gebhart/patrepeval huggingface dataset:
Activation of the E3 ubiquitin ligase Parkin (2015)

The PINK1 (phosphatase and tensin homologue-induced putative kinase 1)/Parkin-dependent mitochondrial quality control pathway mediates the clearance of damaged organelles, but appears to be disrupted in Parkinson's disease (PD) [Springer and Kahle (2011) Autophagy 7, 266-278]. Upon mitochondrial stress, PINK1 activates the E3 ubiquitin (Ub) ligase Parkin through phosphorylation of the Ub-like (UBL) domain of Parkin and of the small modifier Ub itself at a conserved residue [Sauvé and Gehring (2014) Cell Res. 24, 1025-1026]. Recently resolved partial crystal structures of Parkin showed a 'closed', auto-inhibited conformation, consistent with its notoriously weak enzymatic activity at steady state [Wauer and Komander (2013) EMBO J. 32, 2099-2112; Riley et al. (2013) Nat. Commun. 4, 1982; Trempe et al. (2013) Science 340, 1451-1455; Spratt et al. (2013) Nat. Commun. 4, 1983]. It has thus become clear that Parkin must undergo major structural rearrangements in order to unleash its catalytic functions. Recent published findings derived from X-ray structures and molecular modelling present a complete structural model of human Parkin at an all-atom resolution [Caulfield et al. (2014) PLoS Comput. Biol. 10, e1003935]. The results of the combined in silico simulations-based and experimental assay-based study indicates that PINK1-dependent Ser65 phosphorylation of Parkin is required for its activation and triggering of 'opening' conformations. Indeed, the obtained structures showed a sequential release of Parkin's intertwined domains and allowed docking of an Ub-charged E2 coenzyme, which could enable its enzymatic activity. In addition, using cell-based screening, select E2 enzymes that redundantly, cooperatively or antagonistically regulate Parkin's activation and/or enzymatic functions at different stages of the mitochondrial autophagy (mitophagy) process were identified [Fiesel et al. (2014) J. Cell Sci. 127, 3488-3504]. Other work that aims to pin-point the particular pathogenic dysfunctions of Parkin mis-sense mutations have been recently disseminated (Fabienne C. Fiesel, Thomas R. Caulfield, Elisabeth L. Moussaud-Lamodiere, Daniel F.A.R. Dourado, Kotaro Ogaki, Owen A. Ross, Samuel C. Flores, and Wolfdieter Springer, submitted). Such a structure-function approach provides the basis for the dissection of Parkin's regulation and a targeted drug design to identify small-molecule activators of this neuroprotective E3 Ub ligase.
Carbon Microspheres Obtained from Resorcinol-Formaldehyde as High-Capacity Electrodes for Sodium-Ion Batteries (2005)

Microspherical carbon particles were prepared from a mixture of resorcinol and formaldehyde. The resulting gel was annealed at 950°C under an Ar atmosphere. The carbon microparticles exhibit a highly disordered structure and low specific surface area. A maximum reversible capacity of has been achieved in sodium cells, which is mainly developed () below 0.2 V. magic-angle spinning nuclear magnetic resonance results show the interaction between reversibly inserted sodium and carbon. Several electrolytes have been tested, and it has been concluded that tetrahydrofuran solvent improves the electrochemical performance of these carbon microspheres in sodium cells.
Carbonium Ions. VIII. Diarylolefin-Diarylalkyl Cation Equilibria1 (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbonium Ions. VIII. Diarylolefin-Diarylalkyl Cation Equilibria1N. C. Deno, Paul T. Groves, and George SainesCite this: J. Am. Chem. Soc. 1959, 81, 21, 5790–5795Publication Date (Print):November 1, 1959Publication History Published online1 May 2002Published inissue 1 November 1959https://pubs.acs.org/doi/10.1021/ja01530a059https://doi.org/10.1021/ja01530a059research-articleACS PublicationsRequest reuse permissionsArticle Views86Altmetric-Citations53LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Joint admission control and antenna assignment for multiclass QoS in spatial multiplexing MIMO wireless networks (2009)

