gebhart/patrepeval huggingface dataset:
The Eukaryotic Translation Initiation Factor 4E Controls Lettuce Susceptibility to the Potyvirus<i>Lettuce mosaic virus</i>  (2003)

The eIF4E and eIF(iso)4E cDNAs from several genotypes of lettuce (Lactuca sativa) that are susceptible, tolerant, or resistant to infection by Lettuce mosaic virus (LMV; genus Potyvirus) were cloned and sequenced. Although Ls-eIF(iso)4E was monomorphic in sequence, three types of Ls-eIF4E differed by point sequence variations, and a short in-frame deletion in one of them. The amino acid variations specific to Ls-eIF4E(1) and Ls-eIF4E(2) were predicted to be located near the cap recognition pocket in a homology-based tridimensional protein model. In 19 lettuce genotypes, including two near-isogenic pairs, there was a strict correlation between these three allelic types and the presence or absence of the recessive LMV resistance genes mo1(1) and mo1(2). Ls-eIF4E(1) and mo1(1) cosegregated in the progeny of two separate crosses between susceptible genotypes and an mo1(1) genotype. Finally, transient ectopic expression of Ls-eIF4E restored systemic accumulation of a green fluorescent protein-tagged LMV in LMV-resistant mo1(2) plants and a recombinant LMV expressing Ls-eIF4E degrees from its genome, but not Ls-eIF4E(1) or Ls-eIF(iso)4E, accumulated and produced symptoms in mo1(1) or mo1(2) genotypes. Therefore, sequence correlation, tight genetic linkage, and functional complementation strongly suggest that eIF4E plays a role in the LMV cycle in lettuce and that mo1(1) and mo1(2) are alleles coding for forms of eIF4E unable or less effective to fulfill this role. More generally, the isoforms of eIF4E appear to be host factors involved in the cycle of potyviruses in plants, probably through a general mechanism yet to be clarified.
Towards Audio-Visual On-line Diarization Of Participants In Group Meetings (2008)

Abstract. We propose a fully automated, unsupervised, and non-intrusive method of identifying the current speaker audio-visually in a group conversation. This is achieved without specialized hardware, user interaction, or prior assignment of microphones to participants. Speakers are identified acoustically using a novel on-line speaker diarization approach. The output is then used to find the corresponding person in a four-camera video stream by approximating individual activity with computationally efficient features. We present results showing the robustness of the association on over 4.5 hours of non-scripted audio-visual meeting data. 1
Assembly of synthetic laminin peptides into a triple-stranded coiled-coil structure. (1994)

Laminin, a large multidomain glycoprotein specific to basement membranes, is a heterotrimer with alpha, beta, and gamma chains held together in an alpha-helical coiled-coil structure. Synthetic peptides comprising two 51-mers (B1 and B2) from the beta 1 and gamma 1 subunits and a 55-mer (M) from alpha 2 were used to study the molecular mechanisms in laminin chain assembly. Using the synthetic peptides in various mixing experiments, the heterotrimer (B1-B2-M) was preferentially produced. The thermal stability of the heterotrimer increased dramatically (by approximately 20 degrees C) over that of the B1-B2 heterodimer as measured by circular dichroism (CD) spectroscopy. The B1-B1 homodimer (Tm = 60 degrees C) showed higher thermal stability when compared to B1-B2 and B2-B2 dimers. However, the B1 + B2 mixture produced principally the B1-B2 heterodimer. These results suggested that the preferential formations of heterodimer was regulated by kinetic interactions between each chain. The B2 and M peptides have many hydrophobic isoleucine residues which were replaced by leucines. These substitutions were predicted to favor an alpha-helical conformation and a higher propensity for zipper formation. B2L and ML, in which all isoleucine residues were replaced by leucine, showed significantly increased alpha-helicities. While B2L was able to form heterodimers and heterotrimers similar to B2, ML was not able to participate in heterotrimer formation as efficiently as the M peptide. The thermal stability of B1-B2L was comparable to that of B1-B2, but B2L and/or ML containing trimers showed lower thermal stability than B1-B2-M. These results suggest that the isoleucine residues in the alpha 2 and gamma 1 chains are critical for stabilizing the heteromeric triple-stranded coiled-coil structure.
STEM and Sustainability: Creating Aviation Professional Change Agents (2019)

