gebhart/patrepeval huggingface dataset:
Expression of an Expansin Gene Is Correlated with Root Elongation in Soybean  (2003)

Expansin is a family of proteins that catalyze long-term expansion of cell walls and has been considered a principal protein that affects cell expansion in plants. We have identified the first root-specific expansin gene in soybean (Glycine max), GmEXP1, which may be responsible for root elongation. Expression levels of GmEXP1 were very high in the roots of 1- to 5-d-old seedlings, in which rapid root elongation takes place. Furthermore, GmEXP1 mRNA was most abundant in the root tip region, where cell elongation occurs, but scarce in the region of maturation, where cell elongation ceases, implying that its expression is closely related to root development processes. In situ hybridization showed that GmEXP1 transcripts were preferentially present in the epidermal cells and underlying cell layers in the root tip of the primary and secondary roots. Ectopic expression of GmEXP1 accelerated the root growth of transgenic tobacco (Nicotiana tabacum) seedlings, and the roots showed insensitivity to obstacle-touching stress. These results imply that the GmEXP1 gene plays an important role in root development in soybean, especially in the elongation and/or initiation of the primary and secondary roots.
Design, Synthesis, and Antiviral Evaluation of 2-Deoxy-D-Ribosides of Substituted Benzimidazoles as Potential Agents for Human Cytomegalovirus Infections (2000)

Stereoselective glycosylation of 2,5,6-trichlorobenzimidazole (1b), 2-bromo-5,6-dichlorobenzimidazole (1c), 5,6-dichlorobenzimidazole (1d), 5,6-dichlorobenzimidazole-2-thione (1e), 5,6-dichloro-2-(methylthio)benzimidazole (1f), 2-(benzylthio)-5,6-dichlorobenzimidazole (1g), and 2-chloro-5,6-dimethylbenzimidazole (1h) with 2-deoxy-3,5-di-O-p-toluoyl-alpha-D-erythro-pentofuranosyl chloride was achieved to give the desired beta nucleosides 2b-h. Subsequent deprotection afforded the corresponding free beta-D-2-deoxyribosides 3b-h. The 2-methoxy derivative 3i was synthesized by the treatment of 2b with methanolic sodium methoxide. Displacement of the 2-chloro group of 2b with lithium azide followed by a removal of the protective groups gave the 2-azido-5,6-dichlorobenzimidazole derivative (5). The 2-amino derivative (6) was obtained by hydrogenolysis of 5 over Raney nickel. 5,6-Dichloro-2-isopropylamino-1-(2-deoxy-beta-D-erythro- pentofuranosyl)benzimidazole (10) was prepared using 2'-deoxyuridine (7), N-deoxyribofuranosyl transferase and 1d followed by functionalization of the C2 position. Antiviral evaluation of target compounds established that compounds 3b and 3c were active against human cytomegalovirus (HCMV) at non-cytotoxic concentrations. The activity of these 2-deoxy ribosides, however, was less than the activity of the parent riboside, 2,5,6-trichloro-1-beta-D-ribofuranosylbenzimidazole (TCRB). Compared to TCRB, 3b and 3c were somewhat more cytotoxic and active against herpes simplex virus type 1. Compounds 3d-i with other substituents in the 2-position were inactive against both viruses and non-cytotoxic. In contrast, compounds with amine substituents in the 2-position (5, 6, 10) were active against HCMV albeit less so than TCRB. These results establish that 2-deoxy-D-ribosyl benzimidazoles are less active against the DNA virus HCMV than are the corresponding D-ribosides.
Synthesis and characterization of π-conjugated peptide-based supramolecular materials (2012)

We describe the synthesis, characterization, and fabrication of bioelectronic materials derived from small oligopeptides containing π-conjugated subunits directly embedded into peptide backbones. The rapid incorporation of π-conjugated subunits directly into peptide backbones was accomplished through an on-resin dimerization procedure recently explored in our research. We investigated these peptides’ abilities to self-assemble in aqueous environments into 1D nanostructures with intimate π–π interactions. Finally, we discuss a simple processing method to develop aligned networks of 1D π-conjugated peptide nanostructures where the resulting electronic and photophysical properties are altered as a direct impact of the aligned π-conjugated network.
Development of industrial yeast strains for efficient xylose fermentation in lignocellulosic material (2012)