We consider the problem of quality-of-service (QoS) provisioning for multiple traffic classes in a MIMO wireless network. This QoS provisioning is posed as a radio resource management (RRM) problem at a wireless node (e.g., a wireless mesh router) with multiple antennas. We decompose this RRM problem into two tractable subproblems, namely, the antenna assignment and the admission control problems. The objective of antenna assignment is to minimize the weighted packet dropping probability for the different traffic classes under constrained packet delay. The objective of admission control is to maximize the revenue of the wireless node gained from the ongoing connections for different traffic classes under constrained connection blocking probability and average per-connection throughput. The decision of antenna assignment is made in a short-term basis (e.g., for every packet transmission interval) while that of admission control is made in a long-term basis (i.e., when a connection arrives). Constrained Markov decision process (CMDP) models are formulated to obtain the optimal decisions on antenna assignment and admission control. To provide efficient channel utilization, the RRM framework considers adaptive modulation at the physical layer which exploits channel state information. Performance evaluation results show that this joint antenna assignment and admission control framework can provide class-based service differentiation while satisfying both the connection-level and packet-level QoS requirements.
Hybrid genetic algorithms for analogue network synthesis (2003)

Network synthesis involves the selection of a suitable network topology and the choice of component values. Genetic algorithms can be used to perform both of these functions, but it is more efficient to adopt a hybrid approach in which a genetic algorithm is used to determine the network topology whilst the component values are obtained by numerical optimization.
Compound Heterozygote for a Novel Elongated C-Terminal β-Globin Variant (HBB: c.364delG) and Hb E (HBB: c.79G>A) with Heterozygous α-Thalassemia-2 (2019)

This study reports the case of 2-year-old Northeastern Thai girl with β-thalassemia (β-thal) disease who has required regular blood transfusions since she was 8 months old. Hemoglobin (Hb) analysis by high performance liquid chromatography (HPLC) separated Hb A<sub>2</sub>/E (16.5%), Hb F (22.7%), Hb A (51.8%) and an abnormal peak (Hb X) found at a retention time (RT) of 5.05 min. (C-window) with 2.8%. Multiplex gap-polymerase chain reaction (gap-PCR) revealed heterozygous α-thalassemia-2 (α-thal-2) (-α<sup>3.7</sup>/αα; NG_000006.1: g.34164_37967 del3804). This patient was suspected of having a β-globin chain variant and Hb E (<i>HBB</i>: c.79G>A) according to the high Hb F level and disease presentations. Surprisingly, Hb Mahasarakham (the geographic origin of the proband), a novel single nucleotide deletion (-G) at the first nucleotide of codon 121 (<i>HBB</i>: c.364delG), was identified by direct DNA sequencing and secondary confirmation by PCR-restriction fragment length polymorphism (PCR-RFLP). This novel mutation causes a frameshift mutation and added 10 more residues to the β-globin chain that was elongated to 156 amino acids. Molecular basis of this novel mutation in the heterozygous state is required to confirm the mode of inheritance.
Preclinical Investigation of the Novel Histone Deacetylase Inhibitor AR-42 in the Treatment of Cancer-Induced Cachexia (2015)

These findings support further investigation of AR-42 as part of a comprehensive therapeutic strategy for cancer cachexia.
Local ablation therapy for hepatocellular carcinoma. From ethanol injection to radiofrequency ablation. (2007)

This article reviews the current status of local ablation therapy for hepatocellular carcinoma HCC. In the treatment of HCC, non-surgical treatments play important roles since only 20-30% of patients are candidates for surgery. Still worse, even after curative surgical resection, 80% of patients develop recurrence within 5 years. Among non-surgical treatments, image-guided local ablation therapies have been widely used for cases of small-number and small-size lesions, because they are potentially curative, minimally invasive, and easily repeatable. Although percutaneous ethanol injection has long been a standard therapy, there has been a drastic shift from ethanol injection to radiofrequency ablation in recent years. Randomized controlled trials proved that radiofrequency ablation is superior to ethanol injection in the treatment of HCC from the viewpoint of not only treatment response but also long-term survival. Radiofrequency ablation will play more important roles in the treatment of HCC.
Immunohistochemical Analysis of LGR5 Expression in Pediatric Liver Disease (2015)

