gebhart/patrepeval huggingface dataset:
Metasurface for Water-to-Air Sound Transmission (2018)

Effective transmission of sound from water to air is crucial for the enhancement of the detection sensitivity of underwater sound. However, only 0.1% of the acoustic energy is naturally transmitted at such a boundary. At audio frequencies, quarter-wave plates or multilayered antireflection coatings are too bulky for practical use for such enhancement. Here we present an acoustic metasurface of a thickness of only ∼λ/100, where λ is the wavelength in air, consisting of an array of meta-atoms that each contain a set of membranes and an air-filled cavity. We experimentally demonstrate that such a meta-atom increases the transmission of sound at ∼700 Hz by 2 orders of magnitude, allowing about 30% of the incident acoustic power from water to be transmitted into air. Applications include underwater sonic sensing and communication.
Volume flow calculations on gas leaks imaged with infrared gas-correlation (2012)

Two methods for volume flow calculation from images of methane leakages to the atmosphere are presented. The images contain calibrated gas concentration × path length pixel information, and are processed with a block matching method and a theoretical velocity field method. Results from known methane flow in two laboratory setups and one unknown real leakage from a gas processing plant are compared with the image processing methods. The methods are generic and can be implemented in common infrared systems for gas visualization. This work provides a new tool for estimating and reporting volume flow emissions from gas processing plants to the authorities.
Codon choice in genes depends on flanking sequence information—implications for theoretical reverse translation (2008)

Algorithms for theoretical reverse translation have direct applications in degenerate PCR. The conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. In the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. From this, we created a method for theoretical reverse translation that includes information from flanking residues of the protein in question. Our method, named the neighbor correlation method (NCM) and its enhancement, the consensus-NCM (c-NCM) performed significantly better than the conventional codon-usage statistic method (CSM). Using the methods NCM and c-NCM, we were able to increase the average sequence identity from 77% up to 81%. Furthermore, we revealed a significant increase in coverage, at 80% identity, from < 20% (CSM) to > 75% (c-NCM). The algorithms, their applications and implications are discussed herein.
Atomic structure of mutant PPARγ LBD complexed with 15d‐PGJ2: Novel modulation mechanism of PPARγ/RXRα function by covalently bound ligands (2008)

15-deoxy-Delta(12,14)-prostaglandin J(2) (15d-PGJ(2)) activates a nuclear receptor heterodimer, peroxisome proliferators-activated receptor gamma (PPARgamma)/ retinoid X receptor (RXRalpha) through covalent binding to Cys285 in PPARgamma ligand-binding domain (LBD). Here, we present the 1.9A crystal structure of C285S mutant LBD complexed with 15d-PGJ(2), corresponding to the non-covalently bound state. The ligand lies adjacent to a hydrogen-bond network around the helix H2 and the nearby beta-sheet. Comparisons with previous structures clarified the relationships between PPARgamma function and conformational alterations of LBD during the process of covalently binding ligands, such as 15d-PGJ(2), and thus suggested a mechanism, by which these ligands modulate PPARgamma/RXRalpha function through conformational changes of the loop following helix H2' and the beta-sheet.
The Design of Rate-Compatible Protograph LDPC Codes (2012)

This paper presents a simple yet effective method for designing nested families of LDPC codes. Rate compatible codes are essential for many communication applications, e.g. hybrid automatic repeat request (HARQ) systems, and their design is nontrivial due to the difficulty of simultaneously guaranteeing the quality of several related codes. Puncturing can be used to generate rate-compatible LDPC codes, but it produces a gap to capacity that, in practice, often significantly exceeds the gap of the mother code. We propose an alternative method based on successively extending a high-rate protograph. The resulting codes not only inherit the advantages of protograph codes, namely low encoding complexity and efficient decoding algorithms, but also cover a wide range of rates and have very good performance with iterative decoding thresholds that are within 0.2 dB of their capacity limits.
Direct gene transfer into mouse diaphragm (1993)

Direct gene transfer into skeletal muscle is a potential therapeutic strategy for inherited primary myopathies such as Duchenne muscular dystrophy (DMD). In order to affect the life-expectancy of these patients, it will be necessary to carry out gene therapy on the diaphragm. To this end, we report efficient introduction of pure recombinant plasmid DNA into the mouse diaphragm, without causing significant damage. Application of this approach to the diaphragm of the mdx mouse will provide information on the potential usefulness of gene therapy for the treatment of DMD patients.
Protein Transfer of Glycosyl-Phosphatidylinositol (GPI)-Modified Murine B7–1 and B7–2 Costimulators (1999)

