Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling the Multiple Facets of Speciation-with-Gene-Flow toward Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus clupeaformis)

Parallel divergence patterns across replicated species pairs occurring in similar environmental contrasts may arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstructing historical gene flow is therefore of fundamental interest to understand how demography and selection jointly shaped genomic divergence during speciation. Here, we use an extended modeling framework to explore the multiple facets of speciation-with-gene-flow with demo-genetic divergence models that capture both temporal and genomic variation in effective population size and migration rate. We investigate the divergence history of five sympatric Lake Whitefish limnetic (dwarf) and benthic (normal) species pairs characterized by variable degrees of ecological divergence and reproductive isolation. Genome-wide SNPs were used to document the extent of genetic differentiation in each species pair, and 26 divergence models were fitted and compared to the unfolded joint allele frequency spectrum of each pair. We found evidence that a recent (circa 3000-4000 generations) asymmetrical secondary contact between expanding post-glacial populations has accompanied Whitefish diversification. Our results suggest that heterogeneous genomic differentiation patterns have emerged through the combined effects of linked selection generating variable rates of lineage sorting across the genome during geographical isolation, and heterogeneous introgression eroding divergence at different rates across the genome upon secondary contact. This study thus provides a new retrospective insight into the historical demographic and selective processes that shaped a continuum of divergence associated with ecological speciation.
Multiparameter RNA and Codon Optimization: A Standardized Tool to Assess and Enhance Autologous Mammalian Gene Expression

Autologous expression of recombinant human proteins in human cells for biomedical research and product development is often hampered by low expression yields limiting subsequent structural and functional analyses. Following RNA and codon optimization, 50 candidate genes representing five classes of human proteins – transcription factors, ribosomal and polymerase subunits, protein kinases, membrane proteins and immunomodulators – all showed reliable, and 86% even elevated expression. Analysis of three representative examples showed no detrimental effect on protein solubility while unaltered functionality was demonstrated for JNK1, JNK3 and CDC2 using optimized constructs. Molecular analysis of a sequence-optimized transgene revealed positive effects at transcriptional, translational, and mRNA stability levels. Since improved expression was consistent in HEK293T, CHO and insect cells, it was not restricted to distinct mammalian cell systems. Additionally, optimized genes represent powerful tools in functional genomics, as demonstrated by the successful rescue of an siRNA-mediated knockdown using a sequence-optimized counterpart. This is the first large-scale study addressing the influence of multiparameter optimization on autologous human protein expression.
Genetic population structure of broad whitefish, Coregonus nasus, from the Mackenzie River, Northwest Territories: implications for subsistence fishery management

We assayed microsatellite DNA variation among 1013 broad whitefish, Coregonus nasus, from 36 localities within the lower Mackenzie River (Northwest Territories, Canada) to provide the first assessment of fine-scale population structuring of broad whitefish in this large system. Among sampling locations, averaged across all loci, the number of al- leles ranged from 3.00 to 6.71 and heterozygosity averaged 0.54. Population subdivision was generally low, but significant (q = 0.026, P < 0.05), although pairwise comparisons indicated that overall significance was heavily influenced by compar- isons between anadromous and lacustrine groups. Bayesian-based STRUCTURE analysis suggested that there are two main genetic groups within our study area: anadromous and lacustrine broad whitefish. A mixture analysis indicated that all populations contribute to the lower Mackenzie River subsistence fishery, yet catches were dominated by Peel River fish, highlighting the importance of this tributary. Our data also supported the idea that there are several units of conserva- tion among Mackenzie River system broad whitefish populations and that management strategies should be implemented accordingly. Resume´ : Nous avons evaluela variation de l'ADN des microsatellites chez 1 013 coregones tschir, Coregonus nasus ,d e 36 sites sur le cours inferieur du Mackenzie (Territoires du Nord-Ouest, Canada) afin d'obtenir une premiere evaluation de la structure aechelle fine de la population de ces coregones dans ce grand reseau hydrographique. Pour l'ensemble des si- tes d'echantillonnage, le nombre moyen d'alleles pour tous les locus varie de 3,00 a 6,71 et l'heterozygotie moyenne est de 0,54. La subdivision de la population est generalement faible, mais significative (q = 0,026, P < 0,05), bien que des comparaisons appariees indiquent que la signification statistique globale est fortement influencee par les comparaisons en- tre les groupes anadromes et lacustres. Une analyse STRUCTURE de type bayesien laisse croire qu'il y a deux groupes genetiques principaux dans notre region d'etude, les coregones tschir anadromes et les lacustres. Une analyse de melange indique que toutes les populations contribuent a la peche de subsistance dans le cours inferieur du Mackenzie, bien que les captures soient dominees par les poissons de la riviere Peel, ce qui souligne l'importance de ce tributaire. Nos donnees ap- puient aussi la proposition qu'il existe plusieurs unites de conservation au sein des populations de coregones tschir du re ´- seau du Mackenzie et que les strategies d'amenagement devraient en tenir compte. (Traduit par la Redaction)
Preparation of Polylactide/Graphene Composites From Liquid-Phase Exfoliated Graphite Sheets

