gebhart/patrepeval huggingface dataset:
Structure of apolipoprotein B-100 in low density lipoproteins (2001)

There is general consensus that amphipathic alpha-helices and beta sheets represent the major lipid-associating motifs of apolipoprotein (apo)B-100. In this review, we examine the existing experimental and computational evidence for the pentapartite domain structure of apoB. In the pentapartite nomenclature presented in this review (NH(2)-betaalpha(1)-beta(1)-alpha(2)-beta(2)-alpha(3)-COOH), the original alpha(1) globular domain (Segrest, J. P. et al. 1994. Arterioscler. Thromb. 14: 1674;-1685) is expanded to include residues 1;-1,000 and renamed the betaalpha(1) domain. This change reflects the likelihood that the betaalpha(1) domain, like lamprey lipovitellin, is a globular composite of alpha-helical and beta-sheet secondary structures that participates in lipid accumulation in the co-translationally assembled prenascent triglyceride-rich lipoprotein particles. Evidence is presented that the hydrophobic faces of the amphipathic beta sheets of the beta(1) and beta(2) domains of apoB-100 are in direct contact with the neutral lipid core of apoB-containing lipoproteins and play a role in core lipid organization. Evidence is also presented that these beta sheets largely determine LDL particle diameter. Analysis of published data shows that with a reduction in particle size, there is an increase in the number of amphipathic helices of the alpha(2) and alpha(3) domains associated with the surface lipids of the LDL particle; these increases modulate the surface pressure decreases caused by a reduction in radius of curvature. The properties of the LDL receptor-binding region within the overall domain structure of apoB-100 are also discussed. Finally, recent three-dimensional models of LDL obtained by cryoelectron microscopy and X-ray crystallography are discussed. These models show three common features: a semidiscoidal shape, a surface knob with the dimensions of the betaC globular domain of lipovitellin, and planar multilayers in the lipid core that are approximately 35 A apart; the multilayers are thought to represent cholesteryl ester in the smectic phase. These models present a conundrum: are LDL particles circulating at 37 degrees C spheroidal in shape, as generally assumed, or are they semidiscoidal in shape, as suggested by the models? The limited evidence available supports a spheroidal shape.
Effects of oxygen content and oxide layer thickness on interface state densities for metal-oxynitride-oxide-silicon devices (1991)

The interface state density of metal-oxynitride-oxide-silicon (MNOS) devices was investigated as a function of the tunnel oxide thickness and the amount of oxygen in the oxynitride films. Nitrous oxide gas was used to introduce oxygen into the oxynitride film during the deposition process. As 17 at. % oxygen was introduced into the oxynitride film, the lowest oxide-silicon interface state density increased from 3.0 to 3.5×1011 cm−2 eV−1 for 90-Å oxide MNOS devices, and decreased from 5.1 to 3.65×1011 cm−2 eV−1 for 20 Å oxide devices. The increase in interface state density with increasing oxygen for 90-Å oxide devices may be due to an increase in the loss of hydrogen passivation at the interfacial regions as more oxygen is introduced into the film. The higher interface state density for the 20 vs 90 Å oxide samples, for a given oxygen content of the oxynitride films, may be due to additional contributions from the trapping states near or at the oxide-oxynitride interface. However, the decrease in the interface state density for increasing oxygen concentration for 20-Å oxide MNOS devices may be due to passivation of trapping states at the oxide-oxynitride interface by oxygen. The silicon dangling bonds responsible for these trapping states may be compensated by oxygen introduced during the deposition process.
CD1 and Tuberculosis (2004)

