Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature dependence and mechanism of hydrogen incorporation in olivine at 12.5–14.0 GPa

The concentration and incorporation mechanisms of hydrogen into (Mg, Fe)2SiO4 olivine have been studied under water saturated conditions at 12.5–14.0 GPa and 1100–2000°C. The hydrogen content of olivine (Fo90–Fo95) coexisting with enstatite and hydrous melt increases from about 4600 ppmw at 1100°C to a maximum of 6250 ppmw at 1200°C. Above 1400°C, the hydrogen content of olivine decreases non‐linearly, reaching 160–240 ppmw in the 1800–2000°C range where there is a high melt fraction and no enstatite. Polarized infrared spectra of the recovered olivines exhibit OH absorption bands in both the 3450–3650 cm−1 range (group I) and 3160–3450 cm−1 range (group II). Results indicate that hydration of olivine is associated with both Mg and Si site vacancies. Microprobe analyses of the samples show a clear deficit of Si in olivine. The water storage capacity of olivine is probably no more than 1.5–2.0 times less than wadsleyite at 1400°C and transition zone pressures.
Parallel optical interconnect between ceramic BGA packages on FR4 board using embedded waveguides and passive optical alignments

We have studied technologies to design and fabricate high-bit-rate chip-to-chip optical interconnects on printed circuit boards (PCBs) using board-embedded polymer waveguides and surface-mounted component packages or modules. In order to demonstrate the developed technologies, a 4times10 Gb/s optical interconnect was completely integrated on a standard FR4 PCB. The optical link demonstrator consists of 4-channel BGA-mounted transmitter and receiver modules as well as of four parallel multimode optical waveguides fabricated on top of the solder mask of the PCB using lithographic patterning. The transmitters and receivers built on low-temperature co-fired ceramic (LTCC) substrates include 4times10 Gb/s flip-chip mounted VCSEL or photodiode array, wire-bonded driver and receiver ICs, and optical coupling structures. Two microlens arrays and a micro-mirror enable optical coupling between the optoelectronic devices and the waveguide array. The passive optical alignment was based on the marks and structures fabricated both in the LTCC process and in the patterning of the optical layers. The characterized optical alignment tolerances are in the limits of accuracy of the surface-mount technology. The demonstrated technology is suitable for interconnecting CBGA-packaged ICs or multi-chip-modules
A Semi-Supervised Method for Multimodal Classification of Consumer Videos

In large databases, lack of labeled training data leads to major difficulties in classification process. Semi-supervised algorithms are employed to suppress this problem. Video databases are the epitome for such a scenario. Fortunately, graph-based methods have shown to form promising platforms for semi-supervised video classification. Based on multimodal characteristics of video data, different features (SIFT, STIP, and MFCC) have been utilized to build the graph. In this paper, we have proposed a new classification method which fuses the results of manifold regularization over different graphs. Our method acts like a co-training method that tries to find the correct label for unlabeled data during its iterations. But, unlike other co-training methods, it takes into account the unlabeled data in the classification process. After manifold regularization, data fusion is doneby a ranking method which improves the algorithm to become competitive with supervised methods. Our experimental results, run on the CCV database, show the efficiency of the proposed classification method.
Analysis of the discordance between radiographic changes and knee pain in osteoarthritis of the knee.

OBJECTIVE To analyze cross sectional data from the National Health and Nutrition Examination Survey (NHANES I) concerning 3 indicators of osteoarthritis (OA) of the knee: radiographic evidence of structural damage, self-reported knee pain, and self-report of a diagnosis of arthritis at any joint by a physician. METHODS Analysis of NHANES I data for 6880 persons ages 25-74 in the United States. RESULTS Radiographic stage 2-4 knee OA was found in 319 subjects (3.7%); only 47% of these individuals reported knee pain, and only 61% reported that a physician had told them that they had arthritis. Knee pain was reported by 1004 subjects (14.6%), only 15% of whom had radiographic stage 2-4 changes of OA, and 59% of whom reported having a diagnosis of arthritis by a physician. A report of arthritis diagnosed by a physician was given by 1762 subjects (25.6%), of whom only 11% had stage 2-4 radiographic knee OA and 34% reported knee pain. CONCLUSION Substantial discordance exists in this population based study between radiographic OA of the knee versus knee pain, versus a diagnosis of arthritis by a physician. These phenomena may be important in the design of clinical research studies, as well as in criteria for OA.
Structure networks of E. coli glutaminyl‐tRNA synthetase: Effects of ligand binding

