Miracle-dz/UniFAR-FTUs huggingface dataset:
Semisupervised inference for explained variance in high dimensional linear regression and its applications

The paper considers statistical inference for the explained variance βTΣβ under the high dimensional linear model Y=Xβ+ε in the semisupervised setting, where β is the regression vector and Σ is the design covariance matrix. A calibrated estimator, which efficiently integrates both labelled and unlabelled data, is proposed. It is shown that the estimator achieves the minimax optimal rate of convergence in the general semisupervised framework. The optimality result characterizes how the unlabelled data contribute to the estimation accuracy. Moreover, the limiting distribution for the proposed estimator is established and the unlabelled data have also proved useful in reducing the length of the confidence interval for the explained variance. The method proposed is extended to semisupervised inference for the unweighted quadratic functional ‖β‖22 . The inference results obtained are then applied to a range of high dimensional statistical problems, including signal detection and global testing, prediction accuracy evaluation and confidence ball construction. The numerical improvement of incorporating the unlabelled data is demonstrated through simulation studies and an analysis of estimating heritability for a yeast segregant data set with multiple traits.
Pollination Best Practices in Southern Highbush Blueberry in Florida

Southern highbush blueberry is the primary blueberry species grown in Florida. It is dependent upon pollinating insects for adequate pollination and fruit. Some Florida growers have reported cases of low fruit set in recent years, in particular on the cultivars Meadowlark and Emerald, which may have been due in part to poor pollination. This 5-page fact sheet written by Rachel E. Mallinger and Douglas A. Phillips and published by the UF/IFAS Department of Entomology and Nematology will discuss blueberry pollinators, some causes of poor pollination, and current best practices to reduce the possibility of poor pollination of southern highbush blueberry. http://edis.ifas. ufl.edu/in1237
Free Energy Landscape and Conformational Kinetics of Hoogsteen Base-Pairing in DNA vs RNA

Genetic information is encoded in the DNA double helix which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleobase pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen base pairing pattern in naked DNA duplexes and estimated its relative stability and lifetime. In contrast, HG transitions in RNA were not observed. Understanding Hoogsteen (HG) base pairing is important because the underlying "breathing" can modulate significantly DNA/RNA recognition by proteins. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force bias method) and Markov State modeling to obtain accurate free energy, kinetics and the intermediates in the transition pathway between WC and HG base pair for both naked B-DNA and A-RNA duplexes. The Markov state model constructed from our unbiased MD simulation data revealed previously unknown complex extra-helical intermediates in this seemingly simple process of base pair conformation switching in B-DNA. Extending our calculation to A-RNA, for which HG base pair is not observed experimentally, resulted in relatively unstable single hydrogen bonded distorted Hoogsteen like base pair. Unlike B-DNA the transition pathway primarily involved base paired and intra-helical intermediates with transition timescales much higher than that of B-DNA. The seemingly obvious flip-over reaction coordinate, i.e., the glycosidic torsion angle is unable to resolve the intermediates; so a multidimensional picture, involving backbone dihedral angles and distance between atoms participating in hydrogen bonds, is required to gain insight into the molecular mechanism. SIGNIFICANCE Formation of unconventional Hoogsteen (HG) base pairing is an important problem in DNA biophysics owing to its key role in facilitating the binding of DNA repairing enzymes, proteins and drugs to damaged DNA. X-ray crystallography and NMR relaxation experiments revealed the presence of HG base pair in naked DNA duplex and protein-DNA complex but no HG base pair was observed in RNA. Molecular dynamics simulations could reproduce the experimental free energy cost of HG base pairing in DNA although a detailed mechanistic insight is still missing. We performed enhanced sampling simulation and Markov state modeling to obtain accurate free energy, kinetics and the intermediates in the transition pathway between WC and HG base pair for both B-DNA and A-RNA.
Identification of DNA methylation-driven genes by integrative analysis of DNA methylation and transcriptome data in pancreatic adenocarcinoma

