gebhart/patrepeval huggingface dataset:
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon (2011)

The Escherichia coli σ(E) envelope stress response monitors and repairs the outer membrane, a function central to the life of Gram-negative bacteria. The σ(E) stress response was characterized as a single-tier activation network comprised of ~100 genes, including the MicA and RybB noncoding sRNAs. These highly expressed sRNAs were thought to carry out the specialized function of halting de novo synthesis of several abundant porins when envelope homeostasis was perturbed. Using a systematic target profiling and validation approach we discovered that MicA and RybB are each global mRNA repressors of both distinct and shared targets, and that the two sRNAs constitute a posttranscriptional repression arm whose regulatory scope rivals that of the protein-based σ(E) activation arm. Intriguingly, porin mRNAs constitute only ~1/3 of all targets and new nonporin targets predict roles for MicA and RybB in crosstalk with other regulatory responses. This work also provides an example of evolutionarily unrelated sRNAs that are coinduced and bind the same targets, but at different sites. Our finding that expression of either MicA or RybB sRNA protects the cell from the loss of viability experienced when σ(E) activity is inadequate illustrates the importance of the posttranscriptional repression arm of the response. σ(E) is a paradigm of a single-tier stress response with a clear division of labor in which highly expressed noncoding RNAs (MicA, RybB) endow a transcriptional factor intrinsically restricted to gene activation (σ(E)) with the opposite repressor function.
Concentration of Serum Lipids and Aortic Lesion Size in Female and Male Apo E-Deficient Mice Fed Docosahexaenoic Acid (1999)

Apolipoprotein (apo) E-deficient mice were fed an atherogenic diet with either 1% ethyl ester docosahexaenoic acid (DHA) or safflower oil (SO) as a source of linoleic acid for 8 week. Both genders fed DHA had higher proportions of eicosapentaenoic acid and DHA, and lower proportions of linoleic and arachidonic acids in the liver and serum phospholipids than those fed SO. Males fed DHA had greater liver weight and tended to have higher concentrations of serum lipids and liver cholesterol than those fed SO, and there were opposite trends in females. Dietary fats and gender led to no significant effect on lesion sizes in aortic arch and thoracic plus abdominal aorta. These results indicate that the interactive action of sex-related factor(s) with dietary polyunsaturated fatty acids is involved in metabolic changes of serum lipids in apoE-deficient mice, and addition of DHA, compared with addition of SO, is not effective to abolish the atherosclerosis in this animal model.
2‘,5‘-Oligoadenylate synthetase activity in lymphocytes from normal mouse. (1979)

The activity of 2',5'-oligoadenylate synthetase, an enzyme recently discovered in interferon-treated cells, was found in lymphocytes from normal mouse spleen that had received neither exogenous interferon nor its inducers. The oligoadenylate synthesized by lymphocyte cell extracts inhibited protein synthesis in rabbit reticulocyte lysates. The oligomers were composed mainly of trimer and were resistant to digestion by T2 ribonuclease. The level of the enzyme in lymphocytes was about 20 to 30% of that in L929 cells treated with interferon. The activity of the enzyme was further enhanced in lymphocytes in vitro by addition of interferon. The 2',5'-oligoadenylate synthetase was distributed among several lymphoid tissues, but was not detected in cell extracts from brain or liver. The enzyme may play an important role in the regulation of the immune system.
The Dishwasher's Child: education and the end of egalitarianism (1994)

This paper argues that egalitarianism, in itself and as a basis for educational policy, is unacceptable. Three recent defences of it are examined and rejected. Three anti-egalitarian positions, however, all of which stress sufficiency rather than equality, pass muster. Educational implications are followed through, with reference to mixed ability grouping, selection, equal opportunities in education and conflicting views about the minimum content of a common school curriculum.
Intravitreal bevacizumab (Avastin) treatment of macular edema in central retinal vein occlusion: a short-term study. (2006)

Initial treatment results of patients with macular edema secondary to CRVO did not reveal any short-term safety concerns. Intravitreal bevacizumab resulted in a significant decrease in macular edema and improvement in visual acuity. The number of patients in this pilot study was limited and the follow-up is too short to make any specific treatment recommendations, but the favorable short-term results suggest further study is needed.
<title>System for quantitative analysis of coronary calcification via electron-beam computed tomography</title> (1994)