Polylactide (PLA)/graphene nanocomposites were prepared by a facile and low-cost method of solutionblending of PLA with liquid-phase exfoliated graphene using chloroform as a mutual solvent. Transmission electron microscopy (TEM) was used to observe the structure and morphology of the exfoliated graphene. The dispersion of graphene in PLA matrix was examined by scanning electron microscope, X-ray diffraction, and TEM. FTIR spectrum and the relatively low ID/IG ratio in Raman spectroscopy indicate that the structure of graphene sheets (GSs) is intact and can act as good reinforcement fillers in PLA matrix. Thermogravimetric analysis and dynamic mechanical analysis reveal that the addition of GSs greatly improves the thermal stability of PLA/GSs nanocomposites. Moreover, tensile strength of PLA/GSs nanocomposites is much higher than that of PLA homopolymer, increasing from 36.64 (pure PLA) up to 51.14 MPa (PLA/GSs-1.0). POLYM. COMPOS. , 00:000–000, 2013. V C 2013 Society of Plastics Engineers
Antiferroelectric Materials, Applications and Recent Progress on Multiferroic Heterostructures

Antiferroelectric (AFE) materials with adjacent dipoles oriented in antiparallel directions have a double polarization hysteresis loops. An electric field (E-field)-induced AFE–ferroelectric (FE) phase transition takes place in such materials, leading to a large lattice strain and energy change. The high dielectric constant and the distinct phase transition in AFE materials provide great opportunities for the realization of energy storage devices like super-capacitors and energy conversion devices such as AFE MEMS applications. Lots of work has been done in this field since 60–70 s. Recently, the strain tuning of the spin, charge and orbital orderings and their interactions in complex oxides and multiferroic heterostructures have received great attention. In these systems, a single control parameter of lattice strain is used to control lattice–spin, lattice–phonon, and lattice–charge interactions and tailor properties or create a transition between distinct magnetic/electronic phases. Due to the large strain/stress arising from the phase transition, AFE materials are great candidates for integrating with ferromagnetic (FM) materials to realize in situ manipulation of magnetism and lattice-ordered parameters by voltage. In this paper, we introduce the AFE material and it's applications shortly and then review the recent progress in AFEs based on multiferroic heterostructures. These new multiferroic materials could pave a new way towards next generation light, compact, fast and energy efficient voltage tunable RF/microwave, spintronic and memory devices promising approaches to in situ manipulation of lattice-coupled order parameters is to grow epitaxial oxide films on FE/ferroelastic substrates.
Microdevice for aqueous humor drainage Maldonado Bas - Pförtner.

