gebhart/patrepeval huggingface dataset:
DNN-based prediction model for spatio-temporal data (2016)

Advances in location-acquisition and wireless communication technologies have led to wider availability of spatio-temporal (ST) data, which has unique spatial properties (i.e. geographical hierarchy and distance) and temporal properties (i.e. closeness, period and trend). In this paper, we propose a <u>Deep</u>-learning-based prediction model for <u>S</u>patio-<u>T</u>emporal data (DeepST). We leverage ST domain knowledge to design the architecture of DeepST, which is comprised of two components: spatio-temporal and global. The spatio-temporal component employs the framework of convolutional neural networks to simultaneously model spatial near and distant dependencies, and temporal closeness, period and trend. The global component is used to capture global factors, such as day of the week, weekday or weekend. Using DeepST, we build a real-time crowd flow forecasting system called UrbanFlow1. Experiment results on diverse ST datasets verify DeepST's ability to capture ST data's spatio-temporal properties, showing the advantages of DeepST beyond four baseline methods.
Direct Imaging of Multiple Planets Orbiting the Star HR 8799 (2008)

Direct imaging of exoplanetary systems is a powerful technique that can reveal Jupiter-like planets in wide orbits, can enable detailed characterization of planetary atmospheres, and is a key step toward imaging Earth-like planets. Imaging detections are challenging because of the combined effect of small angular separation and large luminosity contrast between a planet and its host star. High-contrast observations with the Keck and Gemini telescopes have revealed three planets orbiting the star HR 8799, with projected separations of 24, 38, and 68 astronomical units. Multi-epoch data show counter clockwise orbital motion for all three imaged planets. The low luminosity of the companions and the estimated age of the system imply planetary masses between 5 and 13 times that of Jupiter. This system resembles a scaled-up version of the outer portion of our solar system.
Biliary Tract Complications after Liver Transplantation: A Review (2008)

Biliary complications continue to be a major cause of morbidity in liver transplant recipients with an incidence of 10-30% following whole-organ transplantation and a mortality rate of up to 10%. Biliary leaks and strictures are most common but sphincter of Oddi dysfunction, hemobilia, and biliary obstruction are also observed. Biliary complications may be related to various factors such as hepatic artery patency, preservation injury, cytomegalovirus infection, chronic ductopenic rejection, ABO incompatibility, and technical reasons. The latter include imperfect anastomosis, T-tube-related complications and the use of partial liver grafts when cut surface biliary leaks or inadvertent bile duct injuries may occur during parenchymal division. The usage of a T-tube for duct-to-duct anastomosis in whole-organ liver transplantation remains controversial, mainly because of the high rates of T-tube-related complications observed in many series. In this article we review the etiology, as well as the main types of biliary complications according to the technique of biliary reconstruction and liver transplant procedure performed. Their management is also discussed with interventional radiology and endoscopic techniques emerging as the preferred treatment option, obviating the need for surgery in a selected majority of patients.
Biophysical modeling of alpha rhythms during halothane-induced unconsciousness (2013)

During the induction of general anesthesia there is a shift in power from the posterior regions of the brain to the frontal cortices; this shift in power is called anteriorization. For many anesthetics, a prominent feature of anteriorization is a shift specifically in the alpha band (8-13 Hz) from posterior to frontal cortices. Here we present a biophysical computational model that describes thalamocortical circuit-level dynamics underlying anteriorization of the alpha rhythm in the case of halothane. Halothane potentiates GABA<sub>A</sub> and increases potassium leak conductances. According to our model, an increase in potassium leak conductances hyperpolarizes and silences the high-threshold thalamocortical (HTC) cells, a specialized subset of thalamocortical cells that fire at the alpha frequency at relatively depolarized membrane potentials (>-60 mV) and are thought to be the generators of quiet awake occipital alpha. At the same time the potentiation of GABA<sub>A</sub> imposes an alpha time scale on both the cortical and the thalamic component of the frontal portion of our model. The alpha activity in the frontal component is further strengthened by reciprocal thalamocortical feedback. Thus, we argue that the dual molecular targets of halothane induce the anteriorization of the alpha rhythm by increasing potassium leak conductances, which abolishes occipital alpha, and by potentiating GABA<sub>A</sub>, which induces frontal alpha. These results provide a computational modeling formulation for studying highly detailed biophysical mechanisms of anesthetic action in silico.
Strong maternal fidelity and natal philopatry shape genetic structure in North Pacific humpback whales (2013)

