gebhart/patrepeval huggingface dataset:
A joint finite mixture model for clustering genes from beta, Gaussian and Bernoulli distributed data (2013)

Background: Expression and protein-protein interaction data are often coupled in gene clustering, which has succeeded in many applications such as pathway discovery and function inference. However, asynchronous relations, which can be measured by protein-DNA binding data, are also crucial in regulatory network and should be taken into account. Thus, how to make efficient use of gene expression, protein-protein interaction and protein-DNA binding data has posed us a huge challenge.\n\nMethod: A beta-Gaussian-Bernoulli mixture model (BGBMM) is proposed to solve the aforementioned problem, assuming that protein-DNA binding probabilities, gene expression data and protein protein interactions can be modeled as beta, Gaussian and Bernoulli distributions, respectively. BGBMM is a natural extension of the beta mixture model, the Gaussian mixture model and the Bernoulli mixture model, which differs from other mixture model based methods by fusing three heterogeneous data types into a unified probabilistic modeling framework with each data type modeled as one component. BGBMM is demonstrated to be an efficient model for data fusion, and is applicable to any data sources that can be modeled as beta, Gaussian or Bernoulli distributed random variables. Further, it is easily extendable to data of any other parametric distributions in principle. A joint standard expectation maximization algorithm is developed to estimate parameters involved in BGBMM. Four approximation-based model selection methods, i.e., the Akaike information criterion, a modified AIC, the Bayesian information criterion, and the integrated classification likelihood-Bayesian information criterion, are compared in BGBMM, based on which the best performing ones are suggested for future use.\n\nResults: The simulation tests and real case application show that combining three data sources into a single joint mixture model with each data type modeled as one component can highly improve the clustering accuracy. Also, applying BGBMM in mouse data reveals genes involved in the process of Toll-like receptor stimulated macrophage activation.\n\nAsiasanat:Joint finite mixture model, gene clustering, gene expression, protein-DNA binding probability, protein protein interaction
Imaging human intra-cerebral connectivity by PET during TMS (1997)

Non-invasive imaging of human inter-regional neural connectivity by positron emission tomography (PET) during transcranial magnetic stimulation (TMS) was performed. The hand area of primary motor cortex (M1) in the left cerebral hemisphere was stimulated with TMS while local and remote effects were recorded with PET. At the stimulated site, TMS increased blood flow (12-20%) in a highly focal manner, without an inhibitory surround. Remote covariances, an index of connectivity with M1, were also focal. Connectivity patterns established in non-human species were generally confirmed. Excitatory connectivity (positive covariance) was observed in ipsilateral primary and secondary somatosensory areas (S1 and S2), in ipsilateral ventral, lateral premotor cortex (M2) and in contralateral supplementary motor area (SMA). Inhibitory connectivity (negative covariance) was observed in contralateral M1.
Evidence‐based sepsis therapy: A hospitalist perspective (2006)

Compelling observational data supports the importance of early, effective antibiotics. Well-designed randomized controlled trials and/or meta-analyses demonstrate the impact of activated protein C, early goal-directed therapy, stress-dose steroids, and intensive insulin in well-defined subgroups of patients. These therapies reduce the absolute mortality risk associated with severe sepsis by 9.5-16%; the corresponding numbers needed to treat to save one life are 6.25-10.5. While major trials are ongoing and the evidence for several sepsis therapies are limited to single trials, the available evidence indicates that appropriate use of these treatments can substantially reduce mortality from severe sepsis.
Nucleic acid specificity of a vertebrate telomere-binding protein: evidence for G-G base pair recognition at the core-binding site. (1992)

