Miracle-dz/UniFAR-FTUs huggingface dataset:
Linkage Maps of a Mediterranean × Continental Tall Fescue Population and their Comparative Analysis with Other Poaceae Species

Temperate grasses belonging to the Festuca–Lolium complex are important throughout the world in pasture and grassland agriculture. Tall fescue (Festuca arundinacea Schreb.) is the predominant species in the United States, covering approximately 15 million ha. Tall fescue has distinctive morphotypes, two of which are Continental (summer active) and Mediterranean (summer semidormant). This is the first report of a linkage map created for Mediterranean tall fescue, while updating the Continental map with additional simple sequence repeat and sequence‐tagged site markers. Additionally, this is the first time that diversity arrays technology (DArT) markers were used in the construction of a tall fescue map. The male parent (Continental), R43‐64, map consisted of 594 markers arranged in 22 linkage groups (LGs) and covered a total of 1577 cM. The female parent (Mediterranean), 103‐2, map was shorter (1258 cM) and consisted of only 208 markers arranged in 29 LGs. Marker densities for R43‐64 and 103‐2 were 2.65 and 6.08 cM per marker, respectively. When compared with the other Poaceae species, meadow fescue (F. pratensis Huds.), annual ryegrass (L. multiflorum Lam.), perennial ryegrass (L. perenne L.), Brachypodium distachyon (L.) Beauv. , and barley (Hordeum vulgare L.), a total of 171 and 98 orthologous or homologous sequences, identified by DArT analysis, were identified in R43‐64 and 103‐2, respectively. By using genomic in situ hybridization, we aimed to identify potential progenitors of both morphotypes. However, no clear conclusion on genomic constitution was reached. These maps will aid in the search for quantitative trait loci of various traits as well as help define and distinguish genetic differences between the two morphotypes.
Draft Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae XPY20 Collected from a Bloodstream Infection Patient

ABSTRACT Bloodstream infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) strains have been a severe problem with high clinical costs and high mortality rates. The blaKPC-2-producing CRKP strain XPY20 was collected from the blood of a patient. The genome characteristics and antimicrobial resistance mechanisms were determined using next-generation sequencing.
Brotherston , James ( 2017 ) Realizability in Cyclic Proof : Extracting Ordering Information for Infinite Descent . In : TABLEAUX 2017 : International Conference on Automated Reasoning with Analytic Tableaux

In program verification, measures for proving the termination of programs are typically constructed using (notions of size for) the data manipulated by the program. Such data are often described by means of logical formulas. For example, the cyclic proof technique makes use of semantic approximations of inductively defined predicates to construct Fermat-style infinite descent arguments. However, logical formulas must often incorporate explicit size information (e.g. a list length parameter) in order to support inter-procedural analysis. In this paper, we show that information relating the sizes of inductively defined data can be automatically extracted from cyclic proofs of logical entailments. We characterise this information in terms of a graph-theoretic condition on proofs, and show that this condition can be encoded as a containment between weighted automata. We also show that under certain conditions this containment falls within known decidability results. Our results can be viewed as a form of realizability for cyclic proof theory.
Efficacy of 2‐hydroxy‐4‐methylthiobutanoic acid compared to DL‐Methionine on growth performance, carcass traits, feather growth, and redox status of Cherry Valley ducks

