gebhart/patrepeval huggingface dataset:
From captions to visual concepts and back (2015)

This paper presents a novel approach for automatically generating image descriptions: visual detectors, language models, and multimodal similarity models learnt directly from a dataset of image captions. We use multiple instance learning to train visual detectors for words that commonly occur in captions, including many different parts of speech such as nouns, verbs, and adjectives. The word detector outputs serve as conditional inputs to a maximum-entropy language model. The language model learns from a set of over 400,000 image descriptions to capture the statistics of word usage. We capture global semantics by re-ranking caption candidates using sentence-level features and a deep multimodal similarity model. Our system is state-of-the-art on the official Microsoft COCO benchmark, producing a BLEU-4 score of 29.1%. When human judges compare the system captions to ones written by other people on our held-out test set, the system captions have equal or better quality 34% of the time.
Fast two-photon imaging of subcellular voltage dynamics in neuronal tissue with genetically encoded indicators (2017)

Monitoring voltage dynamics in defined neurons deep in the brain is critical for unraveling the function of neuronal circuits but is challenging due to the limited performance of existing tools. In particular, while genetically encoded voltage indicators have shown promise for optical detection of voltage transients, many indicators exhibit low sensitivity when imaged under two-photon illumination. Previous studies thus fell short of visualizing voltage dynamics in individual neurons in single trials. Here, we report ASAP2s, a novel voltage indicator with improved sensitivity. By imaging ASAP2s using random-access multi-photon microscopy, we demonstrate robust single-trial detection of action potentials in organotypic slice cultures. We also show that ASAP2s enables two-photon imaging of graded potentials in organotypic slice cultures and in <i>Drosophila</i>. These results demonstrate that the combination of ASAP2s and fast two-photon imaging methods enables detection of neural electrical activity with subcellular spatial resolution and millisecond-timescale precision.
Practical Asymmetric Synthesis of (S)-4-Ethyl-7,8-dihydro-4-hydroxy-1H-pyrano[3,4-f]indolizine- 3,6,10(4H)-trione, a Key Intermediate for the Synthesis of Irinotecan and Other Camptothecin Analogs (1997)

A practical asymmetric synthesis of (S) 4-ethyl-7,8-dihydro-4-hydroxy-1H-pyrano[3,4-f]indolizine-3,6,10(4H)-trione (1), a versatile intermediate for the synthesis of camptothecin analogs, was developed. Commercially available citrazinic acid is converted in four steps into the 2-chloro-6-methoxypyridine 5. An ortho-directed metalation followed by reaction with a formamide produces an aldehyde with the required 2,3,4,6-substituted pyridine (6) with high regioselectivity. After refunctionalization of the aldehyde, the chloropyridine is converted into an ester by a facile palladium-mediated carbonylation reaction. Wittig reaction and racemic osmylation produce the diol 16 which is resolved by an efficient lipase resolution to an ee > 99%, and a one-pot recycle of the unwanted diol enantiomer was developed. A series of high-yielding oxidation and deprotection steps convert (S)-16 into the pyridone 25, which is then converted into 1 with an ee > 99.6%.
Efficient Immunization Strategies for Computer Networks and Populations (2003)

We present an effective immunization strategy for computer networks and populations with broad and, in particular, scale-free degree distributions. The proposed strategy, acquaintance immunization, calls for the immunization of random acquaintances of random nodes (individuals). The strategy requires no knowledge of the node degrees or any other global knowledge, as do targeted immunization strategies. We study analytically the critical threshold for complete immunization. We also study the strategy with respect to the susceptible-infected-removed epidemiological model. We show that the immunization threshold is dramatically reduced with the suggested strategy, for all studied cases.
A Minimal Peptide Scaffold for β-Turn Display:  Optimizing a Strand Position in Disulfide-Cyclized β-Hairpins (2000)