A factor from avian cells formed complexes with telomeric sequences and other single-stranded probes that contained tracts of guanine residues. Nucleoprotein complexes with telomere probes required two or more of the telomeric repeats that were incapable of Watson-Crick base-pairing. Methylation interference and protection experiments identified guanine N7 residues that were critical for the formation of the nucleoprotein complex and for the formation of a higher-order structure that occurred in the absence of the protein. Substitutions of deoxyinosine (dI) for deoxyguanosine (dG) demonstrated that the exocyclic N2 amino groups in the internal telomeric repeat, but not the terminal repeat, were required for the formation of the chemically protected structure and for protein binding. On the basis of these data we propose that the factor specifically recognizes a hairpin DNA structure that is stabilized by intramolecular G-G base-pairing between the telomere repeats. The positions of the critical guanine N2 and N7 groups indicate a G-G base-pairing configuration, where guanines function as hydrogen bond donors at the internal telomeric repeat and hydrogen bond acceptors at the terminal telomeric repeat.
Bromine chloride as an alternative disinfectant to chlorine of human enteric viruses and other pathogens in water and wastewater (1979)

Bromine chloride (BrCl) was evaluated as an alternative disinfectant to chlorine by comparing the inactivation of human enteric viruses and indicator bacteria in water and wastewater by bromine chloride and chlorine. Preliminary studies were conducted under ideal laboratory conditions. In nitrogen-free buffer at pH 6.0, BrCl found to be two to three times as effective as chlorine in inactivating more than 5 logs of poliovirus. Furthermore, BrCl retained its disinfecting ability over a wide range of pH. The primary sit8 of action of BrCl on poliovirus was the virus protein; and infectious RNA was recovered from poliovirus in which more than 3 logs of virus had been inactivated by 0.3 mg/l of BrCl. Bromine chloride was less affected than chlorine by the presence of interfering compounds such as NH 4Cl and glycine, added to the water. Under simulated field conditions in the laboratory, a 5 mg/l dose of BrCl inactivated more than 5 logs of poliovirus in sewage effluent whereas the equivalent dose of chlorine inactivated only 2 logs. Disinfection of wastewater by BrCl and chlorine was also studied under field operating conditions by using a model chlorine contact chamber at a sewage treatment plant to treat large volumes activated sludge sewage effluent. An 8 mg/l dose of BrCl was determined to be more effective than an equivalent dose of chlorine in inactivating more than 4 logs of several types of human enteric viruses added to the effluent as well as viruses naturally present in sewage. BrCl was shown to require a shorter contact time and resulted in unstable residuals as compared to chlorine. Bromine chloride was also shown to be equally effective in inactivating human enteric viruses and coliform bacteria. Chlorine was more effective in inactivating human enteric viruses and coliform bacteria. Chlorine was more effective in inactivating coliform bacteria than viruses. Preliminary experiments also indicate that BrCl is a more effective disinfectant than chlorine of giardia cysts in water. Additional studies demonstrated that residual BrCl was less toxic than residual chlorine for fish. It is concluded that BrCl was a more effective disinfectant than chlorine of human enteric viruses and indicator coliform bacteria in water and wastewater and is therefore strongly recommended as an alternative disinfectant to chlorine.
Macromolecular Contrast Agents for Optical Imaging of Tumors: Comparison of Indotricarbocyanine-labeled Human Serum Albumin and Transferrin¶ (2000)

Macromolecules accumulate in solid tumors and can thus be used as carriers for the delivery of attached contrast agents to tumors. We report the synthesis and use of serum protein-dye conjugates consisting of transferrin (Tf) or human serum albumin (HSA) and an indotricarbocyanine (ITCC) derivative as contrast agents for the optical imaging of tumors. The compounds were characterized with respect to their photophysical properties and tested in vitro for their ability to bind to tumor cells and in vivo for their potential to delineate experimental tumors. In contrast to HAS-ITTC, Tf-ITCC showed receptor-mediated uptake by HT29 human colon cancer cells in vitro. After intravenous injection into HT29 tumor-bearing nude mice both compounds induced increased fluorescence contrast of tumors in vivo. After 24 h the contrast between tumor and normal tissue was significantly higher for Tf-ITCC than for HAS-ITCC. Dye-induced fluorescence was found to be predominantly located in perinecrotic areas of the tumor. Furthermore, Tf-ITCC produced fluorescence of viable tumor cells, whereas HAS-ITCC fluorescence was recorded along connective tissue. We conclude that ITCC-labeled Tf and HSA can serve as macromolecular contrast agents for the optical imaging of tumors, with Tf-ITCC showing higher efficiency.
31Phosphorus magnetic resonance spectroscopy study of tissue specific changes in high energy phosphates before and after sertraline treatment of geriatric depression (2009)