The feasibility of using protein transfer as a means for enhancing the immunogenicity of murine tumor cells was evaluated. Glycosyl-phosphatidylinositol (GPI)-modified variants of the murine costimulators B7-1 (CD80) and B7-2 (CD86), designated B7-1.GPI and B7-2.GPI, respectively, were immunoaffinity-purified from CHO-K1 cells transfected with glutamine synthetase amplification/expression constructs encoding each of these chimeric proteins. The proteins, once purified in detergent-depleted pseudomicelles, were exogenously incorporated into the membranes of several different murine tumor lines (EL-4, SMUCC-1, BW5147.3, P815, Ag104A, and EMT6). Successful membrane painting with the B7.GPI proteins was documented by immunofluorescence and flow cytometry, and membrane integration was verified by demonstrating that the reincorporated proteins were phosphatidylinositol-phospholipase C-sensitive, glycosyl-phosphatidylinositol-phospholipase D-resistant, and refractory to removal with dimyristylphosphatidylcholine vesicles. Significantly, B7-1.GPI and B7-2.GPI could be together copainted onto EL-4 cell surfaces with no interference observed between the two. A standard in vitro proliferation assay was used to show that both of the B7.GPI proteins retained costimulator function after membrane reincorporation. These findings further validate the therapeutic potential of protein-transferred costimulator.GPIs and pave the way for their combinatorial use in animal tumor models.
Properties of pertussis toxin mutant PT-9K/129G after formaldehyde treatment (1991)

Formaldehyde treatment is a method routinely used to detoxify diphtheria, tetanus, and pertussis toxins as well as other molecules suitable for vaccine production. To investigate whether chemical detoxification alters the immunological properties of vaccine components, we have treated the pertussis toxin mutant PT-9K/129G with formaldehyde and tested the properties of the resulting molecules. Very low concentrations of formaldehyde stabilize the molecule without affecting the physicochemical and immunological parameters. Increasing doses of formaldehyde abolish the mitogenic and hemagglutinating activities of PT-9K/129G. At the same time, the molecule loses the ability to be recognized by a monoclonal antibody specific for a major protective epitope on the S1 subunit of pertussis toxin and its affinity for anti-pertussis toxin polyclonal antibodies is also reduced. In marked contrast, the ability of PT-9K/129G to be recognized by human T-cell clones is not affected by Formalin treatment. In vivo, the formaldehyde-treated molecules induce amounts of specific antibodies comparable with those of untreated molecules but significantly lower levels of toxin-neutralizing antibodies. Furthermore, the formaldehyde-treated molecules also show a reduced protective activity in the intracerebral challenge assay.
Molecular targeting of the epidermal growth factor receptor for neutron capture therapy of gliomas. (2002)

Success of boron neutron capture therapy (BNCT) is dependent on cellular and molecular targeting of sufficient amounts of boron-10 to sustain a lethal (10)B (n, alpha) (7)Li capture reaction. The purpose of the present study was to determine the efficacy of boronated epidermal growth factor (EGF) either alone or in combination with boronophenylalanine (BPA) as delivery agents for an epidermal growth factor receptor (EGFR) -positive glioma, designated F98(EGFR). A heavily boronated precision macromolecule [boronated starburst dendrimer (BSD)] was chemically linked to EGF by heterobifunctional reagents. Either F98 wild-type (F98(WT)) receptor (-) or EGFR gene-transfected F98(EGFR) cells, which expressed 5 x 10(5) receptor sites/cell, were stereotactically implanted into the brains of Fischer rats, and 2 weeks later biodistribution studies were initiated. For biodistribution studies rats received an intratumoral (i.t.) injection of (125)I-labeled BSD-EGF and were euthanized either 6 or 24 h later. At 6 h, equivalent amounts of BSD-EGF were detected in F98(EGFR) and F98(WT) tumors. Persistence of the bioconjugate in F98(EGFR) tumors was specifically determined by EGFR expression. By 24 h 33.2% of injected dose/g of EGF-BSD was retained by F98(EGFR) gliomas compared with 9.4% % of injected dose/g in F98(WT) gliomas, and the corresponding boron concentrations were 21.1 microg/g and 9.2 microg/g, respectively. Boron concentrations in normal brain, blood, liver, kidneys, and spleen all were at nondetectable levels (<0.5 microg/g). On the basis of these results, BNCT was initiated at the Brookhaven National Laboratory Medical Research Reactor. Two weeks after implantation of 10(3) F98(EGFR) or F98(WT) tumor cells, rats received an i.t. injection of BSD-EGF (approximately 60 microg (10)B/approximately 15 microg EGF) either alone or in combination with i.v. BPA (500 mg/kg). Rats were irradiated at the Brookhaven Medical Research Reactor 24 h after i.t. injection, which was timed to coincide with 2.5 h after i.v. injection of BPA for those animals that received both capture agents. Untreated control rats had a mean survival time (MST) +/- SE of 27 +/- 1 day, and irradiated controls had a MST of 31 +/- 1 day. Animals bearing F98(EGFR) gliomas, which had received i.t. BSD-EGF and BNCT, had a MST of 45 +/- 5 days compared with 33 +/- 2 days for animals bearing F98(WT) tumors (P = 0.0032), and rats that received i.t. BSD-EGF in combination with i.v. BPA had a MST of 57 +/- 8 days compared with 39 +/- 2 days for i.v. BPA alone (P = 0.016). Our data are the first to show in vivo efficacy of BNCT using a high molecular weight boronated bioconjugate to target amplified EGFR expressed on gliomas, and they provide a platform for the future development of combinations of high and low molecular weight agents for BNCT.
Opposing motor activities are required for the organization of the mammalian mitotic spindle pole. (1996)