It is well known that proteins undergo backbone as well as side chain conformational changes upon ligand binding, which is not necessarily confined to the active site. Both the local and the global conformational changes brought out by ligand‐binding have been extensively studied earlier. However, the global changes have been reported mainly at the protein backbone level. Here we present a method that explicitly takes into account the side chain interactions, yet providing a global view of the ligand‐induced conformational changes. This is achieved through the analysis of Protein Structure Networks (PSN), constructed from the noncovalent side chain interactions in the protein. Here, E. coli Glutaminyl‐tRNA synthetase (GlnRS) in the ligand‐free and different ligand‐bound states is used as a case study to assess the effect of binding of tRNA, ATP, and the amino acid Gln to GlnRS. The PSNs are constructed on the basis of the strength of noncovalent interactions existing between the side chains of amino acids. The parameters like the size of the largest cluster, edge to node ratio, and the total number of hubs are used to quantitatively assess the structure network changes. These network parameters have effectively captured the ligand‐induced structural changes at a global structure network level. Hubs, the highly connected amino acids, are also identified from these networks. Specifically, we are able to characterize different types of hubs based on the comparison of structure networks of the GlnRS system. The differences in the structure networks in both the presence and the absence of the ligands are reflected in these hubs. For instance, the characterization of hubs that are present in both the ligand‐free and all the ligand‐bound GlnRS (the invariant hubs) might implicate their role in structural integrity. On the other hand, identification of hubs unique to a particular ligand‐bound structure (the exclusive hubs) not only highlights the structural differences mediated by ligand‐binding at the structure network level, but also highlights significance of these amino acids hubs in binding to the ligand and catalyzing the biochemical function. Further, the hubs identified from this study could be ideal targets for mutational studies to ascertain the ligand‐induced structure–function relationships in E. coli GlnRS. The formalism used in this study is simple and can be applied to other protein‐ligands in general to understand the allosteric changes mediated by the binding of ligands. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Anisotropic LBP descriptors for robust smoke detection

Image based smoke detection is a difficult problem especially in open areas since it is heavily affected from its environmental objects. This comes from the transparent property of smoke itself. Therefore, to realize robust smoke detection in such situation, it needs to take into account the effect of the degree of transparency, the change of background objects and so forth. To describe smoke information by image features, they are affected from degree of transparency of smoke, background objects, and other environmental conditions such as the direction and the speed of wind. To address such problems, we apply a novel image feature named anisotropic LBP descriptors, which is considered as a extended variants of LBP. The anisotropic LBP descriptors are simply extended from LBP, which are defined as texture operator using anisotropic neighborhood pixel values. Therefore, they can describe anisotropic deformed image information, which are caused from environmental conditions. To obtain more accurate detection results, we also adopt AdaBoost which uses anisotropic LBP descriptors as input vectors. In this study, each AdaBoost classifier is trained for every anisotropic LBP descriptor and the detection result is obtained from the combined result of those AdaBoost classifiers. We evaluate our presented method and confirm that the our approach works well to obtain robust results.
A rapid method for identifying bacterial enzymes.

