Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements

Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process. To better understand TE exaptation, we designed an approach to resolve the phylogenetic context and timing of exaptation events and subsequent patterns of ETE diversification. Starting with known ETEs, we search in diverse genomes for basal ETEs and closely related TEs, carefully curate the numerous candidate sequences, and infer detailed phylogenies. To distinguish TEs from ETEs, we also weigh several key genomic characteristics including repetitiveness, terminal repeats, pseudogenic features, and conserved domains. Applying this approach to the well-characterized plant ETEs MUG and FHY3, we show that each group is paraphyletic and we argue that this pattern demonstrates that each originated in not one but multiple exaptation events. These exaptations and subsequent ETE diversification occurred throughout angiosperm evolution including the crown group expansion, the angiosperm radiation, and the primitive evolution of angiosperms. In addition, we detect evidence of several putative novel ETE families. Our findings support the hypothesis that TE exaptation generates novel genes more frequently than is currently thought, often coinciding with key periods of evolution.
Commentary: how should monetary policy be conducted in an era of price stability?

It is a pleasure to be asked to comment upon Lars Svensson’s thoughtful and ambitious paper, though it raises far too many issues for me to attempt to address them all in the limited time available here. Svensson offers a thorough review of the recent scholarly literature on the conduct of monetary policy, and also reviews one of the most important recent developments in central bank practice as well, namely the evolving methodology of “inflation forecast targeting. ”
American Lobsters (Homarus Americanus) not Surviving During Air Transport: Evaluation of Microbial Spoilage

Eighteen American lobsters (Homarus americanus), dead during air transport, were analysed in order to evaluate the microbial population of meat, gills and gut: no specific studies have ever been conducted so far on the microbiological quality of American lobsters’ meats in terms of spoilage microbiota. The meat samples showed very limited total viable counts, in almost all the cases below the level of 6 Log CFU/g, while higher loads were found, as expected, in gut and gills, the most probable source of contamination. These data could justify the possibility to commercialise these not-surviving subjects, without quality concerns for the consumers. Most of the isolates resulted to be clustered with type strains of Pseudoalteromonas spp. (43.1%) and Photobacterium spp. (24.1%), and in particular to species related to the natural marine environment. The distribution of the genera showed a marked inhomogeneity among the samples. The majority of the isolates identified resulted to possess proteolytic (69.3%) and lipolytic ability (75.5%), suggesting their potential spoilage ability. The maintanance of good hygienical practices, especially during the production of ready-to-eat lobsters-based products, and a proper storage could limit the possible replication of these microorganisms.
Cell Pattern in Adult Human Corneal Endothelium

A review of the current data on the cell density of normal adult human endothelial cells was carried out in order to establish some common parameters appearing in the different considered populations. From the analysis of cell growth patterns, it is inferred that the cell aging rate is similar for each of the different considered populations. Also, the morphology, the cell distribution and the tendency to hexagonallity are studied. The results are consistent with the hypothesis that this phenomenon is analogous with cell behavior in other structures such as dry foams and grains in polycrystalline materials. Therefore, its driving force may be controlled by the surface tension and the mobility of the boundaries.
Document Clustering Analysis Based on Hybrid PSO+K-means Algorithm

: There is a tremendous proliferation in the amount of information available on the largest shared information source, the World Wide Web. Fast and high-quality document clustering algorithms play an important role in helping users to effectively navigate, summarize, and organize the information. Recent studies have shown that partitional clustering algorithms are more suitable for clustering large datasets. The K-means algorithm is the most commonly used partitional clustering algorithm because it can be easily implemented and is the most efficient one in terms of the execution time. The major problem with this algorithm is that it is sensitive to the selection of the initial partition and may converge to a local optima. In this paper, we present a hybrid Particle Swarm Optimization (PSO)+K-means document clustering algorithm that performs fast document clustering and can avoid being trapped in a local optimal solution as well. For comparison purpose, we applied the PSO+K-means, PSO, K-means, and other two hybrid clustering algorithms on four different text document datasets. The number of documents in the datasets range from 204 to over 800, and the number of terms range from over 5000 to over 7000. The results illustrate that the PSO+K-means algorithm can generate the most compact clustering results than other four algorithms.
Comparison of the clinical characteristics and treatment outcomes of patients requiring hospital admission to treat eosinophilic and neutrophilic exacerbations of COPD

