gebhart/patrepeval huggingface dataset:
An African swine fever virus virulence-associated gene NL-S with similarity to the herpes simplex virus ICP34.5 gene (1996)

We described previously an African swine fever virus (ASFV) open reading frame, 23-NL, in the African isolate Malawi Lil 20/1 whose product shared significant similarity in a carboxyl-terminal domain with those of a mouse myeloid differentiation primary response gene, MyD116, and the herpes simplex virus neurovirulence-associated gene, ICP34.5 (M. D. Sussman, Z. Lu, G. Kutish, C. L. Afonso, P. Roberts, and D. L. Rock, J. Virol. 66:5586-5589, 1992). The similarity of 23-NL to these genes suggested that this gene may function in some aspect of ASFV virulence and/or host range. Sequence analysis of additional pathogenic viral isolates demonstrates that this gene is highly conserved among diverse ASFV isolates and that the gene product exists in either a long (184 amino acids as in 23-NL) or a short form (70 to 72 amino acids in other examined ASFV isolates). The short form of the gene, NL-S, encodes the complete highly conserved, hydrophilic, carboxyl-terminal domain of 56 amino acids common to 23-NL, MyD116, and ICP34.5. Recombinant NL-S gene deletion mutants and their revertants were constructed from the pathogenic ASFV isolate E70 and an E70 monkey cell culture-adapted virus, MS44, to study gene function. Although deletion of NL-S did not affect viral growth in primary swine macrophages or Vero cell cultures in vitro, the null mutant, E70/43, exhibited a marked reduction in pig virulence. In contrast to revertant or parental E70 where mortality was 100%, all E70/43-infected animals survived infection. With the exception of a transient fever response, E70/43-infected animals remained clinically normal and exhibited a 1,000-fold reduction in both mean and maximum viremia titers. All convalescent E70/43-infected animals survived infection when challenged with parental E70 at 30 days postinfection. These data indicate that the highly conserved NL-S gene of ASFV, while nonessential for growth in swine macrophages in vitro, is a significant viral virulence factor and may function as a host range gene.
Myeloid-Specific Rictor Deletion Induces M1 Macrophage Polarization and Potentiates In Vivo Pro-Inflammatory Response to Lipopolysaccharide (2014)

The phosphoinositide-3-kinase (PI3K)/protein kinase B (Akt) axis plays a central role in attenuating inflammation upon macrophage stimulation with toll-like receptor (TLR) ligands. The mechanistic target of rapamycin complex 2 (mTORC2) relays signal from PI3K to Akt but its role in modulating inflammation in vivo has never been investigated. To evaluate the role of mTORC2 in the regulation of inflammation in vivo, we have generated a mouse model lacking Rictor, an essential mTORC2 component, in myeloid cells. Primary macrophages isolated from myeloid-specific Rictor null mice exhibited an exaggerated response to TLRs ligands, and expressed high levels of M1 genes and lower levels of M2 markers. To determine whether the loss of Rictor similarly affected inflammation in vivo, mice were either fed a high fat diet, a situation promoting chronic but low-grade inflammation, or were injected with lipopolysaccharide (LPS), which mimics an acute, severe septic inflammatory condition. Although high fat feeding contributed to promote obesity, inflammation, macrophage infiltration in adipose tissue and systemic insulin resistance, we did not observe a significant impact of Rictor loss on these parameters. However, mice lacking Rictor exhibited a higher sensitivity to septic shock when injected with LPS. Altogether, these results indicate that mTORC2 is a key negative regulator of macrophages TLR signalling and that its role in modulating inflammation is particularly important in the context of severe inflammatory challenges. These observations suggest that approaches aimed at modulating mTORC2 activity may represent a possible therapeutic approach for diseases linked to excessive inflammation.
Comprehensive multiomic profiling of somatic mutations in malformations of cortical development (2022)