We use both in vitro and in vivo approaches to examine the roles of Eg5 (kinesin-related protein), cytoplasmic dynein, and dynactin in the organization of the microtubules and the localization of NuMA (Nu-clear protein that associates with the Mitotic Apparatus) at the polar ends of the mammalian mitotic spindle. Perturbation of the function of Eg5 through either immunodepletion from a cell free system for assembly of mitotic asters or antibody microinjection into cultured cells leads to organized astral microtubule arrays with expanded polar regions in which the minus ends of the microtubules emanate from a ring-like structure that contains NuMA. Conversely, perturbation of the function of cytoplasmic dynein or dynactin through either specific immunodepletition from the cell free system or expression of a dominant negative subunit of dynactin in cultured cells results in the complete lack of organization of microtubules and the failure to efficiently concentrate the NuMA protein despite its association with the microtubules. Simultaneous immunodepletion of these proteins from the cell free system for mitotic aster assembly indicates that the plus end-directed activity of Eg5 antagonizes the minus end-directed activity of cytoplasmic dynein and a minus end-directed activity associated with NuMA during the organization of the microtubules into a morphologic pole. Taken together, these results demonstrate that the unique organization of the minus ends of microtubules and the localization of NuMA at the polar ends of the mammalian mitotic spindle can be accomplished in a centrosome-independent manner by the opposing activities of plus end- and minus end-directed motors.
Dietary Unsaturated Long-Chain Fatty Acids Modify D-Glucose Absorption in Weaning Rats (2005)

These results indicate that dietary long-chain polyunsaturated fatty acid supplementation can restore, in part, the kinetic characteristics of intestinal D-glucose absorption in pups from mothers maintained on a low-unsaturated fatty acid diet.
RANTES gene polymorphism in polymyalgia rheumatica, giant cell arteritis and rheumatoid arthritis. (2000)

Three red-fleshed apple cultivars (Malus 'Geneva': GFV-03, Hungarian hybrid: GFV-04, Malus pumila Niedwetzkyana: GFV-05) were investigated for their chemical composition by sHS-SPME-GC-MS and HPLC-DAD-MS/MS analytical techniques. In cultivars GFV-03 and GFV-05 sesquiterpene α-farnesene were dominant while the alphatic esters were present mostly in traces. In GFV-04 - the new disease resistant advanced selection of the Hungarian apple breeding program - hexanol and hexyl 2-methylbutanoate were present in larger amounts while the amount of α-farnesene was lower than the other two cultivars. Using HPLC-DAD-MS/MS four phenolic acid derivatives, four anthocyanins, six flavonoids of quercetin derivatives and two dihydrochalcone phloretin glycosides were identified or characterized among the detected sixteen phenolic compounds.
Participation of Lipopolysaccharide Genes in the Determination of the Enterobacterial Common Antigen: Analysis of R Mutants of Salmonella minnesota (1974)

