Miracle-dz/UniFAR-FTUs huggingface dataset:
Endothelin‐1 protects astrocytes from hypoxic/ischemic injury

Under pathological conditions such as ischemia (I), subarachnoid hemorrhage, and Alzhei¬mer's disease, astrocytes show a large increase in endo¬thelin (ET) ‐like immunoreactivity. However, it is not clear whether ET is protective or destructive to these cells during brain injury. Using astrocytes from ET‐1‐deficient mice, we determined the effect of ET‐1 on these cells under normal, hypoxic (H), and hypoxic/ ischemic (H/I) conditions. Under normal culture con¬ditions, astrocytes from wild‐type and ET‐1‐deficient mice showed no difference in their morphology and cell proliferation rates. ET‐3 and ETA receptor mRNAs were up‐regulated whereas ETB receptor mRNA was down‐regulated in ET‐1‐deficient astrocytes, suggesting that ET‐1 and ET‐3 may complement each other's functions and that the expressions of these endothelins and their receptors are regulated by a complex feed¬back mechanism. Under H and H/I conditions, ET‐1 peptide and mRNA were up‐regulated in wild‐type astrocytes, and the astrocytes without ET‐1 died faster than the wild‐type astrocytes, as indicated by greater efflux of lactate dehydrogenase. The present study suggests that astrocytes without ET‐1 are more vulner¬able to H and H/I injuries and that the up‐regulation of astrocytic ET‐1 is essential for the survival of astrocytes. —Ho, M. C. Y. , Lo, A. C. Y. , Kurihara, H. , Yu, A. C. H. , Chung, S. S. M. , Chung, S. K. Endothelin‐1 protects astrocytes from hypoxic/ischemic injury. FASEB J. 15, 618‐626 (2001)
UNIAXIAL COMPRESSIVE BUCKLING OF BORON NITRIDE NANOTUBES USING MOLECULAR DYNAMICS SIMULATION

The compressive buckling of boron nitrides nanotubes (BNNTs) has been studied using molecular dynamics (MD) simulations. We have used the Lennard-Jones pair potential to characterize the interactions between non-bonded atoms and harmonic potentials for bond stretching and bond angle vibrations. Results of the MD simulations are used to characterize the critical uniaxial compressive buckling loads of BNNTs and indicate that the critical buckling loads increase for larger nanotubes.
The brain's persepective on requirements engineering

Software development is knowledge work. The work of cognitive psychologist offers many insights in respect to knowledge work and these insights suggest an approach to requirements engineering where collaboration and communication plays a much more important role than the documentation of requirements. Such insights must again impact, how requirements knowledge is managed in an organization. This extended abstract promotes the idea to evaluate today's approaches from a brain's perspective.
Gemin5 promotes IRES interaction and translation control through its C-terminal region

Gene expression control largely depends on ribonucleoprotein complexes regulating mRNA translation. Initiation of translation in mRNAs that overcome cap-dependent translation inhibition is often driven by internal ribosome entry site (IRES) elements, whose activity is regulated by multifunctional RNA-binding factors. Here we show that Gemin5 interacts preferentially with a specific domain of a viral IRES consisting of a hairpin flanked by A/U/C-rich sequences. RNA-binding assays using purified proteins revealed that Gemin5–IRES interaction depends on the C-terminal region of the protein. Consistent with this novel finding, the C-terminal region of Gemin5, but not the N-terminal region, impaired translation. Furthermore, RNA selective 2′hydroxyl acylation analysed by primer extension (SHAPE) reactivity demonstrated that addition of purified Gemin5 to IRES mRNA induced the specific protection of residues around the hairpin of the IRES element. We further demonstrate that Gemin5 out-competed SHAPE reactivity variations induced by the IRES-binding factor PTB, leading to a local conformational change in the IRES structure. Together, our data unveil the inhibitory mechanism of Gemin5 on IRES-mediated translation.
Berberine suppresses neuroinflammatory responses through AMP‐activated protein kinase activation in BV‐2 microglia

