gebhart/patrepeval huggingface dataset:
A Chalcone from Ashitaba (Angelica keiskei) Stimulates Myoblast Differentiation and Inhibits Dexamethasone-Induced Muscle Atrophy (2019)

Ashitaba, <i>Angelica keiskei</i> Koidzumi (AK), as a traditional medicine in Korea, Japan, and China, has been known as an elixir of life having therapeutic potential. However, there is no scientific evidence to support that Ashitaba can enhance or maintain muscle strength. To find a new therapeutic agent from the medicinal plant, we evaluated the anti-myopathy effect of chalcones from ethanol extract of AK (EAK) in cellular and animal models of muscle atrophy. To examine anti-myopathy activity, EAK was treated into dexamethasone injected rats and muscle thickness and histopathological images were analyzed. Oral administration of EAK (250 or 500 mg/kg) alleviated muscle atrophic damages and down-regulated the mRNA levels of muscle-specific ubiquitin-E3 ligases. Among ten compounds isolated from EAK, 4-hydroxyderricin was the most effective principle in stimulating myogenesis of C2C12 myoblasts <i>via</i> activation of p38 mitogen-activated protein kinase (MAPK). In three cellular muscle atrophy models with C2C12 myoblasts damaged by dexamethasone or cancer cell-conditioned medium, 4-hydroxyderricin protected the myosin heavy chain (MHC) degradation through suppressing expressions of MAFbx, MuRF-1 and myostatin. These results suggest that the ethanol extract and its active principle, 4-hydroxyderricin from AK, can overcome the muscle atrophy through double mechanisms of decreasing muscle protein degradation and activating myoblast differentiation.
Atomic Layer Deposition of Nanostructured TiO2 Photocatalysts via Template Approach (2007)

Two kinds of TiO2 nanostructures, i.e., TiO2-coated alumina membranes and TiO2-coated Ni nanowires, were prepared by combining different kinds of porous alumina, template-directed electrodeposition and atomic layer deposition. The photocatalytic activities of the nanostructures were tested with methylene blue degradation under UV illumination. All structures showed photocatalytic activity, and the efficiency of the photocatalytic performance was found to be a strong function of the dimensions of the nanostructure.
Prevention of vaginal and rectal HIV transmission by antiretroviral combinations in humanized mice (2017)

With more than 7,000 new HIV infections daily worldwide, there is an urgent need for non-vaccine biomedical prevention (nBP) strategies that are safe, effective, and acceptable. Clinical trials have demonstrated that pre-exposure prophylaxis (PrEP) with antiretrovirals (ARVs) can be effective at preventing HIV infection. In contrast, other trials using the same ARVs failed to show consistent efficacy. Topical (vaginal and rectal) dosing is a promising regimen for HIV PrEP as it leads to low systematic drug exposure. A series of titration studies were carried out in bone marrow/liver/thymus (BLT) mice aimed at determining the adequate drug concentrations applied vaginally or rectally that offer protection against rectal or vaginal HIV challenge. The dose-response relationship of these agents was measured and showed that topical tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) can offer 100% protection against rectal or vaginal HIV challenges. From the challenge data, EC50 values of 4.6 μM for TDF and 0.6 μM for FTC for HIV vaginal administration and 6.1 μM TDF and 0.18 μM for FTC for rectal administration were obtained. These findings suggest that the BLT mouse model is highly suitable for studying the dose-response relationship in single and combination ARV studies of vaginal or rectal HIV exposure. Application of this sensitive HIV infection model to more complex binary and ternary ARV combinations, particularly where agents have different mechanisms of action, should allow selection of optimal ARV combinations to be advanced into pre-clinical and clinical development as nBP products.
Surface-based registration of liver in ultrasound and CT (2015)

