gebhart/patrepeval huggingface dataset:
Ultrasound-Stimulated Vibro-Acoustic Spectrography (1998)

An ultrasound method based on radiation force is presented for imaging the acoustic response of a material to mechanical excitation. Acoustic energy was emitted from solids and tissues in response to an oscillatory radiation force produced by interfering focused beams of ultrasound. Frequency spectra of ultrasound-stimulated acoustic emission exhibited object resonances. Raster-scanning the radiation force over the object and recording the amplitude and phase of the emitted sound resulted in data from which images related to the elastic compositions of the acoustically emitting objects could be computed. Acoustic emission signals distinguished tuning-fork resonances, submillimeter glass spheres, and calcification in excised arteries and detected object motions on the order of nanometers.
TGIF-QA: Toward Spatio-Temporal Reasoning in Visual Question Answering (2017)

Vision and language understanding has emerged as a subject undergoing intense study in Artificial Intelligence. Among many tasks in this line of research, visual question answering (VQA) has been one of the most successful ones, where the goal is to learn a model that understands visual content at region-level details and finds their associations with pairs of questions and answers in the natural language form. Despite the rapid progress in the past few years, most existing work in VQA have focused primarily on images. In this paper, we focus on extending VQA to the video domain and contribute to the literature in three important ways. First, we propose three new tasks designed specifically for video VQA, which require spatio-temporal reasoning from videos to answer questions correctly. Next, we introduce a new large-scale dataset for video VQA named TGIF-QA that extends existing VQA work with our new tasks. Finally, we propose a dual-LSTM based approach with both spatial and temporal attention, and show its effectiveness over conventional VQA techniques through empirical evaluations.
Efficient Genomic DNA Extraction from Low Target Concentration Bacterial Cultures Using SCODA DNA Extraction Technology (2010)

Methods for the extraction of nucleic acids are straightforward in instances where there is ample nucleic acid mass in the sample and contamination is minimal. However, applications in areas such as metagenomics, life science research, clinical research, and forensics, that are limited by smaller amounts of starting materials or more dilute samples, require sample preparation methods that are more efficient at extracting nucleic acids. Synchronous coefficient of drag alteration (SCODA) is a novel electrophoretic nucleic acid purification technology that has been tested successfully with both highly contaminated and dilute samples and is a promising candidate for new sample preparation challenges. In this article, as an example of SCODA's performance with limited sample material, we outline a genomic DNA (gDNA) extraction protocol from low abundance cultures of Escherichia coli DH10B. This method is equally well suited to high biomass samples.
Use of Ultrasound for Characterizing Dairy Products (2005)

It has been known for a long time that acoustic measurements offer some unique features for characterizing liquid food products in their intact state, without any preparation or destruction of the product sample. Acoustic characterization can yield information about fat content, droplet size distribution, and kinetics of product variation with time. Furthermore, acoustic methods are very attractive for on-line process control. This paper addresses several questions: Why does ultrasound attenuate when propagating through a heterogeneous system? What properties of dairy products can be extracted from such ultrasound measurements? Which measurement is better for product characterization: attenuation or sound speed? What measurement precision is required to adequately characterize product properties? What frequency range is of most value for determining these product properties?It is possible to provide answers to many of these questions using experimental data, thereby avoiding, for the moment, any complex mathematical analysis. We present several applications of acoustic spectroscopy for characterizing dairy products, including characterization of the fat content in a wide variety of dairy products; calculation of the fat droplet size distribution in milk without dilution; and calculation of water droplet size in butter, without dilution or melting.
Human Endothelial Cells Effectively Costimulate Cytokine Production by, But Not Differentiation of, Naive CD4+ T Cells (1998)