Fermentation at large industrial scale poses several challenges for the fermenting microorganism to handle. Thus, for an efficient production it is desirable to have robust and efficient strains, which can cope with the specific conditions in the process. For bioethanol production by yeast from lignocellulosic material, one of the largest challenges is the mixture of sugars and the content of inhibitory compounds in the material. Wild-type strains of Saccharomyces cerevisiae can only convert hexose sugars but not the pentoses, xylose and arabinose, which may be present in these materials. However, strains have been genetically modified to allow for xylose conversion, but their performance need to be improved in terms of rate and efficiency. During the pre-treatment of lignocellulosic material the inhibitory compounds are formed; furans, phenolics and organic acids. In an industrial setting, a robust strain back ground (industrial yeast strains) is a prerequisite, in which first pentose fermenting traits should be incorporated and further improvement of the tolerance to inhibitory compounds need to follow. In the present project, we have used directed evolution to simultaneously improve the inhibitor tolerance and xylose conversion capability of recombinant yeast strains with an industrial background. The strains showed increased xylose utilization and ethanol production which was for some strains coupled to decreased xylitol formation. The resulting properties of the strains are highly dependent on the mode of directed evolution applied, which may also give rise to quite a number of clones with different properties.
Disentanglement of sympathetic and parasympathetic activity by instantaneous analysis of human heartbeat dynamics (2016)

Spectral analysis of heart rate variability (HRV) is one of the most effective techniques for the assessment of the influence of the autonomic nervous system (ANS) on the heartbeat. Despite its widespread use, it has been demonstrated that HRV subdivision in the low frequency (LF) and high frequency (HF) bands does not accurately reflect separate sympathetic and parasympathetic influences, respectively, mainly due to overlap of the two branches in the low frequencies. Here we propose two novel indices, namely the instantaneous sympathetic autonomic index (SAI) and parasympathetic autonomic index (PAI), that are able to separately assess the time-varying ANS synergic functions. The application of the paradigm is presented here by associating proper combinations of orthonormal Laguerre functions defined within the heartbeat point-process continuous model. Preliminary results from ten subjects recorded during a tilt-table protocol show that the proposed methodology, differently than the traditional spectral parameters, is able to separately track the independent changes associated with the two ANS branches.
Development of the Selective Hydrophobic Coagulation process (1992)

A novel technique for selectively coagulating and separating coal from dispersed mineral matter has been developed at Virginia Tech. The process, Selective Hydrophobic Coagulation (SHC), has been studied since 1986 under the sponsorship of the US Department of Energy (Contracts AC22-86PC91221 and AC22-90PC90174). The SHC process differs from oil agglomeration, shear or polymer flocculation, and electrolytic coagulation processes in that it does not require reagents or additives to induce the formation of coagula. In most cases, simple pH control is all that is required to (1) induce the coagulation of coal particles and (2) effectively disperse particles of mineral matter. If the coal is oxidized, a small dosage of reagents can be used to enhance the process. During the quarter, the Anutech Mark IV surface force apparatus was used to generate surface force-distance data for the mica/dodecylamine hydrochloride system (Task 2.1.1). Work to characterize the hydrophobicity of this system and the mica/DDOA[sup [minus]] system was also initiated (Task 2.1.2). In Task 3, the mixing/coagulation characteristics of a small Kenics static mixer/agitation system have been investigated (Task 3.2.1), a lamella thickener for the recovery of coagula has been built (Task 3.3.1), and the test program for the recovery of coagula by column flotation has been initiated (Task 3.3.4).
Elimination based Fault Localization in shared resource environments (2011)