Abstract Malformations of cortical development (MCD) are neurological conditions displaying focal disruption of cortical architecture and cellular organization arising during embryogenesis, largely from somatic mosaic mutations. Identifying the genetic causes of MCD has been a challenge, as mutations remain at low allelic fractions in brain tissue resected to treat epilepsy. Here, we report a genetic atlas from 317 brain resections, identifying 69 mutated genes through intensive profiling of somatic mutations, combining whole-exome and targeted-amplicon sequencing with functional validation and single-cell sequencing. Genotype-phenotype correlation analysis elucidated specific MCD gene sets associating distinct pathophysiological and clinical phenotypes. The unique spatiotemporal expression patterns identified by comparing single-nucleus transcriptional sequences of mutated genes in control and patient brains implicate critical roles in excitatory neurogenic pools during brain development, and in promoting neuronal hyperexcitability after birth.
Maria: A Visual Experience Powered Conversational Agent (2021)

Arguably, the visual perception of conversational agents to the physical world is a key way for them to exhibit the human-like intelligence. Image-grounded conversation is thus proposed to address this challenge. Existing works focus on exploring the multimodal dialog models that ground the conversation on a given image. In this paper, we take a step further to study image-grounded conversation under a fully open-ended setting where no paired dialog and image are assumed available. Specifically, we present Maria, a neural conversation agent powered by the visual world experiences which are retrieved from a large-scale image index. Maria consists of three flexible components, i.e., text-to-image retriever, visual concept detector and visual-knowledge-grounded response generator. The retriever aims to retrieve a correlated image to the dialog from an image index, while the visual concept detector extracts rich visual knowledge from the image. Then, the response generator is grounded on the extracted visual knowledge and dialog context to generate the target response. Extensive experiments demonstrate Maria outperforms previous state-of-the-art methods on automatic metrics and human evaluation, and can generate informative responses that have some visual commonsense of the physical world.
Optimized orbitrap HCD for quantitative analysis of phosphopeptides (2009)

Despite the tremendous commercial success of radio frequency quadrupole ion traps for bottom-up proteomics studies, there is growing evidence that peptides decorated with labile post-translational modifications are less amenable to low-energy, resonate excitation MS/MS analysis. Moreover, multiplexed stable isotope reagents designed for MS/MS-based quantification of peptides rely on accurate and robust detection of low-mass fragments for all precursors. Collectively these observations suggest that beam-type or tandem in-space MS/MS measurements, such as that available on traditional triple quadrupole mass spectrometers, may provide beneficial figures of merit for quantitative proteomics analyses. The recent introduction of a multipole collision cell adjacent to an Orbitrap mass analyzer provides for higher energy collisionally activated dissociation (HCD) with efficient capture of fragment ions over a wide mass range. Here we describe optimization of various instrument and post-acquisition parameters that collectively provide for quantification of iTRAQ-labeled phosphorylated peptides isolated from complex cell lysates. Peptides spanning a concentration dynamic range of 100:1 are readily quantified. Our results indicate that appropriate parameterization of collision energy as a function of precursor m/z and z provides for optimal performance in terms of peptide identification and relative quantification by iTRAQ. Using this approach, we readily identify activated signaling pathways downstream of oncogenic mutants of Flt-3 kinase in a model system of human myeloid leukemia.
ChemInform Abstract: Physicochemical Properties of Chitinous Materials (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The EP3-agonist sulprostone, but not prosta glandin E2 potentiates platelet aggregation in human blood (2010)

The EP3-agonist sulprostone, but not prostaglandin E2 potentiates platelet aggregation in human blood -
Science Translational Medicine Podcast: 7 July 2010 (2010)

A conversation with Samuel Broder about early discoveries in HIV-1/AIDS research and strategies for successful translational research in the future.
Experimental and theoretical study of light scattering by individual mature red blood cells by use of scanning flow cytometry and a discrete dipole approximation (2005)