Ultrasound imaging is an attractive modality for real-time image-guided interventions. Fusion of US imaging with a diagnostic imaging modality such as CT shows great potential in minimally invasive applications such as liver biopsy and ablation. However, significantly different representation of liver in US and CT turns this image fusion into a challenging task, in particular if some of the CT scans may be obtained without contrast agents. The liver surface, including the diaphragm immediately adjacent to it, typically appears as a hyper-echoic region in the ultrasound image if the proper imaging window and depth setting are used. The liver surface is also well visualized in both contrast and non-contrast CT scans, thus making the diaphragm or liver surface one of the few attractive common features for registration of US and non-contrast CT. We propose a fusion method based on point-to-volume registration of liver surface segmented in CT to a processed electromagnetically (EM) tracked US volume. In this approach, first, the US image is pre-processed in order to enhance the liver surface features. In addition, non-imaging information from the EM-tracking system is used to initialize and constrain the registration process. We tested our algorithm in comparison with a manually corrected vessel-based registration method using 8 pairs of tracked US and contrast CT volumes. The registration method was able to achieve an average deviation of 12.8mm from the ground truth measured as the root mean square Euclidean distance for control points distributed throughout the US volume. Our results show that if the US image acquisition is optimized for imaging of the diaphragm, high registration success rates are achievable.
A DOI-Dependent Extended Energy Window Method to Control Balance of Scatter and True Events (2008)

In a conventional PET scanner, coincidence events are limited by the energy window for detection of photoelectric events. In contrast, Compton scatter events occur both in a patient and in detector crystals. Scatter events within the patient cause scatter coincidences, but scatter events within crystals have useful information for an activity distribution. The PET scanner with an extended energy window has higher sensitivity but higher scatter fraction than the PET scanner with a default energy window. In this work, we develop a scatter reduction method using a depth-of-interaction (DOI) detector. The DOI detector can make an upper layer act as an absorber of patient scatter, thus shielding a lower layer. Therefore, Compton scatter events with an interaction at the lower layer mainly have more crystal scatter events than patient scatter events. Our method proposes a different energy window for each layer. The energy window of the upper layer is limited to the region of photopeak events, the same as done for the conventional PET scanner. The energy window of the lower layer is extended to the region of crystal scatter events and photopeak events. We tested our proposed technique for a whole-body PET scanner using GATE simulations. Simulation results show the DOI-PET scanner can provide more true events while keeping a low scatter fraction using our scatter reduction method. We conclude this method is promising for obtaining high image quality using DOI information and energy information.
Proceedings of the 5th international conference on automotive user interfaces and interactive vehicular applications, 28-30 October 2013, Eindhoven, The Netherlands (2013)

Innovations in the area of vehicle electronics, sensing technologies and wireless communication (including both vehicle-to-vehicle (V2V) and vehicle-to-roadside (V2X)) are resulting in a rapid change of the driving context. Over the last few years, a rapid increase can be observed in the number of systems aiming to support the driver and increase the safety and comfort. Ultimately, the combination of these support systems may lead to the complete automation of the driving task. In addition, developments in the area of wireless communication have vastly increased the possibilities for drivers and passengers alike to take nomadic appliances within the car for entertainment and communication purposes. These developments create both opportunities and challenges for researchers and developers in the area of automotive user interfaces and interactive vehicular applications.
Vertically aligned carbon nanofibers as sacrificial templates for nanofluidic structures (2003)

We report a method to fabricate nanoscale pipes (“nanopipes”) suitable for fluidic transport. Vertically aligned carbon nanofibers grown by plasma-enhanced chemical vapor deposition are used as sacrificial templates for nanopipes with internal diameters as small as 30 nm and lengths up to several micrometers that are oriented perpendicular to the substrate. This method provides a high level of control over the nanopipe location, number, length, and diameter, permitting them to be deterministically positioned on a substrate and arranged into arrays.
The Effect of Changes in the Leader Sequence of Human Protein C on Biosynthetic Processing and Gamma-Carboxylation (1987)

