Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding

Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.
The relationship between L-arginine/ADMA ratio and coronary collateral development in patients with low glomerular filtration rate.

BACKGROUND It is yet to be established which factors are responsible for differences among patients with the same degree of coronary artery disease in terms of coronary collateral development (CCD). METHODS Patients who had a greater than or equal to 95% stenosis in at least one epicardial coronary artery were classified into two groups according to their glomerular filtration rate (GFR) level. Afterwards, the degree of CCD was evaluated according to their plasma concentration of asymmetric dimethylarginine (ADMA) and GFR levels. RESULTS Rentrop grade 2-3 was found more frequently in patients with GFR > 60 mL/min than in patients with GFR < 60 mL/min (68.6% vs 41.4%, p = 0.032). Then we divided patients into four groups according to their GFR levels and Rentrop grades; whereas we did not find any significant difference for L-arginine or ADMA levels (respectively p = 0.629 and p = 0.076), we did find a statistically significant difference between groups for L-arginine/ /ADMA ratio (p = 0.003) and this statistically significant difference was evident between patients with GFR < 60 mL/min and Rentrop 0-1 and patients with GFR > 60 mL/min and Rentrop 2-3 (1.23 vs 1.69, p < 0.001). Multivariate logistic regression analysis revealed that L-arginine/ADMA ratio was the only variable which had a significant effect on CCD (OR = 1.016; 95% CI 1.001-1.031, Wald = 4.565; p = 0.033). CONCLUSIONS These results showed that CCD was poor in patients with GFR < 60 mL/min, presumably because of the adverse effect of decreased L-arginine/ADMA ratio on endothelial cells and angiogenesis.
The relation of psychological distress to salivary and serum cortisol levels in pregnant women shortly after the diagnosis of a structural fetal anomaly

Objective. To examine the association between psychological distress and levels of salivary cortisol (SalC) and the ratio of serum cortisol to cortisol‐binding globulin (SC/CBG) in pregnant women shortly after the diagnosis of a structural fetal anomaly. Design. A prospective, observational study. Setting. Tertiary referral center for fetal medicine. Population. Pregnant women with (study group, n=126) and without a fetal structural anomaly (comparison group, n=106) were included. Gestational age (GA) was >12weeks. Methods. Psychological distress was assessed by Impact of Event Scale (IES‐22), General Health Questionnaire (GHQ‐28) and Edinburgh Postnatal Depression Scale (EPDS). Salivary cortisol was measured in the evening and SC/CBG in the morning. Main Outcome Measures. Levels of SalC (in nanomoles per liter) and SC/CBG. Results. Median (range) GA at assessment was 19 (12–38) and 19 (13–22)weeks in the study and the comparison group, respectively. The study group had significantly higher psychological distress levels (p≤0.001) than the comparison group in all outcome measures. Salivary cortisol correlated with GA in both groups (p<0.004). In subanalyses including only women with GA 18–22weeks, and excluding smokers or women with chronic diseases or medication which might interfere with cortisol levels, there were no relations of SalC or SC/CBG with the psychometric variables in the study group. Conclusions. Women with detected fetal malformation had high psychological distress scores. The lack of association between psychological distress and SalC or SC/CBG suggests a blunted response of the hypothalamic–pituitary–adrenal axis following recent psychological stress activation in the second trimester of pregnancy.
Engelsk som tredjespråk: Har lærere kompetanse til å støtte flerspråklighet?