ABSTRACT The objective of this study was to compare the bio‐efficacy of 2‐hydroxy‐4‐methylthiobutanoic acid (DL‐HMTBA) with that of DL‐methionine (DLM) as sources of methionine in terms of the growth performance, carcass traits, feather growth, and redox statuses of Cherry Valley ducks. Six hundred and thirty male ducks were randomly allotted to 9 dietary treatment groups with 7 replicates of 10 birds each. The first group received a basal diet (BD) without methionine addition that was deficient in the total number of sulfur amino acids. In Groups 2 to 5 and Groups 6 to 9, the BD was supplemented with 4 increasing doses of methionine as either DLM or DL‐HMTBA. The trial was run from ages 1 to 42 d. Dietary supplementation with DLM and DL‐HMTBA improved body weight gain and feed intake as well as weights of carcasses, breast meat, and feathers compared with the BD. No significant difference was observed between the 2 methionine sources on growth performance, carcass traits, and feather growth. Concentrations of some redox markers in the pectoralis major muscle were improved by addition of methionine to the BD. However, a significant difference was observed between DLM and DL‐HMTBA in this respect, as the supplementation of DL‐HMTBA significantly increased the total antioxidant capacity, the activities of glutathione peroxidase, and the concentration of reduced glutathione in the pectoralis major muscle, compared with DLM. No significant difference between methionine sources was found with regard to the concentrations of oxidized glutathione and malondialdehyde in the pectoralis major muscle. Both DLM and DL‐HMTBA increased malondialdehyde concentrations in the pectoralis major muscle compared with the BD. In conclusion, these results indicated that DLM and DL‐HMTBA have equal biological value for the growth performance, carcass traits, and feather growth of Cherry Valley duck. Moreover, the improved antioxidant capacity observed with DL‐HMTBA makes this a better candidate than DLM for lowering the oxidation process in the meat during post‐mortem storage and thereby contributes to a better duck meat quality.
Digital Predistortion for Hybrid MIMO Transmitters

This paper investigates digital predistortion (DPD) linearization of hybrid beamforming large-scale antenna transmitters. We propose a novel DPD processing and learning technique for an antenna subarray, which utilizes a combined signal of the individual power amplifier (PA) outputs in conjunction with a decorrelation-based learning rule. In effect, the proposed approach results in minimizing the nonlinear distortions in the direction of the intended receiver. This feature is highly desirable, since emissions in other directions are naturally weak due to beamforming. The proposed parameter learning technique requires only a single observation receiver, and therefore supports simple hardware implementation. It is also shown to clearly outperform the current state-of-the-art technique that utilizes only a single PA for learning. Analysis of the feedback network amplitude and phase imbalances reveals that the technique is robust even to high levels of such imbalances. Finally, we also show that the array system out-of-band emissions are well-behaving in all spatial directions, and essentially below those of the corresponding single-antenna transmitter, due to the combined effects of the DPD and beamforming.
Handheld Guides in Inspection Tasks: Augmented Reality versus Picture

Inspection tasks focus on observation of the environment and are required in many industrial domains. Inspectors usually execute these tasks by using a guide such as a paper manual, and directly observing the environment. The effort required to match the information in a guide with the information in an environment and the constant gaze shifts required between the two can severely lower the work efficiency of inspector in performing his/her tasks. Augmented reality (AR) allows the information in a guide to be overlaid directly on an environment. This can decrease the amount of effort required for information matching, thus increasing work efficiency. AR guides on head-mounted displays (HMDs) have been shown to increase efficiency. Handheld AR (HAR) is not as efficient as HMD-AR in terms of manipulability, but is more practical and features better information input and sharing capabilities. In this study, we compared two handheld guides: an AR interface that shows 3D registered annotations, that is, annotations having a fixed 3D position in the AR environment, and a non-AR picture interface that displays non-registered annotations on static images. We focused on inspection tasks that involve high information density and require the user to move, as well as to perform several viewpoint alignments. The results of our comparative evaluation showed that use of the AR interface resulted in lower task completion times, fewer errors, fewer gaze shifts, and a lower subjective workload. We are the first to present findings of a comparative study of an HAR and a picture interface when used in tasks that require the user to move and execute viewpoint alignments, focusing only on direct observation. Our findings can be useful for AR practitioners and psychology researchers.
Template-based scatter correction in clinical brain perfusion SPECT