The AMPK cascade is a sensor of cellular energy change, which monitors the AMP/ATP ratio to regulate cellular metabolism by restoring ATP levels, but its regulation of neuroinflammation mechanism remains unclear. Berberine, one of the major constituents of Chinese herb Rhizoma coptidis, has been shown to improve several metabolic disorders, such as obesity and type II diabetes. However, the effect of berberine on neuroinflammatory responses in microglia are poorly understood. This study shows that berberine represses proinflammatory responses through AMP‐activated protein kinase (AMPK) activation in BV‐2 microglia. Our findings also demonstrate that berberine significantly down‐regulates LPS‐ or interferon (IFN)‐γ‐induced nitric oxide synthase (iNOS) and cyclo‐oxygenase‐2 (COX‐2) expression in BV‐2 microglia cells. Berberine also inhibited LPS‐ or IFN‐γ‐induced nitric oxide production. In addition, berberine effectively inhibited proinflammatory cytokines such as TNF‐α, IL‐1β, and IL‐6 expression. On the other hand, upon various inflammatory stimulus including LPS and IFN‐γ, berberine suppressed the phosphorylated of ERK but not p38 and JNK in BV‐2 microglia. AMPK activation is catalyzed by upstream kinases such as LKB1 and Ca2+/calmodulin‐dependent protein kinase kinase‐II (CaMKK II). Moreover, berberine induced LKB1 (Ser428), CaMKII (Thr286), and AMPK (Thr172) phosphorylation, but not AMPK (Ser485). Furthermore, the inhibitory effect of berberine on iNOS and COX‐2 expression was abolished by AMPK inhibition via Compound C, an AMPK inhibitor. Berberine‐suppressed ERK phosphorylation was also reversed by Compound C treatment. Our data demonstrate that berberine significantly induces AMPK signaling pathways activation, which is involved in anti‐neuroinflammation. J. Cell. Biochem. 110: 697–705, 2010. © 2010 Wiley‐Liss, Inc.
Molecular Image-Guided Theranostic and Personalized Medicine 2014

The growing use of molecular imaging helps to control and monitor dosage for increased safety and effectiveness. Molecular imaging agents become the scientific tools for moving a concept from bench work to clinic product development. This special issue provides original research and review of new trends in molecular imaging agent development. Among clinic molecular imaging modalities, radionuclide imaging technique is the most sensitive and could provide target-specific information. The radiotracer could non-invasively assess disease treatment endpoints which used to rely almost exclusively on biopsies and histopathological assays. L. -H. Shen et al. (Taiwan) reviewed molecular imaging in the diagnosis and management of CNS disorders. F. -L. Kong et al. (USA), N. Tsao et al. (USA), and C. -L. Ho et al. (Taiwan) report pharmacokinetics and dosimetry of molecular imaging compounds in oncology. M. -H. Liao et al. (Taiwan), X. Wang et al. (China), C. Wu et al. (China) and M. Tian et al. (USA) reported that molecular imaging techniques play a major role in the development of novel therapies since they measure target expressions (apoptosis, glycolysis) as well as function, pathway activities, and cell migration in the intact organism. Y. -F. Wang et al. and M. -Y. Chao et al. (Taiwan) described the kit probe for 99mTc-labeling which is crucial for centralized drug process. The kit probe may allow theranostic concept. A theranostic agent would be more accurate in the evaluation of patient response to treatment. The radiotracer could also be used for radionuclide therapy as reported by C. Wang et al. (China). Hybrid molecular imaging modalities (PET/CT, SPECT/CT) provide high-sensitivity functional and high-resolution anatomical imaging which are important in design-personalized treatment. M. -C. Chen et al. (Taiwan) reported the value of using I-131 NP-59 SPECT/CT to diagnose patients with subclinical or atypical features of primary aldosteronism. To proof of concept for molecular biology findings using different imaging modalities (optical, sonography) were described by Z. Pu et al. (China). In summary, molecular imaging enables the comprehensive characterization of therapeutic intervention and can be used in preclinical studies, pharmacokinetic studies, dose-finding studies, and proof-of-concept studies. Molecular imaging technologies promote the discovery and development of personalized medicine. Hong Zhang Mei Tian Carrio Ignasi Zhen Cheng Lie-Hang Shen David J. Yang
Contour deformations for non-holomorphic actions

We show how contour deformations may be used to control the sign problem of lattice Monte Carlo calculations with non-holomorphic actions. Such actions arise naturally in quantum mechanical scattering problems. The approach is demonstrated in conjunction with the holomorphic gradient flow. As our central example we compute the real-time evolution of a particle in a one-dimensional analog of the Yukawa potential.
Targeting Neuronal Populations of the Striatum