We compared costimulatory signals provided by human endothelial cells (ECs) to those provided by conventional bone marrow-derived APCs, i.e., peripheral blood-adherent mononuclear cells (PBAMCs), by measuring their effects on cytokine production by naive or memory CD4+ T cells stimulated by PHA. In these assays, ECs effectively costimulate secretion of IL-2, IFN-gamma, and IL-4 from both naive and memory CD4+ T cells, quantified by ELISA or intracellular cytokine staining. ECs, which lack B7 molecules, use predominantly leukocyte-function associated Ag 3 (LFA-3) to provide costimulation. ECs are comparable to or better than PBAMCs, which use both the LFA-3 and B7 molecules, at costimulating IL-2 and IL-4 production. ECs are less effective than PBAMCs at costimulating IFN-gamma production by naive T cells. ECs do not secrete IL-12, and addition of exogenous IL-12 enables ECs to costimulate IFN-gamma at a level comparable to that observed with PBAMCs. ECs do not promote differentiation of naive T cells to Th1-like cells, whereas PBAMCs do. Again, addition of exogenous IL-12 enables ECs to do so. Transfection of ECs to express B7-1 or B7-2 is less effective than IL-12 supplementation for restoring these responses. These experiments suggest that a deficiency in costimulation due to lack of B7 molecule expression does not fully explain the inability of ECs to activate resting naive CD4+ T cells.
72. Some 4-substituted oxazoles (1961)

A. B. A. Jansen and M. Szelke, J. Chem. Soc., 1961, 405 DOI: 10.1039/JR9610000405
Identification of the human herpesvirus 6 glycoprotein H and putative large tegument protein genes (1991)

Determination of the nucleotide sequences of two molecular clones of human herpesvirus 6 (HHV-6) (strain GS) and comparison with those of human cytomegalovirus (HCMV) has allowed the identification of the genes for the glycoprotein H (gH) and the putative large tegument protein of HHV-6. Two molecular clones of fragments of HHV-6, the BamHI-G fragment (7,981 bp) of the clone termed pZVB43 and a HindIII fragment (8,717 bp) of the clone termed pZVH14, represent approximately 10% of the HHV-6 genome (16,689). An open reading frame within the BamHI-G fragment was designated the gH gene of HHV-6 because of the extensive sequence similarity of its predicted product (79,549 Da) to the HCMV gH gene product. The predicted product (239,589 Da) of an open reading frame within clone pZVH14 showed homology to the predicted product of the proposed gene of HCMV representing the large tegument protein. Computer analyses indicated a closer relationship of the predicted peptides of these HHV-6 genes to those of HCMV than to those of the other human herpesviruses Epstein-Barr virus, herpes simplex virus type 1, and varicella-zoster virus. The gH gene was more conserved among the human herpesvirus group, while significant sequence similarity of the tegument gene could be found only with that of HCMV. The data reported here with one conserved gene (gH) and a more divergent gene (tegument) support previous reports that HHV-6 and HCMV are more closely related to each other than to the other well-characterized human herpesviruses.
Improved Cancer Therapy and Molecular Imaging with Multivalent, Multispecific Antibodies (2010)

Antibodies are highly versatile proteins with the ability to be used to target diverse compounds, such as radionuclides for imaging and therapy, or drugs and toxins for therapy, but also can be used unconjugated to elicit therapeutically beneficial responses, usually with minimal toxicity. This update describes a new procedure for forming multivalent and/or multispecific proteins, known as the dock-and-lock (DNL) technique. Developed as a procedure for preparing bispecific antibodies capable of binding divalently to a tumor antigen and monovalently to a radiolabeled hapten-peptide for pretargeted imaging and therapy, this methodology has the flexibility to create a number of other biologic agents of therapeutic interest. A variety of constructs, based on anti-CD20 and CD22 antibodies, have been made, with results showing that multispecific antibodies have very different properties from the respective parental monospecific antibodies. The technique is not restricted to antibody combination, but other biologics, such as interferon-alpha2b, have been prepared. These types of constructs not only allow small biologics to be sustained in the blood longer, but also to be selectively targeted. Thus, DNL technology is a highly flexible platform that can be used to prepare many different types of agents that could further improve cancer detection and therapy.
Expression of H-RASV12 in a zebrafish model of Costello syndrome causes cellular senescence in adult proliferating cells (2008)