With the evolution of the workforce and the growing needs of the aviation industry, a clear need for concrete sustainability initiatives and actions have emerged. Sustainability in this sense becomes a matter of survival. For this reason, in this chapter, we will attempt to close three gaps in current sustainability studies: Theory vs practice, intention vs behavior, and education vs workplace. Our purpose is to develop a ‘simple’ strategy for integrating all three pillars of sustainability into STEM HE programs that create authentic engagement and real buy-in from the students that are then replicated in the workplace. Based on the literature and our own research projects, we will make concrete recommendations on how sustainability could be integrated and address the workforce opportunities and challenges that this entails.
Passive transfer of protection against cholera toxin in rat intestine (1984)

Passive transfer between rates of protection against cholera toxin (CT) was studied. Extracts of various organs, obtained from CT-immunized rats, were injected intravenously into non-immunized recipient rats. The ability of the extracts to inhibit CT-induced secretion in ligated jejunal loop were tested. A significant inhibition of the response to CT was achieved by extracts from hypophysis, brain and jejunal mucosa. Extracts from pancreas, spleen or adrenal glands were without effect, as were all extracts obtained from control rats. The antisecretory effects of the hypophysis extracts became intensified with increasing numbers of immunizations, and the antisecretory effect was most pronounced when the extract was injected immediately before the CT challenge. The active component of the hypophysis extract was heat-labile and negatively charged, suggesting an acidic protein as the mediator of the protective effect against CT.
Comparison of low complexity turbo-like coding structures (2002)

In this paper we consider the serially concatenated codes where the inner code is an accumulator (rate 1 differential encoder). To compare different constructions we calculated the tangential sphere bounds on word and bit error probabilities for maximum likelihood (ML) decoding and used these bounds as references for simulations. Based on these studies we introduce novel turbo-like schemes called accumulated woven convolutional codes (AWCC) which in some cases provide advantages over considered turbo-like coding structures.
<b>Biocompatibility Studies of the Anaconda Stent-Graft and Observations of Nitinol Corrosion Resistance</b> (2004)

This Anaconda stent-graft has demonstrated its ability to exclude arterial aneurysms. The device used in this study was an experimental prototype, and the manufacturer has incorporated new immobilization features into the model for clinical use. The constituent materials appear to be suitable in terms of biocompatibility, biofunctionality, and short-term durability.
Enhancement of Electric Field inside Metallodielectric Metamaterial (2006)

A metallodielectric metamaterial have been investigated by using FDTD (Finite Difference Time Domain) method and fabricated with a resin based rapid prototyping machine. It was composed of 7 layers of parallel periodic copper wires embedded in resin. The metallodielectric metamaterial shows a different near field distribution with direction of incident electric field E that causes different electromagnetic (EM) properties. In particular, when incident electric field E is vertical to the wires inside resin, we observe enhacement of electric field in the vicinity of the embedded metal wires according to the incident direction of electirc field E as compared with dielectirc wihout metal wires. The enhanced electric field by the embedded metal wire is responsible for the enhancement of effective dielectric constant.
Connection without caution? The role of mobile phone involvement in predicting young people's intentions to use a mobile phone while driving (2012)

The present study examined the predictors of the intentions of young people aged between 17 and 24 years (N = 196) to use their mobile phone while driving. Using convenience sampling, drivers were recruited at petrol station travel centres to complete a cross-sectional survey. The Theory of Planned Behaviour constructs of attitude, subjective norm, and perceived behavioural control (PBC) were measured, as well as mobile phone involvement - a construct based on behavioural addiction components to reflect people's cognitive and behavioural interaction with their mobile phone. Attitudes, PBC, and mobile phone involvement predicted young people's intentions to use their mobile phone while driving, highlighting the need for interventions to address the perceived rewards and costs of the behaviour and to challenge the potentially powerful need to be constantly connected with others by technology irrespective of the associated dangers.
Donor-Derived Mesenchymal Stem Cells Suppress Alloreactivity of Kidney Transplant Patients (2009)