Electron beam computed tomography (EBCT) has provided a new tool for identification and possible quantification of coronary arterial plaque calcium. EBCT is the only imaging modality currently available which generates images of the spatial, temporal, and contrast resolution required for the identification of small foci of calcium and the potential for accurate quantification of calcium. Meanwhile, interest in quantification of coronary arterial calcium via EBCT and its correlation with severity of coronary atherosclerosis is increasing. Data remain inconclusive, but it appears that the reproducibility of quantitative grading of the extent of calcification by EBCT may be limited, in part, by the arbitrary nature of the scoring algorithm employed within the analysis tools currently provided by the EBCT manufacturer. It has not been possible to objectively determine optimum values for minimum plaque area and brightness threshold or to quantitatively determine whether single optimal values even exist. Also, although the current system tabulates the score, area, and mean attenuation for each plaque, the locations of the plaques are not reported.
Effects of Gamma‐Irradiation on Flatulence‐Causing Oligosaccharides in Green Gram ( Phaseolus Areus ) (1983)

ABSTRACT Effects of gamma‐irradiation (l–10 kGy) on flatulence‐causing oligosaccharides of green gram were investigated. Irradiation at 2.5 kGy of hydrated seeds caused nearly 20% loss in their total content; but, 50% each of stachyose and raffinose, the two most gas‐forming sugars, was reduced. However, oligosaccharides disappeared completely from germinated (48 hr) seeds, irradiated at 2.5–10 kGy; though α‐galactosidase activity was not changed. When irradiated green gram flour was subjected to enzymic hydrolysis, significantly more reducing sugars were liberated. Quantitative analysis of the breakdown products of raffinose also suggested that radiation treatment stimulated the glycosidic cleavage of higher sugar molecules to simpler, easily digestible sugars. Thus radiation treatment of green gram is effective for elimination of oligosaccharides during germination.
A Pathogenic Role of Th2 Cells and Their Cytokine Products on the Pulmonary Metastasis of Murine B16 Melanoma (1998)

The role of Th2 cells and the cytokines produced by these cells on experimental pulmonary metastasis of B16 melanoma was investigated in a murine model implanted with high metastatic (B16F10) or low metastatic (B16F1) melanoma cells. An average of 250 colonies of metastasis in the lungs was counted in mice (BF10 mice) at 14 days after the inoculation of 2 x 10(5) B16F10 cells/mouse, while <20 colonies were detected in mice (BF1 mice) inoculated with the same number of B16F1 cells. CD4+ CD11b+ TCR-alphabeta+ T cells (BF10-Th2 cells) were produced in the spleens of BF10 mice, while these cells were not detected in BF1 mice. The BF10-Th2 cells produced IL-4 and IL-10 into culture fluids when stimulated in vitro with anti-CD3 mAb. However, IL-2 and IFN-gamma were not produced. The level of a pulmonary metastasis in BF1 mice increased to the level observed in BF10 mice, when BF10-Th2 cells were adoptively transferred to BF1 mice. Also, an increase in the number of pulmonary melanoma was demonstrated in BF1 mice treated with 10 microg/kg murine rIL-4. The level of pulmonary metastasis in BF10 mice or in BF1 mice inoculated with BF10-Th2 cells decreased to the level observed in BF1 mice when mice were treated with an anti-IL-4 mAb at a dose of 250 microg/kg on days 1, 3, and 5 after tumor inoculation. These results suggest that the severity of pulmonary metastasis in mice receiving B16 melanoma cells is strongly influenced by the IL-4 released from tumor-associated Th2 cells.
ESTIMATION OF THE POLAR SURFACE TENSION PARAMETERS OF GLYCEROL AND FORMAMIDE, FOR USE IN CONTACT ANGLE MEASUREMENTS ON POLAR SOLIDS (1990)

