gebhart/patrepeval huggingface dataset:
Efficient gene transfer of VSV-G pseudotyped retroviral vector to human brain tumor (2001)

A retroviral vector constructed from the murine leukemia virus (MLV) can only express transgenes in cells undergoing mitosis, indicating its suitability as a delivery vehicle for cancer gene therapy. However, the transduction efficiency (TE) of retroviruses embedding endogenous envelope proteins in human cancer cells was found to be unsatisfactory. Recently, several research groups have demonstrated the feasibility of a retroviral vector pseudotyped with a vesicular stomatitis virus G (VSV-G) protein. In this study, the potential of VSV-G pseudotyped MLV-based retrovirus was examined as a delivery vehicle in a variety of human cancer cells including brain tumor cells in vitro and in vivo. The transduction efficiency of the 293T/G/GP/LacZ retrovirus in cell culture was superior in most cancer cells, particularly in brain tumor cells, compared with that of other retroviruses, such as PA317- or PG13-derived. The relative growth rate and phosphatidylserine expression level on the plasma membrane of target cells mainly influenced the transduction efficiency of VSV-G pseudotyped retrovirus, which suggested that both the relative growth rate and phosphatidylserine expression level were major determinants of TE. Furthermore, 293T/G/GP/LacZ could efficiently transduce human cancer cells regardless of the presence of chemical additives, whereas in other retroviruses, cationic chemical additives such as polybrene or liposomes were essential during virus infection. Finally, an average of 10% gene expression was routinely obtained exclusively in the tumor mass when 293T/G/GP/LacZ concentrated by simple ultracentrifugation was directly administrated to pre-established brain tumors in animal models (U251-N nu/nu mice or C6 Wistar rats). All told, the present study suggests that the VSV-G pseudotyped retrovirus is a suitable vector for brain tumor gene therapy.
Supplementary Figures 1-5 from Use of Angiotensin System Inhibitors Is Associated with Immune Activation and Longer Survival in Nonmetastatic Pancreatic Ductal Adenocarcinoma (2023)

&lt;p&gt;Supplementary Figure 1: Clinical status of patients included in the analysis Supplementary Figure 2: Unadjusted Kaplan Meier survival curves of patients who received ACEi (green), ARB (yellow) vs. control group (blue). Supplementary Figure 3: Chronic ASI use in resected patients with hypertension. Supplementary Figure 4: Unadjusted Kaplan Meier survival curve of all resected patients stratified by BMI and chemotherapy. Supplementary Figure 5: Unadjusted Kaplan Meier curves for disease recurrence.&lt;/p&gt;
Thermal Analysis of a Novel Continuous Flow Multi Layered Polymerase Chain Reaction Device (2007)

In this paper are presented the results of a thermal analysis on a high throughput droplet based, nucleic acid amplifier. Initial data of successful amplification of DNA is also presented. The advent of microfluidics offers many opportunities to integrate all functional steps of DNA analysis onto a single platform allowing for reduced analysis times, reduced sample volume requirements and higher throughput. There are many technical challenges facing this goal, thermal control being pivotal. This paper involves fundamental theoretical and experimental characterization of the core element of such a platform; a polymerise chain reaction (PCR) thermal cycler. The PCR process can be either a two-step or three-step temperature cycling procedure, depending on the chemistry involved. Presented in this paper is a thermal analysis of four, two-step thermocyclers arrayed in parallel. Two step PCR requires samples to be cycled through temperature ranges of 92–95°C and 60°C, the preciseness of these temperatures again depending on the chemistry involved. For optimum efficiency, fast heating and cooling between steps, and uniformity within each step is crucial. Our thermocycler design comprises a flow conduit in a serpentine pattern, machined in two segmented aluminium blocks, in which the conduit extends through the denaturation (92–95°C) and the annealing and extension (60°C) zones. Circular tubing, in which the samples are passed through to ensure biocompatibility for the reaction, is embedded in the machined channel which results in high heat transfer from the block to the sample. The device is then positioned in the vertical plane and an array of thermocyclers are formed by combining multiple planar systems. Thermofoil heaters are attached to the underside of the upper blocks creating the denaturation temperature, and by adjusting the air gap, passive thermal control is used to create the temperature required for the annealing and extension zone, thereby reducing the number of heaters and thus the power required. Theoretical thermal analysis of the device is performed, in conjunction with CFD simulations, experimental testing, and thermal imaging. Finally successful PCR of the gene ABL1 was performed.
Mode Dispersion Relations for Quantum Well Assisted Surface Plasmonic Structures (2008)

In this paper, a plasmonic waveguiding structure is presented for effectively compensating the propagation losses of a plasmonic waveguide structure by utilizing a metallic strip sandwiched in between two quantum wells. The mode dispersion relations of the plasmonic waveguide are calculated and the gain requirement on the quantum well structure is also presented.
A review of the environmental pollution originating from the piggery industry and of the available mitigation technologies: towards the simultaneous biofiltration of swine slurry and methaneThis article is one of a selection of papers published in this Special Issue on Biological Air Treatment. (2009)