Constitutively active, 'oncogenic' H-RAS can drive proliferation and transformation in human cancer, or be a potent inducer of cellular senescence. Moreover, aberrant activation of the Ras pathway owing to germline mutations can cause severe developmental disorders. In this study we have generated transgenic zebrafish that constitutively express low levels, or can be induced to express high levels, of oncogenic H-RAS. We observed that fish carrying the integrated transgene in their germline display several hallmarks of Costello syndrome, a rare genetic disease caused by activating mutations in the gene H-RAS, and can be used as a model for the disease. In Costello-like fish, low levels of oncogenic H-RAS expression are associated with both reduced proliferation and an increase in senescence markers in adult progenitor cell compartments in the brain and heart, together with activated DNA damage responses. Overexpression of H-RAS through a heat-shock-inducible promoter in larvae led to hyperproliferation, activation of the DNA damage response and tp53-dependent cell cycle arrest. Thus, oncogene-induced senescence of adult proliferating cells contributes to the development of Costello syndrome and provides an alternative pathway to transformation in the presence of widespread constitutively active H-RAS expression.
How myeloma cells escape bisphosphonate‐mediated killing: development of specific resistance with preserved sensitivity to conventional chemotherapeutics (2003)

Although amino-bisphosphonates (N-BPs) induce apoptosis of myeloma cells in vitro, most in-vivo studies fail to demonstrate a corresponding antitumour effect. This discrepancy might reflect the development of resistance to the antitumour effects of N-BP in myeloma cells when they are exposed to N-BP for a prolonged time. To test this hypothesis, two N-BP-sensitive human myeloma cell lines were continuously exposed to increasing concentrations of the N-BP alendronate for 6 weeks. During this treatment period, 10 out of 10 sublines developed reduced apoptotic and antiproliferative responses to alendronate treatment. This de novo alendronate resistance was accompanied by resistance to another N-BP (zoledronate) but not to an inhibitor of 3-hydroxy-3-methylglutaryl CoA reductase or Fas ligand. Importantly, N-BP-resistant myeloma cells also remained sensitive to conventional myeloma chemotherapeutics (melphalan, doxorubicin and vincristine). Further analysis of the N-BP-resistant cells revealed an increased activity of the N-BP-specific target enzyme farnesyl pyrophosphate synthase, without upregulation of its gene transcription. Our results suggest that continuous exposure of myeloma cells to alendronate leads to the development of N-BP resistance. This is associated with an increased activity of farnesyl pyrophosphate synthase and does not evolve from defective apoptotic pathways. Importantly, the antitumour effects of conventional myeloma chemotherapeutics are preserved in the N-BP-resistant myeloma cells.
Biocatalytic Synthesis of Vanillin (2000)

The conversions of vanillic acid and O-benzylvanillic acid to vanillin were examined by using whole cells and enzyme preparations of Nocardia sp. strain NRRL 5646. With growing cultures, vanillic acid was decarboxylated (69% yield) to guaiacol and reduced (11% yield) to vanillyl alcohol. In resting Nocardia cells in buffer, 4-O-benzylvanillic acid was converted to the corresponding alcohol product without decarboxylation. Purified Nocardia carboxylic acid reductase, an ATP and NADPH-dependent enzyme, quantitatively reduced vanillic acid to vanillin. Structures of metabolites were established by (1)H nuclear magnetic resonance and mass spectral analyses.
Paired Helical Filaments from Alzheimer Disease Brain Induce Intracellular Accumulation of Tau Protein in Aggresomes (2012)

Abnormal folding of tau protein leads to the generation of paired helical filaments (PHFs) and neurofibrillary tangles, a key neuropathological feature in Alzheimer disease and tauopathies. A specific anatomical pattern of pathological changes developing in the brain suggests that once tau pathology is initiated it propagates between neighboring neuronal cells, possibly spreading along the axonal network. We studied whether PHFs released from degenerating neurons could be taken up by surrounding cells and promote spreading of tau pathology. Neuronal and non-neuronal cells overexpressing green fluorescent protein-tagged tau (GFP-Tau) were treated with isolated fractions of human Alzheimer disease-derived PHFs for 24 h. We found that cells internalized PHFs through an endocytic mechanism and developed intracellular GFP-Tau aggregates with attributes of aggresomes. This was particularly evident by the perinuclear localization of aggregates and redistribution of the vimentin intermediate filament network and retrograde motor protein dynein. Furthermore, the content of Sarkosyl-insoluble tau, a measure of abnormal tau aggregation, increased 3-fold in PHF-treated cells. An exosome-related mechanism did not appear to be involved in the release of GFP-Tau from untreated cells. The evidence that cells can internalize PHFs, leading to formation of aggresome-like bodies, opens new therapeutic avenues to prevent propagation and spreading of tau pathology.
SINGLE CYCLE RESONANT CONVERTERS : A NEW FAMILY OF RESONANT CONVERTERS (1989)