PURPOSE A microdevice for the treatment of refractory glaucoma is presented. The underlying concepts, its mechanisms of action and the surgical technique for implanting are explained and the results are analyzed. The microdevice was developed and the surgeries were performed at the Maldonado-Bas Eye Clinic (Cordoba, Argentina), under the rules established in the protocol approved by the provisions of the National Administration of Drugs, Food and Medical Technology 430/7. File No.:1-47-25-649-07-1. METHODS In a prospective study, following the protocol, 16 eyes with refractory glaucoma were included and operated. Intraocular pressure <21mmHg with or without additional medication was considered successful. The follow-up was one year. Averages, percentages and their 95% confidence bands were calculated. Analysis of variance for repeated measures was used to compare averages. RESULTS The average preoperative intraocular pressure was 32.81 mmHg, SD ± 10.94 mmHg in a range of 14 to 50 mmHg. The average post-surgical intraocular pressure at one year was 12.43 mmHg, SD ± 2.85 mmHg in a range of 7 to 19 mmHg. The difference between the pre-and post-surgery average intraocular pressure was 20.38 mmHg. The number of successes was 14 eyes (87.5%, confidence interval (CI) 95% 61.6% - 98.6%). The number of failures was two eyes (12.5%, CI 95% 1.43% - 38.4%). CONCLUSIONS The results show that the microdevice is successful for the treatment of refractory glaucoma.
HOSTING MEGA EVENTS

This study develops and tests a structural model to assess key factors on residents’ perceptions of the impacts of the 2002 Winter Olympics as a mega tourism event and how these perceptions affect their support. The model is based on previous literature and uses data collected during the event. Community backing for mega events is affected directly and/or indirectly by five determinants of support: the level of community concern, ecocentric values, community attachment, perceived benefits, and perceived costs. There are interactions between costs and benefit factors, and support relies heavily on perceived benefits rather than costs. Theoretical and managerial implications are discussed.
Long-Range Wireless Interrogation of Passive Humidity Sensors Using Van-Atta Cross-Polarization Effect and Different Beam Scanning Techniques

This paper presents a method for the remote interrogation of batteryless humidity sensors based on statistical estimations and 3-D beam scanning techniques. As a proof-of-concept demonstration, a Van-Atta reflectarray sensor is interrogated with a 24-GHz frequency-modulated continuous-wave transceiver at various reading ranges. The extension of the proposed approach to passive or moving sensors is reported, and the measurement results are discussed. The relative humidity (RH) is derived from the statistical analysis of multidimensional radar echoes, while method is proposed to detect the sensor among clutter without knowing its exact position. Moreover, it is demonstrated that the cross-polarization effect of the Van-Atta reflectarray combined with the 3-D beam scanning technique allows the indoor measurement of the RH up to 58 m.
PROGRESS IN MEASUREMENTS OF THE GRAVITATIONAL BENDING OF RADIO WAVES USING THE VLBA

We have used the Very Long Baseline Array (VLBA) at 43, 23, and 15 GHz to measure the solar gravitational deflection of radio waves among four radio sources during an 18 day period in 2005 October. Using phase-referenced radio interferometry to fit the measured phase delay to the propagation equation of the parameterized post-Newtonian formalism, we have determined the deflection parameter γ = 0.9998 ± 0.0003 (68% confidence level), in agreement with general relativity. The results come mainly from 43 GHz observations where the refraction effects of the solar corona were negligible beyond 3 deg from the Sun. The purpose of this experiment is three-fold: to improve on the previous results in the gravitational bending experiments near the solar limb; to examine and evaluate the accuracy limits of terrestrial VLBI techniques; and to determine the prospects and outcomes of future experiments. Our conclusion is that a series of improved designed experiments with the VLBA could increase the presented accuracy by at least a factor of 4.
Variability Characterization Using an RO-array Test Structure and Its Impact on Design