BACKGROUND In regenerating liver, hepatic progenitor cells (HPCs) are recruited in response to liver injury; however, there is a lack of highly specific human HPC markers for the hepatocyte lineage. LGR5, a Wnt‐associated adult stem cell marker, has been extensively studied in intestinal stem cells. Although LGR5 appears to be exclusively expressed by HPCs in mice, little is known about its expression in human liver. We hypothesized that LGR5+ cells are induced in the regenerative response to liver injury to potentially rescue dysfunctional hepatocytes. METHODS Using immunohistochemistry, we characterized LGR5 expression in pediatric liver diseases, using mainly liver explants ( n =36 cases total). RESULTS We found cytoplasmic LGR5 over‐expression in all 36 pediatric cases, including acute hepatic necrosis and cholestatic liver diseases. In 44% of cases, &gt;50% of hepatocytes were LGR5+, signifying a robust regenerative response. In contrast, there was only weak staining in bile ducts, suggesting hepatocyte‐specific expression. Marked peri‐portal expression was prominent in cholestatic diseases, consistent with known patterns of regeneration. Comparison to other regeneration markers will further characterize this hepatocyte progenitor cell phenotype. CONCLUSIONS Although we observed some degree of regenerative response in all cases examined, LGR5 was highly expressed in cholestatic liver diseases, possibly due to alternate regeneration pathways. These studies are the first to support a unique role for LGR5 in human hepatocyte regeneration and as a potential predictive marker for recovery of liver function in children. LGR5 INTENSITY TOTAL CASES WEAK + 1+ 2+ 3+ A1AT Deficiency (ATD) 15 0 2 5 8 Biliary Atresia (BA) 5 0 0 2 3 PFIC 10 1 1 5 3 Acute Hepatic Necrosis (ALF) 6 1 4 1 0 TOTAL CASES 36 2 7 13 14 image image
Systematic Error in Lung Nodule Volumetry: Effect of Iterative Reconstruction Versus Filtered Back Projection at Different CT Parameters (2012)

In a phantom model, no clinically relevant differences beyond reported interscan variation levels between lung nodule volumes were measured in nodules 5 mm or larger at reduced tube voltage and tube current-time product, with radiation dose reductions up to 90.6% for both FBP and iterative reconstruction, suggesting that it is safe to convert FBP protocols to iterative reconstruction and reduce tube voltage and tube current-time product for lung nodule follow-up. CT appears to slightly underestimate actual nodule volume.
Global impact of rotavirus vaccines (2010)

The WHO has recently recommended the inclusion of rotavirus vaccine in the national immunization programs of all countries. In countries in the Americas, Europe and Australia that have adopted routine childhood immunization against rotavirus, significant reductions in the burden of severe childhood diarrhea have been observed. Besides protecting vaccinated children, disease rates also appear to be reduced in unvaccinated children, suggesting indirect benefits from vaccination (i.e., herd protection). Early clinical trial data from Africa and Asia are promising, and further efforts are needed to optimize the benefits of vaccination in developing countries where vaccines are likely to have their greatest impact.
Down-Regulation of SOX2 Underlies the Inhibitory Effects of the Triphenylmethane Gentian Violet on Melanoma Cell Self-Renewal and Survival (2016)

Human melanomas contain a population of tumor-initiating cells that are able to maintain the growth of the tumor. We previously showed that the embryonic transcription factor SOX2 is essential for self-renewal and tumorigenicity of human melanoma-initiating cells. However, targeting a transcription factor is still challenging. Gentian violet (GV) is a cationic triphenylmethane dye with potent antifungal and antibacterial activity. Recently, a combination therapy of imiquimod and GV has shown an inhibitory effect against melanoma metastases. Whether and how GV affects melanoma cells remains unknown. Here we show that GV represses melanoma stem cell self-renewal through inhibition of SOX2. Mechanistically, GV hinders EGFR activation and inhibits the signal transducer and activator of transcription-3 [(STAT3)/SOX2] axis. Importantly, we show that GV treatment decreases STAT3 phosphorylation at residue tyrosine 705, thus preventing the translocation of STAT3 into the nucleus and its binding to SOX2 promoter. In addition, GV affects melanoma cell growth by promoting mitochondrial apoptosis and G2 cell cycle arrest. This study shows that in melanoma, GV affects both the stem cell and the tumor bulk compartments, suggesting the potential use of GV in treating human melanoma alone or in combination with targeted therapy and/or immunotherapy.
Canada Thistle (Cirsium arvense) Control in No-Tillage Corn (Zea mays) (1994)

