gebhart/patrepeval huggingface dataset:
A GSM-network for mobile phone localization in disaster scenarios (2011)

This paper deals with an adjustment and an implementation of a modified GSM-network. This network is necessary to enable the localization of mobile phones, primarily in disaster scenarios. In order to localize a mobile phone it is mandatory, that the phone transmits a signal. As a mobile phone transmits only sporadically without request, it has to be enforced to send a signal to be localized. The enforcing of a transmission is done by means of bringing up an auxiliary GSM-network. The configuration of the GSM-network allows the usage of a special handover procedure with frequency hopping. The implementation of frequency hopping considerably increases the accuracy of applied localization techniques.
Ring-Opening Reactions within Porous Metal−Organic Frameworks (2010)

Two new metal-organic framework (MOF) structures, IRMOF-3b and -3c, were prepared by ring-opening reaction of 1,3-propanesultone and 2-methylaziridine with an amine functionalized MOF, IRMOF-3. The new structures are permanently functionalized with covalently linked sulfonate and alkyamine units, respectively. The underlying framework structure is retained after reaction as confirmed by powder X-ray diffraction. The high porosity of IRMOF-3 is also maintained, as evidenced by nitrogen adsorption experiments, which yield Brunauer-Emmett-Teller (BET) surface areas of 1380 and 530 m(2) g(-1) compared to 2040 m(2) g(-1) in the parent material. Ring-opening reactions provide a versatile route to irreversible binding of a range of functionalities that are otherwise difficult to access in MOFs.
Implications of Historical Trends in the Electrical Efficiency of Computing (2010)

The electrical efficiency of computation has doubled roughly every year and a half for more than six decades, a pace of change comparable to that for computer performance and electrical efficiency in the microprocessor era. These efficiency improvements enabled the creation of laptops, smart phones, wireless sensors, and other mobile computing devices, with many more such innovations yet to come. The Web Extra appendix outlines the data and methods used in this study.
Omega-3 Fatty Acids: Evidence Basis for Treatment and Future Research in Psychiatry (2006)

The preponderance of epidemiologic and tissue compositional studies supports a protective effect of omega-3 EFA intake, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), in mood disorders. Meta-analyses of randomized controlled trials demonstrate a statistically significant benefit in unipolar and bipolar depression (p = .02). The results were highly heterogeneous, indicating that it is important to examine the characteristics of each individual study to note the differences in design and execution. There is less evidence of benefit in schizophrenia. EPA and DHA appear to have negligible risks and some potential benefit in major depressive disorder and bipolar disorder, but results remain inconclusive in most areas of interest in psychiatry. Treatment recommendations and directions for future research are described. Health benefits of omega-3 EFA may be especially important in patients with psychiatric disorders, due to high prevalence rates of smoking and obesity and the metabolic side effects of some psychotropic medications.
Exploiting unassigned codons in Micrococcus luteus for tRNA-based amino acid mutagenesis (1997)

An alternative to suppression of stop codons for the biosynthetic insertion of non-natural amino acids has been developed. Micrococcus luteus , a Gram-positive bacterium, is incapable of translating at least two codons. One of these unused codons was inserted in a gene to act as a nonsense site. An aminoacylated tRNA was synthesized which was complementary to this codon. The gene containing the missing codon was expressed in vitro in a M.luteus transcription/translation system. Read-through of the missing codon occurred only when the complementary tRNA was included. The results demonstrate that M.luteus can be used for incorporation of amino acids via synthetically prepared aminoacylated tRNAs. The use of a M. luteus translation system provides a method for incorporation of non-natural amino acids which avoids the use of stop codons.
Stacked Graphical Models for Efficient Inference in Markov Random Fields (2007)

In collective classification, classes are predicted simultaneously for a group of related instances, rather than predicting a class for each instance separately. Collective classification has been widely used for classification on relational datasets. However, the inference procedure used in collective classification usually requires many iterations and thus is expensive. We propose stacked graphical learning, a meta-learning scheme in which a base learner is augmented by expanding one instance's features with predictions on other related instances. Stacked graphical learning is efficient, especially during inference, capable of capturing dependencies easily, and can be implemented with any kind of base learner. In experiments on eight datasets, stacked graphical learning is 40 to 80 times faster than Gibbs sampling during inference.
Taste Receptors in the Gastrointestinal Tract. IV. Functional implications of bitter taste receptors in gastrointestinal chemosensing (2006)