Phage display of peptide libraries has become a powerful tool for the evolution of novel ligands that bind virtually any protein target. However, the rules governing conformational preferences in natural peptides are poorly understood, and consequently, structure-activity relationships in these molecules can be difficult to define. In an effort to simplify this process, we have investigated the structural stability of 10-residue, disulfide-constrained beta-hairpins and assessed their suitability as scaffolds for beta-turn display. Using disulfide formation as a probe, relative free energies of folding were measured for 19 peptides that differ at a one strand position. A tryptophan substitution promotes folding to a remarkable degree. NMR analysis confirms that the measured energies correlate well with the degree of beta-hairpin structure in the disulfide-cyclized peptides. Reexamination of a subset of the strand substitutions in peptides with different turn sequences reveals linear free energy relationships, indicating that turns and strand-strand interactions make independent, additive contributions to hairpin stability. Significantly, the tryptophan strand substitution is highly stabilizing with all turns tested, and peptides that display model turns or the less stable C'-C' ' turn of CD4 on this tryptophan "stem" are highly structured beta-hairpins in water. Thus, we have developed a small, structured beta-turn scaffold, containing only natural L-amino acids, that may be used to display peptide libraries of limited conformational diversity on phage.
Foil Air/Gas Bearing Technology — An Overview (1997)

This paper summarizes the chronological progress of foil air bearings for turbomachinery during the last 25 years. Descriptions of various machines which are in production are provided. The foil bearing air cycle machine on the 747 aircraft has demonstrated an MTBF (mean time between failure) in excess of 100,000 hours. Many advantages of foil air bearings are noted. Various designs of foil air bearings presently in use and their relative merits are described. Analytical methods, their limitations, and their relationships with test results are noted. Descriptions of various machines built and tested in process fluids being gases, other than air, and cryogenic liquids are described. Conclusions are drawn that various high speed turbomachines including high temperature applications can be designed and developed using foil air bearings which will increase efficiency and reduce cost of these machines.
Presentation of Tactile Pleasantness Using Airborne Ultrasound (2021)

In this study, we investigate the physical condition to produce a pleasant feeling by airborne ultrasound stimulus. Since the midair haptic stimulus can precisely control its position and force amplitude, we can evaluate the effect on pleasantness by various spatiotemporal patterns with high reproducibility. In the experiment, we presented a stroke tactile stimulus on a forearm and a palm. We changed the vibration frequency from 0 to 200 Hz while changing the movement speed from 10 to 300 mm/s, evaluating the pleasantness using Likert scale. For objective evaluation, we measured the skin potential level. The experimental result shows that non-modulated stimuli with their speed of 300 mm/s are felt the most pleasant stimulus, while the objective index showed no significant differences.
Attempts to Classify Herbicola Group-Enterobacter agglomerans Strains by Deoxyribonucleic Acid Hybridization and Phenotypic Tests (1984)

There are seven names on the Approved Lists of Bacterial Names that have been treated as partial or total synonyms for strains belonging to the Enterobacter agglomerans-Herbicola group of Erwinia species complex. A total of 124 strains belonging to this complex, isolated mainly from plant and human sources, were studied by deoxyribonucleic acid relatedness and by a variety of biochemical tests. Ninety of these strains fell into 13 deoxyribonucleic acid hybridization groups (2 to 13 strains per group), and the remaining 34 strains did not fit into any hybridization group. Nine of the hybridization groups could be separated biochemically, whereas four hybridization groups could not. Our results point out the inadequacy of the classification schemes presently used for these organisms, the inadequacy of the present nomenclature, the extreme diversity of the strains presently classified in the Enterobacter agglomerans-Herbicola group of Erwinia species complex, and the need for additional, in-depth studies of these organisms.
Whole brain resting-state analysis reveals decreased functional connectivity in major depression (2010)