This chapter reviews the immunobiology of CD1 and its potentially important role in the immune response to Mycobacterium tuberculosis infection. Importantly, CD1 is expressed on dendritic cell (DC) within granulomas from patients with both M. tuberculosis and M. leprae infections, although the role of DC in granuloma formation and maintenance is unclear. One of the hallmarks of M. tuberculosis bacteria is the capacity to survive within the intracellular environment. A significant increase in CD1c-restricted Tcell proliferation was observed in the tuberculosis group compared to the purified protein derivative (PPD)-negative control group. Interestingly, patients with clinically active pulmonary tuberculosis showed no significant response to lipid antigens or whole bacterial sonicates. Lipid-immunized guinea pigs challenged with virulent M. tuberculosis via aerosol administration exhibit reduced pulmonary pathology compared to negative control animals. M. tuberculosis bacilli possess one of the more unusual cell walls in the bacterial kingdom, with many of the lipid molecules being unique to this genus. A more thorough understanding of how CD1 antigen presentation fits into the overall host immune response to infection may lead to novel interventional therapies and improved vaccine formulations for tuberculosis and other infectious diseases.
Cell-replacement therapy for diabetes: Generating functional insulin-producing tissue from adult human liver cells (2005)

Shortage in tissue availability from cadaver donors and the need for life-long immunosuppression severely restrict the large-scale application of cell-replacement therapy for diabetic patients. This study suggests the potential use of adult human liver as alternate tissue for autologous beta-cell-replacement therapy. By using pancreatic and duodenal homeobox gene 1 (PDX-1) and soluble factors, we induced a comprehensive developmental shift of adult human liver cells into functional insulin-producing cells. PDX-1-treated human liver cells express insulin, store it in defined granules, and secrete the hormone in a glucose-regulated manner. When transplanted under the renal capsule of diabetic, immunodeficient mice, the cells ameliorated hyperglycemia for prolonged periods of time. Inducing developmental redirection of adult liver offers the potential of a cell-replacement therapy for diabetics by allowing the patient to be the donor of his own insulin-producing tissue.
Determinants of Viral Clearance and Persistence during Acute Hepatitis C Virus Infection (2001)

The virological and immunological features of hepatitis C virus (HCV) infection were studied weekly for 6 months after accidental needlestick exposure in five health care workers, four of whom developed acute hepatitis that progressed to chronicity while one subject cleared the virus. In all subjects, viremia was first detectable within 1-2 weeks of inoculation, 1 month or more before the appearance of virus-specific T cells. The subject who cleared the virus experienced a prolonged episode of acute hepatitis that coincided with a CD38+ IFN-gamma- CD8+ T cell response to HCV and a small reduction in viremia. Subsequently, a strong CD4+ T cell response emerged and the CD8+ T cells became CD38- and started producing IFN-gamma in response to HCV, coinciding with a rapid 100,000-fold decrease in viremia that occurred without a corresponding surge of disease activity. Chronic infection developed in two subjects who failed to produce a significant T cell response and in two other subjects who initially mounted strong CD4+ T cell responses that ultimately waned. In all subjects, viremia was higher at the peak of acute hepatitis than it was when the disease began, and the disease improved during the viremia. These results provide the first insight into the host-virus relationship in humans during the incubation phase of acute HCV infection, and they provide the only insight to date into the virological and immunological characteristics of clinically asymptomatic acute HCV infection, the commonest manifestation of this disease. In addition, the results suggest that the vigor and quality of the antiviral T cell response determines the outcome of acute HCV infection, that the ability of HCV to outpace the T cell response may contribute to its tendency to persist; that the onset of hepatitis coincides with the onset of the CD8+ T cell response, that disease pathogenesis and viral clearance are mediated by different CD8+ T cell populations that control HCV by both cytolytic and noncytolytic mechanisms, and that there are different pathways to viral persistence in asymptomatic and symptomatic acute HCV infection.
Lung Fibrosis and Emphysema: Divergent Responses to a Common Injury? (1982)

Cadmium chloride, administered intratracheally to golden Syrian hamsters, causes an acute lung injury which evolves into a lesion with functional and morphological features of diffuse fibrosis. With simultaneous feeding of a lathyrogen, beta-aminoproprionitrile, this same injury evolves into functional and morphological changes of bullous emphysema. These results suggest that the same lung injury might result in either fibrosis or emphysema, connective tissue synthesis during the healing phase being the critical determinant.
A way-halting cache for low-energy high-performance systems (2005)