Fault Localization is the process to identify the component(s) that is the exact source of failure given a set of observed failure indications. Despite being a focus of research for a long time, fault localization is still deemed to be a challenge due to the complexity of current distributed environment. Growing adoption of cloud computing wherein multiple applications share multiple resources increases the complexity of the problem. Existing probing techniques are found to be inefficient due to large number of applications and resources. Availability and utilization of such shared resource environment trigger the need for finding other novel techniques to fault localization. In this paper, we present an elimination-based fault localization method that leverages shared resources among applications. Shared resources are used as `Readily Available Probes' to find the real-time state of applications. These probes are used to eliminate non-faulty resources leaving minimal subset of resources that are likely to the faulty components. We show this method significantly reduces the effort required to design and implement probes. Various experiments demonstrate that our method reduces time taken and increases efficiency and accuracy of problem determination.
Sr<sub>2.975−<i>x</i></sub>Ba<sub><i>x</i></sub>Ce<sub>0.025</sub>AlO<sub>4</sub>F: a Highly Efficient Green-Emitting Oxyfluoride Phosphor for Solid State White Lighting (2010)

A new, highly efficient green oxyfluoride phosphor family Sr2.975−xBaxCe0.025AlO4F (SBAF:Ce3+) has been developed as a component of solid state white light emitting diodes (LED). The phosphor emits with a maximum at 502 nm when excited by 405 nm excitation, with a quantum efficiency approaching 100%. When SBAF:Ce3+ (x = 1.0) is incorporated with encapsulant on an ultraviolet (405 nm) LED, greenish-white light with a color rendering index of 62 under a forward bias current of 20 mA is obtained. The results suggest that phosphors deriving from SBAF:Ce3+ have potential for incorporation in formulations for white LEDs and related applications. The preparation and structural and optical characterization of the phosphor family is described. Attempts to understand the origins of the high efficiency on the basis of the thermal quenching characteristics of SBAF:Ce3+ in comparison with related compounds are presented.
Mutations of Francisella novicida that Alter the Mechanism of Its Phagocytosis by Murine Macrophages (2010)

Infection with the bacterial pathogen Francisella tularensis tularensis (F. tularensis) causes tularemia, a serious and debilitating disease. Francisella tularensis novicida strain U112 (abbreviated F. novicida), which is closely related to F. tularensis, is pathogenic for mice but not for man, making it an ideal model system for tularemia. Intracellular pathogens like Francisella inhibit the innate immune response, thereby avoiding immune recognition and death of the infected cell. Because activation of inflammatory pathways may lead to cell death, we reasoned that we could identify bacterial genes involved in inhibiting inflammation by isolating mutants that killed infected cells faster than the wild-type parent. We screened a comprehensive transposon library of F. novicida for mutant strains that increased the rate of cell death following infection in J774 macrophage-like cells, as compared to wild-type F. novicida. Mutations in 28 genes were identified as being hypercytotoxic to both J774 and primary macrophages of which 12 were less virulent in a mouse infection model. Surprisingly, we found that F. novicida with mutations in four genes (lpcC, manB, manC and kdtA) were taken up by and killed macrophages at a much higher rate than the parent strain, even upon treatment with cytochalasin D (cytD), a classic inhibitor of macrophage phagocytosis. At least 10-fold more mutant bacteria were internalized by macrophages as compared to the parent strain if the bacteria were first fixed with formaldehyde, suggesting a surface structure is required for the high phagocytosis rate. However, bacteria were required to be viable for macrophage toxicity. The four mutant strains do not make a complete LPS but instead have an exposed lipid A. Interestingly, other mutations that result in an exposed LPS core were not taken up at increased frequency nor did they kill host cells more than the parent. These results suggest an alternative, more efficient macrophage uptake mechanism for Francisella that requires exposure of a specific bacterial surface structure(s) but results in increased cell death following internalization of live bacteria.
Compiler optimizations for nondeferred reference (2006)

Reference counting is a well-known technique for automatic memory management, offering unique advantages over other forms of garbage collection. However, on account of the high costs associated with the maintenance of up-to-date tallies of references from the stack, deferred variants are typically used in modern implementations. This partially sacrifices some of the benefits of non-deferred reference-counting (RC) garbage collection, like the immediate reclamation of garbage and short collector pause times.This paper presents a series of optimizations that target the stack and substantially enhance the throughput of nondeferred RC collection. A key enabler is a new static analysis and optimization called RC subsumption that significantly reduces the overhead of maintaining the stack contribution to reference counts. We report execution time improvements on a benchmark suite of ten C# programs, and show how RC subsumption, aided with other optimizations, improves the performance of nondeferred RC collection by as much as a factor of 10, making possible running times that are within 32% of that with an advanced traversal-based collector on seven programs, and 19% of that with a deferred RC collector on eight programs. This is in the context of a baseline RC implementation that is typically at least a factor of 6 slower than the tracing collector and a factor of 5 slower than the deferred RC collector.
Protecting Triazabutadienes To Afford Acid Resistance (2016)