Pancreatic adenocarcinoma (PAAD) is a painful and fatal disease that undoubtedly remains a health care priority and offers significant therapeutic challenges. The significance of epigenetic modifications, including DNA methylation in tumor development, has gained the attention of researchers. Identifying DNA methylation-driven genes and investigating the mechanisms underlying the tumorigenesis of PAAD are of substantial importance for developing methods of physiological evaluation, treatment planning and prognostic prediction for PAAD. In the present study, a comprehensive analysis of DNA methylation and gene expression data from 188 clinical samples was performed to identify DNA methylation-driven genes in PAAD. In addition, the diagnostic and prognostic value of DNA methylation-driven genes was evaluated using receiver operating characteristic curve, survival and recurrence analyses. A total of 7 DNA methylation-driven genes, namely zinc finger protein 208 (ZNF208), eomesodermin (EOMES), prostaglandin D2 receptor (PTGDR), chromosome 12 open reading frame 42 (C12orf42), integrin subunit α 4 (ITGA4), dedicator of cytokinesis 8 and protein phosphatase 1 regulatory inhibitor subunit 14D (PPP1R14D), were identified. All of them may be used to diagnose PAAD with excellent specificity and sensitivity (area under curve, >0.8). Of the 7 DNA methylation-driven genes, 6 were significantly associated with overall survival (OS) and recurrence-free survival (RFS) P<0.05). Among them, ZNF208, EOMES, PTGDR, C12orf42 and ITGA4 were significantly negatively associated with the OS rate and positively associated with the recurrence rate, while PPP1R14D was significantly positively associated with the OS rate and negatively associated with the recurrence rate. The present study provides novel insight into the epigenetic alterations associated with the occurrence and progression of PAAD, thereby increasing the mechanistic understanding of this disease, offering potential novel molecular biomarkers and contributing to the development of therapeutic targets for PAAD.
Graph representation and mining applied in comic images retrieval. (Représentation par graphes et fouille de graphes : application à la recherche d'images de bandes dessinées par le contenu)

Nous abordons d’abord le probleme de la representation sous forme d’un graphe de l’image et de ses applications en reconnaissance des formes, en mettant l’accent sur les applications de recherche d’images basees sur le contenu (CBIR). Les images utilisees dans cette these sont des images de bandes dessinees, qui possedent des specificites qui sont des freins pour les methodes de recherche d’information par le contenu utilisees dans la litterature. Le contenu des bandes dessinees, tel que les objets et les personnages, est complexe. La representation des personnages, par exemple, peut, d’une case a l’autre, varier enormement en taille et avec differents effets de perspective, selon la situation que l’auteur souhaite retranscrire. Nous proposons ainsi une representation qui permet d’obtenir des graphes stables et qui conserve des informations structurelles de haut niveau pour les objets d’interet dans les images de bandes dessinees. Ensuite, nous etendons le probleme d’indexation et d’appariement aux structures de graphes representant les images d’une bande dessinee et nous l’appliquons au probleme de la recherche d’information. Un album de bandes dessinees est ainsi transforme en une base de graphes, chaque graphe correspondant a la description d’une seule case. La strategie utilisee pour retrouver un objet ou un personnage donne, consiste donc a rechercher des motifs frequents (ou des sous-structures frequentes) dans cette base de graphes. Cette etape necessite de surmonter le probleme de non-repetabilite provoque par les erreurs introduites dans la structure du graphe pendant la phase de construction dues notamment a la variabilite des dessins. Il apparait donc un ecart semantique entre le graphe et le contenu de l’image de bande dessinee.
Frequency Domain Backoff for Continuous Beamforming Space Division Multiple Access on Massive MIMO Wireless Backhaul Systems

This paper newly proposes a frequency domain backoff scheme dedicated to continuous beamforming space division multiple access (CB-SDMA) on massive antenna systems for wireless entrance (MAS-WE). The entrance base station (EBS) has individual base band signal processing units for respective relay stations (RSs) to be accommodated. EBS then continuously applies beamforming weight to transmission/reception signals. CB-SDMA yields virtual point-to-point backhaul link where radio resource control messages and complicated multiuser scheduling are not required. This simplified structure allows RSs to work in a distributed manner. However, one issue remains to be resolved; overloaded multiple access resulting in collision due to its random access nature. The frequency domain backoff mechanism is introduced instead of the time domain one. It can flexibly avoid co-channel interference caused by excessive spatial multiplexing. Computer simulation verifies its superiority in terms of system throughput and packet delay.
Regularities and systematic trends on Lu III Stark widths

Regularity and systematic trend analysis has been performed on the Stark widths of 27 Lu III spectral lines calculated elsewhere by modified semiempirical method. Possible correlation of those Stark widths with corresponding effective principal quantum numbers or effective ionization potentials have been also considered and discussed. Results obtained in such a way can be used for quick estimate of some other unknown Stark width data for the ions in the same homologous or isoelectronic sequence, especially if the conditions are not satisfied to use more accurate theoretical methods.
Complementary methods for characterization of the corrosion products on the surface of Ag60Cu26Zn14 and Ag58.5Cu31.5Pd10 brazing alloys

