Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for a shape-based recognition of odorants in vivo in the human nose from an analysis of the molecular mechanism of lily-of-the-valley odorants detection in the Lilial and Bourgeonal family using the C/Si/Ge/Sn switch strategy

We performed an analysis of possible mechanisms of ligand recognition in the human nose. The analysis is based on in vivo odor threshold determination and in vitro Ca2+ imaging assays with a C/Si/Ge/Sn switch strategy applied to the compounds Lilial and Bourgeonal, to differentiate between different molecular mechanisms of odorant detection. Our results suggest that odorant detection under threshold conditions is mainly based on the molecular shape, i.e. the van der Waals surface, and electrostatics of the odorants. Furthermore, we show that a single olfactory receptor type is responsible for odor detection of Bourgeonal at the threshold level in humans in vivo. Carrying out a QM analysis of vibrational energies contained in the odorants, there is no evidence for a vibration-based recognition.
A method for improving information synchronization mechanism in Eucalyptus

Cloud computing is a fusion of network technology and traditional computer technology. It aims to deliver the powerful computing capability to end users through the advanced business model such as SaaS, PaaS, and IaaS. IaaS can provide a convenient, flexible and pay-per-use infrastructure for PaaS and SaaS. This paper is focused on Eucalyptus — a famous open source IaaS platform. After a brief introduction to the Eucalyptus, a detailed analysis about information synchronization mechanism shows some issues of information synchronization mechanism. According to the specific scenes, we have given a reasonable solution. With this solution, Eucalyptus can automatically restore to the state before when physical machine reboot for some reason and Eucalyptus can support live migration and dynamic adjustment of the virtual machine resources. At the end of the paper, experiments show the effect of the improvement on the Eucalyptus.
SSDAlloc: Hybrid SSD/RAM Memory Management Made Easy

We introduce SSDAlloc, a hybrid main memory management system that allows developers to treat solid-state disk (SSD) as an extension of the RAM in a system. SSDAlloc moves the SSD upward in the memory hierarchy, usable as a larger, slower form of RAM instead of just a cache for the hard drive. Using SSDAlloc, applications can nearly transparently extend their memory footprints to hundreds of gigabytes and beyond without restructuring, well beyond the RAM capacities of most servers. Additionally, SSDAlloc can extract 90% of the SSD's raw performance while increasing the lifetime of the SSD by up to 32 times. Other approaches either require intrusive application changes or deliver only 6- 30% of the SSD's raw performance.
Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules

Intermolecular interactions in the aqueous phase must compete with the interactions between the two binding partners and their solvating water molecules. In biological systems, water molecules in protein binding sites cluster at well-defined hydration sites and can form strong hydrogen-bonding interactions with backbone and side-chain atoms. Displacement of such water molecules is only favorable when the ligand can form strong compensating hydrogen bonds. Conversely, water molecules in hydrophobic regions of protein binding sites make only weak interactions, and the requirements for favorable displacement are less stringent. The propensity of water molecules for displacement can be identified using inhomogeneous fluid solvation theory (IFST), a statistical mechanical method that decomposes the solvation free energy of a solute into the contributions from different spatial regions and identifies potential binding hotspots. In this study, we employed IFST to study the displacement of water molecules from the ATP binding site of Hsp90, using a test set of 103 ligands. The predicted contribution of a hydration site to the hydration free energy was found to correlate well with the observed displacement. Additionally, we investigated if this correlation could be improved by using the energetic scores of favorable probe groups binding at the location of hydration sites, derived from a multiple copy simultaneous search (MCSS) method. The probe binding scores were not highly predictive of the observed displacement and did not improve the predictivity when used in combination with IFST-based hydration free energies. The results show that IFST alone can be used to reliably predict the observed displacement of water molecules in Hsp90. However, MCSS can augment IFST calculations by suggesting which functional groups should be used to replace highly displaceable water molecules. Such an approach could be very useful in improving the hit-to-lead process for new drug targets.
A Language Based Security Approach for Securing Map-Reduce Computations in the Cloud

We present a model for securing Map/Reduce computation in the cloud. The model uses a language based security approach to enforce information flow policies that vary dynamically due to a restricted revocable delegation of access rights between principals. The decentralized label model (DLM) is used to express these policies. We present a scenario that shows the flexibility and efficiency of our model in securing Map/Reduce computations running on the cloud infrastructure.
An Embedded Microprocessor Radiation Hardened by Microarchitecture and Circuits

