Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary optimization for computationally expensive problems using Gaussian processes

The use of statistical models to approximate detailed analysis codes for evolutionary optimization has attracted some attention [1-3]. However, those early methodologies do suffer from some limitations, the most serious of which being the extra tuning parameter introduceds. Also the question of when to include more data points to the approximation model during the search remains unresolved. Those limitations might seriously impede their successful application. We present here an approach that makes use of the extra information provided by a Gaussian processes (GP) approximation model to guide the crucial model update step. We present here the advantages of using GP over other neural-net biologically inspired approaches. Results are presented for a real world-engineering problem involving the structural optimization of a satellite boom.
Degradation of lateral bearing capacity of piles in soft clay subjected to cyclic lateral loading

Abstract In this article, the degradation of the lateral bearing capacity of piles in soft clay subjected to cyclic lateral loading is studied numerically. A modified kinematic hardening constitutive model is employed to simulate the degradation of soft clay after cyclic loading. The modified model is verified by comparing the numerical simulation results with the results of centrifuge model tests. Furthermore, the modified model is applied to numerical simulations for evaluating the lateral bearing capacity of piles in soft clay subjected to cyclic lateral loading. The degradation of the lateral bearing capacity of piles in soft clay after different cyclic displacement levels and different numbers of cycles is investigated. The study reveals that the modified kinematic hardening constitutive model can effectively estimate the cyclic degradation behavior of piles in soft clay subjected to cyclic lateral loading. The degradation of the ultimate lateral bearing capacity progresses slowly with increasing cyclic displacement level for fewer cycles, and the degradation develops significantly at higher levels of cyclic displacement after applying a larger number of cycles.
Reduced Basis Multiscale Finite Element Methods for Elliptic Problems

In this paper, we propose reduced basis multiscale finite element methods (RB-MsFEMs) for elliptic problems with highly oscillating coefficients. The method is based on MsFEMs with local test functions that encode the oscillatory behavior (see [G. Allaire and R. Brizzi, Multiscale Model. Simul., 4 (2005), pp. 790--812, J. S. Hesthaven, S. Zhang, and X. Zhu, Multiscale Model. Simul. , 12 (2014), pp. 650--666]). For uniform rectangular meshes, the local oscillating test functions are represented by a reduced basis method (RBM), parameterizing the center of the elements. For triangular elements, we introduce a slightly different approach. By exploring oversampling of the oscillating test functions, initially introduced to recover a better approximation of the global harmonic coordinate map, we first build the reduced basis on uniform rectangular elements containing the original triangular elements and then restrict the oscillating test function to the triangular elements. These techniques are also generalized.
Dicaesium diaquabis(methylenediphosphonato-κ2 O,O′)cobaltate(II)

The asymmetric unit of the title compound, Cs2[Co(CH4O6P2)2(H2O)2], is comprised of one bidentate methylenediphosphonate ligand and one water molecule which are coordinated to the CoII atom, as well as a caesium counter-cation. The Co atom occupies a special position on a crystallographic inversion center. The caesium ion is octahedrally coordinated by six O atoms with Cs—O distances ranging from 3.119 (2) to 3.296 (2) Å. A three-dimensional network is formed through O—H⋯O hydrogen bonds.
UHF Propagation Along a Cargo Hold on Board a Merchant Ship

The characterization of a Line of Sight (LOS) and a Non-Line of Sight (NLOS) link is performed over the military Ultra High Frequency (UHF) band (225 to 450 MHz). This is done using experimental results collected inside the cargo hold of a merchant ship. By analyzing the guiding effect associated with the cargo hold and its sub-structures, the channel characteristics of the environment can be determined. This important propagation mechanism is analyzed using the 3-D ray tracing simulator. Path loss for both topologies is studied and linear path loss models are proposed. Small-scale channel characteristics, such as the number of multipath components, decay factor of the multipath components and Root-Mean-Square (RMS) delay spread are studied and compared for the LOS and NLOS scenarios. Due to the guiding effect and multiple reflections along the cargo hold, both the LOS and NLOS scenarios are found to exhibit similar channel characteristics. A linear decay function is proposed to model the average Power Delay Profiles (PDPs). It is concluded that the linear model provides a good representation for the shape of the impulse responses for a cluttered environment with reflective substructures. This study is useful for the implementation of wireless sensor networks for status monitoring in maritime applications.
Solvent-Free Synthesis of Flavour Esters through Immobilized Lipase Mediated Transesterification