We quantified the relative influence of maternal fidelity to feeding grounds and natal fidelity to breeding grounds on the population structure of humpback whales Megaptera novaeangliae based on an ocean-wide survey of mitochondrial (mt) DNA diversity in the North Pacific. For 2193 biopsy samples collected from whales in 10 feeding regions and 8 breeding regions during the winter and summer of 2004 to 2006, we first used microsatellite genotyping (average, 9.5 loci) to identify replicate samples. From sequences of the mtDNA control region (500 bp) we identified 28 unique haplotypes from 30 variable sites. Haplotype frequencies differed markedly among feeding regions (overall F ST = 0.121, ST = 0.178, p < 0.0001), supporting previous evidence of strong maternal fidelity. Haplotype frequencies also differed markedly among breeding regions (overall F ST = 0.093, ST = 0.106, p < 0.0001), providing evidence of strong natal fidelity. Although sex-biased dispersal was not evident, differentiation of microsatellite allele frequencies was weak compared to differentiation of mtDNA haplotypes, suggesting male-biased gene flow. Feeding and breeding regions showed significant differences in haplotype frequencies, even for regions known to be strongly connected by patterns of individual migration. Thus, the influence of migratory fidelity seems to operate somewhat independently on feeding and breeding grounds over an evolutionary time scale. This results in a complex population structure and the potential to define multiple units to conserve in either seasonal habitat.
Coupling of a Targeting Peptide to Plasmid DNA Using a New Type of Padlock Oligonucleotide (2002)

We have recently described a new method for attaching padlock oligonucleotides to supercoiled plasmid DNA at specific sequences. A variant of this method has been developed in order to allow the coupling of targeting moieties to plasmids using a convenient strategy. After sequence-specific winding around the double-stranded target DNA sequence by ligand-induced triple helix formation, the extremities of a triplex-forming oligonucleotide hybridize to each other, leaving a dangling single-stranded sequence, which is then ligated to a hairpin oligonucleotide using T4 DNA ligase. Any targeting moiety may be attached to the hairpin oligonucleotide. This strategy was used to attach an NLS peptide to a luciferase-expressing plasmid. Despite the presence of the padlock oligonucleotide, the reporter gene was efficiently expressed after transfection of the plasmid in HeLa or T24 cells, using either cationic lipids or cationic polymers as transfecting agents. However, no increase in gene expression could be observed as a result of peptide attachment. Nevertheless, the coupling strategy described in this paper may find applications as a tool for plasmid functionalization in other targeting experiments, and may lead to the development of improved vectors for gene therapy.
Autologus saphenous vein femoropopliteal bypass: analysis of 298 cases. (1976)

A retrospective review of 298 saphenous vein femoropopliteal bypasses performed for femoral artery occlusive disease over a 13 year period was carried out. The purpose of the study was to assess factors which influence long-term graft patency. Follow-up was 95.3 percent complete. Results were analyzed with the aid of IBM data processing equipment and standard statistical methods.
Transgene Expression of Drosophila melanogaster Nucleoside Kinase Reverses Mitochondrial Thymidine Kinase 2 Deficiency (2013)