A radiation hardened by design embedded microprocessor is presented. The design uses multiple approaches to minimize the performance reduction from hardening, while simultaneously limiting the power increase. The speculative portions of the pipeline are protected by microarchitecture approaches, i.e., the speculative pipeline is dual redundant, whereby instructions that have errors in one copy cause a pipeline restart - only matching results commit to architectural state. The register file is dual redundant with mechanisms for correction using one copy whose parity is correct. The data cache memory is write-through, allowing protection with parity. The remaining architectural state is protected via hardened circuits. These are implemented with self-correcting triple mode redundant (TMR) flip-flops and TMR logic. The design, implemented here on a 90-nm bulk CMOS process, achieves unprecedented single event effects hardness and 400+ MHz operating frequency at less than 500 mW power consumption. The main constituent circuit hardening approaches have been fabricated and tested separately. Broad beam testing of the constituent circuits has resulted in no uncorrectable soft errors below 100 MeV-cm2/mg LETEFF. We describe the CAD flows used to ensure node separation to achieve high immunity to multiple node charge collection and discuss the relative costs of the chosen hardening techniques.
Cooperative Games with Overlapping Coalitions

In the usual models of cooperative game theory, the outcome of a coalition formation process is either the grand coalition or a coalition structure that consists of disjoint coalitions. However, in many domains where coalitions are associated with tasks, an agent may be involved in executing more than one task, and thus may distribute his resources among several coalitions. To tackle such scenarios, we introduce a model for cooperative games with overlapping coalitions-or overlapping coalition formation (OCF) games. We then explore the issue of stability in this setting. In particular, we introduce a notion of the core, which generalizes the corresponding notion in the traditional (non-overlapping) scenario. Then, under some quite general conditions, we characterize the elements of the core, and show that any element of the core maximizes the social welfare. We also introduce a concept of balancedness for overlapping coalitional games, and use it to characterize coalition structures that can be extended to elements of the core. Finally, we generalize the notion of convexity to our setting, and show that under some natural assumptions convex games have a non-empty core. Moreover, we introduce two alternative notions of stability in OCF that allow a wider range of deviations, and explore the relationships among the corresponding definitions of the core, as well as the classic (non-overlapping) core and the Aubin core. We illustrate the general properties of the three cores, and also study them from a computational perspective, thus obtaining additional insights into their fundamental structure.
Remote Collaborative Depression Care Program for Adolescents in Araucanía Region, Chile: Randomized Controlled Trial

Background Despite evidence on efficacious interventions, a great proportion of depressed adolescents do not receive evidence-based treatment and have no access to specialized mental health care. Remote collaborative depression care (RCDC) may help to reduce the gap between needs and specialized mental health services. Objective The objective of this study was to assess the feasibility, acceptability, and effectiveness of an RCDC intervention for adolescents with major depressive disorder (MDD) living in the Araucanía Region, Chile. Methods A cluster randomized, assessor-blind trial was carried out at 16 primary care centers in the Araucanía Region, Chile. Before randomization, all participating primary care teams were trained in clinical guidelines for the treatment of adolescent depression. Adolescents (N=143; 13-19 years) with MDD were recruited. The intervention group (RCDC, N=65) received a 3-month RCDC treatment that included continuous remote supervision by psychiatrists located in Santiago, Chile’s capital city, through shared electronic health records (SEHR) and phone patient monitoring. The control group (enhanced usual care or EUC; N=78) received EUC by clinicians who were encouraged to follow clinical guidelines. Recruitment and response rates and the use of the SEHR system were registered; patient adherence and satisfaction with the treatment and clinician satisfaction with RCDC were assessed at 12-week follow-up; and depressive symptoms and health-related quality of life (HRQoL) were evaluated at baseline and 12-weeks follow-up. Results More than 60.3% (143/237) of the original estimated sample size was recruited, and a response rate of 90.9% (130/143) was achieved at 12-week follow-up. A mean (SD) of 3.5 (4.0) messages per patient were written on the SEHR system by primary care teams. A third of the patients showed an optimal adherence to psychopharmacological treatment, and adolescents in the RCDC intervention group were more satisfied with psychological assistance than those in EUC group. Primary care clinicians were satisfied with the RCDC intervention, valuing its usefulness. There were no significant differences in depressive symptoms or HRQoL between groups. Satisfaction with psychological care, in both groups, was related to a significant change in depressive symptomatology at 12-weeks follow-up (beta=−4.3, 95% CI −7.2 to −1.3). Conclusions This is the first trial of its kind in Latin America that includes adolescents from vulnerable backgrounds, with an intervention that proved to be feasible and well accepted by both patients and primary care clinicians. Design and implementation issues may explain similar effectiveness across arms. The effectiveness of the intervention seems to be comparable with an already nationwide established treatment program that proved to be highly efficacious under controlled conditions. Trial Registration ClinicalTrials.gov: NCT01860443; https://clinicaltrials.gov/ct2/show/NCT01860443 (Archived by WebCite at http://www.webcitation.org/6wafMKlTY)
Analysis of Local Variation of Soil Surface Parameters With TerraSAR-X Radar Data Over Bare Agricultural Fields