Real silicon variability characterization and modeling are important topics for statistical timing analysis. In this paper, we describe our RO-array test structures in 65nm process and measurement result of WID and D2D variations. We decompose and characterize WID variability into deterministic, systematic, and random components. We also discuss how these components affect circuit timing analysis.
Problem Solving in Human Beings and Computers (formerly: Heuristic Problem Solving)

The process of solving a problem has been traditionally represented as that of searching a graph, describing the problem space, to find a path from the start to the goal state. Prior research on human problem solving has shown that human beings do not perform an exhaustive search of the problem space. Instead, they attempt to identify and use intrinsic properties of the problem. This process involves insight, concept formation, establishing subgoals and invariant features. Such results from psychological research have been used by computer scientists in formalizing the concept of heuristic and applying it in Artificial Intelligence (AI) systems. It has been shown that, in the general case, heuristics allow restriding the search space which speeds up the search process. We first show that if the cosLs of edges in the search graph satisfy metric axioms an algorithm based on the evaluation fundion r develops only one (optimal) path. Second, we show that if a problem can be represented in a metric space, the solution of the problem can be determined by decomposing the problem into local regions and combining the local solutions into a global one. The implications of these analyses were tested in two experiments where human subjects were asked to solve the Traveling Salesman Problem (TSP). Our results show that the subjects are very efficient in metric (Euclidean) TSP, but not in non-metric TSP (where triangle inequality is violated). In the Euclidean TSP, the solution is nearly optimal and time is a linear function of the number of cities. These results suggest that human beings solve problems by building only a single path, rather than by performing a constrained search. We conclude by comparing the human performance to the performance of several conventional Al algorithms. This comparison shows that human beings solve problems by using heuristics that are quite different from existing AI heuristics.
Home fortification of complementary foods with micronutrient supplements is well accepted and has positive effects on infant iron status in Ghana.

BACKGROUND Micronutrient deficiencies are common during infancy, and optimal approaches for their prevention need to be identified. OBJECTIVE The objective was to compare the efficacy and acceptability of Sprinkles (SP), crushable Nutritabs (NT), and fat-based Nutributter (NB; 108 kcal/d), which provide 6, 16, and 19 vitamins and minerals, respectively, when used for home fortification of complementary foods. DESIGN Ghanaian infants were randomly assigned to receive SP (n = 105), NT (n = 105), or NB (n = 103) daily from 6 to 12 mo of age. We assessed dietary intake, morbidity, and compliance weekly. Hemoglobin and plasma ferritin, TfR, C-reactive protein, and zinc were measured at 6 and 12 mo. We used an exit interview to assess acceptability. A randomly selected control group of infants who received no intervention (NI; n = 96) were assessed at 12 mo. RESULTS All supplements were well accepted, and the mean percentage of days that supplements were consumed (87%) did not differ between groups. At 12 mo, all 3 intervention groups had significantly higher ferritin and lower TfR concentrations than did the NI control group. Mean (+/- SD) hemoglobin was significantly higher in NT (112 +/- 14 g/L) and NB (114 +/- 14 g/L) but not in SP (110 +/- 14 g/L) infants than in NI infants (106 +/- 14 g/L). The prevalence of iron deficiency anemia was 31% in the NI control group compared with 10% in the intervention groups combined (P < 0.0001). CONCLUSION All 3 options for home fortification of complementary foods are effective for reducing the prevalence of iron deficiency in such populations.
Postnatal weight and height growth velocities at different ages between birth and 5 y and body composition in adolescent boys and girls.