A strategy to reverse the symptoms of thymidine kinase 2 (TK2) deficiency in a mouse model was investigated. The nucleoside kinase from Drosophila melanogaster (Dm-dNK) was expressed in TK2-deficient mice that have been shown to present with a severe phenotype caused by mitochondrial DNA depletion. The Dm-dNK(+/-) transgenic mice were shown to be able to rescue the TK2-deficient mice. The Dm-dNK(+/-)TK2(-/-) mice were normal as judged by growth and behavior during the observation time of 6 months. The Dm-dNK-expressing mice showed a substantial increase in thymidine-phosphorylating activity in investigated tissues. The Dm-dNK expression also resulted in highly elevated dTTP pools. The dTTP pool alterations did not cause specific mitochondrial DNA mutations or deletions when 6-month-old mice were analyzed. The mitochondrial DNA was also detected at normal levels. In conclusion, the Dm-dNK(+/-)TK2(-/-) mouse model illustrates how dTMP synthesized in the cell nucleus can compensate for loss of intramitochondrial dTMP synthesis in differentiated tissue. The data presented open new possibilities to treat the severe symptoms of TK2 deficiency.
Flow Cytometric Immunophenotypic Analysis of Systemic Mastocytosis Involving Bone Marrow (2014)

Flow cytometry immunophenotyping is a rapid and sensitive technique for characterizing mast cells in bone marrow aspirate specimens. The use of PE-conjugated antibodies for CD2 and CD25 improves the detection rate (CD2) or facilitates analysis (CD25); therefore, PE-conjugated antibodies are suggested. Antibodies reactive with CD35, CD59, CD63, and CD69 are also helpful in detecting SM in bone marrow.
Measurement of material properties of hard and soft biological tissues by means of V(z) and V(f) curves obtained with acoustic microscopy (2001)

Measurement of acoustic propagation speed (C) and attenuation (a) in biological tissues serves to enhance our understanding of how tissue composition and structure affects organ function. We applied the V(z)-technique to measurement of C in embedded cancellous bone at 1 GHz using an acoustic microscope and succeeded in recording the Cs of both longitudinal lateral waves (C<SUB>L</SUB>) and Rayleigh waves (C<SUB>R</SUB>). The former ranged between 2.33 and 4.33 km/s (mean &plusmn;SD: 3.37 &plusmn;0.61 km/s) and the latter between 1.93 and 2.07 km/s (2.00 &plusmn; 0.06 km/s), which is in the range expected on the basis of known properties of bone and acoustic field theory. With respect to soft tissue sections, the V(z)-technique is practically impossible to use, and therefore we applied the V(f)-technique to sections of chordae tendineae. Initial measurements of C and a of aortic tissue, which is well characterized, showed a C of 1.59 &plusmn; 0.04km/s and &alpha; of 0.230 &plusmn;0.001 dB/&mu;m at signal frequencies 0.95 to 1.02 GHz. These results were in agreement with those of others and the chordae subsequently revealed a mean C of 1.79 &plusmn;0.18 km/s and &alpha; of 0.220 &plusmn;0.010 dB/micrometers . The distribution of the properties across the chordal sections showed a regularly undulating pattern which followed the undulating pattern of the collagen fiber arrangement. We conclude that the V(z)- and V(f)-technique are both valuable techniques for microelastic characterization of biological tissues.
Laser-Ablative Synthesis of Stable Aqueous Solutions of Elemental Bismuth Nanoparticles for Multimodal Theranostic Applications (2020)

Elemental bismuth (Bi) nanoparticles (NPs), with the high atomic density of the Bi nuclei, could serve as efficient targeted agents for cancer treatment, with applications such as contrast agents for computed tomography (CT) imaging, sensitizers for image-guided X-ray radiotherapy, and photothermal therapy. However, the synthesis of elemental Bi NPs suitable for biological applications is difficult using conventional chemical routes. Here, we explore the fabrication of ultrapure Bi-based nanomaterials by femtosecond laser ablation from a solid Bi target in ambient liquids and characterize them by a variety of techniques, including TEM, SEM, XRD, FTIR, Raman, and optical spectroscopy. We found that laser-ablative synthesis using an elemental Bi solid target leads to the formation of spherical Bi NPs having the mean size of 20-50 nm and a low size-dispersion. The NPs prepared in water experience a fast (within a few minutes) conversion into 400-500 nm flake-like nanosheets, composed of bismuth subcarbonates, (BiO)<sub>2</sub>CO<sub>3</sub> and (BiO)<sub>4</sub>CO<sub>3</sub>(OH)<sub>2</sub>, while the NPs prepared in acetone demonstrate high elemental stability. We introduce a procedure to obtain a stable aqueous solution of elemental Bi NPs suitable for biological applications, based on the coating of Bi NPs prepared in acetone with Pluronic<sup>®</sup> F68 and their subsequent transfer to water. We also show that the laser-synthesized elemental Bi NPs, due to their vanishing band gap, exhibit remarkable absorption in the infrared range, which can be used for the activation of photothermal therapy in the near IR-to-IR window with maximum optical transparency in biological media. Exempt of any toxic synthetic by-products, laser-ablated elemental Bi NPs present a novel appealing nanoplatform for combination image-guided photoradiotherapies.
Reactions of Cl+at room temperature (1980)

