Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of p75 NTR with Caveolin and Localization of Neurotrophin-induced Sphingomyelin Hydrolysis to Caveolae*

Caveolae are plasma membrane microdomains that are enriched in caveolin, the structural protein of caveolae, sphingomyelin, and other signaling molecules. We previously suggested that neurotrophin-induced p75 NTR -dependent sphingomyelin hydrolysis may be localized to the plasma membrane. Therefore, we examined if caveolae were a major site of p75 NTR -dependent sphingomyelin hydrolysis in p75 NTR -NIH 3T3 fibroblasts. Caveolin-enriched membranes (CEMs) were prepared by either detergent or detergent-free extraction and separated from noncaveolar membranes by centrifugation through sucrose gradients. Immunoblot analysis of the individual gradient fractions indicated that caveolin and p75 NTR were enriched in CEMs. The localization of p75 NTR to CEMs was not an artifact of receptor overexpression in the fibroblasts because a similar distribution of p75 NTR was evident from PC12 cells, which endogenously express p75 NTR . In the p75 NTR fibroblasts, nerve growth factor induced a time-dependent hydrolysis of sphingomyelin only in CEMs with no hydrolysis detected in noncaveolar membranes. Intriguingly, endogenous p75 NTR was found to co-immunoprecipitate with caveolin, suggesting that p75 NTR may associate with caveolin in vivo. This interaction was confirmed in vitro by the co-immunoprecipitation of a glutathione S-transferase fusion protein expressing the cytoplasmic domain of p75 NTR with caveolin. Collectively, these results demonstrate that neurotrophin-induced p75 NTR -dependent sphingomyelin hydrolysis localizes to CEMs and suggest that the interaction of p75 NTR with caveolin may affect signaling through p75 NTR .
A disruption tolerant architecture based on MQTT for IoT applications

In the IoT world, establishing a strong mobile network architecture will be critical for organizations to bring together people, processes, data and things. Among the various available protocols and standards to network IoT entities, the Message Queue Telemetric Transport (MQTT) is already a reference solution. It provides a publish/subscribe messaging transport specifically designed to be used in devices with limited resources over constrained networks. MQTT's main limitation is its low resilience with respect to device mobility, so that the connections could suffer frequent and long lasting disruptions or high bit error rates that severely degrade normal communications. In this work we propose an architecture to increase the robustness of MQTT by integrating a Disruption Tolerant Network (DTN) approach. The architecture has been evaluated through several experiments using real devices to validate its feasibility, and to derive some guidelines for its use.
Reduction of Optical Feedback Originating From Ferroelectric Domains of Periodically Poled Crystals

Optical feedback originating from the interfaces of the periodically poled domains of a nonlinear crystal is usually blocked by a bulky optical isolator to avoid an influence on the pump source. Here, a nonlinear bulk crystal with a slanted design of the periodic poling is used to suppress the optical feedback toward the laser source. This crystal is compared with a conventionally poled crystal, in which the incident radiation propagates perpendicular to the domains. Both crystals are made of magnesium oxide doped congruent lithium niobate (PPMgO:CLN). A distributed Bragg reflector tapered diode lasers with a maximum optical power of 7.0 W at a wavelength of 1122 nm and each nonlinear crystal are employed in a single-pass setup. In comparison with the conventional crystal, the optical feedback of the crystal with slanted domains is reduced by 13.4 dB enabling a stable narrow-band operation of the pump laser source without an optical isolator. The impact of the optical feedback on the diode laser with respect to the optical output power and the spectral behavior is investigated. For the crystal with slanted domains, a frequency doubled output power up to 0.39 W at 561 nm is generated without reaching the coherence collapse regime, as observed in case of the conventional crystal. These results are promising for miniaturization of the setup without a need for a bulky optical isolator.
Adaptive Design, Female Mate Preferences, and Shifts across the Menstrual Cycle