Purpose We compared the clinical characteristics and treatment outcomes of patients with eosinophilic and neutrophilic COPD exacerbations requiring hospital admission. Patients and methods This was a retrospective multicenter study performed between January 2010 and December 2014. In all, 1,688 COPD patients admitted via the outpatient clinics or emergency departments of six university hospitals were enrolled. The patients were grouped by complete blood counts: eosinophilic group, >2% peripheral blood eosinophils, and neutrophilic group, >65% peripheral blood neutrophils or >11,000 leukocytes/mL. The patients with radiographic evidence of pneumonia at the time of admission, those with lung cancer, those admitted for treatment of other medical problems, and those who chronically used steroids were excluded. Results A total of 605 patients hospitalized with COPD exacerbations (177 eosinophilic and 380 neutrophilic) were included. Pulmonary functions, including the forced expiratory volume in 1 second and forced vital capacity, were better in patients with eosinophilic exacerbations. Treatment outcomes, including the rate of admission to the intensive care unit and mortality, were poorer in patients with neutrophilic exacerbations (4.5% vs 12.4%, P=0.004; 1.1% vs 4.5%, P=0.043, respectively). Congestive heart failure (odds ratio [OR] =3.40, 95% confidence interval [CI]: 1.28–9.01) and neutrophilic exacerbation (OR = 2.81, 95% CI: 1.21–6.52) were independent risk factors for intensive care unit admission. Conclusion COPD patients with neutrophilic exacerbations experienced worse clinical outcomes than did those with eosinophilic exacerbations. The peripheral blood eosinophil count may be a useful predictor of clinical progress during hospitalization of COPD patients with acute exacerbations.
A mobile signal transported over a long distance induces systemic transcriptional gene silencing in a grafted partner

Transcriptional gene silencing (TGS) can be induced by promoter-targeted small interfering RNA (siRNA). Long-distance transmission of TGS by viral infection in plants has been reported. However, systemic TGS has not been observed in the case of using an inverted repeat transgene as the silencing trigger. Here it is reported that a mobile signal, presumably the siRNA, produced from a hairpin structure transgene controlled by a companion cell-specific promoter can also induce transmissible TGS in both a modified agroinfiltration and a grafting system. Although the transmissible TGS occurred only in cells located in the vicinity of a leaf vein in the scion, very strong silencing was observed in the root system, especially the lateral roots, including the root apical meristem. The transmissible TGS was maintained through tissue culture and subsequently inherited by the progeny. The results suggest the potential application of mobile promoter-targeting siRNA in horticulture for improvement of plant cultivars by grafting.
Fund Family Tournament and Performance Consequences: Evidence from the UK Fund Industry

By applying tournament analysis to the UK Unit Trusts data, the results support significant risk shifting in the family tournament; i.e. interim winning managers tend to increase their level of risk exposure more than losing managers. It also shows that the risk-adjusted returns of the winners outperform those of the losers following the risk taking, which implies that risk altering can be regarded as an indication of managers’ superior ability. However, the tournament behaviour can still be a costly strategy for investors, since winners can be seen to beat losers in the observed returns due to the deterioration in the performance of their major portfolio holdings.
Accurate Vision-based Vehicle Localization using Satellite Imagery