Recent work on triazabutadienes has shown that they have the ability to release aryl diazonium ions under exceptionally mild acidic conditions. There are instances that require that this release be prevented or minimized. Accordingly, a base-labile protection strategy for the triazabutadiene is presented. It affords enhanced synthetic and practical utility of the triazabutadiene. The effects of steric and electronic factors in the rate of removal are discussed, and the triazabutadiene protection is shown to be compatible with the traditional acid-labile protection strategy used in solid phase peptide synthesis.
Acceleration of spinal fusion using syngeneic and allogeneic adult adipose derived stem cells in a rat model (2008)

Posterolateral spinal fusion is the standard treatment for lumbar compression fractures. Adult adipose tissue-derived stem cells (ASCs) promote osteogenesis in vivo and in vitro. The hypothesis tested in this study was that syngeneic and allogeneic ASCs on a biomaterial scaffold composed of tricalcium phosphate and collagen I will accelerate spinal fusion in a rat model. ASCs from male Fischer or ACI rats were loaded onto scaffolds (53,571 cells/mm(3)) and cultured in stromal media for 48 h. Male Fisher rats were assigned to 4 cohorts (n = 14/cohort) after bilateral decortication of the L4 and L5 transverse processes: (1) No treatment; (2) scaffold only; (3) scaffold + syngeneic ASCs; or (4) scaffold + allogeneic ASCs. Half of each cohort was harvested 4 or 8 weeks after surgery. Spinal fusion was evaluated with radiographs, microcomputed tomography, and light microscopy. Callus did not form in spines without scaffolds. There were no significant differences in callus formation among scaffold cohorts 4 weeks after surgery. Callus formation was more mature in both ASC cohorts versus scaffold alone 8 weeks after surgery based on microstructure as well as radiographic and microcomputed tomographic evidence of active bone formation. Inflammatory cell infiltrate was significantly lower in both ASC cohorts (syngeneic = 18.3 +/- 0.85%; allogeneic = 23.5 +/- 2.33%) versus scaffold alone (46.8 +/- 11.8%) 4 weeks after surgery. Results of this study support syngeneic and allogeneic ASC acceleration of posterior lumbar spinal fusion in a rat model.
Chromate-Free Corrosion Protection Strategies for Magnesium Alloys—A Review: Part III—Corrosion Inhibitors and Combining Them with Other Protection Strategies (2022)

Owing to the unique active corrosion protection characteristic of hexavalent chromium-based systems, they have been projected to be highly effective solutions against the corrosion of many engineering metals. However, hexavalent chromium, rendered a highly toxic and carcinogenic substance, is being phased out of industrial applications. Thus, over the past few years, extensive and concerted efforts have been made to develop environmentally friendly alternative technologies with comparable or better corrosion protection performance to that of hexavalent chromium-based technologies. The introduction of corrosion inhibitors to a coating system on magnesium surface is a cost-effective approach not only for improving the overall corrosion protection performance, but also for imparting active inhibition during the service life of the magnesium part. Therefore, in an attempt to resemble the unique active corrosion protection characteristic of the hexavalent chromium-based systems, the incorporation of inhibitors to barrier coatings on magnesium alloys has been extensively investigated. In Part III of the Review, several types of corrosion inhibitors for magnesium and its alloys are reviewed. A discussion of the state-of-the-art inhibitor systems, such as iron-binding inhibitors and inhibitor mixtures, is presented, and perspective directions of research are outlined, including <i>in silico</i> or computational screening of corrosion inhibitors. Finally, the combination of corrosion inhibitors with other corrosion protection strategies is reviewed. Several reported highly protective coatings with active inhibition capabilities stemming from the on-demand activation of incorporated inhibitors can be considered a promising replacement for hexavalent chromium-based technologies, as long as their deployment is adequately addressed.
Content-based depth estimation in focused plenoptic camera (2010)