Caches contribute to much of a microprocessor system's power and energy consumption. Numerous new cache architectures, such as phased, pseudo-set-associative, way predicting, reactive-associative, way-shutdown, way-concatenating, and highly-associative, are intended to reduce power and/or energy, but they all impose some performance overhead. We have developed a new cache architecture, called a way-halting cache, that reduces energy further than previously mentioned architectures, while imposing no performance overhead. Our way-halting cache is a four-way set-associative cache that stores the four lowest-order bits of all ways' tags into a fully associative memory, which we call the halt tag array. The lookup in the halt tag array is done in parallel with, and is no slower than, the set-index decoding. The halt tag array predetermines which tags cannot match due to their low-order 4 bits mismatching. Further accesses to ways with known mismatching tags are then halted, thus saving power. Our halt tag array has an additional feature of using static logic only, rather than dynamic logic used in highly associative caches, making our cache simpler to design with existing tools. We provide data from experiments on 29 benchmarks drawn from Powerstone, Mediabench, and Spec 2000, based on our layouts in 0.18 micron CMOS technology. On average, we obtained 55% savings of memory-access related energy over a conventional four-way set-associative cache. We show that savings are greater than previous methods, and nearly twice that of highly associative caches, while imposing no performance overhead and only 2% cache area overhead.
Complete Structure of the 11-Subunit Bovine Mitochondrial Cytochrome bc 1 Complex (1998)

Mitochondrial cytochrome bc1 complex performs two functions: It is a respiratory multienzyme complex and it recognizes a mitochondrial targeting presequence. Refined crystal structures of the 11-subunit bc1 complex from bovine heart reveal full views of this bifunctional enzyme. The "Rieske" iron-sulfur protein subunit shows significant conformational changes in different crystal forms, suggesting a new electron transport mechanism of the enzyme. The mitochondrial targeting presequence of the "Rieske" protein (subunit 9) is lodged between the two "core" subunits at the matrix side of the complex. These "core" subunits are related to the matrix processing peptidase, and the structure unveils how mitochondrial targeting presequences are recognized.
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes (2010)

Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here, we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes. A 5' domain of HOTAIR binds polycomb repressive complex 2 (PRC2), whereas a 3' domain of HOTAIR binds the LSD1/CoREST/REST complex. The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1 and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, thereby specifying the pattern of histone modifications on target genes.
Mechanism and conditions for anomalous strain relaxation in graded thin films and superlattices (1992)

Compositionally graded films of SiGe/Si(100) and GaInAs/GaAs were grown under different conditions in order to investigate the different modes of strain relaxation associated with the compositional grading. We show that, when the growth conditions are very clean and the gradient is shallow enough (about 1% misfit per half micron), very good, relaxed films are obtained. This coincides with the introduction of large numbers of dislocations in the substrate itself, which is counter-intuitive at first since the substrate is under negligible strain. We show that this introduction of dislocations is the result of the activation of novel Frank–Read-like sources located in the graded region, and is directly correlated to the lack of other low energy nucleation sites for dislocations. We detail the conditions of growth necessary for this phenomenon to occur, and show that it operates both for the SiGe/Si system and the GaInAs/GaAs system. Pure, relaxed Ge films have been grown in this manner on Si(100), with a defect density as low as 106/cm2.
Variable region sequences of a protective human monoclonal antibody specific for the Haemophilus influenzae type b capsular polysaccharide (1994)

A hybridoma secreting a human immunoglobulin G2 kappa monoclonal antibody (MAb) specific for the capsular polysaccharide of Haemophilus influenzae type b (Hib) was isolated. This MAb, designated CA4, was bactericidal to Hib in vitro and protected infant rats from Hib bacteremia. Nucleotide sequence analysis of CA4 variable (V) region cDNA showed that the heavy (H)-chain V region was of subgroup III and was 96% identical to the VH germ line gene segment DP77 (V3-21). The light (L)-chain V region was of the kappa subgroup III and was 94% identical to the A27 (Humkv325) germ line gene, which is commonly used by rheumatoid factors and other autoantibodies. MAb CA4 did not have rheumatoid factor activity and did not react with histones, DNA, or chromatin. These findings identify an additional VHIII gene segment which can contribute to the anti-Hib capsular polysaccharide repertoire and demonstrate that a VL gene commonly encoding autoantibodies can be utilized for protective immunity.
Hormone replacement therapy and risk of hip fracture: population based case-control study (1998)