These findings demonstrate bioenergetic changes including tissue specific differences in (31)P-MRS metabolites in geriatric depression. Decreased white matter total NTP may reflect alterations in white matter function.
Enhancement of Sucrose Sweetness with Soluble Starch in Humans (2002)

The effect of soluble starch (acid-modified starch) on taste intensity was investigated in human subjects. Different concentrations of sucrose (Suc), six sweeteners, NaCl, quinine-HCl (QHCl) and citric acid (Cit) were dissolved in either distilled water (DW; standard) or starch solution (test solution). The solutions were presented to naive subjects and each subject was requested to taste and compare the sweetness intensity between the standard and test solutions based on a scale ranging from +3 (enhanced) to -3 (inhibited). A greater sweetness intensity occurred with Suc at different concentration (0.1-1.0 M) dissolved in soluble starch (0.125% to 4.0%) than with Suc in DW. Similarly, five other different products of soluble starch at 0.25 and 4.0% resulted in enhancement of sweetness for 0.3 and 1.0 M Suc. With the sole exception of the taste of 0.3 M Suc, sweet enhancement did not occur with 0.43 M fructose, 0.82 M glucose, 0.82 M sorbitol, 0.0037 M aspartame, 0.0042 M saccharin-Na or 0.016 M cyclamate. Neither the saltiness of NaCl (0.01-0.3 M), the bitterness of QHCl (0.00003-0.001 M) nor the sourness of Cit (0.0003-0.01 M) were affected by the soluble starch. These results suggest that the taste enhancing effects of soluble starch on Suc sweetness might depend not only on the taste transduction mechanism, but also on the molecular interaction between Suc and soluble starch.
Ribonuclease T1 has different dimensions in the thermally and chemically denatured states: a dynamic light scattering study (1997)

Ribonuclease T1 can be unfolded and refolded without forming noticeable amounts of aggregates allowing to characterise the dimensions of a protein in different denatured states in terms of the Stokes radius RS. Upon thermal unfolding RS increases from 1.74 nm at 20 degrees C to 2.14 nm at 60 degrees C. By contrast, RS = 2.40 nm was obtained at 5.3 M guanidinium chloride (GuHCl) and 20 degrees C. Heating from 20 degrees C to 70 degrees C in the presence of 5.3 M GuHCl led to a 5% decrease in RS.
Stromal Myofibroblasts Predict Disease Recurrence for Colorectal Cancer (2007)

The results suggest that the abundance of myofibroblasts in cancer-associated stroma may be a useful indicator of disease recurrence after curative colorectal cancer surgery.
Loss of imprinting of IGF2 in Ewing's sarcoma. (1995)

Insulin-like Growth Factor 2 (IGF2) has recently been demonstrated to be maternally imprinted in both mice and humans. We previously reported loss of imprinting (LOI) of IGF2 in rhabdomyosarcoma (RMS) where IGF2 has been shown to act as an autocrine growth factor and play an important role in pathogenesis. Since IGF2 does not appear to play a role in the pathogenesis of Ewing's sarcoma, we sought to determine whether normal IGF2 imprinting was maintained in these tumors. Of 32 Ewing's tumors examined for imprinting of IGF2, 10 were informative heterozygotes and three of these expressed IGF2 biallelically. Furthermore, all three tumors with LOI and five of seven tumors with normal imprinting transcribed IGF2 mRNA at lower levels while relatively higher levels of IGF2 expression was observed in the remaining two tumors with normal imprinting. These data demonstrate altered imprinting of IGF2 occurs in some Ewing's sarcomas. However, LOI of IGF2 in Ewing's sarcoma was not associated with increased expression of IGF2 mRNA, suggesting that LOI may not be involved in the regulation of IGF2 expression and may be related to genetic or epigenetic abnormalities in tumors independent of IGF2 expression.
The significance of experimental models of systemic lupus erythematosus and antiphospholipid syndrome induced by idiotypic manipulation. (1994)

Systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APLS) are two related autoimmune conditions. The pathogenesis of the diseases is unclear and the etiology is multifactorial. During the last 8 years our laboratory has been involved in induction of experimental SLE and APLS both by passive transfer of pathogenic antibodies (e.g., anticardiolipin) and by active immunization with pathogenic idiotypes. The naive mice, following immunization with Ab1, develop anti-autoantibody (Ab2) and eventually anti-autoantibody (Ab3) which has the binding capacities of anti-DNA or anticardiolipin. The mice with the characteristic syndromes were employed to analyze pathogenic mechanisms and new therapeutic modalities.
Characterization of the transient behavior of gated/STI diodes and their associated BJT in the CDM time domain (2007)

A measurement setup for the characterization of very fast transient responses in the CDM time domain is described in this paper. Experimental results are demonstrated on STI and gated diodes with a guard ring in a 65 nm and 130 nm CMOS technology. The superior behavior of gated diodes during triggering is highlighted.
Engineering the Microcirculation (2008)

The ultimate survival of tissue-engineered constructs in vivo depends on the provision of an adequate blood supply to the engineered tissue and the capacity of the engineered microcirculation to connect with the existing recipient circulation. Techniques for the vascularization of tissue-engineered constructs can be broadly grouped into in vitro and in vivo approaches that rely on the presence of a pro-angiogenic microenvironment. Significant advances have been made in resolving the problem of microcirculatory network formation for large 3-dimensional constructs; however, issues concerning construct-host vessel connection, expansion of vascular volume accompanying growing tissue, and prevention of premature or excessive vascular regression remain to be resolved. This review provides an overview of current approaches to creating microcirculatory networks with respect to the cells involved, growth factors, growth factor delivery systems, and scaffold properties required to engineer a permanent microcirculatory network for tissue-engineered constructs. In addition, the review examines concerns related to vascular remodeling and regression reported in some tissue-engineering models.
Matrix Metalloproteinases in the Normal Human Central Nervous System, Microglial Nodules, and Multiple Sclerosis Lesions (1996)

Matrix metalloproteinases (MMPs) comprise a family of proteolytic enzymes that are involved in remodeling of the extracellular matrix (ECM) of many tissues. They have been implicated in degradation of vascular basement membranes thereby facilitating leukocyte migration into inflammatory sites. To determine the cellular localization and levels of MMPs in the normal human central nervous system (CNS), multiple sclerosis (MS) lesions, and other conditions, cryostat sections of CNS samples were immunostained with antisera to MMP-1, -2, -3 and -9. In control white matter the principal cells that express the MMPs were perivascular and parenchymal microglia. Cellular MMP expression was also found in sporadic microglial nodules in MS white matter. Most CNS microvessel endothelial cells expressed MMP-3 and -9 but not MMP-1 or -2. The majority of macrophages in active MS and necrotic lesions were MMP-l-, -2-, -3-, and -9-positive whereas chronic MS lesions had fewer MMP-positive macrophages. Small numbers of astrocytes were MMP-2-, -3- and -9-positive in acute and chronic MS lesions. These data suggest that microglia-derived MMPs may mediate turnover of the CNS ECM under normal conditions and in microglial nodules. In sites of CNS tissue injury there is complex and dynamic regulation of MMP expression by different cell populations. In MS lesions MMP-mediated proteolysis may contribute to breakdown of the blood-brain barrier and leukocyte migration into the CNS, in situ immune activation, demyelination, metabolism of bioactive peptides, and the formation of an ECM that does not promote remyelination or axonal repair.
Cysteine phosphorylation of the glucose transporter of Escherichia coli (1993)