A series of R (rough) Salmonella minnesota mutants with rfb, rfe, and rfa mutations leading to various defects in the biosynthesis of cell wall lipopolysaccharide was analyzed as to their enterobacterial common antigen (CA) content. All mutants that had functional rfe genes were CA(+) as is the wild-type parent. This includes mutants with the most defective lipopolysaccharide core types, demonstrating that core structures are not a necessary part of CA. All rfe(-) mutants (complete lipopolysaccharide core, defective synthesis of O side chains) were defective in the synthesis of CA. A smooth strain was accidentally found to be CA(-); the mutation responsible for this defect was also located, like rfe, very close to ilv.
Epirubicin-encapsulated long-circulating thermosensitive liposome improves pharmacokinetics and antitumor therapeutic efficacy in animals (2010)

In the present work, a long-circulating epirubicin hydrochloride (EPI)-containing thermosensitive liposome aiming at antitumor therapy, DPPC/MSPC/DSPG/DSPE-mPEG(2000) (EPI-LTSL), was developed and evaluated. Nonthermosensitive and traditional liposomes, HSPC/cholesterol/DSPG/DSPE-mPEG(2000) (EPI-NTSL) and HSPC/cholesterol (EPI-LIP), were also prepared at the same time for comparison. Temperature-dependent EPI release from loaded liposomes in vitro was characterized by the fluorescence method. Different liposome preparations were administered in rats by intravenous injection at the same dosage of 12 mg·kg(-1). EPI and internal standard daunorubicin hydrochloride (DAU) were analyzed by high-performance liquid chromatography and verified by LC tandem mass spectrometry. In the pharmacodynamics study, the EPI-LTSL was combined with local hyperthermia for target-specific delivery to the anesthetized and tumor-bearing mice. According to the in vitro results, more than 90% of loaded EPI was released from MSPC-containing liposome (EPI-LTSL) within 4 minutes at 43°C, while at 37°C, less than 5% was released beyond 60 minutes. However, less than 5% of drug was released at 43°C for the other two liposomes without MSPC (EPI-NTSL and EPI-LIP). The results of the pharmacokinetics study in rats showed that not only the circulation time of EPI was prolonged significantly, but also the concentration in vivo was promoted for EPI-LTSL, compared to EPI-NTSL and EPI-solution. The mean tumor inhibitory rate for EPI-LTSL, EPI-NTSL, and EPI-solution were 61.1, 39.6, and 43.1%, respectively.
Application of H and G Indices to Quantify Scientific Productivity of Physicists at JNU, India (2014)

The study aims to quantify the scientific productivity of Physicists using Scientometric h-index and g-index indicators. Paper also identifies that h and g are complementary to each other and g ≥h (1.5 times of h). The most productive and highly cited physicists and their average citation per item at JNU are identified. Also the study enlists the best ten high impact papers published during 2007-2011. Questionnaire was used to know research papers published (2007-2011) by the physicists at JNU. These papers were cross checked for originality, accuracy and completeness from web of science, Scopus, and by visiting journals online. Quantification of scientific productivity of physicists states that Satyabrata Patnaik occupies best three ranks in all categories which make him the high impact and most cited author among others. There is a variation in rankings according to different order h, g and g/h. The study helps to know the research trends of past and present scientific activities of Physicists at JNU
Seizing the Treasure: Transferring Knowledge in Invoice Analysis (2009)

This paper deals with the transfer of knowledge on invoice document layout and extraction strategies, collected by users of the invoice recognition software smartFIX over several years of productive use, to other user's systems. The results of a project analyzing this 'treasure' of knowledge and putting it to use in the smartFIX system are presented. The evaluation shows that this transfer of knowledge using state-of-the-art techniques in transfer learning achieves significantly higher initial recognition rates than the unaugmented system, delivering instant economic advantages by reducing accountant personnel workload.
Interactions of Polyclonal and Monoclonal Anti-Glycoprotein 120 Antibodies with Oligomeric Glycoprotein 120-Glycoprotein 41 Complexes of a Primary HIV Type 1 Isolate: Relationship to Neutralization (1998)