Recent use of hormone replacement therapy is required for optimum fracture protection, but therapy can be started several years after the menopause. The protective effect increases with duration of use, and an oestrogen-sparing effect is achieved when progestins are included in the regimen.
3D In-Vivo Optical Skin Imaging for Topographical Quantitative Assessment of Non-Ablative Laser Technology (2002)

Three-dimensional In-vivo optical skin imaging provided a rapid and quantitative assessment of surface topography and facial fine lines following multiple treatment sessions with a 1064-nm QS Nd:YAG laser, correlating with clinical and subjective responses. This imaging technique provided objective verification and technical understanding of nonablative laser technology. Wrinkle depth and skin roughness decreased at the three and six-month follow-up evaluations by 3D In-vivo assessment, indicating ongoing dermal collagen remodeling after the laser treatment protocol. Future applications may include comparison of nonablative laser technology, optimization of treatment regimens, and objective evaluation of other aesthetic procedures performed by dermatologists.
Inhibition of intratracheal lung cancer development by systemic delivery of E1A. (1996)

Amplification or overexpression of HER-2/neu in human lung cancer has been correlated with poor prognosis and chemoresistance. We have previously reported that the adenovirus type 5 early region 1A (E1A) gene product can suppress HER-2/neu-mediated transformation phenotypes through inhibition of HER-2/neu expression. To find an efficient way to treat HER-2/neu-overexpressing lung cancer with E1A, a replication-deficient adenovirus containing the E1A gene, Ad.E1A(+), was used to transduce E1A into HER-2/neu-overexpressing and low expressing human lung cancer cell lines. Tumour cell growth in vitro and colony formation in soft agarose were greatly inhibited by Ad.E1A(+) transduction in HER-2/neu-overexpressing lung cancer cell lines. In HER-2/neu low expressing cell lines, E1A could not inhibit cell growth in vitro but could reduce the colony formation ability in soft agarose, indicating different effects of E1A in these two types of cancer cells. To test the therapeutic efficacy of E1A to lung cancer by systemic delivery in vivo, tumor-bearing mice were established by intratracheal injection of lung cancer cells and treated by i.v. tail injections of Ad.E1A(+). As a result, Ad.E1A(+) suppressed HER-2/neu overexpression and inhibited intratracheal lung cancer growth. However, no significant tumor suppression effect of Ad.E1A(+) was observed in mice bearing HER-2/neu low expressing cell line when the same therapeutic procedure was followed. Thus, we conclude that systemic delivery of Ad.E1A(+) can efficiently achieve therapeutic effect in HER-2/neu-overexpressing lung cancer in vivo.
Rubber-like shape memory polymeric materials with repeatable thermal-assisted healing function (2012)

A thermo-responsive shape memory polymeric material is reported, which is not only rubber-like from above to below its shape recovery temperature, but also has a repeatable thermal-assisted healing function. The mechanisms behind both features are identified. It is found that while micron-sized inclusions play a part in the shape memory effect (SME), tangled polymer chains contribute to the rubber-like phenomenon and repeatable thermal-assisted healing function atop the SME. This tangling effect enables a perfect combination of high elasticity, SME and repeatable thermal-assisted healing to be simultaneously achieved.
Interaction of Escherichia coli translation‐initiation factor IF‐1 with ribosomes (1988)