Abstract This paper has two aims: first, to review work addressing the functional significance of variation in sexuality across the women's menstrual cycle and its implications for an understanding of human sexual nature; second, to illustrate the more general use of adaptationism in sex research. Adaptationism provides a method for recognizing adaptations, traits that evolved because they bestowed reproductive advantages upon their owners. The telltale sign of adaptation is its special design for a particular function. In recent years, evolutionary psychologists have explored changes in women's sexuality and standards of male attractiveness across the menstrual cycle. Evidence provisionally supports the idea that these changes constitute special design for the function of obtaining genetic benefits through mating with men other than primary partners.
Lymph Node Ratio May Predict the Benefit of Postoperative Radiotherapy in Non–Small-Cell Lung Cancer

Introduction: The use of postoperative radiotherapy (PORT) after resection of non–small-cell lung cancer (NSCLC) is controversial, with some evidence suggesting a benefit in patients with N2 disease. We assessed lymph node ratio (LNR) as a predictor of PORT benefit. Methods: By using the Surveillance, Epidemiology and End Results database, we analyzed resected, node-positive (N1–N2) NSCLC patients diagnosed between 1998 and 2009. LNR, (number of positive nodes/number of resected nodes) was categorized into four groups: LNR less than 12.5%, 12.5 to 24.9%, 25 to 49.9%, and 50% or more. Results: Of 11,324 node-positive NSCLC patients identified, 6551 (57.9%) had N1 disease. The LNR was prognostic for survival in the entire cohort and within each nodal stage. The median survival in LNR groups 1, 2, 3, and 4 was 43, 40, 30, and 23 months in N1 disease and 40, 32, 27, and 22 months in N2 disease, respectively. PORT was associated with a worse survival on univariate analysis (hazard ratio [HR] =1.09; confidence interval [CI] 1.03–1.15; p = 0.002) but no effect on multivariate analysis (HR = 0.96; CI 0.90–1.02; p = 0.201). When analyzed by nodal stage, the benefit of PORT was limited to N2 disease (HR = 0.9; CI 0.84–0.99; p= 0.026) with no benefit in N1 disease (HR = 1.06; CI 0.97–1.15; p=0.2). After stratifying by LNR, the survival benefit of PORT was limited to those with N2 disease and an LNR of 50% or more. Conclusion: A high LNR is associated with a poorer survival in resected, node-positive NSCLC. The survival benefit associated with PORT in this disease seems to be limited to those with an LNR of 50% or more. This warrants further investigation in other cohorts and prospective studies.
The impact of diet on the composition and relative abundance of rumen microbes in goat

Objective This experiment was conducted to explore the impact of diet on the ruminal microbial community in goats. Methods Twelve goats were divided into two groups and fed complete feed (CF) or all forage (AF) diet. The total microbial DNAs in the rumen liquid were extracted. The V4 region of microbial 16S rRNA genes was amplified and sequenced using high-throughput. Information of sequences was mainly analyzed by QIIME 1.8. 0. Results The results showed that Bacteroidetes and Firmicutes were the most predominant microbial phyla in the rumen of all goats. At genus level, the abundance of fiber-digesting bacteria such as Ruminococcus and Lachnospiracea incertae sedis was significantly higher in AF than that in CF, while the levels of fat-degrading bacterium Anaerovibrio and protein-degrading bacterium Pseudomonas were opposite. The core shared genera, Prevotella and Butyrivibrio were widespread in the rumen of goats and no significant difference was observed in relative abundance between groups. Conclusion We concluded that the richness of fiber-, protein-, and fat-digesting bacteria was affected by diet and tended to increase with the rise of their corresponding substrate contents in the ration; some bacteria shared by all goats maintained stable despite the difference in the ration, and they might be essential in maintaining the normal function of rumen.
33 DNA Replication in Tetrahymena