A practical method for scatter compensation in SPECT imaging is the triple energy window technique (TEW) which estimates the fraction of scattered photons in the projection data pixel by pixel. This technique requires an acquisition of counts in three windows of the energy spectrum for each projection bin, which is not possible on every gamma camera. The aim of this study is to set up a scatter template for brain perfusion SPECT imaging by means of the scatter data acquired with the triple energy window technique. This scatter template can be used for scatter correction as follows: the scatter template is realigned with the acquired, by scatter degraded and reconstructed image by means of the corresponding emission template, which also includes scatter counts. The ratios between the voxel values of this emission template and the acquired and reconstructed image are used to locally adjust the scatter template. Finally the acquired and reconstructed image is corrected for scatter by subtracting the thus obtained scatter estimates. We compared the template based approach with the TEW scatter correction technique for data acquired with same gamma camera system and found a similar performance for both correction methods.
Continuous Integration and Visual GUI Testing: Benefits and Drawbacks in Industrial Practice

Continuous integration (CI) is growing in industrial popularity, spurred on by market trends towards faster delivery and higher quality software. A key facilitator of CI is automated testing that should be executed, automatically, on several levels of system abstraction. However, many systems lack the interfaces required for automated testing. Others lack test automation coverage of the system under test's (SUT) graphical user interface (GUI) as it is shown to the user. One technique that shows promise to solve these challenges is Visual GUI Testing (VGT), which uses image recognition to stimulate and assert the SUT's behavior. Research has presented the technique's applicability and feasibility in industry but only limited support, from an academic setting, that the technique is applicable in a CI environment. In this paper we presents a study from an industrial design research study with the objective to help bridge the gap in knowledge regarding VGT's applicability in a CI environment in industry. Results, acquired from interviews, observations and quantitative analysis of 17.567 test executions, collected over 16 weeks, show that VGT provides similar benefits to other automated test techniques for CI. However, several significant drawbacks, such as high costs, are also identified. The study concludes that, although VGT is applicable in an industrial CI environment, its severe challenges require more research and development before the technique becomes efficient in practice.
Statistical Optimality of Stochastic Gradient Descent on Hard Learning Problems through Multiple Passes

We consider stochastic gradient descent (SGD) for least-squares regression with potentially several passes over the data. While several passes have been widely reported to perform practically better in terms of predictive performance on unseen data, the existing theoretical analysis of SGD suggests that a single pass is statistically optimal. While this is true for low-dimensional easy problems, we show that for hard problems, multiple passes lead to statistically optimal predictions while single pass does not; we also show that in these hard models, the optimal number of passes over the data increases with sample size. In order to define the notion of hardness and show that our predictive performances are optimal, we consider potentially infinite-dimensional models and notions typically associated to kernel methods, namely, the decay of eigenvalues of the covariance matrix of the features and the complexity of the optimal predictor as measured through the covariance matrix. We illustrate our results on synthetic experiments with non-linear kernel methods and on a classical benchmark with a linear model.
Modeling Unit Commitment in Political Context: Case of China's Partially Restructured Electricity Sector

Restructuring an electricity sector entails a complex realignment of political and economic institutions, which may both delay and distort the achievement of satisfactorily competitive conditions. In research and planning for policy interventions in power systems under these varied regulatory environments, typical operational models may neglect important interactions between techno-economic criteria and political constraints, leading to poor understanding of underlying causes of inefficiency and to inappropriate recommendations. We develop tractable formulations of the unit commitment problem based on integer clustering of similar units that endogenize important political factors in the Northeast grid region of China. We demonstrate the importance of these interactions on operations and provide a set of options for researchers to explore further pathways for China's ongoing power system reforms. For example, wind integration, a key policy priority, is inhibited by the interaction of institutions limiting short- and long-term sources of flexibilities in interprovincial trade.
LipidMediators in Acne Monica Ottaviani , Emanuela Camera , andMauro Picardo