Denne artikkelen handler om norske engelsklaereres kompetanse i a arbeide med barn som har et annet morsmal enn norsk, og som laerer engelsk som fremmedsprak. Problemstillingene er "Hva slags utdanning og kunnskap innen flerspraklighet har engelsklaerere i Norge? ," "I hvilken grad foler engelsklaerere i Norge seg forberedt pa a undervise i flerkulturelle og flerspraklige klasserom? " og "Hvilken type kunnskap, ferdigheter og ressurser foler de behov for? ". Vi presenterer resultater fra en nasjonal sporreundersokelse hvor i alt 176 engelsklaerere deltok. I tillegg presenterer vi resultater fra fokusintervjuer med i alt fire laerere fra to skoler. Resultatene viser at selv om engelsklaererne til en viss grad foler seg forberedt pa arbeid med elever som ikke har norsk som morsmal, har svaert fa av dem utdanning som fokuserer pa flerspraklighet. Svarene fra sporreundersokelsen og fra intervjuene viser at engelsklaererne gjerne vil ha mer kompetanse pa dette omradet. Vi vil derfor understreke betydningen av utdanning i teori og praksis om flerspraklig utvikling og flerkulturell utdanningsteori, og ikke minst betydningen av tilgang til faglig utvikling som fokuserer pa flerspraklighet i skolen og i samfunnet for engelsklaerere i Norge.Nokkelord: engelsklaerere, kompetanse, sprakpedagogisk kunnskap,flerspraklighet, laererutdanningAbstractThis paper examines the extent to which English teachers in Norway are prepared to work with children whose mother tongue is not Norwegian, and who are acquiring English as a foreign language. The research questions are “What type of education and knowledge in the area of multilingualism do English teachers in Norway have? ,” To what extent do English teachers in Norway feel they are prepared to teach in a multicultural and multilingual classroom? ,” and “What kinds of knowledge, skills and resources do they feel a need for? ” We present the results of a national survey completed by 176 teachers. In addition, we present results from focused interviews with four English teachers from two schools. The results show that although English teachers feel somewhat prepared for work with students who are not native speakers of Norwegian, very few of them have an education with focus on multilingualism. Responses from the survey and the interviews show that English teachers would like to have more expertise in this area. Therefore, we want to emphasize the importance of providing English teachers in Norway with education in theory and practice of multilingual development and multicultural education as well as access to professional development that focuses on multilingualism in schools and in society.Key words: English teachers, preparedness, knowledge of language teaching methods, multilingualism, teacher education
Communicating accuracy of tests to general practitioners: a controlled study

Abstract Objective: To assess the extent to which different forms of summarising diagnostic test information influence general practitioners' ability to estimate disease probabilities. Design: Controlled questionnaire study. Setting: Three Swiss conferences in continuous medical education. Participants: 263 general practitioners. Intervention: Questionnaire with multiple choice questions about terms of test accuracy and a clinical vignette with the results of a diagnostic test described in three different ways (test result only, test result plus test sensitivity and specificity, test result plus the positive likelihood ratio presented in plain language). Main outcome measures: Doctors' knowledge and application of terms of test accuracy and estimation of disease probability in the clinical vignette. Results: The correct definitions for sensitivity and predictive value were chosen by 76% and 61% of the doctors respectively, but only 22% chose the correct answer for the post-test probability of a positive screening test. In the clinical vignette doctors given the test result only overestimated its diagnostic value (median attributed likelihood ratio (aLR)=9.0, against 2.54 reported in the literature). Providing the scan's sensitivity and specificity reduced the overestimation (median aLR=6.0) but to a lesser extent than simple wording of the likelihood ratio (median aLR=3.0). Conclusion: Most general practitioners recognised the correct definitions for sensitivity and positive predictive value but did not apply them correctly. Conveying test accuracy information in simple, non-technical language improved their ability to estimate disease probabilities accurately. What is already known on this topic Many doctors confuse the sensitivity of clinical tests and their positive predictive value Doctors tend to overestimate information derived from such tests and underestimate information from a patient's clinical history Most primary research on diagnostic accuracy is reported using sensitivity and specificity or likelihood ratios What this study adds In a cohort of experienced Swiss general practitioners most were unable to interpret correctly numerical information on the diagnostic accuracy of a screening test When presented with a positive result alone they grossly overestimated its value Adding information on the test's sensitivity and specificity moderated these overestimates, and expressing the same numerical information as a positive likelihood ratio in simple, non-technical language brought the estimates still closer to their true values
Can recidivism be predicted among rapists and pedophiles during their first year of parole in the state of California