The interaction between Escherichia coli translation-initiation factor IF-1 and ribosomes was studied in binding experiments by Airfuge centrifugation. IF-1 binds to the 30S, but not to the 50S, ribosomal subunit and its binding is strongly stimulated by IF-3 and IF-2, either alone or in combination. From the dependence of the Kd of the 30S-subunit--IF-1 complex on ionic strength, it can be concluded that IF-1 binds primarily via an ionic interaction, most likely with the 16S rRNA, with the minimum number of ion pairs involved being 2.7-3.6. The 30S-subunit--IF-1 interaction is unaffected by temperature changes between 11 degrees C and 44 degrees C and is thus accompanied by a negligible enthalpy change. It is concluded that the interaction is an entropy-driven process triggered mainly by the release of counter ions from the RNA phosphates. Titration of 30S-subunit--IF-1 complexes with 50S subunits causes the ejection of the factor indicating that IF-1 is released from the ribosomes during the subunit association step which marks the transition from a 30S-initiation-complex to a 70S initiation complex.
Regulation of type II iodothyronine 5'-deiodinase by thyroid hormone. Inhibition of actin polymerization blocks enzyme inactivation in cAMP-stimulated glial cells. (1990)

The cellular events mediating the rapid, thyroid hormone-dependent modulation of membrane-bound, type II iodothyronine 5'-deiodinase were studied in dibutyryl cyclic AMP(bt2cAMP)-treated brain astrocytes. Unstimulated cells had undetectable type II 5'-deiodinating activity. Treating the cells with bt2cAMP and hydrocortisone induced enzyme expression by increasing transcription of the enzyme or an essential enzyme related protein(s), with steady-state levels of type II 5'-deiodinase attained after 8 h of bt2cAMP treatment. Glial cells grown in the absence of thyroid hormone had 10-15-fold higher levels of 5'-deiodinating activity than cells grown in the presence of serum. The increased type II 5'-deiodinating activity observed in serum-free cultures was due to a prolonged enzyme half-life with no change in the rate of enzyme synthesis. Addition of thyroxine or 3,3',5'-triiodothyronine to the serum-free culture medium resulted in a concentration-dependent fall in steady-state enzyme levels, with EC50 values of approximately 0.4 nM. 3,5,3'-Triiodothyronine was at least 100-fold less effective. Chloroquine, NH4Cl, tunicamycin, colchicine, and monodansylcadavarine had no effect on the t1/2 of the enzyme, while both carbonyl cynanide m-chlorophenylhydrazone and cytochalasins completely blocked the inactivation of the type II 5'-deiodinase. These data indicate that in glial cells, an intact actin-cytoskeleton is required for thyroid hormone to modulate the energy-dependent regulation of the half-life of the short-lived, membrane-bound enzyme, type II 5'-deiodinase.
Strategies for production of pharmaceutical proteins in milk (1994)

Although it is only a decade since the use of transgenic livestock for the production of pharmaceutical proteins in milk was first suggested, great progress has been made. There is every reason to expect that, as methods for the transfer of genomic clones are applied with efficient regulatory elements, many proteins will be produced at high concentrations in the milk of livestock species. In most cases, these proteins will be biologically active, however, it remains to be shown whether they will be identical in structure and function to the natural product.
BREEDING ECOLOGY OF WHITE-WINGED DOVES IN A RECENTLY COLONIZED URBAN ENVIRONMENT (2005)

Using field-implanted subcutaneous radio transmitters, we monitored the breeding biology of White-winged Doves (Zenaida asiatica) in a recently colonized urban area (Waco, Texas). We implanted transmitters in June 2002 (n = 39; 16 males, 23 females) and February and March 2003 (n = 40; 17 males, 17 females, 6 unknown sex), and tracked radio-tagged doves every 3rd day until transmitters no longer functioned (90–120 days). We tracked 26 doves to 36 nests in nine tree species. The maximum number of nesting attempts was four. Nest success of first and second nesting attempts was 62 and 24%, respectively, and overall nest success for both years combined was 52%. Mean nest height—as a proportion of tree height—ranged from 0.31 to 0.75. Urban White-winged Doves had an extended breeding season; nesting attempts occurred both before and after the traditional dove breeding period in native brush habitats of the lower Rio Grande Valley of Texas. Field-implantation of subcutaneous radio transmitters was a viable technique for monitoring nesting activities of White-winged Doves.