Multiple factors are involved in acne pathogenesis, and sebum secretion is one of the main ones. The role sebum plays in acne development has not been completely elucidated yet; however, increasing amounts of data seem to confirm the presence of alterations in sebum from acne patients. Altered ratio between saturated and unsaturated fatty acids has been indicated as an important feature to be considered in addition to the altered amount of specific fatty acids such as linoleic acid. Furthermore, particular attention has been focused on squalene peroxide that seems to be able to induce an inflammatory response beyond cytotoxicity and comedones formation. Moreover, recent data suggest that lipid mediators are able to interfere with sebocytes differentiation and sebogenesis through the activation of pathways related to peroxisome proliferators-activated receptors. Understanding the factors and mechanisms that regulate sebum production is needed in order to identify novel therapeutic strategies for acne treatment.
Chromosome architecture constrains horizontal gene transfer in bacteria

Despite significant frequencies of lateral gene transfer between species, higher taxonomic groups of bacteria show ecological and phenotypic cohesion. This suggests that barriers prevent panmictic dissemination of genes via lateral gene transfer. We have proposed that most bacterial genomes have a functional architecture imposed by Architecture IMparting Sequences (AIMS). AIMS are defined as 8 base pair sequences preferentially abundant on leading strands, whose abundance and strand-bias are positively correlated with proximity to the replication terminus. We determined that inversions whose endpoints lie within a single chromosome arm, which would reverse the polarity of AIMS in the inverted region, are both shorter and less frequent near the replication terminus. This distribution is consistent with the increased selection on AIMS function in this region, thus constraining DNA rearrangement. To test the hypothesis that AIMS also constrain DNA transfer between genomes, AIMS were identified in genomes while ignoring atypical, potentially laterally-transferred genes. The strand-bias of AIMS within recently acquired genes was negatively correlated with the distance of those genes from their genome’s replication terminus. This suggests that selection for AIMS function prevents the acquisition of genes whose AIMS are not found predominantly in the permissive orientation. This constraint has led to the loss of at least 18% of genes acquired by transfer in the terminus-proximal region. We used completely sequenced genomes to produce a predictive road map of paths of expected horizontal gene transfer between species based on AIMS compatibility between donor and recipient genomes. These results support a model whereby organisms retain introgressed genes only if the benefits conferred by their encoded functions outweigh the detriments incurred by the presence of foreign DNA lacking genome-wide architectural information.
Potential Synergies of β-Hydroxybutyrate and Butyrate on the Modulation of Metabolism, Inflammation, Cognition, and General Health

The low-carbohydrate high-fat diet (LCHFD), also known as the ketogenic diet, has cycled in and out of popularity for decades as a therapeutic program to treat metabolic syndrome, weight mismanagement, and drug-resistant disorders as complex as epilepsy, cancer, dementia, and depression. Despite the benefits of this diet, health care professionals still question its safety due to the elevated serum ketones it induces and the limited dietary fiber. To compound the controversy, patient compliance with the program is poor due to the restrictive nature of the diet and symptoms related to energy deficit and gastrointestinal adversity during the introductory and energy substrate transition phase of the diet. The studies presented here demonstrate safety and efficacy of the diet including the scientific support and rationale for the administration of exogenous ketone bodies and ketone sources as a complement to the restrictive dietary protocol or as an alternative to the diet. This review also highlights the synergy provided by exogenous ketone, β-hydroxybutyrate (BHB), accompanied by the short chain fatty acid, butyrate (BA) in the context of cellular and physiological outcomes. More work is needed to unveil the molecular mechanisms by which this program provides health benefits.
Optimizing the Metric for Brain White Matter Comparisons

N. Lepore*, C. Brun*, M. Descoteaux, Y-Y. Chou, G. de Zubicaray, K. McMahon, M. Wright, N. Martin, J. Gee, and P. Thompson *equal contribution Department of Radiology, Children's Hospital, Los Angeles, Los Angeles, CA, United States, Department of Radiology, Penn Image Computing and Science Laboratory, University of Pennsylvania, Philadelphia, PA, United States, Universite de Sherbrooke, Canada, Laboratory of NeuroImaging, UCLA, United States, University of Queensland, Australia, Genetic Epidemiology Lab, QIMR, Australia, Laboratory of NeuroImaging, UCLA, Los Angeles, CA, United States
Time-Soundness of Time Petri Nets Modelling Time-Critical Systems