ABSTRACT By measuring contact angles with water, glycerol and formamide on a number of polar surfaces, an estimate could be made of the electron-acceptor (γ+ ) and the electron-donor (γ− ) parameters of glycerol (G) and formamide (F), relative to the parameters of. water (W), for which a reference value of γ+ W = γ− W = 25.5 mJ/m2 has been assumed. The values thus found are: γ+ G ≈ 3.92 mJ/m2 (which yields γ− G ≈ 57.4 mJ/m2) and γ+ F ≈2.28 mJ/m2 (which yields γ− F ≈ 39.6 mJ/m2).
BIOCHEMISTRY OF ENDOTOXINS (1990)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Coaggregation: specific adherence among human oral plaque bacteria (1993)

Nearly all human oral bacteria exhibit coaggregation, cell-to-cell recognition of genetically distinct cell types. Clumps or coaggregates composed of the two kinds of cells are formed immediately upon mixing two partner cell types. Members of all 18 genera tested exhibit lactose-reversible coaggregation. Many of these interactions appear to be mediated by a lectin on one cell type that interacts with a complementary carbohydrate receptor on the other cell type. A lactose-sensitive adhesin has been isolated from Prevotella loescheii PK1295, and it exhibits the adherence properties observed with whole cells. Other adhesins have been identified and the genes for some of them have been cloned and sequenced. One Streptococcus sanguis adhesin is a lipoprotein that appears to have a dual function of recognizing both a bacterial carbohydrate receptor and a receptor in human saliva. Carbohydrate receptors for some adhesins have been purified from five oral streptococci, and they specifically block the coaggregations with the streptococcal partners that express the complementary adhesins. Coaggregation offers an explanation for the temporally related accretion of dental plaque and bacterial recognition of mucosal surfaces. Early colonizers of the tooth surface coaggregate with each other and late colonizers of the tooth surface coaggregate with each other, but with few exceptions, early colonizers do not recognize late colonizers. Furthermore, bacteria that colonize mucosal surfaces coaggregate with each other, indicating the high degree of specificity of coaggregation in the oral bacterial population.
Back Cover: Macromol. Chem. Phys. 15/2004 (2004)

Back Cover: The Cover shows the absorption and emission spectra of alkyl‐ and alkoxy‐substituted dialdehydes, and their respective poly[(phenylene ethynylene)‐ alt ‐(phenylene vinylene)] hybrid polymers, obtained by the polycondensation of the dialdehydes with alkoxy‐substituted bisphosphonates. Photophysical investigations and quantum chemical calculations reveal remarkable differences between alkyl‐ and alkoxy‐substituted dialdehydes. On the contrary, their polymers exhibit similar photophysical properties, indicating an identical fluorophore system located around the lower energy phenylene‐vinylene segment of the polymers. Further details can be found in the Full Paper by D. A. M. Egbe, * S. Sell, C. Ulbricht, E. Birckner, and U.‐W. Grummt on page 2105.
Monte Carlo-minimization approach to the multiple-minima problem in protein folding. (1987)

A Monte Carlo-minimization method has been developed to overcome the multiple-minima problem. The Metropolis Monte Carlo sampling, assisted by energy minimization, surmounts intervening barriers in moving through successive discrete local minima in the multidimensional energy surface. The method has located the lowest-energy minimum thus far reported for the brain pentapeptide [Met5]enkephalin in the absence of water. Presumably it is the global minimum-energy structure. This supports the concept that protein folding may be a Markov process. In the presence of water, the molecules appear to exist as an ensemble of different conformations.
Full-Length Dystrophin Reconstitution with Adeno-Associated Viral Vectors (2014)

Duchenne muscular dystrophy (DMD) is the most common lethal muscle disorder in children. It is caused by mutations of the dystrophin gene. Adeno-associated virus (AAV)-mediated gene replacement therapy has been actively pursued to treat DMD. However, this promising therapeutic modality has been challenged by the small packaging capacity of the AAV vector. The size of the full-length dystrophin cDNA is >11 kb, while an AAV virus can carry only a 5 kb genome. Innovative high-capacity AAV vectors may offer an opportunity to express the full-length dystrophin coding sequence. Here we describe several sets of tri-AAV vectors for full-length human dystrophin delivery. In each set, the full-length human dystrophin cDNA was split into three fragments and independently packaged into separate recombinant AAV vectors. Each vector was engineered with unique recombination signals for directional recombination. Tri-AAV vectors were coinjected into the tibialis anterior muscle of dystrophin-deficient mdx4cv mice. Thirty-five days after injection, dystrophin expression was examined by immunofluorescence staining. Despite low reconstitution efficiency, full-length human dystrophin was successfully expressed from the tri-AAV vectors. Our results suggest that AAV can be engineered to express an extra-large (up to 15 kb) gene that is approximately three times the size of the wild-type AAV genome. Further optimization of the trivector strategy may expand the utility of AAV for human gene therapy.
Voiced/Unvoiced classification of speech with applications to the U.S. government LPC-10E algorithm (2005)