Biochemical tests for characterizing bacteria are often time-consuming. They generally involve detecting one or more bacterial enzyme by using colour changes, coagulation, turbidity or gas for-mation as indices of enzyme activity. These visual changes depend on the conversion of relatively large amounts of substrate by the enzyme. Qualitative tests for bacterial enzyme activity could be made much more rapid by increasing the sensitivity of detection of the reaction products by the human eye. We describe here a simple and rapid method for detecting bacterial enzymes that depends on the release of a fluorescent reaction product (methylum-belliferone) from a non-fluorescent substrate (methyl-umbelliferyl substrate).
Reductive Decomposition Reactions of Ethylene Carbonate by Explicit Electron Transfer from Lithium: An eReaxFF Molecular Dynamics Study

A detailed understanding of the mechanism of the formation of the solid electrolyte interphase (SEI) is crucial for designing high-capacity and longer-lifecycle lithium-ion batteries. The anode-side SEI primarily consists of the reductive dissociation products of the electrolyte molecules. Any accurate computational method for studying the reductive decomposition mechanism of electrolyte molecules is required to include an explicit electronic degree of freedom. In this study, we employed our newly developed eReaxFF method to investigate the major reduction reaction pathways of SEI formation with ethylene carbonate (EC) based electrolytes. In the eReaxFF method, electrons are treated explicitly in a pseudoclassical manner. The method has the ability to simulate explicit electrons in a complex reactive environment. Our eReaxFF-predicted results for the EC decomposition reactions are in good agreement with the quantum chemistry data available in the literature. Our molecular dynamics (MD) simulations capture.
Agrobacterium rhizogenes mediated hairy root induction for increased Colchicine content in Gloriosa superba

Gloriosa superba L. a medicinally important monocot, member of the family Liliaceae, was investigated for callusing, direct regeneration and induction of hairy root using soil bacterium Agrobacterium rhizogenes. Friable callus was initiated from corms on basal MS medium amended with 2,4-D (1 mg L) and kinetin (1 mg L). Callus generated from such effective combinations were co-cultivated with the bacterium in vitro. Infection was facilitated by acetosyringone (AS) (20 mg L) supplemented during co-cultivation. Extensive hairy roots were induced from the callus within 15-18 d. These roots were then established on MS basal broth medium. Alkaloids like colchicine and colchicoside were extracted from hairy roots and compared with authentic standard colchicines in HPLC. Statistical media optimization was employed to select effective media composition. The findings indicated that nitrogen, inoculum and ferric ions have the highest f value that influenced colchicine production (22.7 mM) and hairy root growth.
Mechanisms of erythropoietin‐mediated cardioprotection during ischemia‐reperfusion injury: role of protein kinase C and phosphatidylinositol 3‐kinase signaling

Langendorff‐perfused rat hearts treated with EPO exhibited significantly improved postischemic recovery of left ventricular developed pressure (LVDP) and reduced infarct size compared with control hearts. Perfusion with the mitogen/extracellular signal‐regulated kinase (MEK) inhibitor U0126 just before and concomitant with EPO treatment abolished EPO‐induced phosphorylation of the MEK substrate extracellular signal‐regulated kinase (ERK) but had no effect of EPO‐mediated cardioprotection. EPO treatment of the perfused hearts induced translocation of protein kinase C (PKC) ε isoform to the membrane fraction of the hearts and the protective effect of EPO was significantly inhibited by the PKC catalytic inhibitor chelerythrine added before and concomitant with EPO. These data demonstrate that EPO‐mediated activation of the PKC signaling pathway before or during ischemia is required for the cardioprotective effect of EPO during ischemia‐reperfusion injury. Perfusion with the phosphatidylinositol 3‐kinase (PI3K) inhibitors LY294002 or wortmannin just before and concomitant with EPO treatment attenuated EPO‐induced phosphorylation of the PI3K substrate Akt but had no effect on EPO‐mediated cardioprotection. However, when wortmannin was added during EPO treatment and continued during reperfusion, EPO‐mediated cardioprotection was significantly inhibited. We also show that postischemia EPO treatment at the onset of reperfusion significantly improved recovery of LVDP and reduced infarct size. Postischemia cardioprotection by EPO required the PI3K pathway but was not affected by inhibition of PKC at the time of EPO treatment.
Activation of Adenosine 2A Receptors Attenuates Allograft Rejection and Alloantigen Recognition1