The striatum is critically involved in motor and motivational functions. The dorsal striatum, caudate–putamen, is primarily implicated in motor control and the learning of habits and skills, whereas the ventral striatum, the nucleus accumbens, is essential for motivation and drug reinforcement. The GABA medium-sized spiny neurons (MSNs, about 95% of striatal neurons), which are targets of the cerebral cortex and the midbrain dopaminergic neurons, form two pathways. The dopamine D1 receptor-positive (D1R) striatonigral MSNs project to the medial globus pallidus and substantia nigra pars reticulata (direct pathway) and co-express D1R and substance P, whereas dopamine D2 receptor-positive (D2R) striatopallidal MSNs project to the lateral globus pallidus (indirect pathway) and co-express D2R, adenosine A2A receptor (A2AR) and enkephalin (Enk). The specific role of the two efferent pathways in motor and motivational control remained poorly understood until recently. Indeed, D1R striatonigral and D2R striatopallidal neurons, are intermingled and morphologically indistinguishable, and, hence, cannot be functionally dissociated with techniques such as chemical lesions or surgery. In view of the still debated respective functions of projection D2R striatopallidal and D1R striatonigral neurons and striatal interneurons, both in motor control and learning but also in more cognitive processes such as motivation, the present review sum up the development of new models and techniques (bacterial artificial chromosome transgenesis, optogenetic, viral transgenesis) allowing the selective targeting of these striatal neuronal populations in adult animal brain to understand their specific roles.
A Catalog of Security-oriented Program Transformations

Security requirements change, but the typical way of improving system security by patches is ad hoc and has not produced good results. Security improvements should be systematic, just as new features can be added to software systematically. It would be easier to improve the security of a system if we had a catalog of security-oriented program transformations that could be used to plan changes, to divide the work to make changes, and as a target of automation. This paper describes a catalog of security-oriented program transformations that were derived from security patterns. It describes several ways of categorizing these transformations, our first attempts at validating the catalog, and how the catalog can be used to improve the security of systems.
A study of the size effect on the temperature-dependent resistivity of bismuth nanowires with rectangular cross-sections

Rectangular cross-section bismuth nanowires with dimensions of 50 nm by 70–200 nm (thickness by width) were fabricated using an electron beam writing technique. Individual nanowire measurement is possible using this method. The resistivities of the 50 nm thick nanowires were dependent on line width. The measured resistivity of 70, 120 and 200 nm wide nanowires was 4.05 × 10−3, 2.87 × 10−3 and 2.30 × 10−3 Ω cm at 300 K respectively. Temperature-dependent resistance measurements indicated that the electrical conductivity of the Bi nanowires was carrier dependent, and the carrier density decreased at low temperature, showing that the all the Bi nanowires exhibited semiconductor behaviour. The size-dependent resistivity of the Bi nanowires was an indication of the ordinary size effect in the one-dimensional nanowire, where the carrier mobility was grain boundary scattering dominated.
Maximizing SB3 Waste Throughput Melt Rate Tests

The Defense Waste Processing Facility (DWPF) is presently vitrifying Sludge Batch 3 (SB3) and preparing to process Sludge Batch 4 (SB4) in late 2006 or early 2007. Previous laboratory testing and DWPF operational experience has indicated that the maximum waste throughput peak for the Sludge Batch 2 (SB2) system occurs at a waste loading in the mid-30's. This trend has been shown as well for SB3 on a lab-scale basis. These SB3 tests used SRAT product that targeted a REDuction/OXidation (REDOX) of 0.2 and an acid stoichiometry of 135%. Acid stoichiometry, however, has been shown to impact melt rate of MRF tests at one waste loading (35%). Due to the impact of acid stoichiometry on melt rate, it is possible that the current target acid stoichiometry (155%) with SB3 may not exhibit the same maximum waste throughput peak, or there may not even be a discernable peak. In fact, current DWPF operational experience with SB3 and Frit 418 has not shown the same drop off in melt rate and hence waste throughput as was observed with SB2 and Frit 320. The objective of this testing is to determine if increasing the overall alkali content in the feed (via using the more » higher alkali Frit 320 versus Frit 418) will either result in a shift in the waste throughput to higher waste loadings or an increase in the overall waste throughput at waste loadings of interest (31 to 41%). For these tests, the target Sludge Receipt and Adjustment Tank (SRAT) product REDOX was 0.2 and the target acid stoichiometry was 155%. The incentive for this series of tests stems from a previous Slurry-Fed Melt Rate Furnace (SMRF) test with SB3/Frit 320 feed which showed an increase in melt rate versus SB3/Frit 418 at 35% waste loading. This single data point suggests that overall waste throughput for the SB3/Frit 320 system is higher at 35% waste loading (i.e., the melt rate versus waste loading curve has potentially shifted upward). To address the potential shift in waste throughput, the strategy was to fully characterize the impact of waste loading (ranging from about 30 to 40%) on melt rate for the SB3/Frit 320 and SB3/Frit 418 feed systems. This will allow for potential shifts in waste throughput to be assessed via a change in frit composition. Initially, the dry-fed Melt Rate Furnace (MRF) was utilized. Based on the MRF results, the tests had a decision point on whether or not to continue testing using the SMRF. « less
Therapeutic alliance, empathy, and genuineness in individual adult psychotherapy: A meta-analytic review