Elastic light scattering by mature red blood cells (RBCs) was theoretically and experimentally analyzed by use of the discrete dipole approximation (DDA) and scanning flow cytometry (SFC), respectively. SFC permits measurement of the angular dependence of the light-scattering intensity (indicatrix) of single particles. A mature RBC is modeled as a biconcave disk in DDA simulations of light scattering. We have studied the effect of RBC orientation related to the direction of the light incident upon the indicatrix. Numerical calculations of indicatrices for several axis ratios and volumes of RBC have been carried out. Comparison of the simulated indicatrices and indicatrices measured by SFC showed good agreement, validating the biconcave disk model for a mature RBC. We simulated the light-scattering output signals from the SFC with the DDA for RBCs modeled as a disk-sphere and as an oblate spheroid. The biconcave disk, the disk-sphere, and the oblate spheroid models have been compared for two orientations, i.e., face-on and rim-on incidence, relative to the direction of the incident beam. Only the oblate spheroid model for rim-on incidence gives results similar to those of the rigorous biconcave disk model.
Boron‐Containing Two‐Photon‐Absorbing Chromophores: Electronic Interaction through the Cyclodiborazane Core (2006)

Through-Bond-Kopplung über einen Cyclodiborazankern führt zu großen Absorptionsquerschnitten bei neuartigen zweiphotonenabsorbierenden Chromophoren (siehe Bild; B rosa, N blau, C grau; alle H-Atome außer BH (weiß) weggelassen). Dies ist ein erster Schritt zur Entwicklung von Chromophoren mit dualen Eigenschaften für Anwendungen in der Biologie oder Medizin (z. B. Zweiphotonenbildgebung und Borneutroneneinfangtherapie).
Mesoporous silica nanoparticles functionalized with folic acid/methionine for active targeted delivery of docetaxel (2016)

Mesoporous silica nanoparticles (MSNs) are known as carriers with high loading capacity and large functionalizable surface area for target-directed delivery. In this study, a series of docetaxel-loaded folic acid- or methionine-functionalized mesoporous silica nanoparticles (DTX/MSN-FA or DTX/MSN-Met) with large pores and amine groups at inner pore surface properties were prepared. The results showed that the MSNs were successfully synthesized, having good pay load and pH-sensitive drug release kinetics. The cellular investigation on MCF-7 cells showed better performance of cytotoxicity and cell apoptosis and an increase in cellular uptake of targeted nanoparticles. In vivo fluorescent imaging on healthy BALB/c mice proved that bare MSN-NH<sub>2</sub> are mostly accumulated in the liver but MSN-FA or MSN-Met are more concentrated in the kidney. Importantly, ex vivo fluorescent images of tumor-induced BALB/c mice organs revealed the ability of MSN-FA to reach the tumor tissues. In conclusion, DTX/MSNs exhibited a good anticancer activity and enhanced the possibility of targeted drug delivery for breast cancer.
A High-Efficiency High Step-Up Interleaved Converter with a Voltage Multiplier for Electric Vehicle Power Management Applications (2016)

This paper proposes a novel high-efficiency high-step-up interleaved converter with a voltage multiplier, which is suitable for electric vehicle power management applications. The proposed interleaved converter is capable of achieving high step-up conversion by employing a voltage-multiplier circuit. The proposed converter lowers the input-current ripple, which can extend the input source's lifetime, and reduces the voltage stress on the main switches. Hence, large voltage spikes across the main switches are alleviated and the efficiency is improved. Finally, a prototype circuit with an input voltage of 24 V, an output voltage of 380 V, and an output rated power of 1 kW is implemented and tested to demonstrate the functionality of the proposed converter. Moreover, satisfying experimental results are obtained and discussed in this paper. The measured full-load efficiency is 95.2%, and the highest measured efficiency of the proposed converter is 96.3%.
The first febrile convulsion: an analysis of 108 children in Saudi Arabia (1982)