The current studies investigated the in vitro and in vivo effect of adenosine 2A receptor (A2AR) agonists to attenuate allogenic immune activation. We performed MLRs with spleen T lymphocytes and APCs isolated from wild-type and A2AR knockout mice of both C57BL/6 and BALB/c background strains. Two-way MLR-stimulated T cell proliferation was reduced by ATL313, a selective A2AR agonist in a dose-responsive manner (∼70%; 10 nM), an effect reversed by the A2AR antagonist ZM241385 (100 nM). By one-way MLRs, we observed that ATL313’s inhibitory effect was due to effects on both T cells and APCs. ATL313 suppressed the activation markers CD25 and CD40L and the release of inflammatory cytokines IFN-γ, RANTES, IL-12P70, and IL-2. ATL313 also increased negative costimulatory molecules programmed death-1 and CTLA-4 expressed on T cells. In lymphocytes activated with anti-CD3e mAb, ATL313 inhibited the phosphorylation of Zap70, an effect that was reversed by the protein kinase A inhibitor H-89. In skin transplants, allograft survival was enhanced with ATL313, an effect blocked by ZM241385. These results indicate that A2AR agonists attenuate allogenic recognition by action on both T lymphocytes and APCs in vitro and delayed acute rejection in vivo. We conclude that A2AR agonists may represent a new class of compounds for induction therapy in organ transplantation.
Field swimming behavior in largemouth bass deviates from predictions based on economy and propulsive efficiency

ABSTRACT Locomotion is energetically expensive. This may create selection pressures that favor economical locomotor strategies, such as the adoption of low-cost speeds and efficient propulsive movements. For swimming fish, the energy expended to travel a unit distance, or cost of transport (COT), has a U-shaped relationship to speed. The relationship between propulsive kinematics and speed, summarized by the Strouhal number (St=fA/U, where f is tail beat frequency, A is tail tip amplitude in m and U is swimming speed in m s−1), allows for maximal propulsive efficiency where 0.2<St<0.4. Largemouth bass adopted field speeds that were generally below the range predicted to minimize their COT. This may reflect speed modulation to meet competing functional demands such as enabling effective prey detection and capture. St exceeded the optimal range for the lowest observed swimming speeds. Mechanical and physiological constraints may prevent adoption of efficient St during low-speed swimming. Highlighted Article: Video analysis of largemouth bass swimming behavior in the field suggests that they do not use swimming speeds or propulsive movements that maximize economy and efficiency.
At A Glance : NetIDE An integrated development environment for portable network applications Project

This document is the second deliverable produced by WP4 and corresponds to the first release of the NetIDE Debugging Toolset. This docum t includes a initial description of the Debugging Tools and a proposal for integrating the to ls in the NetIDE Architecture, an analysis of the related work on debuggi g tools for SDN ecosystems and a description of the requirements and fu ctionality of each of the tools (Logger, Resource Manager, Garbage Collector, Model Checker, P ofiler, Debugger and Simulator). Finally, this deliverable includes the software release of the NetIDE Logger and its related documentation.
Interactive Multimedia Module with Pedagogical Agents: Formative Evaluation.

Electrochemistry is found to be a difficult topic to learn due to its abstract concepts that involve three representation levels. Research showed that animation and simulation using Information and Communication Technology can help students to visualize and thus enhance students’ understanding in learning abstract chemistry topics. As a result, an interactive multimedia module with a pedagogical agent (IMMPA) named EC Lab was developed to assist students in the learning of Electrochemistry. There were 35 students and seven experts involved in this formative evaluation to test the usability and effectiveness of the module developed. Instruments involved were module evaluation questionnaire, module reliability questionnaire, module validity questionnaire, pretest, post-test and motivation questionnaire. Results showed that the students and experts rated the module developed as high (M = 3.94) and very high quality (M = 4.45). Besides, the respondents also see the module as reliable (M = 3.87) and valid (M = 4.51). Students have higher scores on their post-test and have gained higher motivation level after learning with the IMMPA EC Lab. However, some corrections and modifications have been made based on feedback and suggestions from the respondents to improve the quality of IMMPA EC Lab.
Oncologic Effectiveness and Safety of Bursectomy in Patients with Advanced Gastric Cancer: A Systematic Review and Updated Meta-Analysis