The reactions of Cl+ with NH3, H2S, O2, CH3Cl, NO, COS, C2H4, H2, CH4, and N2O have been studied at room temperature using a selected ion flow tube (SIFT). No evidence was found for the presence of long-lived excited states of Cl+. Ground-state rate constants are given for the above reactions together with product ion branching ratios where applicable.
Effect of morphological structure on photosensitivity of chemically deposited PbS thin films (1980)

Chemically deposited PbS thin films have been prepared for use as infrared detectors. A systematic and elaborate study using scanning electron microscopy shows that the structure and crystallite size are related to the photosensitivity. Both the role of chemical oxidant influencing the type of conductivity and morphological details such as crystallite size distribution have been investigated. It is observed that in the absence of oxidant the average size of crystallites is about 0.9 mu m. This decreases to 0.3 mu m for the concentration of oxidant imparting maximum photosensitivity and further reduces to 0.2 mu m or less at higher concentrations. A good photosensitive film is electronically p-type and has a more uniform crystallite size distribution with relatively loose compact structure. Annealing of the films at 393K under vacuum (5*10-2 Torr) for 4-5 h affects the electronic properties considerably but does not cause any appreciable change in the structure except in smoothing the grain boundaries to a certain extent. A qualitative explanation in terms of rate of chemical reaction is offered for the morphological parameters observed in these experiments. It is also suggested that the photocharacteristics could be viewed partly as a support for barrier modulation but having its origin in the physical nature of the films.
Characterization of Fscl cDNA for a Mouse Sperm Fibrous Sheath Component1 (1995)

The fibrous sheath is a major cytoskeletal structure in the principal piece of the mammalian sperm flagellum. We have cloned a cDNA and used it to characterize the expression of mRNA for a mouse sperm fibrous sheath protein. Peptides from a tryptic digest of fibrous sheath proteins were separated by HPLC and a 31 amino acid sequence was obtained from one of the peptides. Through the use of degenerate oligonucleotide polymerase chain reaction (PCR) primers predicted from this sequence, an 80-bp product was amplified from mouse testis first-strand cDNA. This was utilized as a probe to isolate a 2.9-kb cDNA clone from a mouse round spermatid cDNA library. Sequence analysis of the cDNA clone showed that it encodes a protein with an open reading frame of 849 amino acids and includes the original peptide sequence. The predicted protein has a molecular weight of 93,795 and contains 32 cysteine residues and 32 potential phosphorylation sites. It has no significant homology with other known cytoskeletal proteins. Northern blot analysis detected an mRNA of approximately 3 kb that was abundant in round spermatids of the mouse and in testes from six other mammalian species, but not in twelve somatic tissues from the mouse. In situ hybridization analysis indicated that the mRNA is first detected in step 1-6 spermatids, is most abundant in step 8-12 spermatids, and decreases in amount in step 13-15 spermatids, suggesting that expression of the mRNA occurs in the postmeiotic phase of spermatogenesis.(ABSTRACT TRUNCATED AT 250 WORDS)
On expander codes based on hypergraphs (2003)