In 108 children admitted to the Maternity and Children's Hospital, Riyadh with their first febrile convulsion, clinical course, management and underlying causes were analysed. There was a preponderance of boys (69%) and a mean age of 18.6 months with a peak incidence (82%) between six months and three years. The commonest precipitating conditions were upper respiratory infection and gastroenteritis. Physical findings were confined to those of the primary disease. Routine investigations, including CSF analysis were not helpful. Convulsions were mainly of the simple type, single and symmetrical, and did not last for more than 30 minutes. Two thirds of the children reached hospital within two hours of the onset of their first convulsion, and the remainder up to ten hours after the convulsion had ceased. In only 18 patients did the parents take measures to lower the temperature or revive the child. Management of febrile convulsions is discussed. Since the condition is common and, if repeated, may have serious effects, methods of educating parents are suggested.
In Vivo and In Vitro Expression of iC1, a Methylation-Controlled J Protein (MCJ) in Bovine Liver, and Response to In Vitro Bovine Fatty Liver Disease Model (2023)

Mitochondrial complex I inhibitor (iC1) is a methylation-controlled J protein (MCJ) that decreases cellular respiration by inhibiting oxidative phosphorylation. Recent rodent studies showed that loss or inhibition of iC1 was associated with preventing lipid accumulation. A common metabolic disorder of dairy cattle is a fatty liver disease (FLD), which often occurs during the periparturient period. In humans and rodents, iC1 is expressed in the liver and acts as a mitochondrial "brake". However, iC1 expression in bovine liver and its possible role in FLD development have not yet been characterized. We hypothesized that iC1 is expressed in the bovine liver and that the expression of iC1 is correlated with FLD in periparturient dairy cattle. To test this hypothesis, we collected bovine liver tissue samples from an abattoir and isolated primary hepatic cells immediately following harvest. Utilizing an in vitro model of bovine FLD developed in our laboratory, we cultured primary hepatic cells in low-glucose DMEM supplemented with 10% FBS. The basal media was made to induce lipid accumulation and cytotoxicity in the primary liver cells with three treatments. To the basal media (control) we added 0.4 mM palmitate (treatment 1) or 20 ng/mL TNFα (treatment 2), or both 0.4 mM palmitate and 20 ng/mL TNFα (treatment 3). Consistent with our hypothesis, we present the novel characterization of iC1 expression in primary bovine liver cells cultured with or without the addition of lipotoxic factors made to emulate bovine FLD. We demonstrate both in situ and in vitro expression of iC1 in bovine liver and mRNA expression in hepatic cells and in the precipitates of conditioned media. The results of RT-qPCR, IHC, and western blot all demonstrated the expression of iC1 in bovine liver. In addition, we isolated precipitates of conditioned media further demonstrated iC1 expression by RT-qPCR. The transcript of iC1 tended to be more concentrated (4-fold; <i>p</i> > 0.05) in TNFα-treated conditioned media when compared with the control. Taken together, we present the novel finding that iC1 transcript and protein are expressed in liver tissue from dairy cattle, primary hepatic cells isolated from that liver tissue, and, finally, in the conditioned media derived from those cells. These novel findings and the prior findings on the role of iC1 in rodents and humans indicate that further investigation of the role of iC1 in the etiology and pathology of FLD in periparturient dairy cows is warranted.
Nonadiabatic Effects and the Quantum Geometric Tensor in Charge Density Wave Systems (2007)

We studied the energy corrections to the mean-field theory on a charge density wave (CDW) system in terms of the random phase approximation (RPA). An energy correction with a logarithmic singular behavior has been found in the ground-state energy. There exists a region where this correction gives a considerable contribution to the mean-field gap equation. By estimating the validity of the adiabatic approximation, the global phase diagram of the ground state in the \((\Delta/\varepsilon_{\text{F}},\hbar\omega/\varepsilon_{\text{F}})\)-plane (Δ: CDW mean-field gap, ε F : Fermi energy, \(\hbar\omega\): phonon energy quantum) has been revealed. In particular, we have found a crossover between adiabatic states and nonadiabatic states in the quantum liquid region in the phase diagram. In this paper, we also explain that the logarithmic singular term corresponds to the fourth-order energy correction, which is represented by the so-called quantum geometric tensor, in the adiabatic approximation.
SERUM LEVELS OF THE PRO-INFLAMMATORY CYTOKINE HMGB1 CORRELATE WITH VAGUS NERVE ACTIVITY (2004)