Donor MSC significantly inhibited the proliferation of alloactivated recipient T cells before and after kidney transplantation. We believe these findings should encourage MSC-based intervention in clinical organ transplantation.
Rapid nucleic acid diagnostics for the detection of antimicrobial resistance in Gram-negative bacteria: is it time for a paradigm shift? (2014)

A key component for tackling the ever more serious antimicrobial resistance problem in Gram-negative bacteria is the introduction of rapid nucleic acid diagnostics. Successful incorporation of new diagnostic technologies has the potential benefit of improving not only patient treatment but also infection control and antimicrobial stewardship. However, there are still many hurdles to overcome, such as the complexity of resistance mechanisms in Gram-negative bacteria, the discrepancy between phenotype and genotype and the difficulty in distinguishing pathogens from background commensals. A small number of manufacturers have introduced tests to the market that concentrate partly or specifically on resistance determinants in Gram-negative bacteria. These are currently predominantly based on different types of PCR technology. The development of new technologies, such as whole-genome sequencing and the combination of MALDI-TOF with PCR, holds much promise for the introduction of improved diagnostics for the future.
Long Term Profile Variability of Double-Peaked Emission Lines in AGNs (2003)

An increasing number of AGNs exhibit broad, double-peaked Balmer emission lines, which are thought to arise from the outer regions of the accretion disk which fuels the AGN. The line profiles are observed to vary on a characteristic timescales of 5-10 years. The variability is not a reverberation effect; it is a manifestation of physical changes in the disk. Our group has monitored a set of 20 double-peaked emitters for the past 8 years (longer for some objects). Here, we characterize the variability of the double-peaked H alpha line profiles in five objects from our sample. By experimenting with simple models, we find that disks with a single precessing spiral arm are able to reproduce many of the variability trends that are seen in the data.
Voice based biometric authentication using collapsing classes discriminative space transform (2014)

A novel method of voice based biometric authentication system is proposed in this paper. The proposed method utilizes the distance between i-vectors to minimize the intra-class variation and maximizing the inter-class variation. This problem is formulated as a convex optimization problem, such that the i-vectors of the same speaker collapsed to a single point. On the other hand, i-vectors of the impostors are pushed away by a large margin. Additionally, the distance matrix is itself learned using the data (i-vectors of the speakers). The transformation matrix obtained herein linearly transforms the input i-vectors into a new discriminative space. The i-vectors in the new transformed space give improved speaker authentication performance. Speaker authentication experiments are conducted on NIST 2004 and YOHO speaker verification databases. Experimental results obtained indicate a reasonable improvement in the performance, when compared to state of the art voice based biometric authentication systems.
Metals and Alzheimer's disease (2006)

There is increasing evidence to support a role for both the amyloid beta-protein precursor (AbetaPP) and its proteolytic fragment, amyloid beta (Abeta), in metal ion homeostasis. Furthermore, metal ions such as zinc and copper can interact with both AbetaPP and Abeta to potentiate Alzheimer's disease by participating in the aggregation of these normal cellular proteins and in the generation of reactive oxygen species. In addition, metal ions may interact on several other AD-related pathways, including those involved in neurofibrillary tangle formation, secretase cleavage of AbetaPP and proteolytic degradation of Abeta. As such, a dysregulation of metal ion homeostasis, as occurs with both aging and in AD, may foster an environment that can both precipitate and accelerate degenerative conditions such as AD. This offers a broad biochemical front for novel therapeutic interventions.
Calcitonin Receptor-stimulating Peptide, a New Member of the Calcitonin Gene-related Peptide Family (2003)