A new family of resonant converters, which is named as Sin­gle Cycle Resonant Convertcr [SCRC] is proposed Conventional 6-basic DC/DC converters are simplified and unified using the concepts of switch so called PWM switch By adding additional LC resonant elements to the switch a general resonant switch cell which includes newly proposed Single Cycle Resonant Switch[SCRS] cell, can be made. The conven­tional 6-basic dc/dc converters can be easily changed to corresponding resonant converters simply by replacing each switch cell with the proposed general resonant switch cell. As a special case, a new family of SCRC's which have the same charac­teristics as those of conventional converters with zero cross switching capabilities, is obtained using the SCRS cell According to type of switches, they can be applied to fixed frequency AC/AC converter(electronic slidacs) as well as DC/DC converter. The steady state operation and characteristics of buck type SCRC is analyzed, and verified through the simulation.
On the matched filter bound of transmit diversity techniques (2002)

Diversity transmission at the base station is an effective technique to combat the adverse effects of fading. This is suggested as an alternative to diversity at the terminal, thereby reducing the implementation complexity. We evaluate the matched filter bound (MFB) for two transmit diversity schemes with two transmit antennas: delay diversity and space-time block coding. Theoretical results show that even though the expected value of the matched filter bound is the same for both approaches, the diversity order exhibited by the space-time block coding approach is larger than that of delay diversity for any frequency selective channel with more than 1 tap. In fact for a frequency selective channel with L+1 taps with equal energy, the diversity order exhibited by the space-time coding MFB is 2/spl times/(L+1) while that of delay diversity is L+2.
Cross-Polarization/Magic Angle Spinning (CP/MAS) 13C Nuclear Magnetic Resonance (NMR) Analysis of Chars from Alkaline-Treated Pyrolyzed Softwood (2008)

Pyrolysis chemistry of alkaline-treated loblolly pine is investigated in this study. The pyrolysis experiments were accomplished under an argon atmosphere at 200−400 °C, to determine the effect of alkaline treatment on the char formation. Solid-state cross-polarization/magic angle spinning (CP/MAS) 13C nuclear magnetic resonance (NMR) spectroscopy was used to characterize the chars of the treated and untreated loblolly pine. These studies showed that, in the samples treated with NaOH, there is a shift in the chemical composition of the thermally modified char from cellulosic/hemicellulosic structures to more aryl C structures. At 300 °C, carbohydrate peaks were still present in the char of untreated wood but not in the char of the alkaline-treated wood. This indicated that the addition of NaOH enhanced the thermal degradation of the sugars in the pine sawdust. Our studies also showed that there was an emergence of an aliphatic peak around 12 ppm in the treated pine, which is absent in the spectra of the untreated pine. In addition to the relative increase in aryl and aliphatic C species, there is also an increase in the signals seen for the carbonyl species centered around 210 ppm at the higher end of the temperature range in this study for the treated samples. This investigation showed that solid-state NMR provided a facile methodology to investigate the types of changes that occur to wood chars during pyrolysis.
Antibody-dependent cell-mediated cytotoxicity (ADCC) in Aujeszky's disease (1979)

Antibody-dependent cell-mediated cytotoxicity (ADCC) was studied using as targets 51Cr-labelled Vero cells infected with the Bartha strain of Aujeszky's disease virus (ADV). Using hyperimmune anti-ADV serum to sensitize the targets, porcine leukocytes from dextran-sedimented blood were found to be efficient effector cells yielding maximal 51Cr release by 16 hours. Whilst complement-dependent cytotoxic antibody could be demonstrated no enhancement of ADCC by complement was found. The sera of pigs vaccinated i.m. with Bartha virus were titrated in ADCC using leukocytes as effector cells and the results compared with those obtained by virus neutralization. ADCC proved to be a much more sensitive technique and might, therefore, provide the basis for a reliable diagnostic test. Partially purified lymphocytes and polymorphonuclear leukocytes from blood and peritoneal exudates, and macrophages from exudates were found to mediate ADCC with hyperimmune serum, but differences were observed in the efficiency and timing of their cytotoxic effects.
Copyright protection of images using robust digital signatures (2002)