Canada thistle control in no-tillage corn was studied in Western Maryland from 1990 to 1992. The best treatment at planting for controlling Canada thistle was a tank mixture of 2240 g/ha glyphosate plus 560 g/ha 2,4-D. Clopyralid applied at 210 and 280 g/ha alone and 106 g/ha tank mixed with 560 g/ha 2,4-D effectively controlled Canada thistle in no-tillage corn (85 to 96%). Nicosulfuron applied at 35 g/ha and 20 or 40 g/ha primisulfuron suppressed Canada thistle (59 to 75%). Tank mixtures of nicosulfuron or primisulfuron with 2,4-D or dicamba generally increased Canada thistle control (75 to 87%) compared with control by these herbicides applied alone. Treatments that controlled Canada thistle generally increased corn yields compared with the weedy controls. Yield increases were most dramatic in 1991 when precipitation was low.
Potential links between the emerging risk factors for food allergy and vitamin D status (2012)

A variety of hypotheses have been proposed to explain the recently described increase in food allergy among children living in developed countries. In this study, we summarize the emerging risk factors for IgE-mediated food allergy in early life, and then review the evidence for and against an association between low vitamin status (VDS) and food allergy. We consider whether each of the epidemiological variables that have been associated with food allergy may also be associated with VDS; and argue that future studies must adequately account for the potential relationships between risk factors for food allergy and VDS, and must also discriminate between vitamin D derived by sun exposure, diet and oral supplementation.
Asthma and corticosteroids: time for a more precise approach to treatment (2017)

It is well known that corticosteroids improve asthma in a subgroup of patients and that this responder subgroup is invariably large enough to drive statistically significant differences in asthma outcomes when steroids are compared to placebo in unselected patients. The consistency of clinical trial data showing benefit from corticosteroids, especially in less severe patients, is the reason why asthma treatment guidelines consistently advocate their daily use in all but the mildest forms of asthma. Guidelines also typically advocate an empiric approach to corticosteroid dosing in which the dose of corticosteroid is increased as disease severity worsens. Such empiric approaches to treatment are now considered flawed and the emphasis is switching to development of treatment approaches that are guided by mechanism-based molecular endotypes rather than trait-based clinical phenotypes. The reason is simple: asthma traits such as symptoms and airflow limitation result from heterogeneous molecular mechanisms, and a one-size-fits all treatment paradigm to treat these traits does not make sense. Prescribing corticosteroids for asthma based on mechanism-based endotypes rather than trait-based phenotypes <http://ow.ly/HiHq30cA6Da>
Immunosuppression management in renal transplant recipients with normal-immunological risk: 10-year results from the Swiss Transplant Cohort Study (2020)

The available data show that primary maintenance immunosuppression with tacrolimus has displaced ciclosporin-based therapies. The tacrolimus-based immunosuppression therapy showed consistently better results across almost all assessed clinically relevant outcomes. (ClinicalTrials.gov Number: NCT01204944).
MURINE PGK PROMOTER IN A LENTIVIRAL VECTOR IN CANINE LEUKOCYTE ADHESION DEFICIENCY AND IN HUMAN LAD-1 CD34+CELLS IN NSG MICE (2012)

The safety of lentiviral (LV) vectors for gene therapy of genetic hematopoietic diseases would be considerably enhanced by the identification of a non-viral promoter capable of driving therapeutic levels of transgene expression in the target cell. Here, we tested the efficacy of the murine phosphoglycerate kinase (mPgk) promoter in a self-inactivating (SIN) LV vector to express canine CD18 in animals with canine leukocyte adhesion deficiency (CLAD) and in human LAD-1 CD34+ cells in NSG mice. Despite high transduction levels and high levels of CD18 expression per cell in CLAD CD34+ cells in vitro using the mPgk vector to drive canine CD18 expression, only two of five CLAD animals treated with ex vivo gene therapy achieved therapeutic levels of CD18+ neutrophils in vivo. Similarly, despite high transduction efficiency and high levels of CD18 expression in human LAD-1 CD34+ cells in vitro, the mPgk-hCD18 promoter resulted in a low percentage of CD45+/CD18+ cells and low levels of CD18 expression per neutrophil, when the transduced cells were transplanted into NSG mice. In contrast, human LAD-1 CD34+ cells transduced with a LV vector containing the viral MND promoter (MND-hCD18) and injected into NSG mice displayed a high percentage of CD45+/CD18+ cells and high levels of CD18 expression per neutrophil. These studies demonstrated that the mPgk promoter does not direct sufficient CD18 expression in neutrophils to replace a viral promoter for gene therapy of children with LAD-1.
The Effects of Increased Levels of Niacin Supplementation on Growth Rate and Carcass Composition of Broiler Chickens (1985)