In Canada, the piggery industry is an essential part of the agricultural sector, but the main waste product of this industry, swine slurry, is particularly harmful to the environment. The anaerobic storage conditions and the excessive use of slurry for agricultural fertilization contribute, respectively, to the emission of greenhouse gases and to aquatic pollution. This paper provides a review of these environmental concerns and of the existing mitigation technologies. Water pollution from swine slurry is associated with the nutrients it contains, such as nitrogen and phosphorous, while the main greenhouse gases produced by the piggery industry are methane and nitrous oxide. Available technologies can valorize the slurry through agricultural fertilization, reduce greenhouse gas emissions, by limiting nutrient availability for example, or treat the effluents using solid–liquid separation, flaring or biological processes. Specific attention is paid to biofiltration due to its potential to simultaneously treat these two types of pollution.
Meta-analysis of Transperitoneal Versus Extraperitoneal Robot-Assisted Radical Prostatectomy for Prostate Cancer (2013)

This meta-analysis suggests that perioperative parameters, including OR time and LOS, may be more favorable for EP-RARP than for TP-RARP. However, the oncologic outcome of margin positivity did not demonstrate a significant difference between the EP and TP approaches.
Secondary structure of Src homology 2 domain of c-Abl by heteronuclear NMR spectroscopy in solution. (1992)

The Src homology 2 (SH2) domain is a recognition motif thought to mediate the association of the cytoplasmic proteins involved in signal transduction by binding to phosphotyrosyl-containing sequences in proteins. Assignments of nearly all 1H and 15N resonances of the SH2 domain from the c-Abl protein-tyrosine kinase have been obtained from homonuclear and heteronuclear NMR experiments. The secondary structure has been elucidated from the pattern of nuclear Overhauser effects, from vicinal coupling constants, and from observation of slowly exchanging amino hydrogens. The secondary structure contains two alpha-helices and eight beta-strands, six of which are arranged in two contiguous, antiparallel beta-sheets. Residues believed to be involved in phosphotyrosyl ligand binding are on a face of one beta-sheet. The alignment of homologous sequences on the basis of secondary structure suggests a conserved global fold in a family of SH2 domains.
A cytotoxic and cytostatic gold(iii) corrole (2014)

We have synthesized and characterized a water-soluble gold(III) corrole (1-Au) that is highly toxic to cisplatin-resistant cancer cells. Relative to its 1-Ga analogue, axial ligands bind only weakly to 1-Au, which likely accounts for its lower affinity for human serum albumin (HSA). We suggest that the cytotoxicity of 1-Au may be related to this lower HSA affinity.
Electrically Assisted Extraction of Soluble Matter from Chardonnay Grape Skins for Polyphenol Recovery (2009)

The objective of this study was to investigate the effects of pulsed electric field (PEF) and high-voltage electrical discharges (HVED) application on the efficiency of aqueous extraction of total soluble matter and polyphenols from grape skins ( Vitis vinifera L.) at different temperatures within 20-60 degrees C. The highest level of polyphenol concentration C was reached after about 60 min of extraction for HVED treatment: C(HVED) = 21.4 +/- 0.8 micromol of gallic acid equivalent (GAE)/g of dry matter (DM). Almost the same level of C was reached after 180 min of extraction for the PEF-treated skins. These levels exceeded the value C = 19.1 +/- 0.5 micromol of GAE/g of DM for the untreated samples. The difference between degrees Brix values for HVED-treated and untreated systems decreased with temperature increase (from 40 to 60 degrees C), but a large difference in the total amount of polyphenols was observed for HVED-treated and untreated systems. The activation energies were W(u) = 31.3 +/- 3.7 kJ/mol and W(PEF) = 28.9 +/- 5.5 kJ/mol for untreated and PEF-treated systems, respectively.
Analysis of human leukocyte antigen associations in human papillomavirus–positive and –negative head and neck cancer: Comparison with cervical cancer (2022)

Cervical cancer studies highlight that human papillomavirus (HPV)-driven cancer risk is linked with human leukocyte antigen (HLA) polymorphism. Hence, the current study was designed to investigate the HLA associations in HPV-positive and HPV-negative head and neck cancer (HNC) and compare these associations with cervical cancer. Several lead signals reported by previous HNC and cervical genome-wide association studies were replicated in the current study. However, these associations were limited to the HPV-positive HNC group, and this suggests that HPV-positive HNC risk is associated with distinct HLA variants, and some of them are shared by both cervical cancer and HPV-positive HNC.
Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process (2021)

Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry. This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and colocalize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. This interactome dataset will serve as a useful resource for functional studies of P. infestans effectors and of effector-targeted host processes.
Nucleophilic Aliphatic Substitution (2007)

This chapter contains sections titled: Ion-pair Phenomena and Bordeline Mechanisms Solvent and Medium Effects Kinetic Isotope Effects and Other Isotope Studies Intramolecular Catalysis Ambident Nucleophiles Substitution at Vinylic Carbon S N2 processes Displacement at Elements Other than Carbon Metals in Nucleophilic Substitution Reactions Other Reactions
A novel MONOS nonvolatile memory device ensuring 10-year data retention after 10/sup 7/ erase/write cycles (1993)

A highly reliable nonvolatile memory device suitable for high-density electrically erasable and programmable read only memories (EEPROMs) is described. A metal-oxide-nitride-oxide-semiconductor (MONOS) structure whose top oxide is fabricated by chemical vapor deposition (CVD) on the nitride is proposed. This CVD oxide is densified by pyrogenic annealing and has stoichiometric SiO/sub 2/ characteristics. Its potential barrier, which prevents stored charges from decaying through the top oxide to the gate, thus becomes sharper than that of the thermally grown top oxide used in the conventional MONOS structure. For comparison between the proposed MONOS, conventional MONOS, and MNOS structures, three devices were fabricated on the same process line. The 16.7-nm nitride thickness in combination with a top oxide thickness of 4.0 nm results in a gate capacitance equivalent to that of the conventional NMOS structure with a 23.5-nm nitride thickness. Moreover, an asymmetric erase/write programming voltage has been adapted to the MONOS device operation by considering both erased-state degradation and written-state retention. At 85 degrees C, the proposed MONOS device has 10/sup 7/-cycle endurance with 10-year data retention.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A major genetic determinant of autoimmune diseases is associated with the presence of autoantibodies in hypersensitivity pneumonitis (2020)

A subset of hypersensitivity pneumonitis patients presents circulating autoantibodies and higher mortality that are associated with some alleles of 8.1 ancestral haplotype.
Impact of multiple access on uplink scheduling (2002)

We consider uplink scheduling for bursty traffic. We characterize the achievable rate region for Gaussian multiple access in terms of minimum required powers, with a constraint on average transmission delay for all users. We show that delay and rate constrained, power minimizing schemes perform scheduling accompanied with power control. Further, for the class of randomized stationary schedulers, it is shown that the achievable region is a convex polytope. We highlight that power requirements of a user can be reduced by either allowing additional delay (time scheduling gain) or increasing the power of another user (multiuser power exchange). Results are presented for two user additive white Gaussian noise channel and can be extended to finite state fading channels.
Efficient Traffic Control for Optical Switching with Different Granularity (2006)

Through the result of analysis on Internet traffic characteristics, we propose efficient traffic control method in optical switching environment with different granularity. According to the classified traffic flows, we can use both Optical Circuit Switching (OCS) and Optical Burst Switching (OBS) simultaneously.
In Vivo MRI of Endogenous Remyelination in a Nonhuman Primate Model of Multiple Sclerosis (2021)

ABSTRACT Remyelination is crucial for recovery from inflammatory demyelination in multiple sclerosis (MS). Investigating remyelination in vivo using magnetic resonance imaging (MRI) is difficult in MS, where collecting serial short-interval scans is challenging. Using experimental autoimmune encephalomyelitis (EAE) in common marmosets, a model of MS that recapitulates focal cerebral MS lesions, we investigated whether remyelination can be detected and characterized noninvasively. In 6 animals followed with multisequence 7-tesla MRI, 36 focal lesions, classified as demyelinated or remyelinated based on signal intensity on proton density-weighted images, were subsequently assessed with histopathology. Remyelination occurred in 5 of 6 marmosets and 51% of lesions. Radiological-pathological comparison showed high sensitivity (88%) and specificity (90%) for detecting remyelination by in vivo MRI. This study demonstrates the prevalence of spontaneous remyelination in marmoset EAE and the ability of in vivo MRI to detect it, with implications for preclinical testing of pro-remyelinating agents and translation to clinical practice.
Memory T Cells Migrate to and Reject Vascularized Cardiac Allografts Independent of the Chemokine Receptor CXCR3 (2011)

CXCR3 is not critical for the migration of memory T cells to vascularized organ allografts. Blocking CXCR3 or CXCR3 and CCR5 does not delay acute rejection mediated by memory T cells. These findings suggest that the mechanisms of memory T cell-homing to transplanted organs may be distinct from those required for their migration to sites of infection.
Daytime spikes in dopaminergic activity drive rapid mood-cycling in mice (2015)