Protein C is the precursor to a serine protease in plasma which contains gamma-carboxy glutamic acid and functions as a potent anticoagulant. Protein C shows considerable structural homology with the other vitamin K-dependent coagulation factors including prothrombin, factor VII, factor IX and factor X. This homology includes the putative pro-peptide region of the prepro leader sequences for these proteins, as well as the leader sequences for gamma-carboxylated proteins from bone. Deletion mutants have been constructed in the cDNA for human protein C in order to test the possibility that the pro-peptide portion of the 42 amino acid leader sequence serves as a molecular signal for gamma-carboxylation. Accordingly, these mutants contain the pre-peptide (hydrophobic leader) plus portions of the pro-peptide at the amino terminus of the light chain. The mutant proteins were expressed in carboxylation-competent mammalian cells and analyzed by barium citrate precipitation and N-terminal amino acid sequencing. These studies have shown that deletions in the pro-peptide region interfere with gamma-carboxylation and removal of the pro-peptide. Deletion of residues −1 through −12 had little effect on the carboxylation or secretion. Deletion of −1 through −17 completely abolished gamma-carboxylation, but had no measurable effect on secretion. Amino terminal sequence analysis of the latter mutant showed that the light chain began with Thr-Pro-Ala-Pro... This corresponds to a sequence in the prepro leader starting at −24. This indicates that the signal peptidase cleavage site for human protein C is between residues −25 and −24 and removal of the pro-peptide had been blocked by the deletion.
The Impact of Protein Corona Formation on the Macrophage Cellular Uptake and Biodistribution of Spherical Nucleic Acids (2017)

The effect of serum protein adsorption on the biological fate of Spherical Nucleic Acids (SNAs) is investigated. Through a proteomic analysis, it is shown that G-quadruplexes templated on the surface of a gold nanoparticle in the form of SNAs mediate the formation of a protein corona that is rich in complement proteins relative to SNAs composed of poly-thymine (poly-T) DNA. Cellular uptake studies show that complement receptors on macrophage cells recognize the SNA protein corona, facilitating their internalization, and causing G-rich SNAs to accumulate in the liver and spleen more than poly-T SNAs in vivo. These results support the conclusion that nucleic acid sequence and architecture can mediate nanoparticle-biomolecule interactions and alter their cellular uptake and biodistribution properties and illustrate that nucleic acid sequence is an important parameter in the design of SNA therapeutics.
The amino terminus of tau inhibits kinesin‐dependent axonal transport: Implications for filament toxicity (2008)

The neuropathology of Alzheimer's disease (AD) and other tauopathies is characterized by filamentous deposits of the microtubule-associated protein tau, but the relationship between tau polymerization and neurotoxicity is unknown. Here, we examined effects of filamentous tau on fast axonal transport (FAT) using isolated squid axoplasm. Monomeric and filamentous forms of recombinant human tau were perfused in axoplasm, and their effects on kinesin- and dynein-dependent FAT rates were evaluated by video microscopy. Although perfusion of monomeric tau at physiological concentrations showed no effect, tau filaments at the same concentrations selectively inhibited anterograde (kinesin-dependent) FAT, triggering the release of conventional kinesin from axoplasmic vesicles. Pharmacological experiments indicated that the effect of tau filaments on FAT is mediated by protein phosphatase 1 (PP1) and glycogen synthase kinase-3 (GSK-3) activities. Moreover, deletion analysis suggested that these effects depend on a conserved 18-amino-acid sequence at the amino terminus of tau. Interestingly, monomeric tau isoforms lacking the C-terminal half of the molecule (including the microtubule binding region) recapitulated the effects of full-length filamentous tau. Our results suggest that pathological tau aggregation contributes to neurodegeneration by altering a regulatory pathway for FAT.
SBPOR (2007)

RLC circuits have been shown to be better formulated as second-order systems instead of first-order systems. The corresponding model order reduction techniques for second- order systems have been developed. However, existing techniques are mainly based on moment-matching concept. While suitable for the reduction of large-scale circuits, those approaches cannot generate reduced models as compact as desired. To achieve smaller models with better error control, a novel technique, SBPOR (Second-order Balanced truncation for Passive Order Reduction), is proposed in this paper, which is the first second-order balanced truncation method proposed for passive reduction of RLC circuits. SBPOR is superior to the pioneering work in the control community because second-order systems can be balanced via congruency transformation without any accuracy loss. In addition, compared with the first-order balanced truncation approaches, SBPOR is a better choice for RLC reduction. SBPOR preserves not only passivity but also the structure information inherent to RLC circuits, which is a special need for RLC reduction. In addition, SBPOR is computationally more efficient as it only needs to solve one linear matrix equation instead of two quadratic matrix equations.
Differential expression of stathmin during neoplastic conversion of human prostate epithelial cells is reversed by hypomethylating agent, 5-azacytidine. (1999)