Changes in the luminal contents of the gastrointestinal tract modulate gastrointestinal functions, including absorption of nutrients, food intake, and protection against harmful substances. The current notion is that mucosal enteroendocrine cells act as primary chemoreceptors by releasing signaling molecules in response to changes in the luminal environment, which in turn activate nerve terminals. The recent discovery that taste receptors and G protein subunits alpha-gustducin and alpha-transducin, involved in gustatory signal transduction, are expressed in the gastrointestinal mucosa supports the concept of a chemosensory machinery in the gastrointestinal tract. An understanding of luminal sensing processes responsible for the generation of the appropriate functional response to specific nutrients and nonnutrients is of clinical importance since aberrant or unsteady responses to changes in luminal contents might result in disease states ranging from intoxication to feeding disorders and inflammation. The purpose of this theme article is to discuss the functional implications of bitter taste signaling molecules in the gastrointestinal tract deduced by their localization in selected populations of epithelial cells and their relationship with neural pathways responsible for the generation of specific responses to luminal contents.
Langerhans Cells and T Cells in Langerhans Cell Histiocytosis Have Distinct Cytokine and Growth Factor Gene Expression Profiles Depending on the Clinical Risk Groups. (2004)

Abstract Langerhans cell histiocytosis (LCH) can present in several clinical forms with expected response to therapy categorized by the organ systems involved. Low Risk patients (unifocal bone, skin, or lymph nodes disease) are nearly always cured of the disease, patients with multifocal bone involvement are more likely to have relapses, and High Risk patients (involving liver, lung, spleen, or bone marrow) have only a 50% chance of cure. The etiology of LCH is unknown and controversy exists whether this is purely an immunologic dysfunction or a neoplastic disease since the Langerhans cells have been identified as a clonal proliferation. Understanding interaction of Langerhans cells (LC) with T lymphocytes and macrophages in the lesions of Langerhans cell histiocytosis (LCH) is critical to elucidating LCH pathophysiology. We have used laser capture microdissection to isolate CD1a+ LC and CD3+ T cells from frozen LCH lesions. RNA from the dissected cells was enzymatically amplified, hybridized to a cytokine/growth factor array and analyzed for quantity of gene expression after normalizing to b-actin. A complex expression profile has emerged: Gene Expression in LCH Clinical Groups Low Risk Multifocal Bone High Risk * to ***= low to high expression of a gene, VEGF:vascular endothelial growth factor, FGF: fibroblast growth factor CD1a Cytokines IL-9**, -11***, -17**, Leptin*,TGF- β IL-10**, IL-11**,TGF- β IL-9*,11*,Leptin** CD1a Growth Factors FGF-6*, VGEF*** FGF-6**, VEGF** FGF-6***, VEGF* CD3 Cytokines IL-9**, Lymphotoxin- α IL-9*,-10 IL-9*** Lymphotoxin- α** CD3 Growth Factors GM-CSF* GM-CSF** FGF-5* GM-CSF*** FGF-5** Growth factor and cytokine interactions from these LCH patients with different clinical presentations illustrates the importance of both LC and T-cells as well as the known influence of macrophages on the type of LCH. Although previous studies have shown TNF-a is an important factor, our data illustrates that other cytokines and growth factors may play critical roles, because of their relative higher gene expression when compared with TNF-a. These data will facilitate development of in vitro systems to test our hypotheses that a combination of cytokines/growth factors may be important in varying LCH clinical presentations.
A model for receptor–peptide binding at the glucagon‐like peptide‐1 (GLP‐1) receptor through the analysis of truncated ligands and receptors (2003)