The correctness of a time-critical system is closely related to the time of responding and performing every event. Our motivation example, alternating bit protocol, and application example, multi-track level crossing with sensors, both demonstrate that some nondeterministic behaviours can take place if the time associated with events is configured inappropriately or some concurrent events are controlled imperfectly in an overlapping period. These nondeterministic behaviours decrease the reliability and/or safety of a time-critical system. Therefore, it is valuable to formalise and check (non)determinacy. Time Petri Nets (TPN) in which the firing of every event is limited to a fix time interval are used to model time-critical systems in this article. We proposes a novel notion for TPN named time-soundness. It guarantees that the system always owns deterministic behaviours after any event is performed no matter when the event is performed. We utilise the notion of bisimulation to prove that the time-soundness can guarantee the behavioural determinacy. We propose an algorithm to check time-soundness, develop the related tool, and do experiments to show the usefulness and effectiveness of our notion and method.
D-Ary Cuckoo Filter: A Space Efficient Data Structure for Set Membership Lookup

Many networking and distributed systems use Bloom filters and their variants for high speed set membership tests. Such probabilistic techniques provide very good space efficiency at the cost of a small fraction of false positive answers. The original Bloom filters do not permit deletion of items from the set and most attempts to extend Bloom filters to support deletions suffer from either space or time performance degradation. Recently, inspired by Cuckoo Hashing, Fan et. al. proposed a data structure called Cuckoo filter that achieves even better space performance than Bloom filters while supporting dynamic insertion and deletion of items. By allowing that each element has more than two candidate buckets, d-ary Cuckoo Hashing is capable of providing much higher space utilization. Motivated by this study, we generalize Cuckoo filter to d-ary Cuckoo filter for further reduction in space cost. The main difficulty here is that increasing the number of candidate buckets is not as easy as it appears because only fingerprints are available for the calculation of candidate locations. To solve this problem, we introduce the base-d digitwise xor operations as the foundation for computing the d candidate buckets of each element in a cyclic fashion. Theoretical analysis and experiment study show that d-ary Cuckoo filters can save up to one bit for each element at the cost of increased lookup and insertion performance.
Influence of brightness and contrast adjustments on the diagnosis of proximal caries lesions.

OBJECTIVES To assess the influence of brightness and contrast adjustments of digital radiographs on the diagnosis of proximal caries lesions, and to compare with observers' preferences for subjective image quality. METHODS 80 proximal surfaces of posterior teeth were radiographed using an intraoral digital system (Digora Toto, Soredex, Finland). Initial images and four different combinations of brightness and contrast for each radiography were analysed. Five observers scored the images for the presence and extension of caries lesions. Micro-CT images were used as gold standard. In a second stage, the observers were asked which of the radiographs they preferred for the assessment of caries lesions. RESULTS No differences were found between the original and adjusted radiographic images regarding the area under the receiver operating characteristic curve, sensitivity, and specificity (p > 0.05). There was a significant difference between the micro-CT and the intraoral radiographs (p < 0.0001). Images with high brightness and low contrast presented higher number of true negative cases, but also a decrease in caries detection. On the other hand, there were more cases of overestimation of the presence and extension of caries lesions in images with low brightness and high contrast. The subjective evaluation of image quality showed that radiographs with lower brightness and higher contrast tended to be preferred by observers. CONCLUSIONS Brightness and contrast adjustments in digital intraoral radiographs within the range tested in this study do not significantly influence the diagnosis of proximal caries lesions, although observers tend to prefer lower brightness and higher contrast images.