Abstract Objective: Alliance, empathy, and genuineness are each integral parts of the therapeutic relationship. No previous meta-analysis has explored the extent to which therapist empathy and genuineness contribute to the therapeutic alliance. Method: In this meta-analysis, a multifaceted search strategy yielded 53 studies. Forty studies reported alliance/empathy relationships, eight studies reported alliance/genuineness relationships, and five studies reported both. Results: Random effects meta-analyses revealed that therapeutic alliance was significantly related to perceptions of therapist empathy with a mean r = 0.50 (95% CI = 0.42, 0.57). Therapeutic alliance was also significantly related to perceptions of therapist genuineness with a mean r = 0.59 (95% CI = 0.45, 0.71). Tests of publication bias indicated a low likelihood of publication bias affecting the strength and direction of the results. Potential moderating variables were explored, including rater perspective, measure of therapeutic relationship variables, and client race/ethnicity. Conclusions: Therapeutic alliance has a moderate relationship with perceptions of therapist empathy and genuineness. Of note, there may be reason to believe that when rated by the same person, these constructs have significant overlap and lack discreteness. Future directions for study of the therapeutic relationship are discussed. Implications for practice are provided.
A Proximity Grid Optimization Method to Improve Audio Search for Sound Design

Sound designers organize their sound libraries either with dedicated applications (often featuring spreadsheet views), or with default file browsers. Content-based research applications have been favoring cloud-like similarity layouts. We propose a solution combining the advantages of these: after feature extraction and dimension reduction (Studentt Stochastic Neighbor Embedding), we apply a proximity grid, optimized to preserve nearest neighborhoods between the adjacent cells. By counting direct vertical / horizontal / diagonal neighbors, we compare this solution over a standard layout: a grid ordered by filename. Our evaluation is performed on subsets of the One Laptop Per Child sound library, either selected by thematic folders, or filtered by tag. We also compare 3 layouts (grid by filename without visual icons, with visual icons, and proximity grid) by a user evaluation through known-item search tasks. This optimization method can serve as a human-readable metric for the comparison of dimension reduction techniques.
Common Process Demands of Two Complex Dynamic Control Tasks: Transfer Is Mediated by Comprehensive Strategies

Although individual differences in complex problem solving (CPS) are well–established, relatively little is known about the process demands that are common to different dynamic control (CDC) tasks. A prominent example is the VOTAT strategy that describes the separate variation of input variables (“Vary One Thing At a Time”) for analyzing the causal structure of a system. To investigate such comprehensive knowledge elements and strategies, we devised the real-time driven CDC environment Dynamis2 and compared it with the widely used CPS test MicroDYN in a transfer experiment. One hundred sixty five subjects participated in the experiment, which completely combined the role of MicroDYN and Dynamis2 as source or target problem. Figural reasoning was assessed using a variant of the Raven Test. We found the expected substantial correlations among figural reasoning and performance in both CDC tasks. Moreover, MicroDYN and Dynamis2 share 15.4% unique variance controlling for figural reasoning. We found positive transfer from MicroDYN to Dynamis2, but no transfer in the opposite direction. Contrary to our expectation, transfer was not mediated by VOTAT but by an approach that is characterized by setting all input variables to zero after an intervention and waiting a certain time. This strategy (called PULSE strategy) enables the problem solver to observe the eigendynamics of the system. We conclude that for the study of complex problem solving it is important to employ a range of different CDC tasks in order to identify components of CPS. We propose that besides VOTAT and PULSE other comprehensive knowledge elements and strategies, which contribute to successful CPS, should be investigated. The positive transfer from MicroDYN to the more complex and dynamic Dynamis2 suggests an application of MicroDYN as training device.
Evaluation of a Mobile Phone Image-Based Dietary Assessment Method in Adults with Type 2 Diabetes