We isolated a novel biologically active peptide, designated calcitonin receptor-stimulating peptide (CRSP), from the acid extract of the porcine brain by monitoring cAMP production in the porcine kidney cell line LLC-PK(1). Determination of the amino acid sequence and cDNA analysis encoding a CRSP precursor showed that this peptide has approximately 60% identity in the amino acid sequence with human calcitonin gene-related peptide type-alpha (alphaCGRP), type-beta (betaCGRP), and porcine CGRP. Northern blot analysis and radioimmunoassay demonstrated that CRSP is expressed mainly in the thyroid gland and the central nervous system, in which the calcitonin receptor was abundantly expressed. Synthetic CRSP elicited a potent stimulatory effect on the cAMP production in LLC-PK(1) cells. Although it shows significant sequence similarity with CGRPs, this peptide did not elicit cAMP elevation in cells that endogenously expressed a CGRP receptor or an adrenomedullin receptor or were transfected with either of these recombinant receptors. Administration of CRSP into anesthetized rats did not alter the blood pressure but induced a transient decrease in the plasma calcium concentration. In fact, this peptide potently increased the intracellular cAMP concentration in COS-7 cells that expressed the recombinant calcitonin receptor. These unique properties indicate that CRSP is not a porcine counterpart of betaCGRP and probably elicits its biological effects via the calcitonin receptor.
An X-Band Balanced Fin-Line Mixer (1978)

The fin-line technique has been used in a balanced 9-11-GHz mixer with a 70-MHz intermediate frequency. The mixer without an IF amplifier has an available conversion loss of less than 5 dB with a 3.8-dB minimum and a SSB noise figure of less than 6.9 dB with a 5.3-dB minimum. The mixer is tunable by variable shorts. It is possible to scale the device to millimeter-wave frequencies.
A phase I dose-escalation and immune biomarker study of intravenous FF-10832, liposomal gemcitabine, in patients with advanced solid tumors. (2019)

TPS3163 Background: FF-10832 (832) is a liposomal formulation of gemcitabine (GEM) that demonstrates a prolonged half-life and preferential uptake in tumor vs normal tissues and marrow in pre-clinical models. Macrophage uptake has been shown in the tumor microenvironment (TME), with subsequent GEM release in tumor cells. This relative selectivity and anti-tumor immunological changes observed in the TME may lead to decreased toxicity and increased efficacy compared to GEM. Ferumoxytol (FMX) may be a surrogate for nanoparticle penetration into tissue and is being examined as a potential correlate for activity. Methods: This ongoing Phase 1, 3+3 dose-escalation study of 832 will determine the safety profile, maximum tolerated dose, dose-limiting toxicities (DLT) and recommended Phase 2 dose, and will be followed by expansion. Enrollment of up to 60 patients (pts) with advanced solid tumors is planned. Pre-treatment (tx) FMX MRI scans are performed, followed by 832 administration on Days 1 &15 of each 28-day cycle until disease progression or unacceptable toxicity. In addition to standard biomarker and imaging evaluations, change in macrophage polarity, myeloid-derived suppressor cell (MDSC) and regulatory T cell populations are being investigatedin peripheral blood and tumor tissue. Clinical trial information: NCT03440450.
An investigation of feedback guided dynamic scheduling of nested loops (2002)

In previous papers (J.M. Bull, 1998; J.M. Bull et al., 1996; R.W. Ford et al., 1994) feedback guided loop scheduling algorithms have been shown to be very effective for certain loop scheduling problems. In particular they perform well for problems that involve a sequential outer loop and a parallel inner loop, and timing information gathered during one execution of the parallel inner loop can be used to inform the scheduling of the subsequent execution of this loop. The authors consider the extension of these feedback guided scheduling algorithms to the more important case of nested parallel loops, again within a sequential outer loop. We describe three alternative ways of scheduling nested loops; two are based on reducing the nested loops to a single loop and applying one-dimensional techniques; the third addresses the multidimensionality of the nested loops directly.
The N-Glycome of Human Plasma (2010)

N-linked glycans isolated from human plasma proteins have been profiled and sequenced by mass spectrometry using an ion trap instrument (ITMSn). The released glycans were prepared as reduced, methylated analogues and directly infused into a chip-based nanoelectrospray ionization system and analyzed by ITMSn. The resulting mass profiles (MS1) of IgG-depleted and nondepleted plasma samples were contrasted and these results were again compared with recent literature reports. Before depletion, approximately 50 independent glycan ions were detected; this more than doubled to 106 after depletion. The mass range profiled was 1-5 kDa which included many doubly and triply charged ions that were resolved by higher MS resolution. Selected ions in the depleted sample were disassembled to define their detailed structure providing a high-performance sequencing result. The simplicity of this nonchromatographic, direct infusion and gas-phase structural characterization compares most favorably with the latest reports using alternative instrumentation and adjunct techniques.
Studies on synthetic LuxR solo hybrids (2015)