The glucose transporter (IIBCGlc/IIAGlc complex) of the bacterial phosphotransferase system couples vectorial translocation to phosphorylation of the transported sugar. The IIAGlc subunit transfers the phosphoryl group from the phosphoryl carrier protein P-HPr to the IIBCGlc subunit. IIBCGlc translocates and phosphorylates glucose. The site of IIBCGlc phosphorylation is cysteine 421 as shown by mass spectrometric and biochemical analyses of phosphorylated peptides. Site-directed mutagenesis of Cys421 (C421S) afforded a stable but completely inactive protein (Nuoffer, C., Zanolari, B., and Erni, B. (1988) J. Biol. Chem. 263, 6647-6655). Cys421 is located in the C-terminal cytoplasmic domain of the IIBCGlc subunit in a sequence context (LDACITRL) which is well conserved in other transporters of the bacterial phosphotransferase system. Phosphocysteine has been shown previously to be the catalytic intermediate of the mannitol transporter (Pas, H. H., Meyer, G. H., Kruizinga, W. H., Tamminga, K. S., van Weeghel, R. P., and Robillard, G. T.
The GB viruses: a review and proposed classification of GBV-A, GBV-C (HGV), and GBV-D in genus Pegivirus within the family Flaviviridae (2010)

In 1967, it was reported that experimental inoculation of serum from a surgeon (G.B.) with acute hepatitis into tamarins resulted in hepatitis. In 1995, two new members of the family Flaviviridae, named GBV-A and GBV-B, were identified in tamarins that developed hepatitis following inoculation with the 11th GB passage. Neither virus infects humans, and a number of GBV-A variants were identified in wild New World monkeys that were captured. Subsequently, a related human virus was identified [named GBV-C or hepatitis G virus (HGV)], and recently a more distantly related virus (named GBV-D) was discovered in bats. Only GBV-B, a second species within the genus Hepacivirus (type species hepatitis C virus), has been shown to cause hepatitis; it causes acute hepatitis in experimentally infected tamarins. The other GB viruses have however not been assigned to a genus within the family Flaviviridae. Based on phylogenetic relationships, genome organization and pathogenic features of the GB viruses, we propose to classify GBV-A-like viruses, GBV-C and GBV-D as members of a fourth genus in the family Flaviviridae, named Pegivirus (pe, persistent; g, GB or G). We also propose renaming 'GB' viruses within the tentative genus Pegivirus to reflect their host origin.
Thermal formation of mesoporous single-crystal Co3O4 nano-needles and their lithium storage properties (2008)

In this work, we report the simple solid-state formation of mesoporous Co3O4 nano-needles with a 3D single-crystalline framework. The synthesis is based on controlled thermal oxidative decomposition and re-crystallization of precursor β-Co(OH)2 nano-needles. Importantly, after thermal treatment, the needle-like morphology can be completely preserved, despite the fact that there is a large volume contraction accompanying the process: β-Co(OH)2 → Co3O4. Because of the intrinsic crystal contraction, a highly mesoporous structure with high specific surface area has been simultaneously created. The textual properties can be easily tailored by varying the annealing temperature between 200–400 °C. Interestingly, thermal re-crystallization at higher temperatures leads to the formation of a perfect 3D single-crystalline framework. Thus derived mesoporous Co3O4 nano-needles serve as a good model system for the study of lithium storage properties. The optimized sample manifests very low initial irreversible loss (21%), ultrahigh capacity, and excellent cycling performance. For example, a reversible capacity of 1079 mA h g−1 can be maintained after 50 cycles. The superior electrochemical performance and ease of synthesis may suggest their practical use in lithium-ion batteries.
Adaptive control with NeuCOP, the neural control and optimization package (2002)

NeuCOP is the neural control and optimization package that has been jointly developed by Texaco and NeuralWare. It is a state-of-the-art, multivariable, adaptive controller that combines the nonlinear modeling power of neural networks with nonlinear optimization algorithms. The NeuCOP controller belongs to the general class of model predictive controllers. One novel feature of the NeuCOP controller is its use of a nonlinear, neural network process model. We describe the identification subsystem that has been developed. More specifically, we address the issue of system re-identification, after the system is put online. The re-identification process allows the model to adapt to changing process conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cardiocerebral Resuscitation Is Associated With Improved Survival and Neurologic Outcome from Out‐of‐hospital Cardiac Arrest in Elders (2010)

Cardiocerebral resuscitation is associated with better survival from OHCA in most age groups. The majority of patients in all age groups who survived to hospital discharge and who could be reached for follow-up had good neurologic outcome. Among patients receiving CCR for OHCA, witnessed arrest, Vfib/Vtach, agonal respirations, and early response time are significant predictors of survival, and these do not change significantly based on age.