The objective of this paper is to analyze the sensitivity of very high resolution TerraSAR-X radar data taken over bare soils to surface soil parameters and to study the spatial variability of these parameters at a fine scale (within a field plot). The relationship between the backscattering coefficient and the soil's parameters (moisture, surface roughness, texture, and local topography) was examined by means of four satellite images, as well as ground truth measurements, of each of the three agricultural plots, recorded during several field campaigns in the winter and spring of 2008. TerraSAR images demonstrate high potential for the identification of local variations of roughness and texture. An approach for the estimation of local moisture is proposed using an empirical method adapted to the scale of an individual field. The results show that, by using TerraSAR-X data to study bare agricultural fields, local variations in soil moisture can be retrieved with a root-mean-square error of 0.05 cm3 ·cm-3.
Priority based addressing method for the components of on chip communication

Abstract: In this paper we propose a priority based addressing method for Network-on-Chip applications. This method will facilitate a user to transmit a lesser number of overhead bits while transmitting a message to some other user. The number of overhead bits required will be dependent on the distance (in terms of number of routing nodes or routers) from source IP to destination IP. We also define a channel utility factor and show how the overall utilization of the channel increases with this method.
The genetic burden of inflammatory bowel diseases: implications for the clinic?

ABSTRACT Introduction: Inflammatory bowel diseases (IBD), which include Crohn’s disease (CD) and ulcerative colitis (UC), are characterized by chronic intestinal inflammation. Their etiology is multifactorial, with complex interactions between genetic and environmental factors, which are still largely unclear. Areas covered: The influence of genetics is clearly demonstrated by important epidemiological data, including familial aggregation and concordance in twins. In 2001, the first genetic susceptibility gene for IBD, the NOD2 gene, was identified. Currently, thanks to genetic wide association studies, over 200 susceptibility genetic markers are know. Expert commentary: However, clinically highly relevant gene associations are still very limited and the usefulness of these information in the current clinical strategies for treatment and surveillance of IBD is weak. Nevertheless, the recent identification of some genetic risk variants has clarified some newbiological pathways of these diseases thus paving the way for the discoveries in the near future of new targeted therapies.
Effects of testosterone, 17β-estradiol, and progesterone on the differentiation of bovine intramuscular adipocytes

The aim of this study was to investigate the effects of testosterone, 17β-estradiol, and progesterone on the differentiation of bovine intramuscular adipocytes (BIA). Stromal-vascular (SV) cells were obtained from M. longissimus dorsi of 20 months old Korean (Hanwoo) steers, and were cultured in DMEM containing 5% FBS. The proliferated BIA were induced to differentiate with 0.25 µM dexamethasone, 0.5 mM 1-methyl-3-isobutyl-xanthine and 10 µg/ml insulin. During differentiation, the cells were treated with testosterone, 17β-estradiol, and progesterone at concentrations of 10 -10 , 10 -9 , and 10 -8 M, respectively, for 12 days. Regardless of its concentration, testosterone remarkably reduced lipid droplets in the cytosol of BIA. On the other hand, 17β-estradiol and progesterone increased the accumulation of lipid droplets in BIA. Testosterone significantly (p<0.05) decreased GPDH activities with a dose-dependent pattern. 17β-Estradiol treatment onto BIA during differentiation, however, increased GPDH activity showing the highest activity (11.3 nmol/mg protein/min) at 10 -10 M. Treatment of BIA with progesterone also increased (p<0.05) GPDH activity with the highest activity (13.8 nmol/mg protein/min) at 10 -9 M. In conclusion, the results in the current study suggest that testosterone inhibits differentiation of BIA by suppressing GPDH activity while 17β-estradiol and progesterone have adverse effects. (Asian-Aust. J. Anim. Sci. 2005. Vol 18, No. 11 : 1589-1593)
Metabolic Regulation of Invadopodia and Invasion by Acetyl-CoA Carboxylase 1 and De novo Lipogenesis