The linear ribosomal RNA gene (rDNA) minichromosome in the somatic macronucleus of Tetrahymena thermophila serves as a paradigm for multiple mechanisms of regulation of chromosomal DNA replication. Whereas chromosomal DNA replication in most eukaryotes is under strict cell cycle control, additional mechanisms appear to be involved in the regulation of rDNA replication in vegetatively growing Tetrahymena cells (Anderson 1972; Engberg et al. 1972; Truett and Gall 1977). All macronuclear chromosomes, including the rDNA minichromosome, segregate randomly and thus appear to lack centromeres. The macronucleus divides by a poorly understood amitotic mechanism, and DNA is often distributed unequally between daughter macronuclei (Doerder 1979). To explain how cells compensate for inequalities that arise from such divisions, it was proposed that a copy number control mechanism is superimposed on cell cycle control of the macronuclear DNA (Preer and Preer 1979; for review, see Larson et al. 1991). In addition, different allelic forms of the rDNA compete with each other for replication in the same macronucleus, and additional copies of the origin region confer a replication advantage to rDNA molecules. These observations are at odds with strict cell cycle control. Therefore, it was concluded that copy number control facilitates the maintenance of rDNA levels in vegetative cells (Larson et al. 1986). Cell cycle control of DNA replication is also suppressed during developmentally programmed rDNA amplification (Yao et al. 1974). cis- Acting determinants controlling the formation and propagation of the rDNA minichromosome have been identified by classic genetic and DNA transformation approaches (Larson et al. 1986;.
GUARD: A Genetic Unified Approach for Recommendation

Recommender systems suggest new items to users based on his/her interests. They appear in distinct contexts, such as movies, e-commerce, search engines, program guides for digital TV. In this work we propose a framework to generate ranking functions for items recommendation based on genetic programming, which we call GUARD (Genetic Unified Approach for Recommendation). The framework was developed under a collaborative filtering approach, but can be easily extended to work with content-based or hybrid recommender systems. The GP-based framework is flexible, works under a multi-objective approach and is able to combine different features and deal with data uncertainty and noisy. GUARD generates ranking functions considering four different measures: precision, recall, diversity and novelty. The framework was tested in the scenario of movies recommendation, using the Movielens 100k and Movielens 1M datasets. The results obtained were compared to those generated by PureSVD, the state-of-the-art algorithm for collaborative filtering. Considering the Movielens 100k, the results of precision and recall were superior to those of SVD. The framework can also generate more diverse and novel recommendations, with a small loss in precision. For Movielens 1M, the results are not as good as those obtained by PureSVD, but the functions slighly sacrifice accuracy over simplicity.
Recognition and Stabilization of A Unique CPRI—Structural Motif in Cucurbitaceae Family Trypsin Inhibitor Peptides: Molecular Dynamics Based Homology Modeling Using the X-ray Structure of MCTI-II

Abstract The high resolution crystallographic structure of MCTI-II complexed with beta trypsin (PDB entry 1MCT) was used to model the corresponding structures of the six inhibitor peptides belonging to Cucurbitaceae family (MCTI-I, LA-1, LA-2, CMTI-I, CMTI-III, CMTI- IV). Two model inhibitors, LA-1 and LA-2 were refined by molecular dynamics to estimate the average solution structure. The difference accessible surface area (DASA) study of the inhibitors with and without trypsin revealed the Arginine and other residues of the inhibitors which bind to trypsin. The hydration dynamics study of LA1 and LA2 also confirm the suitability of water molecules at the active Arg site. Moreover, the presence of a unique 3D-structural motif comprises with the four CPRI residues from the amino terminal is thought to be conserved in all the six studied inhibitors, which seems essential for the directional fixation for proper complexation of the Arg (5) residue towards the trypsin S1-binding pocket. The role of the disulphide linkage in the geometrical stabilization of CPRI (Cysteine, Proline, Arginine, Isoleucine) motif has also been envisaged from the comparative higher intra molecular Cys (3) -Cys (20) disulphide dihedral energies.
Cross‐species amplification of 44 microsatellite loci developed for Chaetodon trifascialis, C. lunulatus and C. vagabundus in 22 related butterflyfish species

Forty‐four microsatellite primers developed for three species of butterflyfish were cross‐tested against 22 related confamilial species. Amplification success and cross‐species transferability of these markers were moderately high. Between 24 and 37 loci were amplified successfully in each species, with a mean success rate per species of 71.7% (± 1.8 SE). Rates of amplification success were comparable among primers designed for the three source species, ranging from a mean success rate per species of 16.9 loci (± 0.8 SE) for Chaetodon trifascialis source loci to 13.7 loci (± 1.5 SE) for C. vagabundus source loci. Polymorphism rates were high (76.1%± 3.1 SE of all successfully amplified loci), and 10 loci were polymorphic in all successfully amplified species (Tri14, B11, C5, D3, D113, D6, D117, D120, D111, D118). The number of alleles per polymorphic locus ranged from 2 to 8, and the average number of alleles across all polymorphic loci and all species was 3.6 (± 0.07 SE). Polymorphism rates were higher overall in primers designed for C. vagabundus (89.9%± 3.9 SE). Overall cross‐testing success was lowest for Heniochus chrysostomus, the most phylogenetically divergent species. The significant cross‐testing reported here provides a valuable resource that will enable population genetics studies to be undertaken on a range of butterflyfishes without the need for expensive and time‐consuming de novo microsatellite development.
A performance analysis of the active memory system