Recently, both increases and decreases in resting-state functional connectivity have been found in major depression. However, these studies only assessed functional connectivity within a specific network or between a few regions of interest, while comorbidity and use of medication was not always controlled for. Therefore, the aim of the current study was to investigate whole-brain functional connectivity, unbiased by a priori definition of regions or networks of interest, in medication-free depressive patients without comorbidity. We analyzed resting-state fMRI data of 19 medication-free patients with a recent diagnosis of major depression (within 6 months before inclusion) and no comorbidity, and 19 age- and gender-matched controls. Independent component analysis was employed on the concatenated data sets of all participants. Thirteen functionally relevant networks were identified, describing the entire study sample. Next, individual representations of the networks were created using a dual regression method. Statistical inference was subsequently done on these spatial maps using voxel-wise permutation tests. Abnormal functional connectivity was found within three resting-state networks in depression: (1) decreased bilateral amygdala and left anterior insula connectivity in an affective network, (2) reduced connectivity of the left frontal pole in a network associated with attention and working memory, and (3) decreased bilateral lingual gyrus connectivity within ventromedial visual regions. None of these effects were associated with symptom severity or gray matter density. We found abnormal resting-state functional connectivity not previously associated with major depression, which might relate to abnormal affect regulation and mild cognitive deficits, both associated with the symptomatology of the disorder.
The Diverse Roles of Extracellular Leucine-rich Repeat-containing Receptor-like Proteins in Plants (2010)

Plant cells use various types of cell surface receptor molecules to sense extracellular signals and modulate cell-to-cell communication in many biological processes. Extracellular leucine-rich repeat (eLRR) receptor-like proteins (RLPs) represent an important class of such cell surface receptors. RLPs differ from receptor-like kinases (RLKs), which compose the largest class of cell surface receptors in many plant species, because they lack a cytoplasmic kinase domain. RLPs play roles in both developmental processes and disease resistance. A total of 57 RLP encoding genes has been identified in Arabidopsis. Two of them, CLAVATA2 (CLV2) and Too Many Mouths (TMM) have a function in meristem maintenance and stomatal distribution, respectively, whereas few others act in basal defense against pathogens. Although the function of most RLPs in Arabidopsis remains unclear, considerable progress has been made in understanding RLP functioning and signaling over the years. This review focuses on the function of RLPs in plants. Furthermore, the function of distinct RLP domains and the role of conserved residues important for perception and ligand specificity are discussed. The role of RLP proteins in multimeric complexes to sense biotic and abiotic extracellular signals is also addressed.
New insight into drug-DNA interactions at individual drug binding sites probed by RNA polymerase during active transcription of the DNA. (1990)

An in vitro transcription assay has been used to probe drug-DNA interactions during active transcription of the DNA. The method relies upon the formation of a stable, synchronized population of initiated transcripts comprising a short length of RNA, achieved by the absence of one nucleotide in the initiation mixture. Subsequent equilibration of the transcription complex with drug, followed by elongation of the initiated transcripts, yields lengths of RNA determined by transcription up to each drug-occupied site. A variety of site-specific phenomena have been observed, including delayed termination of transcription 5-10 bp downstream of actinomycin binding sites; 10-20% probability of termination at most echinomycin sites; drug residence-time-dependent termination of bacteriophage polymerases; enhanced residence time compared to physicochemical measurement of drug-DNA dissociation rates. The use of two counter-directed promoters separated by 100 bp results in a sensitive bidirectional transcription footprinting procedure able to resolve adjacent drug sites separated by only 1 bp. The significance of the method of in vitro transcription is the ability to quantitate a range of parameters describing individual drug sites in situations where multiple drug-DNA interactions exist.
Production of nitric oxide by murine bone marrow cells. Inverse correlation with cellular proliferation (1992)

The present studies were designed to assess the ability of primary cultures of bone marrow cells to produce nitric oxide. We found that two inflammatory stimuli, IFN-gamma and LPS, were potent inducers of nitric oxide production by bone marrow cells. In addition, the CSF granulocyte-macrophage (GM)-CSF and IL-3 as well as TNF-alpha, while inactive by themselves, were synergistic with LPS and IFN-gamma in inducing nitric oxide production. Maximal effects were observed with combinations of GM-CSF and LPS. Nitric oxide production by bone marrow cells was found to be dependent on the presence of L-arginine in the culture medium and inhibitable by NG-monomethyl-L-arginine and L-canavanine, two nitric oxide synthase inhibitors. Nitric oxide produced by the cells was also suppressed by TGF-beta 1 and the tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate. Separation of bone marrow cells by density gradient centrifugation and flow cytometry revealed that the granulocyte-containing fraction was largely responsible for nitric oxide production. In additional experiments we found that treatment of bone marrow cells with GM-CSF significantly stimulated bone marrow cell growth. In contrast, the combination of GM-CSF and LPS or IFN-gamma markedly suppressed cellular proliferation. This suppression was completely reversed by treatment of the cells with NG-monomethyl-L-arginine. Taken together, these data demonstrate that various inflammatory stimuli and cytokines induce nitric oxide production by primary cultures of bone marrow cells and that this mediator may play a role in the regulation of bone marrow cell growth and development.
Synthesis and antimicrobial activity of some bis-quinazoline derivatives. (1997)