ABSTRACT Purpose/Aim: In the past few decades some researchers have questioned whether bursectomy for gastric cancer is essential from an oncological point of view and no consistent recommendations have been proposed. The aim of this systematic review with meta-analysis is to investigate the oncologic effectiveness and safety of bursectomy for the treatment of advanced gastric cancer patients. Materials and Methods: We planned and performed this systematic review and meta-analysis in accordance with Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) statement and Cochrane Handbook for Systematic Reviews of Intervention. Results: Overall, four studies with a total of 1,340 patients met inclusion criteria. The pooled hazard ratio for overall survival between the bursectomy versus nonbursectomy groups was [HR = 0.85, 95% CI 0.66–1.11, p =. 252]. Interestingly, the pooled HR between the two groups in serosa-positive cases subgroup, showed a significant improvement of overall survival rate in favor of bursectomy [HR = 0.72, 95% CI 0.73–0.99, p <. 05]. Conclusions: Bursectomy represents a surgical procedure that might be able to improve overall survival in serosa positive gastric cancer patients. However, a definitive conclusion could not be made because of the studies’ methodological limitations. This meta-analysis points to the urgent need of high quality, large-scaled, clinical trials with short- as well as long-term evaluation comparing bursectomy with non bursectomy procedures, in a controlled randomized manner, helping future researches and establishing a modern and tailored approach to gastric cancer.
A Simple, Novel Method for Assessing Medication Adherence: Capsule Photographs Taken With Cellular Telephones

Objectives:Medication nonadherence is an important factor in clinical practice and research methodology. Although many methods of measuring adherence have been investigated, there is as yet no “gold standard. ” We compared the usefulness and accuracy of a novel measure of adherence, photographs taken by cellular telephones with 2 incumbents: capsule count and the Medication Event Monitoring System (MEMS). Method:Twenty subjects participated in a clinical trial of the efficacy of modafinil for the treatment of methamphetamine dependence. Subjects were issued cell phones and medication in MEMS Cap equipped bottles and were instructed to take 1 capsule a day for 8 weeks, recording adherence with both systems. Pill counts were recorded at weekly inpatient visits. Subjects were paid for participation and for each capsule photograph and the returned medication bottle with MEMS Cap. Results:Capsule count-indicated adherence (proportion of prescribed medication taken) was 94.9%. When compared with capsule count, the novel method was found to underestimate adherence, whereas MEMS overestimated adherence. By using the dosing time data collected, we determined that subjects who dosed at a consistent time daily were more likely to adhere to the prescribed regimen. We also detected discrepancies in the timestamps recorded by MEMS. Conclusions:Capsule photographs are a useful measure of adherence, allowing more accurate time measures and more frequent adherence assessment than MEMS or capsule count. Given the ubiquity of cellular telephone use, and the relative ease of this adherence measurement method, we believe it is a useful and cost-effective approach.
MCCC1/LAMP3 reduces risk of sporadic Parkinson's disease in Han Chinese

A recent large‐scale replication and heterogeneity study reported the new described GWAS locus (MCCC1/LAMP3 rs11711441) was associated with a reduced risk of Parkinson disease (PD) in Asian and Caucasian populations. Its role is still unknown in a Han Chinese population from mainland China. We genotyped the rs11711441 variant to investigate the association with risk of PD.
Bayesian estimation of parameters of a damped sinusoidal model by a Markov chain Monte Carlo method

A dynamic Monte Carlo method is proposed to compute the posterior means and covariances of the parameters of a damped sinusoidal model when an informative prior distribution is known. The Bayesian framework provides a sound mathematical ground, which possibly allows one to overcome the approximations commonly used to cope with this difficult problem. Some simulations results are provided, which support the conclusion that the prior information can also be significantly improved when the data have a low signal-to-noise ratio.