We propose a method for accurately localizing ground vehicles with the aid of satellite imagery. Our approach takes a ground image as input, and outputs the location from which it was taken on a georeferenced satellite image. We perform visual localization by estimating the co-occurrence probabilities between the ground and satellite images based on a ground-satellite feature dictionary. The method is able to estimate likelihoods over arbitrary locations without the need for a dense ground image database. We present a ranking-loss based algorithm that learns location-discriminative feature projection matrices that result in further improvements in accuracy. We evaluate our method on the Malaga and KITTI public datasets and demonstrate significant improvements over a baseline that performs exhaustive search.
Distribution of Influenza-Like Illness (ILI) by Occupation in Washington State, September 2009–August 2010

Objectives : We aim to estimate the prevalence of influenza-like illness (ILI) by occupation and to identify occupations associated with increased ILI prevalence. Methods Between September 2009 and August 2010, the Centers for Disease Control (CDC) included questions on ILI symptoms on the Behavioral Risk Factor Surveillance System (BRFSS). Washington State collects the occupation of all employed BRFSS respondents. ILI prevalence and prevalence ratios (PR) were calculated by occupational group. Results There were 8,758 adult, currently employed, non-military respondents to the Washington BRFSS during the study period. The ILI prevalence for all employed respondents was 6.8% (95% Confidence Interval (95% CI) = 6.1, 7.6). PRs indicated a lower prevalence of ILI in Technicians (PR = 0.4, 95% CI = 0.2, 0.9) and Truck Drivers (PR = 0.2, 95% CI = 0.1, 0.7) and higher prevalence in Janitors and Cleaners (PR = 2.5, 95% CI = 1.3, 4.7) and Secretaries (PR = 2.4, 95% CI = 1.1, 5.4). Conclusions Some occupations appear to have higher prevalence of ILI than others. These occupational differences may be explained, in part, by differing levels of social contact with the public or contact with contaminated surfaces at work, or by other occupational factors such as stress or access to health care resources.
Automated patient-specific classification of premature ventricular contractions

In this paper, we present an automated patient-specific electrocardiogram (ECG) beat classifier designed for accurate detection of premature ventricular contractions (PVCs). In the proposed feature extraction scheme, the principal component analysis (PCA) is applied to the dyadic wavelet transform (DWT) of the ECG signal to extract morphological ECG features, which are then combined with the temporal features to form a resultant efficient feature vector. For the classification scheme, we selected the feed-forward artificial neural networks (ANNs) optimally designed by the multi-dimensional particle swarm optimization (MD-PSO) technique, which evolves the structure and weights of the network specifically for each patient. Training data for the ANN classifier include both global (total of 150 representative beats randomly sampled from each class in selected training files) and local (the first 5 min of a patient's ECG recording) training patterns. Simulation results using 40 files in the MIT/BIH arrhythmia database achieved high average accuracy of 97% for differentiating normal, PVC, and other beats.
Geographic patterning of variation in segment number in geophilomorph centipedes: clines and speciation

SUMMARY Since their origin as a metameric group, arthropods have diversified considerably in their number of segments. Present‐day geophilomorph centipedes provide a model system for investigating the evolutionary origins of this diversification, because they exhibit intraspecific variation in segment number. (This variation is, however, derived; it is not a plesiomorphic condition within the Chilopoda.) Previous studies have shown that there are significant differences in segment number between populations within several geophilomorph species. In one (arguably two) species, it has been demonstrated that there is a particular form of geographic patterning of the variation, namely a latitudinal cline, with the segment number decreasing with increasing distance north. Here, we provide additional data on four more species, all of which show evidence of a latitudinal cline in either one or both sexes. It is therefore becoming clear that this is a general phenomenon, applying widely (perhaps universally) across the Geophilomorpha, a group consisting of some 1000 known species. It may be that latitudinal clines are a frequent part of the speciation cycle in this group.
Scaling learning algorithms towards AI