Abstract Corrosion products formed on the surface of two silver brazing alloys after the potentiostatic polarization in 3.5% sodium chloride solution were characterized by the standard methods such as, the X-ray diffraction, micro-Raman spectroscopy, and scanning electron microscopy with energy-dispersive spectroscopy. This paper presents the results of a laser desorption/ionization mass spectrometry (LDI MS) analysis as a new approach to the characterization of corrosion products. The potential of the anodic polarization was 0.5 V versus saturated calomel electrode, and the process duration was 300 s. The corrosion layers on both investigated alloys were similar in composition with cuprous chloride and silver chloride as the main components and had strong indications of cuprous oxide formation. The major difference between these two layers was the existence of zinc hydroxychloride as the corrosion product of Ag-Cu-Zn alloy. Palladium compounds were not found in the case of Ag-Cu-Pd alloy. The results of different methods have shown a good consistency. Complementarity between the used methods was useful in the interpretation of the results for each used method. This study has demonstrated that LDI MS can be used as an efficient additional method together with the traditional ones.
Constrained Subspace Method for the Identification of Structured State-Space Models (COSMOS)

In this article, a unified identification framework called constrained subspace method for structured state-space models (COSMOS) is presented, where the structure is defined by a user-specified linear or polynomial parametrization. The new approach operates directly from the input and output data, which differs from the traditional two-step method that first obtains a state-space realization followed by the system-parameter estimation. The new identification framework relies on a subspace inspired linear regression problem which may not yield a consistent estimate in the presence of process noise. To alleviate this problem, the linear regression formulation is imposed by structured and low-rank constraints in terms of a finite set of system Markov parameters and the user specified model parameters. The nonconvex nature of the constrained optimization problem is dealt with by transforming the problem into a difference-of-convex optimization problem, which is then handled by the sequential convex programming strategy. Numerical simulation examples show that the proposed identification method is more robust than the classical prediction-error method initialized by random initial values in converging to local minima, but at the cost of heavier computational burden.
Selection and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR Analysis in Needles of Larix olgensis under Abiotic Stresses

Larix olgensis Henry is an important afforestation species in northeastern China because of its fast juvenile growth, high-quality timber, and significant economic and ecological values. The selection of appropriate reference genes is necessary for the normalization of gene expression determination during quantitative real-time polymerase chain reaction (qRT-PCR) experiments. In this study, qRT-PCR was used to study gene expression. Three software packages geNorm, NormFinder, BestKeeper were used, and a comprehensive ranking of candidate reference genes was produced based on their output to evaluate the expression stability of 16 candidate reference genes from L. olgensis under drought, salt, cold, and heat stress. PP2A-1 and GAPDH ranked as the most stable reference genes under drought and cold stress, PP2A-1 and UBQ10 were most stable under salt stress, and TIP41 and ACT2 were most stable under heat stress. The least stable gene was ADP, which ranked the last under all treatments. Expression profile analysis of the antioxidant gene CAT using the two most stable and the single least stable reference genes under each stress further verified that the selected reference genes were suitable for gene expression normalization. This study provides an important foundation for the selection of suitable reference genes for the normalization and quantification of L. olgensis gene expression under abiotic stress conditions.
Employment Trade-Offs under Different Family Policy Constellations

This article examines how employees consolidate the spheres of work and family in three countries with different family policy constellations: Sweden, Germany and Great Britain. The analyses are based on data from the International Social Survey Programme, 2015. Building on family policy typologies, the study demonstrates how gender and family and employment demands interact with the institutional setting regarding how people make employment trade-offs. The results show that (1) employees in Sweden make the fewest employment trade-offs, (2) family demands exert a gendered effect on employment trade-offs in Germany and (3) employment demands have both similar and distinct gender effects across countries. The article contributes to the literature by showing how individual characteristics interact with family policy constellations. The findings provide little support for a welfare-state paradox regarding family demands but some support with regard to employment demands.
Post Operative Sore Throat : Incidence after nebulization with Ketamine, Lidocaine and Budesonide

Post operative sore throat and hoarseness are common complications after endotracheal intubation. We conducted an experimental, randomized, double- blind study to compare the effectiveness of preoperative nebulisation with ketamine, budesonide and lignocaine in reducing the incidence and severity of post operative sore throat. MATERIAL & METHODS 120 patients (aged 20-60 years) scheduled for elective surgery under general anaesthesia were enrolled. Preoperatively , patients were nebulized with ketamine (Group 1) , Budesonide (Group 2 ) , Lignocaine (Group 3 ) and distilled water (Group 4). Number of attempts required for intubation, duration of laryngoscopy and anaesthesia were recorded. Patients were evaluated post operatively at various time intervals for sore throat, hoarseness and cough, pain and signs of mucositis in laryngopharynx. RESULTS The incidence of sore throat at different time intervals was found to be least in ketamine group at 1 hr, by lignocaine at 24 hrs and budesonide at 48 hrs. Lignocaine reduced cough at 1 and 24 hrs. Incidence of hoarseness was comparable in all the groups. CONCLUSION Nebulisation with lignocaine was efficacious in reducing cough , and ketamine reduced sore throat in early post operative period , whereas long term outcome was better with budesonide.
Super-Resolution Based on Residual Dense Network for Agricultural Image