1. The receptor for glucagon-like peptide-1 (GLP-1) can be activated by both its physiological hormone and a peptide discovered in the venom of the Gila Monster, exendin-4, which shows promise as an antidiabetic agent. 2. Exendin-4 displays receptor-binding properties not observed for GLP-1. Firstly, exendin-4 can be truncated by up to eight residues at its N-terminus without a significant loss of affinity. Secondly, exendin-4 maintains high affinity for the isolated N-terminal domain of the receptor, suggesting that exendin-4 makes additional contacts with this domain of the receptor, which nullify the requirement for ligand-receptor interactions involving the extracellular loops and/or transmembrane helices of the receptor's core domain. 3. In order to further understand the nature of the receptor-peptide interaction, a variety of full length and truncated peptide analogues were used to quantify the contribution of each distinct region of exendin-4 and GLP-1 to receptor affinity. 4. Our data show that, for both exendin-4 and GLP-1, the primary interaction is between the putative helical region of the peptide and the extracellular N-terminal domain of the receptor. 5. However, we demonstrate that the contribution to receptor affinity provided by the N-terminal segment of GLP-1 is greater than that of exendin-4, while the C-terminal nine residue extension of exendin-4, absent in GLP-1, forms a compensatory interaction with the N-terminal domain of the receptor. 6. We describe a peptide-receptor binding model to account for these data.
Understanding spontaneous speech (1989)

When speech understanding systems are used in real applications, they will have to deal with phenomena peculiar to spontaneous speech. People use language differently when they speak than when they write. Spoken language contains many interjections, filled pauses, etc. Speakers often don't use well-formed sentences. They speak in phrases, have restarts, etc. Systems designed for written or read text will encounter serious difficulties processing such input. This paper outlines our strategy for dealing with spontaneous spoken input in a speech recognition system.
Enhancement of the thermostability of subtilisin E by introduction of a disulfide bond engineered on the basis of structural comparison with a thermophilic serine protease. (1990)

Sites for Cys substitutions to form a disulfide bond were chosen in subtilisin E from Bacillus subtilis, a cysteine-free bacterial serine protease, based on the structure of aqualysin I of Thermus aquaticus YT-1 (a thermophilic subtilisin-type protease containing two disulfide bonds). Cys residues were introduced at positions 61 (wild-type, Gly) and 98 (Ser) in subtilisin E by site-directed mutagenesis. The Cys-61/Cys-98 mutant subtilisin appeared to form a disulfide bond spontaneously in the expression system used and showed a catalytic efficiency equivalent to that of the wild-type enzyme for hydrolysis of a synthetic peptide substrate. The thermodynamic characteristics of these enzymes were examined in terms of enzyme autolysis (t1/2) and thermal stability (Tm). The half-life of the Cys-61/Cys-98 mutant was found to be 2-3 times longer than that of the wild-type enzyme. Similar results were obtained by differential scanning calorimetry. The disulfide mutant showed a Tm of 63.0 degrees C, which was 4.5 degrees C higher than that observed for the wild-type enzyme. Under reducing conditions, however, the characteristics of the mutant enzyme were found to revert to those of the wild-type enzyme. These results strongly suggest that the introduction of a disulfide bond by site-directed mutagenesis enhanced the thermostability of subtilisin E without changing the catalytic efficiency of the enzyme.
Design and specificity of hammerhead ribozymes against calretinin mRNA (1993)

We obtained a partial sequence of mouse calretinin mRNA from cDNA clones, and designed hammerhead ribozymes to cleave positions within it. With a view to optimising hammerhead ribozymes for eliminating the mRNA in vivo, we varied the length and sequence of the three duplex 'arms' and measured the cleavage of long RNA substrates in vitro at 37 degrees C (as well as 50 degrees C). Precise cleavage occurred, but it could only go to completion with a large excess of ribozyme. The evidence suggests that the rate-limiting step with a large target is not the cleavage, but the formation of the active ribozyme: substrate complex. The efficiency varied unpredictably according to the target site, the length of the substrate RNA, and the length of the ribozyme; secondary structure in vitro may be responsible. We particularly investigated the degree of sequence-specificity. Some mismatches could be tolerated, but shortening of the total basepairing with the substrate to less than 14 bp drastically reduced activity, implying that interaction with weakly-matched RNAs is unlikely to be a serious problem in vivo. These results suggest that specific and complete cleavage of a mRNA in vivo should be possible, given high-level expression of a ribozyme against a favourable target site.
Tyrosine phosphorylation of the asialoglycoprotein receptor. (1990)