In a variety of human tumor tissues, including those of prostate and breast, CpG hypermethylation represents one of the mechanisms downregulating the expression of specific proteins, including tumor suppressor proteins. Using 267B1-XR cells generated by ionizing radiation-induced transformation of epithelial cells, derived from neonatal human prostate and immortalized by SV40 (267B1), we now report markedly low levels of expression of the cytoplasmic phosphoprotein stathmin, in addition to several proteins of the actin microfilaments and intermediate filaments that characterize the altered phenotype. Stathmin is emerging as a relay protein integrating signals from diverse pathways during differentiation and neoplastic progression. In this in vitro prostate carcinogenesis model system, where loss of specific-protein expression is a major feature of the transformed 267B1-XR cells, we employed 5-azacytidine treatment followed by 2D-PAGE to reveal if experimental genomic hypomethylation reinstated the levels of any of the differentially expressed proteins. Our data suggest that stathmin represents one such example.
Lymphomatoid Granulomatosis: A Clinicopathologic Study of a Series of Cases in a Single Institution (2011)

Abstract Abstract 4960 Introduction: Lymphomatoid granulomatosis is a rare lymphoproliferative disorder with a proclivity for extranodal involvement, including the lungs, brain, kidney, liver, and skin. It usually affects middle-age adults, with male predominance (M:F ratio &gt;2:1). Its association with EBV (Epstein Barr Virus) infection has been described. Objectives: To present our experience of 8 cases of lymphomatoid granulomatosis at Moffitt Cancer Center (MCC) in the last 10 years. Results: We collected the data of 8 cases of lymphomatoid granulomatosis that were diagnosed and treated at MCC from January 2000 to January 2011. The median follow up was 7.5 months. Five out 8 (63%) cases were males. The median age was 65. 3/8 (12.5%) had a performance status (PS) more than 2. 4/8 (50%) of cases had elevated LDH. All patients (100%) had an Ann Arbor Stage IVE. The IPI (International Prognostic Index) was more than high-intermediate in 6/8 (75%) cases. 4/8 (50%) of cases were positive for EBV. 6/8 (75%) have received chemotherapy to date, most commonly R+CHOP. The median time to progression was 8.6 months (1-8 months) following the first treatment and was shorter after the second treatment (4.8 months). 2/8 (25%) are disease free after chemotherapy, all remaining patients have active disease. 2/8 (25%) have died at 7 and 13 months after diagnosis. Conclusions: Lymphomatoid granulomatosis is a rare lymphoproliferative disease. In our experience it presents as an advanced and high risk disease. Interestingly, EBV was found in only 50% of cases. The overall response to standard chemotherapy is suboptimal and further strategies are needed for optimal management. These might include aggressive chemotherapy and up front stem cell transplantation. Disclosures: No relevant conflicts of interest to declare.
Xq26.3 Duplication in a Boy With Motor Delay and Low Muscle Tone Refines the X-Linked Acrogigantism Genetic Locus (2018)

We describe a 4-year-old boy with developmental delay who was found to carry by clinical grade (CG) molecular cytogenetics (MCs) a chromosome Xq26 microduplication. The report prompted a referral of the patient for possible X-linked acrogigantism (X-LAG), a well-defined condition (MIM300942) due to chromosomal microduplication of a nearby region. The patient was evaluated clinically and investigated for endocrine abnormalities related to X-LAG and not only did he not have acrogigantism, but his growth parameters and other hormones were all normal. We then performed high definition MCs and the duplication copy number variant (CNV) was confirmed to precisely map outside the X-LAG critical region and definitely did not harbor the X-LAG candidate gene, <i>GPR101</i>. The patient's phenotype resembled that of other patients with Xq26 CNVs. The case is instructive for the need for high definition MCs when CG MCs' results are inconsistent with the patient's phenotype. It is also useful for further supporting the contention that <i>GPR101</i> is the gene responsible for X-LAG.
IKOMA at TAC2011: A Method for Recognizing Textual Entailment using Lexical-level and Sentence Structure-level features (2011)