,. C. iii IMPLICATIONS FOR SOCIAL WORK AND OTHER THERAPEUTIC THEORETICAL ORIENTATIONS AS EXPLANATIONS OF acknowledgments;,. ^ iv INTRODUCTION . 1 PROBLEM STATEMENT/PROBLEM FOCUS . 3 COMMUNITIES. ,. v. 7 SEXUAL DEVIANCE . 11 LITERATURE REVIEW . 15 RESEARCH DESIGN AND METHODS . 25 RESULTS . V. 28 LIMITATIONS IN FINDINGS/NEED^ FOR APPENDIX C: ITEM LEVEL RESULTS FROM THE MULTIPLE REGRESSION . 5d DISCUSSION . ;. 36 ADDITIONAL RESEARCH . 43 APPENDIX A: AGE AT RELEASE BY SUCCESS ON PAROLE 48 APPENDIX B: NUMBER OF ARRESTS BY SUCCESS ON PAROLE . 49 APPENDIX D: LETTER OF PERMISSION 51 REFERENCES . 52
Infrared imaging and millimetre continuum mapping of Herbig Ae/Be and FU Orionis stars

The goal of this paper is a detailed analysis of the dusty environment of Herbig Ae/Be stars and FU Orionis ob- jects. For this purpose we mapped 22 regions at 1.3 mm wave- length containing 25 target objects. We found that it is indispens- able to perform mapping in contrast to pointed On-On measure- ments in order to obtain the correct distribution of cold material around young stellar objects and to relate 1.3 mm flux densi- ties to individual sources. To get reliable information about the structure and shape of the dust configurations and their relation to the stellar sources, we superimposed the millimetre maps on near-infrared images. The comparison of the data demon- strated that some of the Herbig Ae/Be stars are not associated with the peak of the millimetre emission. This is obviously the case for V 376 Cas/LkH 198, MWC 137, CoD-4211721, and V 1685 Cyg/V 1686 Cyg. We found two different morphologies of the dust envelopes: 6 regions show a compact structure, whereas 12 regions are characterized by a core/envelope structure. The "disk" objects AB Aur and HD 163296 show only a compact core and are not surrounded by an extended envelope. We did not detect HK Ori, HD 250550, LkH 25, and V 1515 Cyg which all have low IRAS luminosities. Based on the flux densities derived from the millimetre maps, we estimated characteristic physical parameters like den- sity and mass assuming optically thin emission. The total masses of the circumstellar regions around the Herbig Ae/Be stars with core/envelope structure and with "genuine" point-like millime- tre sources are 8060 M and 0.150. 15 M, respectively. The lowest and highest masses of the circumstellar material were found around AB Aur (0.03 M) and CoD-4211721 (1100 M), respectively. The average densities in the cores range from 10 5 to 10 8 cm 3 . The densities of the extended envelopes are of the order of 10 4 to 10 5 cm 3 . In addition, we combined the measured millimetre flux den- sities with infrared and optical data and modelled the broad- band spectral energy distributions using spherically symmet- ric models. We found good fits for both the core sources Send offprint requests to: Th. Henning ? Partially based on observations collected at the European Southern
The Female Encounter Test: A Novel Method for Evaluating Reward-Seeking Behavior or Motivation in Mice

Background: Reduced motivation is an important marker of psychiatric disorders, including depression. We describe the female encounter test, a novel method of evaluating reward-seeking behavior in mice. Methods: The test apparatus consists of three open chambers, formed with partitions that allow the animal to move freely from one chamber to another. A test male mouse is habituated in the apparatus, and subsequently a female and male mouse are introduced into a wire-mesh box in the left and right chamber, respectively. The time the test male mouse spends in the female or male area is measured for 10min. Results: All six strains of mice tested showed a significant preference for female encounters. The preference was observed in 7–30-week-old mice. The preference was blocked by castration of the resident male test mouse, and was not affected by the phase of the menstrual cycle of the female intruder. The preference was impaired in mouse models of depression, including social isolation-reared, corticosterone-treated, and lipopolysaccharide-treated mice. The impairment was alleviated by fluvoxamine in isolation-reared and lipopolysaccharide-treated mice, and it was improved by the metabotropic glutamate 2/3 receptor antagonist LY341495 in corticosterone-treated mice. Encounter with a female, but not male, mouse increased c-Fos expression in the nucleus accumbens shell of test male mice. Furthermore, both the preference and encounter-induced increases in c-Fos expression were blocked by dopamine D1 and D2 receptor antagonists. Conclusions: These findings indicate that motivation in adult male mice can be easily evaluated by quantitating female encounters.
RPC: A Large-Scale Retail Product Checkout Dataset