One long-term goal of machine learning research is to produce methods that are applicable to highly complex tasks, such as perception (vision, audition), reasoning, intelligent control, and other artificially intelligent behaviors. We argue that in order to progress toward this goal, the Machine Learning community must endeavor to discover algorithms that can learn highly complex functions, with minimal need for prior knowledge, and with minimal human intervention. We present mathematical and empirical evidence suggesting that many popular approaches to non-parametric learning, particularly kernel methods, are fundamentally limited in their ability to learn complex high-dimensional functions. Our analysis focuses on two problems. First, kernel machines are shallow architectures, in which one large layer of simple template matchers is followed by a single layer of trainable coefficients. We argue that shallow architectures can be very inefficient in terms of required number of computational elements and examples. Second, we analyze a limitation of kernel machines with a local kernel, linked to the curse of dimensionality, that applies to supervised, unsupervised (manifold learning) and semi-supervised kernel machines. Using empirical results on invariant image recognition tasks, kernel methods are compared with deep architectures, in which lower-level features or concepts are progressively combined into more abstract and higher-level representations. We argue that deep architectures have the potential to generalize in non-local ways, i.e., beyond immediate neighbors, and that this is crucial in order to make progress on the kind of complex tasks required for artificial intelligence.
Assessing the potential long-term increase of oceanic fossil fuel CO 2 uptake due to CO 2 -calcification feedback

Abstract. Plankton manipulation experiments exhibit a wide range of sensitivities of biogenic calcification to simulated anthropogenic acidification of the ocean, with the "lab rat" of planktic calcifiers, Emiliania huxleyi apparently not representative of calcification generally. We assess the implications of this observational uncertainty by creating an ensemble of realizations of an Earth system model that encapsulates a comparable range of uncertainty in calcification response to ocean acidification. We predict that a substantial reduction in marine carbonate production is possible in the future, with enhanced ocean CO2 sequestration across the model ensemble driving a 4–13% reduction in the year 3000 atmospheric fossil fuel CO2 burden. Concurrent changes in ocean circulation and surface temperatures in the model contribute about one third to the increase in CO2 uptake. We find that uncertainty in the predicted strength of CO2-calcification feedback seems to be dominated by the assumption as to which species of calcifier contribute most to carbonate production in the open ocean.
Universality classes for extreme-value statistics

The equilibrium low-temperature physics of disordered systems is governed by the statistics of extremely low-energy states. It is thus relevant to discuss the possible universality classes for extreme-value statistics. We compare the usual probabilistic classification to the results of the replica approach. We show in detail for several problems (including the random energy model and the decaying Burgers turbulence) that one class of independent variables corresponds exactly to the so-called one step replica symmetry breakingsolution in the replica language. We argue that this universality class holds if the correlations are sufficiently weak, and propose a conjecture on the level of correlations which leads to different universality classes.
Improvement of Hydraulic and Water Quality Renovation Functions by Intermittent Aeration of Soil Treatment Areas in Onsite Wastewater Treatment Systems

Abstract: We tested intermittent aeration of the soil treatment area (STA) of onsite wastewater treatment systems (OWTS) for its ability to restore and maintain STA hydraulic flow and improve the water quality functions of conventional OWTS. Evaluation was conducted on hydraulically-failed conventional OWTS at three state-owned medical group homes in Washington County, RI, USA. Testing was conducted in two phases, with Phase I (before intermittent soil aeration (ISA)) comprising the first 6 months of the study, and Phase II (during ISA) the remaining 7 months. Intermittent soil aeration restored STA hydraulic function in all three systems despite a marked reduction in the STA total infiltrative surface. Soil pore water was collected from 30 and 90 cm below the STA during both phases and analyzed for standard wastewater parameters. Although the STA infiltrative surface was reduced—and the contaminant load per unit of area increased—after installation of the ISA system, no differences were observed between phases in concentration of total N, NO
Spectrophotometric evaluation of shade reproduction of pressable all-ceramic system on un-stained and stained tooth: An in vitro study