The synthesis of methyl butyrate and octyl acetate through immobilized Rhizopus oryzae NRRL 3562 lipase mediated transesterification was studied under solvent-free conditions. The effect of different transesterification variables, namely, molarity of alcohol, reaction time, temperature, agitation, addition of water, and enzyme amount on molar conversion (%) was investigated. A maximum molar conversion of 70.42% and 92.35% was obtained in a reaction time of 14 and 12 h with the transesterification variables of 0.6 M methanol in vinyl butyrate and 2 M octanol in vinyl acetate using 80 U and 60 U immobilized lipase with the agitation speed of 200 rpm and 0.2% water addition at 32°C and 36°C for methyl butyrate and octyl acetate, respectively. The immobilized enzyme has retained good relative activity (more than 95%) up to five and six recycles for methyl butyrate and octyl acetate, respectively. Hence, the present investigation makes a great impingement in natural flavour industry by introducing products synthesized under solvent-free conditions to the flavour market.
The Effect of Fast Normal Mode Structure and Magnetopause Forcing on FLRs in a 3‐D Waveguide

This paper investigates the excitation of waveguide modes in a nonuniform dipole equilibrium and, further, their coupling to field line resonances (FLRs). Waveguide modes are fast compressional ultralow frequency (ULF) waves, whose structure depends upon the magnetospheric equilibrium and the solar wind driving conditions. Using magnetohydrodynamic simulations, we consider how the structure of the excited waveguide mode is affected by various forms of magnetopause driving. We find that the waveguide supports a set of normal modes that are determined by the equilibrium. However, the particular normal modes that are excited are determined by the structure of the magnetopause driver. A full understanding of the spatial structure of the normal modes is required in order to predict where coupling to FLRs will occur. We show that symmetric pressure driving about the noon meridian can excite normal modes which remain around to drive resonances for longer than antisymmetric driving. Further, the critical quantity in terms of efficient coupling is the magnetic pressure gradient aligned with the resonance.
Hippocampal CA3 Transcriptome Signature Correlates with Initial Precipitating Injury in Refractory Mesial Temporal Lobe Epilepsy

Background Prolonged febrile seizures constitute an initial precipitating injury (IPI) commonly associated with refractory mesial temporal lobe epilepsy (RMTLE). In order to investigate IPI influence on the transcriptional phenotype underlying RMTLE we comparatively analyzed the transcriptomic signatures of CA3 explants surgically obtained from RMTLE patients with (FS) or without (NFS) febrile seizure history. Texture analyses on MRI images of dentate gyrus were conducted in a subset of surgically removed sclerotic hippocampi for identifying IPI-associated histo-radiological alterations. Methodology/Principal Findings DNA microarray analysis revealed that CA3 global gene expression differed significantly between FS and NFS subgroups. An integrative functional genomics methodology was used for characterizing the relations between GO biological processes themes and constructing transcriptional interaction networks defining the FS and NFS transcriptomic signatures and its major gene-gene links (hubs). Co-expression network analysis showed that: i) CA3 transcriptomic profiles differ according to the IPI; ii) FS distinctive hubs are mostly linked to glutamatergic signalization while NFS hubs predominantly involve GABAergic pathways and neurotransmission modulation. Both networks have relevant hubs related to nervous system development, what is consistent with cell genesis activity in the hippocampus of RMTLE patients. Moreover, two candidate genes for therapeutic targeting came out from this analysis: SSTR1, a relevant common hub in febrile and afebrile transcriptomes, and CHRM3, due to its putative role in epilepsy susceptibility development. MRI texture analysis allowed an overall accuracy of 90% for pixels correctly classified as belonging to FS or NFS groups. Histological examination revealed that granule cell loss was significantly higher in FS hippocampi. Conclusions/Significance CA3 transcriptional signatures and dentate gyrus morphology fairly correlate with IPI in RMTLE, indicating that FS-RMTLE represents a distinct phenotype. These findings may shed light on the molecular mechanisms underlying refractory epilepsy phenotypes and contribute to the discovery of novel specific drug targets for therapeutic interventions.
Role of Norepinephrine in Modulating Inhibitory Avoidance Memory Storage: Critical Involvement of the Basolateral Amygdala

© 2012 Ferry and Quirarte, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Role of Norepinephrine in Modulating Inhibitory Avoidance Memory Storage: Critical Involvement of the Basolateral Amygdala
High resolution tiling‐path BAC array deletion mapping suggests commonly involved 3p21‐p22 tumor suppressor genes in neuroblastoma and more frequent tumors