The asialoglycoprotein (ASGP) receptor undergoes constitutive endocytosis through the coated pit/coated vesicle pathway in hepatocytes. Studies on HepG2 cells have shown that the receptor is phosphorylated at serine under control conditions and following protein kinase C stimulation. This study examined whether the ASGP receptor could also serve as a substrate for a tyrosine kinase in HepG2 cells. 32P labeling was performed in membrane preparations, in permeabilized cells at 4 degrees C, and in intact cells at 37 degrees C. The phosphorylated ASGP receptor was isolated by immunoprecipitation, hydrolyzed in 6 N HCl at 110 degrees C, and analyzed by two-dimensional high voltage electrophoresis. The receptor isolated from a membrane preparation incubated in vitro with [gamma-32P]ATP incorporated radiolabel predominantly (greater than 90%) into phosphotyrosine. ASGP receptor phosphorylation at both tyrosine and serine was detected in intact cells incubated with phosphatase inhibitors for 60 min at 37 degrees C. The presence of both phenylarsine oxide (20 microM) and sodium orthovanadate (200 microM) was required for tyrosine phosphorylation. Use of these inhibitors together resulted in a 16.4-fold increase in phosphorylation of the immunoprecipitated ASGP receptor, whereas phosphorylation of total HepG2 membrane proteins was not significantly augmented by this procedure. Selective proteolytic digestion of ASGP receptors in isolated vesicles demonstrated that the phosphorylation site identified in these studies is located at tyrosine 5 in the cytoplasmic tail.
The accuracy of extrapolation (time series) methods: Results of a forecasting competition (1982)

Abstract In the last few decades many methods have become available for forecasting. As always, when alternatives exist, choices need to be made so that an appropriate forecasting method can be selected and used for the specific situation being considered. This paper reports the results of a forecasting competition that provides information to facilitate such choice. Seven experts in each of the 24 methods forecasted up to 1001 series for six up to eighteen time horizons. The results of the competition are presented in this paper whose purpose is to provide empirical evidence about differences found to exist among the various extrapolative (time series) methods used in the competition.
General mechanisms of metastasis (1997)

In the present article, the steps involved in the process of tumor metastasis are discussed. Several events are required for malignant cells to leave the primary tumor and proliferate at a distant site: vessel formation (angiogenesis), cell attachment, invasion (matrix degradation, cell motility), and cell proliferation. Molecular mechanisms underlying each of these steps are described. Based on blocking these processes, new anti-metastasis therapies are being developed.
Development of an implantable centrifugal blood pump. (1993)

The efficacy of centrifugal pumps for short-term (0-30 days) ventricular support has been widely reported and favorably compared with pulsatile systems. A small, durable, implantable centrifugal blood pump is being developed for medium-term use (up to 6 months). The pump is based on the Medtronic Hemadyne system that has existed in multiple forms over the past 30 years. The pump is approximately the size of a tennis ball, weighs 240 g, and is comprised of a 2.5 cm plastic impeller driven by a radially coupled brushless DC motor. In vitro hydraulic performance was recorded over a wide range of flow conditions on a mock circulatory loop. The pump generated 7 L/min flow against an afterload of 100 mmHg pressure, with a maximum power draw of 10.4 watts. Pulsatile flow was preserved when placed in conjunction with a simulated left ventricle. In vivo testing was performed in 10 healthy sheep for 10-292 hr. Heparin was used to facilitate cannulation, and no anticoagulation was administered after pump implantation. Blood chemistries reflecting hematologic, pulmonary, renal, and hepatic functions were recorded and demonstrated no adverse effects with normal pump operation. Complications were related to kinking of blood conduits and thrombus formation within the cannulae. These results are encouraging and warrant further studies to prove feasibility of this pump as a medium-term implantable ventricular assist device.
Expression of Engineered Nuclear Male Sterility in Brassica napus (Genetics, Morphology, Cytology, and Sensitivity to Temperature) (1993)