Goldstein, R.; Gallowitsch, M.; Amella, C. A.; Czura, C. J.; Friedman, S.; Sama, A.; Tracey, K. J. Author Information
P4–034: Beta amyloid deposition and hyperphosphorylated tau are also present in the degenerating pancreas in type 2 diabetes (2006)

Strong epidemiologic evidence supports an association between Alzheimer's disease (AD) and type 2 diabetes. Inflammation and amyloidosis play an important role in the pathogenesis of both. The 4 kDa amyloid beta peptide (AB) aggregates in AD and amylin (37 kDa) in diabetes type 2. Previously “curly fibers” and “tangles” with an ultrastructure similar to paired helical filaments of neurofibrillary tangles were also observed in other organs than the brain, including the pancreas. The goal of the present study was to analyze whether amyloid beta and hyperphosphorylated tau, the two biological markers of AD, may also be present in the affected pancreas in type 2 diabetes. An immunonohistochemical analysis of brains and pancreas of 37 autopsy cases including 20 definite AD and 8 type 2 diabetes cases was performed. A panel of different antibodies to detect AB, amylin, tau, ubiquitin and Apo–E was used. Using infrared microspectrophotometry (SIRMS) we analyzed the presence of a beta sheet formation in islet amyloid deposits. Antibodies to the inflammatory markers for activated macrophages and complement proteins C3d, C4d and the membrane attack complex were also used to detect whether in the pancreas, similarly to the brain in AD, local inflammation was also present. Amylin, beta amyloid, AT8, ubiquitin and Apo–E were all expressed in the degenerating pancreas in type 2 diabetes. The islet amyloid, similar to senile plaques, showed a beta sheet conformation by SIRMS. Amyloid beta and hyperphosphorylated tau are both present in degenerating islets in the pancreas of type 2 diabetes. CR3/43 positive activated macrophages and complement activation in the lesions were also seen in the affected pancreas. These observations indicate a common pathogenic link between AD and type 2 diabetes.
The expression and the nuclear activity of the caretaker gene ku86 are modulated by somatostatin (2009)

Somatostatin is a peptide hormone that exerts antisecretory and antiproliferative activities on some human tumors. The Ku70/86 heterodimer acts as regulatory subunit of the DNA dependent protein kinase and its DNA binding activity mediates DNA double strands breaks repair that is crucial to maintain the genetic integrity of the genome. The activation of the heterodimer regulates cell cycle progression and the activity of nuclear transcription factors involved in DNA replication and cell proliferation. Moreover Ku86 behaves as a receptor for the growth inhibitory tetradecapeptide, somatostatin. Herein we report that somatostatin treatment to a colon carcinoma cell line (Caco-2) inhibits cell growth and, at same time, strongly modulates the activation of Ku70/86 heterodimer and the levels of Ku86 in the nucleus by increasing its specific mRNA level. Our findings are consistent with the hypothesis that somatostatin controls cell cycle progression and DNA repair through a new signalling pathway that involves the regulation of Ku86 level and modulates the Ku70/86 activity in the nucleus.
Charge Recombination in Phosphorescent Organic Light-Emitting Diode Host–Guest Systems through QM/MM Simulations (2016)

Host–guest systems are crucial for achieving high efficiency in most organic light-emitting diode (OLED) devices. However, charge recombination in such systems is poorly understood due to complicated molecular environment, making the rational design of host–guest systems difficult. In this article, we present a computational study of a phosphorescent OLED with 2,8-bis(triphenylsilyl)dibenzofuran (BTDF) as the host and fac-tris(2-phenylpyridine) iridium (fac-Ir(ppy)3) as the guest, using a combined quantum mechanics/molecular mechanics (QM/MM) scheme. A new reaction coordinate is introduced to measure the electrostatic interactions between the host and guest molecules. Ionization potentials and electron affinities of the host show broader distributions as the host–guest interaction increases. On the basis of these distributions, we describe a molecular picture of charge recombination on the guest and find a direct charge trapping route for this system. Our results suggest several strategies for the design of more efficient host and guest combinations.