One major problem of using Java in real-time and embedded devices is the non-deterministic turnaround time of dynamic memory management systems (memory allocation and garbage collection). For the allocation, the nondeterminism is often contributed by the time to perform searching, splitting, and coalescing. For the garbage collection, the turnaround time is usually determined by the size of the heap, the number of live objects, the number of object collected, and the amount of garbage collected Even with the current state-of-the-art garbage collectors (generational and incremental schemes), they may or may not guarantee the worst case latency. Moreover such schemes often prolong overall garbage collection time. In this paper, the performance analysis of the proposed Active Memory Module (AMM) for embedded systems is presented Unlike the software counterparts, the AMM can perform a memory allocation in a predictable and hounded fashion (14 cycles). Moreover it can also yield a bounded sweeping time regardless of the number of live objects or heap size. By utilizing the proposed system, the overall speed-up can be as high as 23% over the JDK 1.2. 2 running in classic mode.
Sodium Pump Activity in Uremic Erythrocytes: A Microcalorimetric Study

Erythrocyte thermogenesis was studied by flow microcalorimetry in 25 healthy subjects and 27 uremic patients. The heat production (HP) from cells in plasma, decrease in HP induced by ouabain (a specific sodium pump inhibitor) and index of rate response to ouabain action were measured. HP was higher in uremic patients than controls. Sodium pump inhibition with ouabain induced the same decrease in HP in the two groups. The index of rate response to ouabain action was lower in uremic patients than in controls. The difference in total HP may be due to a different age distribution of erythrocytes. Mean sodium pump activity was identical in the two groups, but some patients had lower activity than controls. Ouabain seems to act more slowly in many patients than in controls, perhaps because of hindered binding of the inhibitor.
Hybrid flooding and tree-based broadcasting for reliable and efficient link-state dissemination

Current link-state routing protocols (e.g., OSPF) use flooding to disseminate link-state information throughout the network. Despite its simplicity and reliability, flooding incurs unnecessary communications overhead since nodes may receive multiple copies of the same advertisement. This extra overhead becomes an Issue in the context of quality-of-service (QoS) routing, where link state is dynamic and needs to be advertised frequently. The advertisement overhead can be significantly reduced by using tree-based broadcasting approaches. Although several of these approaches have been proposed in the literature, they are not used in practice because of their complexity and/or unreliability. We propose a new link-state dissemination approach that combines the best features of flooding and tree-based broadcasting. Our hybrid approach is particularly suited for "dynamic" link metrics (e.g., available bandwidth). It uses periodic flooding to advertise topology changes and first-time LSAs (link-state advertisements), and uses tree-based broadcasting to disseminate subsequent refresh LSAs. The broadcast trees in our approach are constructed dynamically during the flooding of the first LSA, without the need for the complex algorithms of previous tree-based approaches. Two versions of our dissemination approach are presented, with one being more suitable for networks with frequent topological changes. We prove the correctness of our approach and contrast its communications overhead with flooding and pure tree-based broadcasting. The results indicate that our hybrid approach has a significantly lower overhead than flooding; yet It enjoys the simplicity, reliability, and fast convergence of flooding. Finally, we outline how OSPF can be extended to support the proposed dissemination approach.
Nutritional and antinutritional components of vetiver grass (Chrysopogon zizanioides L. Roberty) at different stages of growth

Vetiver grass was harvested at 4, 6 and 8-week old re-growth. The chemical composition and quantitative analyses of anti-nutritional components were determined. The result showed that dry matter and fiber content increased with age while crude protein, mineral content and anti-nutritional components reduced with age. It was concluded that age of re-growth significantly affect the nutrient and anti-nutrients contents of vetiver grass.
Quantum hyperbolic metamaterials with exciton-polaritons in semiconductor Bragg mirrors