The recurrent loss of 3p segments in neuroblastoma suggests the implication of 1 or more tumor suppressor genes but thus far few efforts have been made to pinpoint their detailed chromosomal position. To achieve this goal, array‐based comparative genomic hybridization was performed on a panel of 23 neuroblastoma cell lines and 75 primary tumors using a tiling‐path bacterial artificial chromosome array for chromosome 3p. A total of 45 chromosome 3 losses were detected, including whole chromosome losses, large terminal deletions and interstitial deletions. The latter, observed in cell lines as well as a number of distal deletions detected in primary tumors, allowed us to demarcate 3 minimal regions of loss of 3.6 Mb [3p21.31‐p21.2, shortest regions of overlap (SRO)1], 1.4 Mb (3p22.3‐3p22.2, SRO2) and 3.8 Mb (3p25.3‐p25.1, SRO3) in size. The present data significantly extend previous findings and now firmly establish critical regions on 3p implicated in neuroblastoma. Interestingly, the 2 proximal regions coincide with previously defined SROs on 3p21.3 in more frequent tumors including lung and breast cancer. As such, similar tumor suppressor genes may play a critical role in development or progression of a variety of neoplasms, including neuroblastoma. © 2006 Wiley‐Liss, Inc.
Adjuvant capecitabine, docetaxel, cyclophosphamide, and epirubicin for early breast cancer: final analysis of the randomized FinXX trial.

PURPOSE Capecitabine is an active agent in the treatment of breast cancer. It is not known whether integration of capecitabine into an adjuvant regimen that contains a taxane, an anthracycline, and cyclophosphamide improves outcome in early breast cancer. PATIENTS AND METHODS Women with axillary node-positive or high-risk node-negative breast cancer were randomly assigned to receive either three cycles of docetaxel and capecitabine (TX) followed by three cycles of cyclophosphamide, epirubicin, and capecitabine (CEX; n = 753) or three cycles of docetaxel (T) followed by three cycles of cyclophosphamide, epirubicin, and fluorouracil (CEF; n = 747). The primary end point was recurrence-free survival (RFS). RESULTS During a median follow-up time of 59 months, 214 RFS events occurred (local or distant recurrences or deaths; TX/CEX, n = 96; T/CEF, n = 118). RFS was not significantly different between the groups (hazard ratio [HR], 0.79; 95% CI, 0.60 to 1.04; P = .087; 5-year RFS, 86.6% for TX/CEX v 84.1% for T/CEF). Fifty-six patients assigned to TX/CEX died during the follow-up compared with 75 of patients assigned to T/CEF (HR, 0.73; 95% CI, 0.52 to 1.04; P = .080). In exploratory analyses, TX/CEX improved breast cancer-specific survival (HR, 0.64; 95% CI, 0.44 to 0.95; P = .027) and RFS in women with triple-negative disease and in women who had more than three metastatic axillary lymph nodes at the time of diagnosis. We detected little severe late toxicity. CONCLUSION Integration of capecitabine into a regimen that contains docetaxel, epirubicin, and cyclophosphamide did not improve RFS significantly compared with a similar regimen without capecitabine.
Autumn Cooling of Western East Antarctica Linked to the Tropical Pacific

Over the past 60 years, the climate of East Antarctica cooled while portions of West Antarctica were among the most rapidly warming regions on the planet. The East Antarctic cooling is attributed to a positive trend in the Southern Annular Mode (SAM) and a strengthening of the westerlies, while West Antarctic warming is tied to zonally asymmetric circulation changes forced by the tropics. This study finds recent (post‐1979) surface cooling of East Antarctica during austral autumn to also be tied to tropical forcing, namely, an increase in La Niña events. The recent increase in La Niña conditions forces a Rossby wave into the Southern Hemisphere that increases anticyclonic circulation over the South Atlantic. The South Atlantic anticyclone is associated with cold air advection, weakened northerlies, and increased sea ice concentrations across the western East Antarctic coast, which has increased the rate of cooling at Novolazarevskaya and Syowa stations after 1979. This enhanced cooling over western East Antarctica is tied more broadly to a zonally asymmetric temperature trend pattern across East Antarctica during autumn that is consistent with a tropically forced Rossby wave rather than a SAM pattern; the positive SAM pattern is associated with ubiquitous cooling across East Antarctica, which is not seen in temperature observations after 1979. We conclude that El Niño–Southern Oscillation‐related circulation anomalies, particularly zonal asymmetries that locally enhance meridional wind, are an important component of East Antarctic climate variability during autumn, and future changes in tropical Pacific climate will likely have implications for East Antarctica.
A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism.
Neural evolution in the bat-free habitat of Tahiti: partial regression in an anti-predator auditory system

Abstract Noctuid moths endemic to the mountains of Tahiti have evolved in an environment without bats and these insects have lost a defensive behaviour against these predators, the acoustic startle response (ASR). The ASR in noctuid moths is presumed to be activated by a single auditory receptor neuron (A2 cell) and we report that while this cell still exists in endemic species and possesses similar sensitivity thresholds compared to the A2 cell of recently introduced species, it exhibits reduced firing activity to ASR-evoking sounds. This partial neural regression suggests that the evolutionary disappearance of the ASR in these insects is incomplete and that sensoribehavioural integration decays gradually following the removal of stabilizing selective forces.
Physiological levels of S-nitrosothiols in human plasma.