A dominant genetic male sterility trait obtained through transformation in rapeseed (Brassica napus) was studied in the progenies of 11 transformed plants. The gene conferring the male sterility consists of a ribonuclease gene under the control of a tapetum-specific promoter. Two ribonuclease genes, RNase T1 and barnase, were used. The chimaeric ribonuclease gene was linked to the bialophos-resistance gene, which confers resistance to the herbicide phosphinotricine (PPT). The resistance to the herbicide was used as a dominant marker for the male sterility trait. The study presented here concerns three aspects of this engineered male sterility: genetics correlated with the segregation of the T-DNA in the progenies; expression of the male sterility in relation to the morphology and cytology of the androecium; and stability of the engineered male sterility under different culture conditions. Correct segregation, 50% male-sterile, PPT-resistant plants, and 50% male-fertile, susceptible plants were observed in the progeny of seven transformants. The most prominent morphological change in the male-sterile flowers was a noticeable reduction in the length of the stamen filament. The first disturbances of microsporogenesis were observed from the free microspore stage and were followed by a simultaneous degeneration of microspore and tapetal cell content. At anthesis, the sterile anthers contained only empty exines. In some cases, reversion to fertility of male-sterile plants has been observed. Both ribonuclease genes are susceptible to instability. Instability of the RNase T1-male sterility trait increased at temperatures higher than 25[deg] C. Our results do not allow us to confirm this observation for the barnase male-sterile plants. However, the male-sterile plants of the progeny of two independent RNase T1 transformants were stably male sterile under all conditions studied.
Revisiting detrended fluctuation analysis (2012)

Half a century ago Hurst introduced Rescaled Range (R/S) Analysis to study fluctuations in time series. Thousands of works have investigated or applied the original methodology and similar techniques, with Detrended Fluctuation Analysis becoming preferred due to its purported ability to mitigate nonstationaries. We show Detrended Fluctuation Analysis introduces artifacts for nonlinear trends, in contrast to common expectation, and demonstrate that the empirically observed curvature induced is a serious finite-size effect which will always be present. Explicit detrending followed by measurement of the diffusional spread of a signals' associated random walk is preferable, a surprising conclusion given that Detrended Fluctuation Analysis was crafted specifically to replace this approach. The implications are simple yet sweeping: there is no compelling reason to apply Detrended Fluctuation Analysis as it 1) introduces uncontrolled bias; 2) is computationally more expensive than the unbiased estimator; and 3) cannot provide generic or useful protection against nonstationaries.
Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target (2006)

D-amino acids are much less common than their L-isomers but are widely distributed in most organisms. Many D-amino acids, including those necessary for bacterial cell wall formation, are synthesized from the corresponding L-isomers by alpha-amino acid racemases. The important class of pyridoxal phosphate-independent racemases function by an unusual mechanism whose details have been poorly understood. It has been proposed that the stereoinversion involves two active-site cysteine residues acting in concert as a base (thiolate) and an acid (thiol). Although crystallographic structures of several such enzymes are available, with the exception of the recent structures of glutamate racemase from Bacillus subtilis and of proline racemase from Trypanosoma cruzi, the structures either are of inactive forms (e.g., disulfide) or do not allow unambiguous modeling of the substrates in the active sites. Here, we present the crystal structures of diaminopimelate (DAP) epimerase from Haemophilus influenzae with two different isomers of the irreversible inhibitor and substrate mimic aziridino-DAP at 1.35- and 1.70-A resolution. These structures permit a detailed description of this pyridoxal 5'-phosphate-independent amino acid racemase active site and delineate the electrostatic interactions that control the exquisite substrate selectivity of DAP epimerase. Moreover, the active site shows how deprotonation of the substrates' nonacidic hydrogen at the alpha-carbon (pKa approximately 29) by a seemingly weakly basic cysteine residue (pKa approximately 8-10) is facilitated by interactions with two buried alpha-helices. Bacterial racemases, including glutamate racemase and DAP epimerase, are potential targets for the development of new agents effective against organisms resistant to conventional antibiotics.