With the rapid development of convolutional neural network in image processing, its image processing performance is becoming more and more outstanding. With the development of agricultural informatization, our demand for effectively accessing to agricultural information is also increasing. For example, greenhouse image monitoring equipment for crops is only in a low level. In this paper, we propose a method to apply image super resolution to the processing of greenhouse monitoring images, and use residual dense network to enhance the learning of global and local features in agricultural images. Therefore, more detailed information can be obtained from the low resolution images. Experiments on the data sets are made from the greenhouse agriculture images, and experimental results show that our method can effectively enhance the quality of agricultural monitoring images. It can better meet the needs of agricultural monitoring.
Sampling high dimensional tables with applications to assessing linkage disequilibrium

We propose a sequential importance sampling strategy to sample high dimensional tables with ﬁxed one way margins. The proposal distribution for the method is constructed by adapting an approximation to the total number of tables available in the literature. We apply the method to estimating the total number of tables and assessing linkage disequilibrium in multimarker genetic data with the table representing haplotype count data. We demonstrate eﬃcient and accurate performance in these practical, real-world examples. The method may be applied in any situation in which uniformly sampling high dimensional tables with ﬁxed one way margins is of interest. Detailed derivations are provided in the appendix.
Chlorpyrifos and deltamethrin degradation potentials of two Lactobacillus plantarum (Orla-Jensen, 1919) (Lactobacillales: Lactobacillaceae) strains

Bircok toprak bakterisi chlorpyrifos ve deltamethrin gibi sentetik insektisitleri esteraz enzimleriyle ve/veya bunlari karbon ve enerji kaynagi olarak kullanarak parcalayabilmektedir. Bizim bu calismadaki hipotezimiz gida fermantasyonu asamalarinda kullanilan Lactobacillus plantarum (Orla-Jensen, 1919) (Lactobacillales: Lactobacillaceae)’un benzer bir insektisit parcalama potansiyelinin gosterilmesidir. Bu calisma,raroa ei Lactobacillus plantarum ’un iki farkli susunun (LB-1 ve LB-2) asilamadan sonraki 4 gun icinde, iki farkli insektisit parcalama mekanizmasini gostermek amaciyla 2017-2018 yillarinda, Bursa Uludag Universitesi laboratuvarlarinda, in-vitro kosullarda gerceklestirilmistir. Herhangi bir karbon ve enerji kaynagi icermeyen MS ortami ile karsilastirildiginda, chlorpyrifos ve deltamethrin iceren MS ortaminda onemli duzeyde LB-1 gelisimi saptanmistir. Ayrica, bu sus icin onemli duzeyde artan hidroliz aktivitesi de gozlemlenmistir. Bu ozellikler LB-2’de bir miktar daha dusuk bulunmustur. GC-MS cihazi ile yapilan periyodik analizler sonucunda, LB-1 ve LB-2 inokule edilmis MS ortami icinde chlorpyrifos ve deltamethrin’in parcalama oranlari, 3 gun sonra chlorpyrifos icin sirasiyla %96 ve 90, deltamethrin icin %24 ve 53 olarak belirlenmistir. Deltamethrin icin onemli duzeyde bir parcalanma (%86-82) inkubasyondan 10 gun sonra gerceklesmistir. Bu calisma, denemede kullanilan L. plantarum suslarinin chlorpyrifos ve deltamethrin parcalama potansiyellerinin oldugunu gostermistir. Ileride bazi meyve sebzelerin fermentasyon sureclerinde kullanimi ve bu suslarin farkli inokulasyon oranlarinda etkinliginin belirlenmesi amaciyla daha fazla calisma yapilmasi gerekmektedir.
Public Opinion Toward a Misunderstood Predator: What do People Really Know about Wolverine and Can Educational Programs Promote its Conservation?

ABSTRACT Among the least known of Canada's large predators, the wolverine's status as threatened, or endangered throughout its eastern range, makes it a candidate for conservation programs. A lack of public support, however, can dramatically reduce the chances of such programs being successful. To assess the current state of support for wolverine conservation, knowledge and perceptions toward this species among the public, adults visiting the St. Félicien zoo were surveyed. Knowledge among participants was generally low and misconceptions were abundant, even among repeat visitors to the zoo. Attitudes, however, were mostly positive. To assess how exposure can influence perceptions, children were surveyed who had or had not attended a 5-day camp at the zoo. Both groups demonstrated similar levels of knowledge about wolverine. However, children who had attended the camp demonstrated a greater aesthetic appreciation and fewer negative associations with wolverines. These results suggest that while the wolverine is not a well-known species, people's perceptions toward this species are not necessarily negative. Additionally, information provided by zoos, in a variety of forms, may not always be acquired by visitors, but may still have a positive influence on how the public perceives cryptic misunderstood species such as the wolverine.