BACKGROUND Rapid weight gain in the first years of life is associated with adult obesity. Whether there are critical windows for this long-term effect is unclear. OBJECTIVE The objective was to study anthropometric measures in adolescence by sex according to weight and height growth velocities at different ages between birth and 5 y. DESIGN Anthropometric measures, including fat and fat-free mass by bipodal impedancemetry, were measured in 468 adolescents aged 8-17 y. We retrospectively collected early infancy data and individually estimated weight and height growth velocities in 69.4% of them using a mathematical model. Associations between birth variables, growth velocities, and anthropometric measures in adolescence were studied. RESULTS Weight growth velocity at 3 mo was associated with overweight (odds ratio for a 1-SD increase: 1.52; 95% CI: 1.04, 2.22), fat mass, and waist circumference in adolescence in both sexes and with fat-free mass in boys (r = 0.29, P < 0.001) but not in girls (r = -0.01, NS). Weight growth velocities after 2 y were associated with all anthropometric measures in adolescence, in both sexes. Between 6 mo and 2 y, weight growth velocities were significantly associated only with adolescent height in boys; in girls, associations with fat mass in adolescence were weaker. CONCLUSION Our results support the hypothesis of 2 critical windows in early childhood associated with the later risk of obesity: up to 6 mo and from 2 y onward. The study of the determinants of growth during these 2 periods is of major importance for the prevention of obesity in adolescence.
Whole-grain intake may reduce the risk of ischemic heart disease death in postmenopausal women: the Iowa Women's Health Study.

BACKGROUND A recent review of epidemiologic literature found consistently reduced cancer and heart disease rates in persons with high compared with low whole-grain intakes. OBJECTIVE We hypothesized that whole-grain intake was associated with a reduced risk of ischemic heart disease (IHD) death. DESIGN We studied 34,492 postmenopausal women aged 55-69 y and free of IHD at baseline in 1986. There were 438 IHD deaths between baseline and 1995. Usual dietary intake was determined with use of a 127-item food-frequency questionnaire. RESULTS Whole-grain intake in median servings/d was 0.2, 0.9, 1.2, 1.9, and 3.2 for quintiles of intake. The unadjusted rate of IHD death was 2.0/1 x 10(3) person-years in quintile 1 and was 1.7, 1.2, 1.0, and 1.4 IHD deaths/1 x 10(3) person-years in succeeding quintiles (P for trend < 0.001). Adjusted for demographic, physiologic, behavioral, and dietary variables, relative hazards were 1.0, 0.96, 0.71, 0.64, and 0.70 in ascending quintiles (P for trend = 0.02). The lower risk with higher whole-grain intake was not explained by intake of fiber or several other constituents of whole grains. CONCLUSION A clear inverse association between whole-grain intake and risk of IHD death existed. A causal association is plausible because whole-grain foods contain many phytochemicals, including fiber and antioxidants, that may reduce chronic disease risk. Whole-grain intake should be studied further for its potential to prevent IHD and cancer.
Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes

Non-aureus staphylococci (NAS) are most commonly isolated from subclinical mastitis. Different NAS species may, however, have diverse effects on the inflammatory response in the udder. We determined the genome sequences of 20 staphylococcal isolates from clinical or subclinical bovine mastitis, belonging to the NAS species Staphylococcus agnetis, S. chromogenes, and S. simulans, and focused on the putative virulence factor genes present in the genomes. For comparison we used our previously published genome sequences of four S. aureus isolates from bovine mastitis. The pan-genome and core genomes of the non-aureus isolates were characterized. After that, putative virulence factor orthologues were searched in silico. We compared the presence of putative virulence factors in the NAS species and S. aureus and evaluated the potential association between bacterial genotype and type of mastitis (clinical vs. subclinical). The NAS isolates had much less virulence gene orthologues than the S. aureus isolates. One third of the virulence genes were detected only in S. aureus. About 100 virulence genes were present in all S. aureus isolates, compared to about 40 to 50 in each NAS isolate. S. simulans differed the most. Several of the virulence genes detected among NAS were harbored only by S. simulans, but it also lacked a number of genes present both in S. agnetis and S. chromogenes. The type of mastitis was not associated with any specific virulence gene profile. It seems that the virulence gene profiles or cumulative number of different virulence genes are not directly associated with the type of mastitis (clinical or subclinical), indicating that host derived factors such as the immune status play a pivotal role in the manifestation of mastitis.