The hitherto unknown bis[quinazolin-4-one-2-yl]-m-phenylene (2d), and its 3-N-substituted derivatives were prepared from the corresponding bis[3,1-benzoxazin-4-one-2-yl]-m-phenylene (1) as precursor. The quinazolinone derivative 2d was converted into bis[quinazolin-4-thioxo-2-yl]-m-phenylene (3) via different routes, bis[4-chloroquinazolin-2-yl]-m-phenylene (8) and bis[4-hydrazinoquinazolin-2-yl]-m-phenylene (11), respectively. The structures of the compounds 2, 3, 8, and 11 were supported by elemental, spectroscopic analysis as well as, chemical proofs. Biological activities of some of the produced compounds were evaluated.
Synthesis of queuine, the base of naturally occurring hypermodified nucleoside (queuosine), and its analogues (1988)

A convenient new method for synthesizing queuine (1){2-amino-5-[(1S,2R,3S)-2,3-dihydroxycyclopent-4-enylaminomethyl]pyrrolo[2,3-d]pyrimidin-4(3H)-one}, the base of the naturally occurring hypermodified nucleoside, queuosine, present in certain transfer RNAs, and its biosynthetic precursor, 2-amino-5-aminomethylpyrrolo[2,3-d] pyrimidin-4(3H)-one (2)(Pre Q1 base), was successfully exploited. This method involved two critical reactions: the Mannich reaction using dibenzylamine–formaldehyde of 2-acylaminopyrrolo[2,3-d] pyrimidin-4(3H)-one (7), which resulted in the selective introduction of the dibenzylaminomethyl group into the 5-position of (7), and an amine exchange reaction of the 5-dibenzylamine function in the resulting Mannich base (17) with (1S,2R,3S)-2,3-isopropylidenedioxycyclopent-4-enylamine, which yielded the desired queuine (1). Similar reaction of (17) with ammonia gave the biosynthetic precursor of queuine (2)(Pre Q1 base). Thus, a series of queuine analogues with structural variations in their 5-aminomethyl side-chains was synthesized by the amine exchange reaction of (17) with appropriate amines or by acylation of (2) with appropriate acylating agents.
A heparin-binding protein involved in inhibition of smooth-muscle cell proliferation (1988)

A heparin-binding protein was isolated from bovine uteri and purified to homogeneity. This protein appears as a double band of approx. 78 kDa in SDS/polyacrylamide-gel electrophoresis and has an isoelectric point of 5.2. The binding of heparin to this protein is saturable. No other glycosaminoglycan from mammalian tissue, such as hyaluronic acid, chondroitin sulphate, dermatan sulphate or keratan sulphate, binds to the 78 kDa protein. Dextran sulphate binds in a non-saturable fashion. Certain heparan sulphate polysaccharide structures are required for binding to the 78 kDa protein. Some proteoheparan sulphates, such as endothelial cell-surface proteoheparan sulphate, show only weak interaction with the 78 kDa protein in contrast with a basement-membrane proteoheparan sulphate from HR-9 cells. Antibodies against the 78 kDa protein inhibit binding of proteoheparan [35S]sulphate from basement membranes to smooth-muscle cells. Conventional antibodies, Fab fragments and some monoclonal antibodies, inhibit smooth-muscle cell proliferation in a similar range as that observed for heparin. The protein was detected in a variety of tissues and cells but not in blood cells. A possible role of this protein as a receptor for heparin or heparan sulphate and its function in the control of the arterial wall structure are discussed.
The variant call format and VCFtools (2011)

http://vcftools.sourceforge.net
Terminal Ligand Influence on the Electronic Structure and Intrinsic Redox Properties of the [Fe4S4]2+ Cubane Clusters (2004)