Expander codes where introduced in (1996) by Sipser and Spielman. These codes are related to low-density parity-check codes (LDPC-codes) from (R.G. Gallager, 1963) and other codes described in (R.M. Tanner, 1981), but with the restriction that any code symbol is involved in only two check equations. Gallager showed in (1963) that this is not suitable for constructing LDPC-codes. Therefore we generalize expander codes by using hypergraphs. Good expander graphs are obtained by using algebraic constructions from (G.A. Margulis, 1973) and (A. Lubotzky, et al., 1988). Since such constructions are not very flexible, we present a simple probabilistic method for constructing expander codes.
Learning Labeled Robot Affordance Models Using Simulations and Crowdsourcing (2020)

Affordance models are widely used in robotics to represent a robot's possible interactions with its environment. However, robot affordance models are inherently quantitative, making them difficult for humans to understand and interact with. To address this problem, previous works have constructed affordance models by grounding (connecting) them to natural language, but primarily used expert-defined actions, effects, or labels to do so. In this paper, we use short text responses provided by humans and simple randomized robot manipulation actions to construct a labeled affordance model that defines a relationship between English-language labels and robots' internal affordance representations. We first collect label data from a combination of crowdsourced real-world human-robot interactions and online user studies. We then use this data to train classifiers predicting whether or not a particular quantitative affordance will receive a specific label from a person, achieving an average affordance prediction score of 0.87 (area under Receiver Operating Characteristic curve). Our results also show that labels are more accurately predicted by affordance effects than affordance actions-a result that has been hypothesized in prior work but has never been directly tested. Finally, we develop a technique for automatically constructing a hierarchy of labels from crowdsourced data, discovering structure within the learned labels and suggesting the existence of a more universal set of affordance primitives.
Transposon mutagenesis of Rickettsia felis sca1 confers a distinct phenotype during flea infection (2022)

Since its recognition in 1994 as the causative agent of human flea-borne spotted fever, Rickettsia felis, has been detected worldwide in over 40 different arthropod species. The cat flea, Ctenocephalides felis, is a well-described biological vector of R. felis. Unique to insect-borne rickettsiae, R. felis can employ multiple routes of infection including inoculation via salivary secretions and potentially infectious flea feces into the skin of vertebrate hosts. Yet, little is known of the molecular interactions governing flea infection and subsequent transmission of R. felis. While the obligate intracellular nature of rickettsiae has hampered the function of large-scale mutagenesis strategies, studies have shown the efficiency of mariner-based transposon systems in Rickettsiales. Thus, this study aimed to assess R. felis genetic mutants in a flea transmission model to elucidate genes involved in vector infection. A Himar1 transposase was used to generate R. felis transformants, in which subsequent genome sequencing revealed a transposon insertion near the 3' end of sca1. Alterations in sca1 expression resulted in unique infection phenotypes. While the R. felis sca1::tn mutant portrayed enhanced growth kinetics compared to R. felis wild-type during in vitro culture, rickettsial loads were significantly reduced during flea infection. As a consequence of decreased rickettsial loads within infected donor fleas, R. felis sca1::tn exhibited limited transmission potential. Thus, the use of a biologically relevant model provides evidence of a defective phenotype associated with R. felis sca1::tn during flea infection.
7-Substituted 5-amino-1-cyclopropyl-6,8-difluoro-1,4-dihydro-4-oxo-3-quinolinecarboxylic acids: synthesis and biological activity of a new class of quinolone antibacterials (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT7-Substituted 5-amino-1-cyclopropyl-6,8-difluoro-1,4-dihydro-4-oxo-3-quinolinecarboxylic acids: synthesis and biological activity of a new class of quinolone antibacterialsJohn M. Domagala, Susan E. Hagen, Carl L. Heifetz, Marland P. Hutt, Thomas F. Mich, Joseph P. Sanchez, and Ashok K. TrehanCite this: J. Med. Chem. 1988, 31, 3, 503–506Publication Date (Print):March 1, 1988Publication History Published online1 May 2002Published inissue 1 March 1988https://pubs.acs.org/doi/10.1021/jm00398a003https://doi.org/10.1021/jm00398a003research-articleACS PublicationsRequest reuse permissionsArticle Views275Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Novozym 435: the “perfect” lipase immobilized biocatalyst? (2019)

Novozym 435 (N435) is a commercially available immobilized lipase produced by Novozymes with its advantages and drawbacks.