Invadopodia are membrane protrusions that facilitate matrix degradation and cellular invasion. Although lipids have been implicated in several aspects of invadopodia formation, the contributions of de novo fatty acid synthesis and lipogenesis have not been defined. Inhibition of acetyl-CoA carboxylase 1 (ACC1), the committed step of fatty acid synthesis, reduced invadopodia formation in Src-transformed 3T3 (3T3-Src) cells, and also decreased the ability to degrade gelatin. Inhibition of fatty acid synthesis through AMP-activated kinase (AMPK) activation and ACC phosphorylation also decreased invadopodia incidence. The addition of exogenous 16∶0 and 18∶1 fatty acid, products of de novo fatty acid synthesis, restored invadopodia and gelatin degradation to cells with decreased ACC1 activity. Pharmacological inhibition of ACC also altered the phospholipid profile of 3T3-Src cells, with the majority of changes occurring in the phosphatidylcholine (PC) species. Exogenous supplementation with the most abundant PC species, 34∶1 PC, restored invadopodia incidence, the ability to degrade gelatin and the ability to invade through matrigel to cells deficient in ACC1 activity. On the other hand, 30∶0 PC did not restore invadopodia and 36∶2 PC only restored invadopodia incidence and gelatin degradation, but not cellular invasion through matrigel. Pharmacological inhibition of ACC also reduced the ability of MDA-MB-231 breast, Snb19 glioblastoma, and PC-3 prostate cancer cells to invade through matrigel. Invasion of PC-3 cells through matrigel was also restored by 34∶1 PC supplementation. Collectively, the data elucidate the novel metabolic regulation of invadopodia and the invasive process by de novo fatty acid synthesis and lipogenesis.
Environmental Change and Prehistoric Polynesian Settlement in Hawai'i

IT HAS NOW BEEN A LITTLE MORE than a decade since Patrick Kirch (1982a) summarized the available and rather uneven evidence for environmental change in Hawai'i, compiling information from both archaeological and natural history sources. The actual data, which from today's perspective were quite limited, con­ cerned various aspects of the native flora and fauna of Hawai'i in addition to aspects of geomorphological alteration of the Hawaiian landscape. Taken together, these data suggested to Kirch that the prehistoric Polynesian colonizers of Hawai'i had (Kirch 1982a: 1) "a far greater impact on the Hawaiian ecosystem than has heretofore been realized. " According to Kirch's thesis, the use of fire, primarily for agricultural clearing, was a major factor in the Polynesian transformation of the Hawaiian environment. This view contrasted with the then-prevalent notion that it was only after Western contact that massive environmental degradation oc­ curred. The causes included the introduction of hoofed mammals for ranching, plantation agriculture, and the proliferation of introduced plant and animal species that often had no competitors and flourished at the expense of the local biota. Although Kirch's article paved the way for establishing a productive domain of research relating to an understanding of Polynesian adaptations to their island en­ vironment in Hawai'i, until recently there have been few in-depth or focused studies. Investigations that go beyond simple generalizations based on limited or uneven data and anecdotal accounts or programs of intensive field and laboratory research followed by quantifiable and replicable presentations of the data are rare.
Allometric Scaling of the Optic Tectum in Cartilaginous Fishes

In cartilaginous fishes (Chondrichthyes; sharks, skates and rays (batoids), and holocephalans), the midbrain or mesencephalon can be divided into two parts, the dorsal tectum mesencephali or optic tectum (analogous to the superior colliculus of mammals) and the ventral tegmentum mesencephali. Very little is known about interspecific variation in the relative size and organization of the components of the mesencephalon in these fishes. This study examined the relative development of the optic tectum and the tegmentum in 75 chondrichthyan species representing 32 families. This study also provided a critical assessment of attempts to quantify the size of the optic tectum in these fishes volumetrically using an idealized half-ellipsoid approach (method E), by comparing this method to measurements of the tectum from coronal cross sections (method S). Using species as independent data points and phylogenetically independent contrasts, relationships between the two midbrain structures and both brain and mesencephalon volume were assessed and the relative volume of each brain area (expressed as phylogenetically corrected residuals) was compared among species with different ecological niches (as defined by primary habitat and lifestyle). The relatively largest tecta and tegmenta were found in pelagic coastal/oceanic and oceanic sharks, benthopelagic reef sharks, and benthopelagic coastal sharks. The smallest tecta were found in all benthic sharks and batoids and the majority of bathyal (deep-sea) species. These results were consistent regardless of which method of estimating tectum volume was used. We found a highly significant correlation between optic tectum volume estimates calculated using method E and method S. Taxon-specific variation in the difference between tectum volumes calculated using the two methods appears to reflect variation in both the shape of the optic tectum relative to an idealized half-ellipsoid and the volume of the ventricular cavity. Because the optic tectum is the principal termination site for retinofugal fibers arising from the retinal ganglion cells, the relative size of this brain region has been associated with an increased reliance on vision in other vertebrate groups, including bony fishes. The neuroecological relationships between the relative size of the optic tectum and primary habitat and lifestyle we present here for cartilaginous fishes mirror those established for bony fishes; we speculate that the relative size of the optic tectum and tegmentum similarly reflects the importance of vision and sensory processing in cartilaginous fishes.