We used photoelectron spectroscopy (PES) to study how the terminal ligands influence the electronic structure and redox properties of the [4Fe-4S] cubane in several series of ligand-substituted analogue complexes: [Fe(4)S(4)Cl(4-x)(CN)(x)](2-), [Fe(4)S(4)Cl(4-x)(SCN)(x)](2-), [Fe(4)S(4)Cl(4-x)(OAc)(x)](2-), [Fe(4)S(4)(SC(2)H(5))(4-x)(OPr)(x)](2-), and [Fe(4)S(4)(SC(2)H(5))(4-x)Cl(x)](2-) (x = 0-4). All the ligand-substituted complexes gave similar PES spectral features as the parents, suggesting that the mixed-ligand coordination does not perturb the electronic structure of the cubane core significantly. The terminal ligands, however, have profound effects on the electron binding energies of the cubane and induce significant shifts of the PES spectra, increasing in the order SC(2)H(5)(-) --> Cl(-) --> OAc(-)/OPr(-) --> CN(-) --> SCN(-). A linear relationship between the electron binding energies and the substitution number x was observed for each series, indicating that each ligand contributes independently and additively to the total binding energy. The electron binding energies of the gaseous complexes represent their intrinsic oxidation energies; the observed linear dependence on x is consistent with similar observations on the redox potentials of mixed-ligand cubane complexes in solution. The current study reveals the electrostatic nature of the interaction between the [4Fe-4S] cubane core and its coordination environment and provides further evidence for the electronic and structural stability of the cubane core and its robustness as a structural and functional unit in Fe-S proteins.
Cells previously identified as retinal stem cells are pigmented ciliary epithelial cells (2009)

It was previously reported that the ciliary epithelium (CE) of the mammalian eye contains a rare population of cells that could produce clonogenic self-renewing pigmented spheres in culture. Based on their ability to up-regulate genes found in retinal neurons, it was concluded that these sphere-forming cells were retinal stem cells. This conclusion raised the possibility that CE-derived retinal stem cells could help to restore vision in the millions of people worldwide who suffer from blindness associated with retinal degeneration. We report here that human and mouse CE-derived spheres are made up of proliferating pigmented ciliary epithelial cells rather than retinal stem cells. All of the cells in the CE-derived spheres, including the proliferating cells, had molecular, cellular, and morphological features of differentiated pigmented CE cells. These differentiated cells ectopically expressed nestin when exposed to growth factors and low levels of pan-neuronal markers such as beta-III-tubulin. Although the cells aberrantly expressed neuronal markers, they retained their pigmented CE cell morphology and failed to differentiate into retinal neurons in vitro or in vivo. Our results provide an example of a differentiated cell type that can form clonogenic spheres in culture, self-renew, express progenitor cell markers, and initiate neuronal differentiation that is not a stem or progenitor cell. More importantly, our findings highlight the importance of shifting the focus away from studies on CE-derived spheres for cell-based therapies to restore vision in the degenerating retina and improving techniques for using ES cells or retinal precursor cells.
Automatic virtual machine configuration for database workloads (2008)

Virtual machine monitors are becoming popular tools for the deployment of database management systems and other enterprise software applications. In this paper, we consider a common resource consolidation scenario, in which several database management system instances, each running in a virtual machine, are sharing a common pool of physical computing resources. We address the problem of optimizing the performance of these database management systems by controlling the configurations of the virtual machines in which they run. These virtual machine configurations determine how the shared physical resources will be allocated to the different database instances. We introduce a virtualization design advisor that uses information about the anticipated workloads of each of the database systems to recommend workload-specific configurations offine. Furthermore, runtime information collected after the deployment of the recommended configurations can be used to refine the recommendation. To estimate the effect of a particular resource allocation on workload performance, we use the query optimizer in a new what-if mode. We have implemented our approach using both PostgreSQL and DB2, and we have experimentally evaluated its effectiveness using DSS and OLTP workloads.
Pattern of recurrence following complete resection of esophageal carcinoma and factors predictive of recurrent disease (2003)

Depth of tumor invasion should be used to identify patients who will have recurrence within 12 months of operation, so that these patients may be either entered into trials of multimodality treatment or offered nonsurgical palliation.