Disruptions in circadian rhythms and dopaminergic activity are involved in the pathophysiology of bipolar disorder, though their interaction remains unclear. Moreover, a lack of animal models that display spontaneous cycling between mood states has hindered our mechanistic understanding of mood switching. Here, we find that mice with a mutation in the circadian Clock gene (ClockΔ19) exhibit rapid mood-cycling, with a profound manic-like phenotype emerging during the day following a period of euthymia at night. Mood-cycling coincides with abnormal daytime spikes in ventral tegmental area (VTA) dopaminergic activity, tyrosine hydroxylase (TH) levels and dopamine synthesis. To determine the significance of daytime increases in VTA dopamine activity to manic behaviors, we developed a novel optogenetic stimulation paradigm that produces a sustained increase in dopamine neuronal activity and find that this induces a manic-like behavioral state. Time-dependent dampening of TH activity during the day reverses manic-related behaviors in ClockΔ19 mice. Finally, we show that CLOCK acts as a negative regulator of TH transcription, revealing a novel molecular mechanism underlying cyclic changes in mood-related behavior. Taken together, these studies have identified a mechanistic connection between circadian gene disruption and the precipitation of manic episodes in bipolar disorder.
Neutralizing Monoclonal Antibody to Edema Toxin and Its Effect on Murine Anthrax (2010)

Edema factor (EF) is a component of an anthrax toxin that functions as an adenylate cyclase. Numerous monoclonal antibodies (MAbs) have been reported for the other Bacillus anthracis toxin components, but relatively few to EF have been studied. We report the generation of six murine hybridoma lines producing two IgM and four IgG1 MAbs to EF. Of the six MAbs, only one IgM neutralized EF, as assayed by an increase in cyclic AMP (cAMP) production by Chinese hamster ovary (CHO) cells. Analysis of the variable gene elements revealed that the single neutralizing MAb had a different binding site than the others. There was no competition between the neutralizing IgM and the nonneutralizing IgG MAbs indicative of different specificity. MAb-based capture enzyme-linked immunosorbent assay (ELISA) detected EF in liver lysates from mice infected with B. anthracis Sterne 34F2. Administration of the neutralizing IgM MAb to A/JCr mice lethally infected with B. anthracis strain Sterne had no significant effect on median time to death, but mice treated with the MAb were more likely to survive infection. Combining the neutralizing IgM to EF with a subprotective dose of a neutralizing MAb to protective antigen (PA) prolonged mean time to death of infected mice, suggesting that neutralization of EF and PA could produce synergistic beneficial effects. In summary, the results from our study and literature observations suggest that the majority of Abs to EF are nonneutralizing, but the toxin has some epitopes that can be targeted by the humoral response to generate useful Abs that may contribute to defense against anthrax.
Challenges During Shallow and Deep Carbonate Reservoirs Stimulation (2014)

Carbonate reservoir stimulation has been carried out for years using HCl or HCl-based fluids. High HCl concentration should not be used when the well completion has Cr-based alloy in which the protective layer is chrome oxide which is very soluble in HCl. HCl or its based fluids are not recommended either in shallow reservoirs where the fracture pressure is low (face dissolution) or in deep reservoirs where it will cause severe corrosion problems to the well tubular. Different chelating agents have been proposed to be used as alternatives to HCl in the cases that HCl cannot be used. Chelating agents, such as HEDTA (hydroxyl ethylene diamine triacetic acid) and GLDA (glutamic –N, N-diacetic acid), have been used to stimulate carbonate cores. The benefits of chelating agents over HCl are the low reaction, low leak-off rate, and low corrosion rates. In this study, the different equations and parameters that can be used in matrix acid treatment were summarized to scale up the laboratory conditions to the field conditions. The conditions where HCl or chelating agents can be used were optimized and in this paper. The leak-off rate was determined using the data from coreflood experiments and computed tomography (CT) scans. Indiana limestone cores of average permeability of 1 md and core lengths of 6 and 20 in. were used in this study. Chelating agents will be used at pH value of 4 and at concentration of 0.6M, and their performance will be compared with the 15 wt.% HCl. The experimental results showed that HCl has high leak-off rate and caused face dissolution at low injection rate. The model to scale up the linear coreflood results to radial field conditions was developed and can be used to design for the optimum conditions of the matrix acid treatments. Chelating agents can be used to stimulate shallow reservoirs in which HCl may cause face dissolution, because they can penetrate deep with less volume and also they can be used in deep reservoirs where HCl may cause severe corrosion to the well tubular.
In Vivo activity of a PSA-activated doxorubicin prodrug against PSA-producing human prostate cancer xenografts (2000)

The PSA-specific peptide/doxorubicin prodrug can be used to deliver higher intratumoral levels of Dox for longer duration while avoiding systemic toxicity. In addition, these results validate the specificity of the PSA-specific peptide as a targetable drug carrier. This PSA-specific peptide could also be used as a carrier to target a wide variety of cytotoxic agents for specific activation within sites of metastatic prostate cancer.