Four experiments were conducted to examine the response of broiler chickens to different levels of niacin. Practical-type diets, calculated to contain from 20.7 to 23.7 mg niacin per kg from intact ingredients, were fortified with a complete vitamin mixture which provided 33 mg supplemental niacin per kg of diet, in excess of the National Research Council (1977) suggested requirement of 27 mg per kg through 6 weeks of age. A niacinamide supplement was used to provide additional levels of 0, 33, or 66 mg per kg. Diets differed in content of added fat and energy levels in two of the experiments and in the presence or absence of animal protein sources in two others. The addition of niacinamide at 33 and 66 mg per kg to a diet already supplemented with 33 mg per kg from a complete vitamin premix, calculated to exceed the present NRC suggested requirement, resulted in improved body weight gains with sex differences noted in some experiments. Feed utilization was improved in some studies. There was no effect on the amount of abdominal fat or carcass dressing percentage. The results of these studies indicate that the modern rapidly growing broiler chick may require niacin levels greater than those generally recommended by the National Research Council (1977), which are based largely on studies where performance was considerably lower than obtained with the modern strains of broilers.
Cold Sintered Ceramics and Cements for Part Encapsulation (2021)

In this project, ceramic encapsulation materials were studied for high temperature (>~500 o C) applications where typical polymer encapsulants are unstable. A new low temperature (<~200 o C) method of processing ceramics, the cold sintering process was examined. Additionally, commercially available high temperature ceramic cements were investigated. In both cases, the mechanical strengths of available materials are less than desired (i.e., desired strengths similar to Si 3 N 4 ), limiting applicability. Composite designs to increase mechanical strength are suggested. Additionally, non-uniformities in stresses and densification while embedding alumina sheets in encapsulants via cold sintering using uni-axial pressing led to fracture of sheets, and an alternative iso-static based approach is recommended for future studies.
Social Alignment for Preprocessing User-Constructed Ontologies (2007)

User-constructed ontologies have caused some difficulties in being discriminated from other user-constructed ontologies. For efficiently annotating resources in their own repositories, people simply append ontology fragments retrieved from standard ontologies and from other neighbors' ontologies along to social links. In this paper, we propose a preprocessing method to extract preferential concepts for comparing with social semantics. In order to prune out irrelevant concepts from user-constructed ontologies, alignment-based concept classification process is designed by checking these two main criteria; i) redundancy (e.g., if there already exist semantically identical concepts), and ii) tendency (e.g., if there exist semantically declined concepts). Finally, we want to show an application scenario to demonstrate our contributions.
ALMDS laser system (2003)

The ALMDS (Airborne Laser Mine Detection System) has been developed utilizing a solid-state laser operating at 532nm for naval mine detection. The laser system is integrated into a pod that mounts externally on a helicopter. This laser, along with other receiver systems, enables detailed underwater bathymetry. CEO designs and manufactures the laser portion of this system. Arete Associates integrates the laser system into the complete LIDAR package that utilizes sophisticated streak tube detection technology. Northrop Grumman is responsible for final pod integration. The laser sub-system is comprised of two separate parts: the LTU (Laser Transmitter Unit) and the LEU (Laser Electronics Unit). The LTU and LEU are undergoing MIL-STD-810 testing for vibration, shock, temperature storage and operation extremes, as well as MIL-STD-704E electrical power testing and MIL-STD-461E EMI testing. The Nd:YAG MOPA laser operates at 350 Hz pulse repetition frequency at 45 Watts average 532nm power and is controlled at the system level from within the helicopter. Power monitor circuits allow real time laser health monitoring, which enables input parameter adjustments for consistent laser behavior.