A method for copyright protection of digital images is presented. Copyright protection is achieved by embedding an "invisible" signal, known as digital signature, in the digital image. Signature casting is performed in the spatial domain by slightly modifying the intensity level of randomly selected image pixels. Signature detection is done by comparing the mean intensity value of the marked pixels against that of the not marked pixels. Statistical hypothesis testing is used for this purpose. The signature can be designed in such a way that it is resistant to JPEG compression and lowpass filtering. This is done by minimizing the energy content of the signature signal in higher frequencies. Experiments on real image data verify the effectiveness of the method.
Effect of branched-chain amino acids on muscle atrophy in cancer cachexia (2007)

In the present study, the BCAAs (branched-chain amino acids) leucine and valine caused a significant suppression in the loss of body weight in mice bearing a cachexia-inducing tumour (MAC16), producing a significant increase in skeletal muscle wet weight, through an increase in protein synthesis and a decrease in degradation. Leucine attenuated the increased phosphorylation of PKR (double-stranded-RNA-dependent protein kinase) and eIF2alpha (eukaryotic initiation factor 2alpha) in skeletal muscle of mice bearing the MAC16 tumour, due to an increased expression of PP1 (protein phosphatase 1). Weight loss in mice bearing the MAC16 tumour was associated with an increased amount of eIF4E bound to its binding protein 4E-BP1 (eIF4E-binding protein 1), and a progressive decrease in the active eIF4G-eIF4E complex due to hypophosphorylation of 4E-BP1. This may be due to a reduction in the phosphorylation of mTOR (mammalian target of rapamycin), which may also be responsible for the decreased phosphorylation of p70(S6k) (70 kDa ribosomal S6 kinase). There was also a 5-fold increase in the phosphorylation of eEF2 (eukaryotic elongation factor 2), which would also decrease protein synthesis through a decrease in translation elongation. Treatment with leucine increased phosphorylation of mTOR and p70(S6k), caused hyperphosphorylation of 4E-BP1, reduced the amount of 4E-BP1 associated with eIF4E and caused an increase in the eIF4G-eIF4E complex, together with a reduction in phosphorylation of eEF2. These changes would be expected to increase protein synthesis, whereas a reduction in the activation of PKR would be expected to attenuate the increased protein degradation.
The effect of intranasal fluticasone propionate irrigations on salivary cortisol, intraocular pressure, and posterior subcapsular cataracts in postsurgical chronic rhinosinusitis patients (2013)

Fluticasone propionate irrigations did not suppress salivary cortisol levels or result in ocular changes. Irrigation with fluticasone propionate 3 mg in 240 mL saline twice daily may be a safe alternative to other intranasal or systemic corticosteroid treatments for chronic rhinosinusitis patients.
Adenovirus 5 E2 transcription unit: an E1A-inducible promoter with an essential element that functions independently of position or orientation. (1984)

Utilizing deletion mutants of a plasmid containing the adenovirus E2 gene, an E1A-inducible transcription unit, we determined the promoter sequences required for full expression in transient transfection assays. Wild-type expression was obtained from plasmids containing only 79 nucleotides of upstream sequence relative to the transcription initiation site. Removal of an additional nine nucleotides lowered expression 10-fold, and deletion to -59 resulted in near total loss of transcription. Wild-type levels of expression were restored to a -28 deletion mutant by insertion of the sequence from -21 to -262 from the wild-type promoter at the -28 position, in either orientation, even though when inserted in the opposite orientation the relevant sequences were ca. 270 nucleotides upstream from their normal position. Finally, this sequence could be placed at a distance of 4,000 nucleotides from the E2 cap site and still retain near total function. Thus, the E2 promoter element can function independent of orientation and position, properties characteristic of enhancer elements.