A novel mechanism for realization of hyperbolic metamaterials with use of spatially periodic semiconductor Bragg mirrors containing periodically arranged quantum wells is proposed. The hyperbolic dispersion of exciton-polariton modes is realized near the top of the first allowed photonic mini-band in the structure. We predict formation of low amplitude breather-like oscillatory structures: oscillons described by kink shaped solutions of the effective Ginzburg-Landau-Higgs equation.
Prion protein participates in the regulation of classical and alternative activation of BV2 microglia

The cellular prion protein (PrPC) is a glycoprotein anchored by glycosylphosphatidylinositol (GPI) to the cell surface and is abundantly expressed in the central nervous system. Numerous studies have suggested a protective function for PrPC, including protection from ischemic and excitotoxic lesions and several apoptotic insults, and recent reports have shown that PrPC has a context‐dependent neuroprotective function. In this study, we investigated the effect of PPNP down‐regulation on various forms of microglial activation. We first examined the mRNA expression of PRNP upon exposure to IFN‐γ, IL‐4, or IL‐10 in BV2 microglia. We then analyzed the effect of si‐RNA‐mediated disruption of PRNP on different parameters of microglial activation in IFN‐γ‐, IL‐4‐, or IL‐10‐stimulated microglia. The results showed that PRNP mRNA expression was invariably down‐regulated in microglia upon exposure to IFN‐γ, IL‐4, or IL‐10. PRNP silencing prior to cytokines treatment reduced the responsiveness of microglia to INF‐γ treatment, significantly altered IL‐4‐induced microglial activation phenotype, and had no effect on IL‐10‐induced microglial activation. Together, these results support a role of PrPC in the modulation of the shift of microglia from a quiescent state to an activated phenotype and in the regulation of the microglial response during classical and alternative activation.
REPEATABILITY OF CLUTCH SIZE IN FEMALE STARLINGS (STURNUS VULGARIS)

Theories of clutch size determination have focused on first broods or on seasonal trends in clutch size. Clutch size is controlled by combination of genetic, ontological and environmental factors (KENNEDY & WHITE, 1991). In recent years, an increasing number of studies have demonstrated the existence of significant repeatability in ecologically important traits in natural bird populations (e.g. GOODBURN, 1991; JERZAK et al., 2000; AMAT et al., 2001; YOSEF & ZDUNIAK, 2004). Repeatability expresses the proportion of the variation between measurements that is due to consistent differences between the objects measured (HORAK et al., 1995). According to van NOORDWIJK et al. (1980), no single optimum value exists for clutch size. In some years small clutches are optimal, in other years large clutches contribute more to NAT. CROAT. VOL. 14 No 4 357? 361 ZAGREB December 31, 2005
The 'balanced force' concept for instrumentation of curved canals revisited

The principal characteristics of K-type files are described and the succession of operations as prescribed by the 'balanced force' method of preparation of root canals, particularly curved root canals, examined. On the basis of a simple mathematical model, the motions of a file in a straight canal and in a curved canal are successively considered, and the merits of the recommended method highlighted and confirmed.
Renal transplantation from extended criteria cadaveric donors: problems and perspectives overview

The critical shortage of organs available for renal transplantation has led to the consideration of alternative strategies for increasing the donor pool. Recently, the cadaveric kidney donor pool extended to donors who might have been deemed unsuitable in early times, leading to the concept of marginal donors and more recently to the notion of expanded criteria donors. Such organs are eligible for organ donation but, because of extreme age and other clinical characteristics, are expected to produce allograft at risk for diminished post‐transplant function. Thus, the challenge is now to reduce the difference between graft outcome from patients grafted with marginal and ‘optimal’ donors. This implies appropriate transplantation strategies during pre‐, peri‐ and post‐transplantation phases including reduction of cold ischemia time, recipient selection, adaptation of immunosuppressive drug regimens, increase in nephron mass by dual kidney transplantation, and improvement in the graft selection process using histological criteria. This review summarizes current definition of a marginal donor and provides some guidance for clinical management of such transplant.