Purpose: To evaluate the shade reproduction of a pressable all-ceramic system placed on unstained and stained extracted maxillary central incisor using a color measurement spectrophotometer. In addition, to compare shade reproduction of this material with low translucency and medium opacity on unstained tooth and medium and high opacity on stained tooth. Materials and Methods: Total 45 discs, with difference in the opacity of core, were used. After spectrophotometric evaluation, shade reproduction of the discs was compared and calculated by formula: Δ E+ = ([Δ L+]2+ [Δ a+]2+ [Δ b+]2) 1/2. Results: Student's t-test showed that in a sample of 15, the values of Δ E+ for Group I - LT (Us.T.) lie between 0 and l, for Group II - MO (for Us. as well as S.T.) between l and 2, for Group III - HO (S.T.) are all above 5. Comparison among groups after t-test showed that mean Δ E+ values of Group I - LT is less than Group II - MO for the unstained tooth, Δ E+ for Group II - MO is less than average Δ E+ value of Group III - HO for stained tooth. Conclusion: All-ceramic with low translucency can be used for the fabrication of restoration on the unstained tooth as it gives the best shade reproduction. The medium opacity material may be used on the unstained as well as on stained tooth. However, the clinical implication of high opacity is limited when applied over the stained tooth as it is giving a shade reproduction, which is not within acceptable limits.
Adoption, Use and Environmental Impact of Feminine Hygiene Products among College Going Girls of Udaipur

Feminine hygiene products are personal care products used by women during menstruation, which can be either disposable (sanitary napkins, tampons and panty liners) or reusable (menstrual cups, cloth pad). A significant portion of the Indian disposable hygiene market, accounts for these feminine hygiene products. Euromonitor, a market research company, estimates that the Indian feminine hygiene product market has reached Rupees 22.21 billion ($340 million) in 2017 and is expected to reach Rupees 34.68 billion ($522 million) by 2020. Increase in demand was attributed to rising income and choice of a comfortable and convenient lifestyle. Despite demand, the penetration rate of the sanitary napkins market was only 24% in 2014 and is expected to grow to 42% by 2018. (Nonwovens Industry Magazine, March 2017).
Information Dissemination on Asset Markets with Endogenous and Exogenous Information: An Experimental Approach

In this paper we study information revelation on asset markets with endogenous and exogenous information. Our results indicate that superior information can only be exploited in the beginning of trading. Information disseminates on the market and informational advantages are counter-balanced over time. This result holds true for both exogenous and precise endogenous information. Vague endogenous information, however, has no impact on individual payoff. Furthermore, we find that excessive trading decreases individual earnings.
Posterior approach compared to direct lateral approach resulted in better patient-reported outcome after hemiarthroplasty for femoral neck fracture

Background and purpose — Hemiarthroplasty (HA) is the most common treatment for displaced femoral neck fractures in many countries. In Norway, there has been a tradition of using the direct lateral surgical approach, but worldwide a posterior approach is more often used. Based on data from the Norwegian Hip Fracture Register, we compared the results of HA operated through the posterior and direct lateral approaches regarding patient-reported outcome measures (PROMs) and reoperation rate. Patients and methods — HAs due to femoral neck fracture in patients aged 60 years and older were included from the Norwegian Hip Fracture Register (2005–2014). 18,918 procedures were reported with direct lateral approach and 1,990 with posterior approach. PROM data (satisfaction, pain, quality of life (EQ-5D), and walking ability) were reported 4, 12, and 36 months postoperatively. The Cox regression model was used to calculate relative risk (RR) of reoperation. Results — There were statistically significant differences in PROM data with less pain, better satisfaction, and better quality of life after surgery using the posterior approach than using the direct lateral approach. The risk of reoperation was similar between the approaches. Interpretation — Hemiarthroplasty for hip fracture performed through a posterior approach rather than a direct lateral approach results in less pain, with better patient satisfaction and better quality of life. The risk of reoperation was similar with both approaches.