This paper describes the development and application of a new voicing algorithm used in the 2400 bit per second U.S. Government's Enhanced Linear Predictive Coder (LPC-10E). Correct voicing is crucial to perceived quality and naturalness of LPC systems and therefore to user acceptance of LPC systems. This new voicing algorithm uses a smoothed adaptive linear discriminator to classify the signal as voiced or unvoiced speech. The classifier was determined using Fisher's method of linear discriminant analysis. The voicing decision smoother is a modified median smoother that uses both the linear discriminant and speech onsets to determine its smoothing. The voicing classifier adapts to various acoustic noise levels and features a powerful new set of signal measurements: biased zero crossing rate, energy measures, reflection coefficients, and prediction gains. The LPC-10E voicing algorithm improves upon other 2400 bps LPC voicing algorithms by providing higher quality synthesized speech. Higher quality is due to halving of the error rate and graceful degradation in the presence of acoustic noise.
Characterization of double-stranded ribonucleic acid sequences present in the initial transcription products of rat liver chromatin (1977)

At low ionic strength and with a low exogenous RNA polymerase/DNA ratio, rat liver chromatin directs the synthesis in vitro of RNA sequences rich in double-stranded segments. All the transcripts contain at least one double-stranded sequence. Most of the double-stranded segments are formed by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. They are heterogeneous in size, 35-45% of them being more than 80 nucleotides long. They contain 61-64% G+C, whether synthesized by rat liver RNA polymerase (form B) or Escherichia coli RNA polymerase. The largest double-stranded sequences are found in the largest transcripts, and are the most thermostable. The fidelity of base-matching is better in double-stranded transcripts synthesized on rat liver chromatin by homologous polymerase than in those synthesized on it by a bacterial polymerase, or in those synthesized by either of the two polymerases on pure DNA.
Myosin VI is required for the proper maturation and function of inner hair cell ribbon synapses (2009)

The ribbon synapses of auditory inner hair cells (IHCs) undergo morphological and electrophysiological transitions during cochlear development. Here we report that myosin VI (Myo6), an actin-based motor protein involved in genetic forms of deafness, is necessary for some of these changes to occur. By using post-embedding immunogold electron microscopy, we showed that Myo6 is present at the IHC synaptic active zone. In Snell's waltzer mutant mice, which lack Myo6, IHC ionic currents and ribbon synapse maturation proceeded normally until at least post-natal day 6. In adult mutant mice, however, the IHCs displayed immature potassium currents and still fired action potentials, as normally only observed in immature IHCs. In addition, the number of ribbons per IHC was reduced by 30%, and 30% of the remaining ribbons were morphologically immature. Ca2+-dependent exocytosis probed by capacitance measurement was markedly reduced despite normal Ca2+ currents and the large proportion of morphologically mature synapses, which suggests additional defects, such as loose Ca2+-exocytosis coupling or inefficient vesicular supply. Finally, we provide evidence that Myo6 and otoferlin, a putative Ca2+ sensor of synaptic exocytosis also involved in a genetic form of deafness, interact at the IHC ribbon synapse, and we suggest that this interaction is involved in the recycling of synaptic vesicles. Our findings thus uncover essential roles for Myo6 at the IHC ribbon synapse, in addition to that proposed in membrane turnover and anchoring at the apical surface of the hair cells.
Prospective study of equine colic incidence and mortality (1997)