A sub-group of LuxR family of proteins that plays important roles in quorum sensing, a process of cell-cell communication, is widespread in proteobacteria. These proteins have a typical modular structure consisting of N-ter autoinducer binding and C-ter helix-turn-helix (HTH) DNA binding domains. The autoinducer binding domain recognizes signaling molecules which are most often N-acyl homoserine lactones (AHLs) but could also be other novel and yet unidentified molecules. In this study we carried out a series of specific domain swapping and promoter activation experiments as a first step to engineer synthetic signaling modules, taking advantage of the modularity and the versatile/diverse signal specificities of LuxR proteins. In our experiments the N-ter domains from different LuxR homologs were either interchanged or placed in tandem followed by a C-ter domain. The rational design of the hybrid proteins was supported by a structure-based homology modeling studies of three members of the LuxR family (i.e., LasR, RhlR, and OryR being chosen for their unique ligand binding specificities) and of selected chimeras. Our results reveal that these LuxR homologs were able to activate promoter elements that were not their usual targets; we also show that hybrid LuxR proteins retained the ability to recognize the signal specific for their N- ter autoinducer binding domain. However, the activity of hybrid LuxR proteins containing two AHL binding domains in tandem appears to depend on the organization and nature of the introduced domains. This study represents advances in the understanding of the modularity of LuxR proteins and provides additional possibilities to use hybrid proteins in both basic and applied synthetic biology based research.
Unsupervised image ranking (2009)

In the paper, we propose and test an unsupervised approach for image ranking. Prior solutions are based on image content and the similarity graph connecting images. We generalize this idea by directly estimating the likelihood of each photo in a feature space. We hypothesize the photos at the peaks of this distribution are the most likely photos for any given category and therefore these images are the most representative.
Denoising scheme for realistic digital photos from unknown sources (2009)

This paper targets denoising of digital photos taken by cameras with unknown sensor parameters and image processing pipeline. Common noise characteristics in such images originate from camera-internal processing, such as demosaicing, tone mapping, and JPEG compression. Three of the noise characteristics that are not adequately addressed by existing denoising algorithms are spatially correlated low-frequency noise, strong signal dependency of the noise level and high levels of the chrominance noise relative to the luminance noise. We propose a generic scheme that extends existing denoisers such as the bilateral filter to account for all the problems above. Our solution combines a novel progressive pyramidal filtering scheme to address the correlated noise, filter adaptation via local noise level estimation and luminance-guided chrominance filtering to address the low-SNR of the chrominance channels. We demonstrate the effectiveness of our solution for challenging realistic noisy photos.
Jak2 Tyrosine Kinase and Cancer: How Good Cells Get HiJAKed (2007)

Cloned in 1992, Jak2 tyrosine kinase has emerged as a critical molecule in mammalian development, physiology, and disease. Here, we will review the early history of Jak2 as it pertains to its role in classical cellular signaling. We also review how specific structural determinants within Jak2 dictate its overall function. Finally, we will review relatively recent literature as it pertains to the role of Jak2 in neoplastic growth as well as the identification of novel Jak2 inhibitors. It is our hope that by reviewing these specific areas, we will have a better understanding of the role of Jak2 in cancer, and in turn, we may have a better idea as to how to block aberrant Jak2 function.
Efficient Synthesis of Highly Luminescent Copper Indium Sulfide-Based Core/Shell Nanocrystals with Surprisingly Long-Lived Emission (2011)

We report an efficient synthesis of copper indium sulfide nanocrystals with strong photoluminescence in the visible to near-infrared. This method can produce gram quantities of material with a chemical yield in excess of 90% with minimal solvent waste. The overgrowth of as-prepared nanocrystals with a few monolayers of CdS or ZnS increases the photoluminescence quantum efficiency to > 80%. On the basis of time-resolved spectroscopic studies of core/shell particles, we conclude that the emission is due to an optical transition that couples a quantized electron state to a localized hole state, which is most likely associated with an internal defect.