Depth estimation in focused plenoptic camera is a critical step for most applications of this technology and poses interesting challenges, as this estimation is content based. We present an iterative algorithm, content adaptive, that exploits the redundancy found in focused plenoptic camera captured images. Our algorithm determines for each point its depth along with a measure of reliability allowing subsequent enhancements of spatial resolution of the depth map. We remark that the spatial resolution of the recovered depth corresponds to discrete values of depth in the captured scene to which we refer as slices. Moreover, each slice has a different depth and will allow extraction of different spatial resolutions of depth, depending on the scene content being present in that slice along with occluding areas. Interestingly, as focused plenoptic camera is not theoretically limited in spatial resolution, we show that the recovered spatial resolution is depth related, and as such, rendering of a focused plenoptic image is content dependent.
The Role of Adenovirus in Cancer Therapy (2020)

This series of 13 articles (7 original articles, 6 reviews) is presented by international leaders in adenovirus-based cancer therapy [...].
Isolation and characterization of a new chimpanzee lentivirus (simian immunodeficiency virus isolate cpz-ant) from a wild-captured chimpanzee (1992)

This study shows that natural infection of wild-captured chimpanzees with an HIV-related virus may not be uncommon. The diversity of the two chimpanzee isolates, the different geographical origin and the absence of disease suggest that chimpanzees have not recently become SIVcpz-infected.
Multivariate backhaul compression for the downlink of cloud radio access networks (2014)

In the downlink of cloud radio access networks, a central encoder is connected to multiple multi-antenna base stations (BSs) via finite-capacity backhaul links. At the central encoder, precoding is followed by compression in order to produce the rate-limited bit streams delivered to each BS over the corresponding backhaul link. In current state-of-the-art schemes, the signals intended for different BSs are compressed independently. In contrast, this work proposes to leverage joint compression, also referred to as multivariate compression, of the signals for different BSs in order to better control the effect of the additive quantization noises at the mobile stations (MSs). The problem of maximizing the weighted sum-rate over precoding and compression strategies is formulated subject to power and backhaul capacity constraints. An iterative algorithm is proposed that achieves a stationary point of the problem. From numerical results, it is confirmed that the proposed joint precoding and compression strategy outperforms conventional approaches based on independent compression across the BSs.
Photobiomodulation and Cancer: What Is the Truth? (2018)

PBM therapy may have benefits in cancer patients and should be further investigated.
Novel Mammalian Group XII Secreted Phospholipase A<sub>2</sub>Lacking Enzymatic Activity<sup>,</sup> (2003)

An increasing number of mammalian secreted phospholipases A(2) (sPLA(2)s) has been identified over the past few years. Here, we report the identification and recombinant expression of a novel sPLA(2)-like protein in mouse and human species that has been called group XIIB (GXIIB). The mature protein has a molecular mass of 19.7 kDa and structural features similar to those of the previously identified GXII sPLA(2), now called GXIIA. Strikingly, the GXIIB sPLA(2) has a mutation in the active site, replacing the canonical histidine by a leucine, suggesting that this sPLA(2) is catalytically inactive. Recombinant expression of human (hGXIIB) and mouse (mGXIIB) sPLA(2)s in Escherichia coli indicates that GXIIB sPLA(2)s display no measurable lipolytic activity on various types of phospholipid substrates. Furthermore, these sPLA(2)-like proteins display relatively weak affinity to phospholipid vesicles. Binding experiments indicate that these proteins are also unable to bind to the well-known M-type sPLA(2) receptor. The RNA tissue distribution of GXIIB sPLA(2)s is distinct from that of other sPLA(2)s including the homologous GXIIA. Strong expression was observed in liver, small intestine, and kidney in both human and mouse species. Interestingly, the expression of the novel sPLA(2) is dramatically decreased in human tumors from the same tissues. The absence of enzymatic activity suggests that the GXIIB sPLA(2)-like proteins probably exert their biological roles by acting as ligands for as yet unidentified receptors.
Optical pulse compression reflectometry with 10 cm spatial resolution based on pulsed linear frequency modulation (2015)

A new scheme based on pulsed linear frequency modulation is proposed to improve the stability and spatial resolution of optical pulse compression reflectometry. 10 cm spatial resolution over 5.4 km measurement range is experimentally demonstrated.