A prospective study of one year was conducted on 31 horse farms to obtain population based estimates of incidence, morbidity and mortality rates of equine colic. Farms with greater than 20 horses were enrolled by randomly selecting horse owners from 2 adjacent counties of Virginia and Maryland. Descriptive information for 1427 horses was collected at the initiation of the study and updated at 3 month intervals. Time on the farm during the study was tabulated for each horse. When colic was reported by the owner, investigators visited the farm to obtain information about the colic. The crude incidence density rate of colic was 10.6 colic cases/100 horse-years, based on 104 cases/358,991 horse-days. The median farm specific incidence density rate was 7 cases/100 horse-years, and the range for individual farms varied from 0 to 30 colic cases/100 horse-years. A specific diagnosis was not made for 84 (81%) of colic episodes. Seventy colic episodes (67%) were treated by a veterinarian. Drugs were used in 83 (80%) colic episodes, and 78 (75%) of colic cases were mild, requiring no treatment or resolving after only one treatment. Four horses required colic surgery. Fourteen (13%) horses had more than one episode of colic during the year. Mortality from all causes of death was 2.5 deaths/100 horse-years, mortality rate for colic was 0.7 deaths/100 horse-years. Proportional mortality rate of colic, 28%, was higher than for any other cause of death. Horses less than age 2 years or greater than age 10 years had lower incidence than horses age 2-10 years. No difference in colic risk between genders was identified. Arabian horses had the lowest and Thoroughbreds the highest breed specific incidence rates. Horses used for eventing, or in training had a statistically significant higher incidence rate of colic compared to mature horses with no use (pets, retired, on pasture with no stated purpose). Horses used for lessons or with no use had the lowest incidence rates.
Molecular pathology of MELAS and MERRF. The relationship between mutation load and clinical phenotypes (1997)

Many patients with inherited mitochondrial encephalopathies have one of two pathogenic mutations of mitochondrial DNA (mtDNA): A3243G or A8344G. Individuals who harbour these mutations carry both mutant and wild-type alleles within each cell (heteroplasmy). Despite clear evidence of a direct relationship between the level of mutation and mitochondrial respiratory chain function in vitro, it has been more difficult to demonstrate a clear correlation between clinical phenotype and the level of mutant mtDNA in vivo. To address this issue, we identified 245 individuals who carry either the A3243G or A8344G mutations, and studied the relationship between the incidence of specific clinical features and the level of mutant mtDNA in blood (for A3243G, n = 73; for A8344G, n = 25) and/or skeletal muscle (for A3234G, n = 111; for A8344G, n = 55). Within this study group, the frequency of key clinical features was significantly different for individuals harbouring the A3243G and A8344G mutations. For both mutations, there was a correlation between the frequency of the more common clinical features and the level of mutant mtDNA in muscle. In contrast, we did not observe a correlation between the frequency of clinical features and the level of mutant mtDNA in blood. Therefore, measurement of the level of the A3243G and A8344G mutations in muscle will allow the identification of individuals who are at risk of developing specific complications, thus improving the prognostic advice that can be given to patients and family members who carry these mutations.
Instrumentation in medical systems (2002)

The demand for clinical use of accelerated heavy charged particle (proton and light-ion) beams for cancer treatment is now burgeoning worldwide. Clinical trials are underway at more than a dozen accelerators. Several hospital-based accelerator facilities dedicated to radiation treatment of human cancer have been constructed, and their number is growing. Many instruments in medical systems have been developed for modifying extracted particle beams for clinical application, monitoring the delivery of the treatment beams, and controlling the treatment processes to ensure patient safety. These in turn demand new developments of instruments in controlling beam extraction, beam tuning, and beam transportation at the medical systems.
Mobile Advertisement System Utilizing User&amp;#146;s Contextual Information (2006)

With the continuous advances in mobile technology, numerous applications are being developed to empower the mobile users. Mobile commerce (m-commerce) is starting to make a mark following the success of the internet and e-commerce. With this, application development aims to optimize the performance of the mobile environment such as PDA and cellular phones. Mobile advertisement is one example of mobile applications that provide a lot of potentials. In this paper, we introduce a new method of personalizing mobile advertisement by considering not only the user’s location but also his/her interest. A prototype system called ‘Concierge’ has been developed and tested on a shopping environment. The result of the experiment shows good potential for this kind of service.