-embryonic ventricles in vivo. However, the isoenzyme profile of the 7-day-old culture differs from that of its counterpart in vivo, as well as from that of the young and adult rat ventricles, the last two containing the predominant fast-migrating component, V1. When embryonic cardiac myocytes were grown in vitro for 7 days in a medium containing a physiological concentration of L-thyroxine (T4), myosin isoenzyme profiles of these cells shifted to the adult form, with isoenzyme V1 predominating after day 4 of culture. The 7-day-old intact embryonic-chicken ventricles and isolated myocytes showed a single myosin isoenzyme band after 7 days of culture that resembles the pattern seen for the adult chicken. T4 had no effect on the electrophoretic mobility of this isoenzyme pattern. ATPase activity of isoenzyme V1 in cultured rat myocytes treated with T4 was comparable with that of V1 in the untreated adult heart. This study demonstrates that ATPase activity of the chicken myosin isoenzyme is significantly lower than that of isoenzyme V1, but is comparable with that of rat V3. This study shows that the expression of myosin isoenzyme profiles in cultured rat cardiac myocytes does not fully represent the situation in vivo. Physiological concentrations of T4 can modulate the predominant foetal-type isoenzyme V3 to the adult type V1 in cultured embryonic-rat cardiac myocytes within a brief period.
Similar Effects on Infants of n-3 and n-6 Fatty Acids Supplementation to Pregnant and Lactating Women (2001)

This study shows neither harmful nor beneficial effects of maternal supplementation of long-chain n-3 PUFAs regarding pregnancy outcome, cognitive development, or growth, as compared with supplementation with n-6 fatty acids. However, it confirms that DHA concentration may be related to gestational length and cerebral maturation of the newborn.
Evaluation of protective immunity in gilts inoculated with the NADC-8 isolate of porcine reproductive and respiratory syndrome virus (PRRSV) and challenge-exposed with an antigenically distinct PRRSV isolate. (1999)

Exposure of swine to enzootic PRRSV will provide protection against homologous PRRSV-induced reproductive losses. Extent and duration of protection against heterologous PRRSV may be variable and dependent on antigenic relatedness of the virus strains used for inoculation and CE.
Acyclic analogue of lipid A stimulates TNF- alpha and arachidonate release via a unique LPS-signaling pathway. (1994)

LPS has been implicated in the pathogenesis of Gram-negative bacterial sepsis. Despite intensive efforts to define the LPS-signal transduction pathway, CD14 is the sole molecule clearly demonstrated to possess signaling capabilities. However, it remains unclear whether CD14 is the only LPS-signaling molecule expressed in phagocytes and how CD14-mediated signaling occurs. Compound SDZ 280.961 is a synthetic triacylated amino acid that structurally resembles the reducing sugar moiety of lipid A. SDZ 280.961 effectively stimulated TNF-alpha release from human PBMC. Co-incubation of PBMC with the specific LPS inhibitor Rhodobacter sphaeroides lipid A inhibited SDZ 280.961-mediated stimulation of TNF-alpha release, indicating that this analogue signals mononuclear cells via a LPS-activated signaling pathway. Induction of TNF-alpha release from mononuclear cells by SDZ 280.961 was strongly dependent on the presence of serum and was enabled by the presence of purified LPS-binding protein, characteristics of CD14-mediated signaling. In contrast, SDZ 280.961-mediated signaling was not inhibited by blocking anti-CD14 mAbs. A Chinese hamster ovary fibroblast line transfected with human CD14, which responds to LPS in a manner qualitatively similar to that of macrophage cell lines, failed to respond to SDZ 280.961. Taken together, these data suggest that the lipid A analogue SDZ 280.961 activates monocytes via a unique LPS-signal transduction pathway that appears to be independent of CD14.