We have studied antibody reactivity with monomeric and oligomeric forms of the gp120 envelope glycoprotein from the macrophage-tropic primary virus, HIV-1 JR-FL. We find that the correlation between oligomer reactivity and virus neutralization is not absolute for MAbs to epitopes overlapping the CD4-binding site on gp120. An MAb (205-46-9) with very limited neutralizing ability for JR-FL binds about as avidly to oligomeric JR-FL envelope glycoproteins as the strongly neutralizing IgG1b12 MAb does. In addition, neutralizing and nonneutralizing sera from HIV-1-infected people are similar in their reactivities to oligomeric JR-FL envelope glycoproteins; the correlation between oligomer reactivity and virus neutralization is weak. Although oligomer reactivity of an anti-gp120 antibody is necessary for virus neutralization, it is not always sufficient to cause it.
Tn4563 transposition in Streptomyces coelicolor and its application to isolation of new morphological mutants (1991)

The Tn3-like transposon Tn4556 (and its derivatives Tn4560 and Tn4563) has been used for insertion mapping of genetic loci cloned on plasmids, but it has been difficult to obtain chromosomal insertions, largely because of the lack of a strong selection against transposon donor molecules. In this communication, we report two efficient selection techniques for transposition and their use in the isolation of chromosomal insertion mutations. A number of independent Streptomyces coelicolor morphological mutants (bld and whi) were obtained. Two of the bld mutations were mapped to locations on the chromosome by SCP1-mediated conjugation; at least one mutation, bld-5m1, appears to define a novel locus involved in control of S. coelicolor morphogenesis and antibiotic production.
Roles of vestibular nuclei for bodily balance (2008)

The purpose of this paper is to give an account of the vestibular nuclei from the point of view of phylogeny, behaviors, and neural networks of the vestibular nuclei. In the early vertebrates, the vestibular endorgans developed by isolation of the lateral line organ from the body surface. Although vestibular control based on inertial inputs works ideally under a stationary space, it breaks down in moving spaces. To compensate for the shortcoming, discomfort (motion sickness) was utilized to avoid moving spaces. Along with progress of locomotion, the vestibular cerebellum developed as a supplementary route of the vestibular nuclei to stabilize the gaze and posture; the flocculus for visual-inertial integration, and the uvula-nodulus for gravito-inertial integration. Further, the vestibular cerebellum (vermis) and the somatically arranged lateral vestibular nucleus developed for coordination of posture and four-limb locomotion. The superior vestibular nucleus is distributed centrally by the canal fibers and flocculus fibers of visual origin, and peripherally by the uvula-nodulus fibers of otolith origin. The nucleus carries spatial rotation with gravito-inertial axis to the ocular motor nuclei. Body balance is maintained by a somatic-to-spatial transformation of the coordinates, that is, transfer of contents of the cerebellum-fastigial-and-vestibular nuclues routes to the vestibular nucleus-motor nucleus routes. Thus, gaze and posture are stable when spatial coordinates remain still in space, but they become unstable when the coordinates are moving in space.
High-speed bulk InGaAsP-InP electroabsorption modulators with bandwidth in excess of 20 GHz (1990)

Bulk InGaAsP-InP electroabsorption optical modulators with high extinction ratio, low drive voltage, and high modulation bandwidth at lambda =1.3 mu m are reported. The devices have a tapered-fiber-to-modulator-to-tapered-fiber extinction ratio greater than 20 dB at a drive voltage of <5 V. Very low capacitance modulators (<0.2 pF) were fabricated using SiO/sub 2/ bonding pad isolation, resulting in a measured electrical modulation bandwidth in excess of 20 GHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Phase 3 Trial of l -Glutamine in Sickle Cell Disease (2018)

Oxidative stress contributes to the complex pathophysiology of sickle cell disease. Oral therapy with pharmaceutical
Face Image Quality Assessment Based on Learning to Rank (2014)

Face image quality is an important factor affecting the accuracy of automatic face recognition. It is usually possible for practical recognition systems to capture multiple face images from each subject. Selecting face images with high quality for recognition is a promising stratagem for improving the system performance. We propose a learning to rank based framework for assessing the face image quality. The proposed method is simple and can adapt to different recognition methods. Experimental result demonstrates its effectiveness in improving the robustness of face detection and recognition.
Translating Videos to Natural Language Using Deep Recurrent Neural Networks (2015)

Subhashini Venugopalan, Huijuan Xu, Jeff Donahue, Marcus Rohrbach, Raymond Mooney, Kate Saenko. Proceedings of the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2015.
Methods in Molecular Biology, Volume 302: HANDBOOK OF ELISPOT: METHODS AND PROTOCOLS (2005)

Immunology and Cell Biology (2005) 83, 586; doi:10.1111/j.1440‐1711.2005.01381.x