This paper describes the Recognizing Textual Entailment (RTE) system that our teams developed for TAC 2011. Our system combines the entailment score calculated by lexicallevel matching with the machine-learningbased filtering mechanism using various features obtained from lexical-level, chunk-level and predicate argument structure-level information. In the filtering mechanism, we try to discard the T-H pairs that have high entailment score and are actually not entailment. That is, for filtering false positive T-H pairs caused by our lexical-level manner, we use additional information like features from word chunks and predicate-argument structures.
Ketosynthases in the Initiation and Elongation Modules of Aromatic Polyketide Synthases Have Orthogonal Acyl Carrier Protein Specificity (2003)

Many bacterial aromatic polyketides are synthesized by type II polyketide synthases (PKSs) which minimally consist of a ketosynthase-chain length factor (KS-CLF) heterodimer, an acyl carrier protein (ACP), and a malonyl-CoA:ACP transacylase (MAT). This minimal PKS initiates polyketide biosynthesis by decarboxylation of malonyl-ACP, which is catalyzed by the KS-CLF complex and leads to incorporation of an acetate starter unit. In non-acetate-primed PKSs, such as the frenolicin (fren) PKS and the R1128 PKS, decarboxylative priming is suppressed in favor of chain initiation with alternative acyl groups. Elucidation of these unusual priming pathways could lead to the engineered biosynthesis of polyketides containing novel starter units. Unique to some non-acetate-primed PKSs is a second catalytic module comprised of a dedicated homodimeric KS, an additional ACP, and a MAT. This initiation module is responsible for starter-unit selection and catalysis of the first chain elongation step. To elucidate the protein-protein recognition features of this dissociated multimodular PKS system, we expressed and purified two priming and two elongation KSs, a set of six ACPs from diverse sources, and a MAT. In the presence of the MAT, each ACP was labeled with malonyl-CoA rapidly. In the presence of a KS-CLF and MAT, all ACPs from minimal PKSs supported polyketide synthesis at comparable rates (k(cat) between 0.17 and 0.37 min(-1)), whereas PKS activity was attenuated by at least 50-fold in the presence of an ACP from an initiation module. In contrast, the opposite specificity pattern was observed with priming KSs: while ACPs from initiation modules were good substrates, ACPs from minimal PKSs were significantly poorer substrates. Our results show that KS-CLF and KSIII recognize orthogonal sets of ACPs, and the additional ACP is indispensable for the incorporation of non-acetate primer units. Sequence alignments of the two classes of ACPs identified a tyrosine residue that is unique to priming ACPs. Site-directed mutagenesis of this amino acid in the initiation and elongation module ACPs of the R1128 PKS confirmed the importance of this residue in modulating interactions between KSs and ACPs. Our study provides new biochemical insights into unusual chain initiation mechanisms of bacterial aromatic PKSs.
The internal transcribed spacers and 5.8S rRNA gene show extensive diversity among isolates of the species complex (2003)

Sequences of the internal transcribed spacer (ITS) region including the 5.8S rRNA gene delineated seven genotypes within the three varieties of Cryptococcus neoformans via specific combinations of eight nucleotide differences located at positions 10, 11, 15, 19, 108 (ITS1), 221 (5.8S), 298 and 346 (ITS2). The ITS types correlated to polymerase chain reaction fingerprint/random amplification of polymorphic DNA (RAPD) molecular types: with ITS type 1 (ATACTAGC)=C. neoformans var. grubii, molecular types VNI+VNII and the serotype A allele of the AD hybrid, VNIIIA; ITS type 2 (ATATAGGC)=the serotype D allele of the AD hybrid, VNIIIB, and C. neoformans var. neoformans, VNIV; and ITS type 3 (GCGCTGGC) and ITS type 7 (ACGCTGGC)=VGI=RAPD type III, ITS type 4 (ACACTGAC)=VGII=RAPD type II, ITS type 5: (ACACTGGG)=VGIII=RAPD type I, ITS type 6 (ACACTGGC)=VGIV=RAPD type IV, all corresponding to C. neoformans var. gattii. Cloned sequences from serotype AD revealed that the hybrid serotype is diploid at the ITS1-5.8S-ITS2 locus carrying the ITS type 1 (ATACTAGC) and the ITS type 2 (ATATAGGC) alleles. ITS sequencing is a useful technique for genotyping the three C. neoformans varieties and for subtyping within C. neoformans var. gattii.