Image-based dietary records have limited evidence evaluating their performance and use among adults with a chronic disease. This study evaluated the performance of a 3-day mobile phone image-based dietary record, the Nutricam Dietary Assessment Method (NuDAM), in adults with type 2 diabetes mellitus (T2DM). Criterion validity was determined by comparing energy intake (EI) with total energy expenditure (TEE) measured by the doubly-labelled water technique. Relative validity was established by comparison to a weighed food record (WFR). Inter-rater reliability was assessed by comparing estimates of intake from three dietitians. Ten adults (6 males, age: 61.2 ± 6.9 years old, BMI: 31.0 ± 4.5 kg/m2) participated. Compared to TEE, mean EI (MJ/day) was significantly under-reported using both methods, with a mean ratio of EI:TEE 0.76 ± 0.20 for the NuDAM and 0.76 ± 0.17 for the WFR. Correlations between the NuDAM and WFR were mostly moderate for energy (r = 0.57), carbohydrate (g/day) (r = 0.63, p < 0.05), protein (g/day) (r = 0.78, p < 0.01) and alcohol (g/day) (rs = 0.85, p < 0.01), with a weaker relationship for fat (g/day) (r = 0.24). Agreement between dietitians for nutrient intake for the 3-day NuDAM (Intra-class Correlation Coefficient (ICC) = 0.77–0.99) was lower when compared with the 3-day WFR (ICC = 0.82–0.99). These findings demonstrate the performance and feasibility of the NuDAM to assess energy and macronutrient intake in a small sample. Some modifications to the NuDAM could improve efficiency and an evaluation in a larger group of adults with T2DM is required.
Second order sliding mode control for inverted pendulum

This paper presents a second order sliding mode control for an inverted pendulum which is a nonlinear and unstable system. Two second order sliding mode algorithms are presented: Twisting algorithm and super-twisting algorithm. They are used to ensure not only a better robustness against parametric uncertainties, modeling errors and external disturbances, by the attenuation of chattering, but also a finite time convergence of state variables. Simulations results are shown to manifest the efficiency of these approaches.
Dense core secretory vesicles revealed as a dynamic Ca2+ store in neuroendocrine cells with a vesicle-associated membrane protein aequorin chimaera

The role of dense core secretory vesicles in the control of cytosolic-free Ca2+ concentrations ([Ca2+]c) in neuronal and neuroendocrine cells is enigmatic. By constructing a vesicle-associated membrane protein 2–synaptobrevin.aequorin chimera, we show that in clonal pancreatic islet β-cells: (a) increases in [Ca2+]c cause a prompt increase in intravesicular-free Ca2+ concentration ([Ca2+]SV), which is mediated by a P-type Ca2+-ATPase distinct from the sarco(endo) plasmic reticulum Ca2+-ATPase, but which may be related to the PMR1/ATP2C1 family of Ca2+ pumps; (b) steady state Ca2+ concentrations are 3–5-fold lower in secretory vesicles than in the endoplasmic reticulum (ER) or Golgi apparatus, suggesting the existence of tightly bound and more rapidly exchanging pools of Ca2+; (c) inositol (1,4,5) trisphosphate has no impact on [Ca2+]SV in intact or permeabilized cells; and (d) ryanodine receptor (RyR) activation with caffeine or 4-chloro-3-ethylphenol in intact cells, or cyclic ADPribose in permeabilized cells, causes a dramatic fall in [Ca2+]SV. Thus, secretory vesicles represent a dynamic Ca2+ store in neuroendocrine cells, whose characteristics are in part distinct from the ER/Golgi apparatus. The presence of RyRs on secretory vesicles suggests that local Ca2+-induced Ca2+ release from vesicles docked at the plasma membrane could participate in triggering exocytosis.