To the Editor: The hypothesis that endothelial-derived relaxing factor (EDRF) is nitric oxide (NO) has stimulated a wealth of research into the significance of this novel, intriguing molecule. Given its short life, many forms of storage and targeting have been postulated: among these, a pool of derivatives of NO (RSNOs) covalently bound to SH groups of proteins and low molecular weight thiols (eg, glutathione) has been identified in various biological systems. The importance of RSNOs results from the very similar biological actions exhibited by both NO and RSNOs in vivo as well as in vitro. S -nitroso derivatives of GSH, cysteine, hemoglobin, BSA, and many other protein or nonprotein thiols are potent, fast-acting vasodilators, as well as strong inhibitors of platelet aggregation, like NO itself. Moreover, several nitrosovasodilators, such as nitrosoglycerin, have been reported to function through the formation of S -nitrosothiol intermediates. S -nitrosothiols in biological samples have been measured by a wide spectrum of different techniques. However, in our opinion, most of these techniques are not devoid of …
The In Vitro Mass-Produced Model Mycorrhizal Fungus, Rhizophagus irregularis, Significantly Increases Yields of the Globally Important Food Security Crop Cassava

The arbuscular mycorrhizal symbiosis is formed between arbuscular mycorrhizal fungi (AMF) and plant roots. The fungi provide the plant with inorganic phosphate (P). The symbiosis can result in increased plant growth. Although most global food crops naturally form this symbiosis, very few studies have shown that their practical application can lead to large-scale increases in food production. Application of AMF to crops in the tropics is potentially effective for improving yields. However, a main problem of using AMF on a large-scale is producing cheap inoculum in a clean sterile carrier and sufficiently concentrated to cheaply transport. Recently, mass-produced in vitro inoculum of the model mycorrhizal fungus Rhizophagus irregularis became available, potentially making its use viable in tropical agriculture. One of the most globally important food plants in the tropics is cassava. We evaluated the effect of in vitro mass-produced R. irregularis inoculum on the yield of cassava crops at two locations in Colombia. A significant effect of R. irregularis inoculation on yield occurred at both sites. At one site, yield increases were observed irrespective of P fertilization. At the other site, inoculation with AMF and 50% of the normally applied P gave the highest yield. Despite that AMF inoculation resulted in greater food production, economic analyses revealed that AMF inoculation did not give greater return on investment than with conventional cultivation. However, the amount of AMF inoculum used was double the recommended dose and was calculated with European, not Colombian, inoculum prices. R. irregularis can also be manipulated genetically in vitro, leading to improved plant growth. We conclude that application of in vitro R. irregularis is currently a way of increasing cassava yields, that there is a strong potential for it to be economically profitable and that there is enormous potential to improve this efficiency further in the future.
Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs

Evolution drives changes in a protein’s sequence over time. The extent to which these changes in sequence lead to shifts in the underlying preference for each amino acid at each site is an important question with implications for comparative sequence-analysis methods such as molecular phylogenetics. To quantify the extent that site-specific amino-acid preferences shift during evolution, we performed deep mutational scanning on two homologs of human influenza nucleoprotein with 94% amino-acid identity. We found that only a modest fraction of sites exhibited shifts in amino-acid preferences that exceeded the noise in our experiments. Furthermore, even among sites that did exhibit detectable shifts, the magnitude tended to be small relative to differences between non-homologous proteins. Given the limited change in amino-acid preferences between these close homologs, we tested whether our measurements could inform site-specific substitution models that describe the evolution of nucleoproteins from more diverse influenza viruses. We found that site-specific evolutionary models informed by our experiments greatly outperformed non-site-specific alternatives in fitting phylogenies of nucleoproteins from human, swine, equine, and avian influenza. Combining the experimental data from both homologs improved phylogenetic fit, partly because measurements in multiple genetic contexts better captured the evolutionary average of the amino-acid preferences for sites with shifting preferences. Our results show that site-specific amino-acid preferences are sufficiently conserved that measuring mutational effects in one protein provides information that can improve quantitative evolutionary modeling of nearby homologs.