Over recent years, emerging interest has occurred in integrating computer vision technology into the retail industry. Automatic checkout (ACO) is one of the critical problems in this area which aims to automatically generate the shopping list from the images of the products to purchase. The main challenge of this problem comes from the large scale and the fine-grained nature of the product categories as well as the difficulty for collecting training images that reflect the realistic checkout scenarios due to continuous update of the products. Despite its significant practical and research value, this problem is not extensively studied in the computer vision community, largely due to the lack of a high-quality dataset. To fill this gap, in this work we propose a new dataset to facilitate relevant research. Our dataset enjoys the following characteristics: (1) It is by far the largest dataset in terms of both product image quantity and product categories. (2) It includes single-product images taken in a controlled environment and multi-product images taken by the checkout system. (3) It provides different levels of annotations for the check-out images. Comparing with the existing datasets, ours is closer to the realistic setting and can derive a variety of research problems. Besides the dataset, we also benchmark the performance on this dataset with various approaches. The dataset and related resources can be found at \url{this https URL}.
Expression of the transcriptional cofactors/histone acetyltransferases CBP and P300 during mouse development and their functional interactions with Gli transcription factors

Normal embryonic development requires precise regulation and coordination of different signaling pathways. One of these signaling cascades. the hedgehog (Hh) pathway, has been of major interest for developmental biologists. Sonic hedgehog (Shh). a vertebrate Hh protein. is involved in patterning several tissues during embryogenesis. Gli transcription factors (Gli 1. GliZ, Gli3) mediate Shh signaling in venebrates. In vertebrates there are two co-factors CBP and p300 that interact with several transcription factors and modify their activity. They are thought to act in the cell nuclei as integrators of different signaling pathways. Evidence for co-operation between vertebrate Gli proteins and CBPlp300 comes from phenotypes of human developmental disorders and studies in Drosophila. Mutations in Gli3 cause Greig cephalic polysyndactyly syndrome (GCPS) in humans. which is characterized by limb abnormalities and craniofacial defects. A similar phenotype is observed in Rubinstein-Taybi syndrome (RTS) patients. who have a mutation in CBP gene suggesting functional interactions between GIis and CBP. Furthermore. Drosophila CBP. dCBP. was shown to interact with the Drosophila Gli homologue Cubitus intemptus (Ci) and was required for activation of Hh target genes. The research presented in this thesis contributes to a better understanding of the roles of transcriptional cofactor CBPfp300 in vertebrate development and in activation/modification of Gli protein function. I describe in detail how CBP and p300 proteins are expressed during mouse neurogenesis and organogenesis providing the first evidence for developmentally regulated expression of CBP and p300 in the thesis. Interestingly. there is a good correlation between CBPfp300 expression and phenotypes in mutant mice lacking CBP or p300 function and in patients with Rubinstein-Taybi syndrome. These studies indicate that CBP and p300 are coexpressed with Gli genes in the limb mesenchyme. dorsal neural tube and craniofacial mesenchyme. However. absence of CBPlp300 expression in some Shh responsive tissues like in the floor plate suggests that CBPlp300 is not always required for Shh signaling. I further demonstrate that p300 functions as a transcriptional co-activator for all Glis. I also examined whether CBP directly interacts with Glil, Gli2 and Gli3 in vitro. 1 could not detect any interaction between Gli proteins and CBP-CREB binding domain. CHAPTER 1: GENERAL INTRODUCTION
Specimen-Specific Natural, Pathological, and Implanted Knee Mechanics Using Finite Element Modeling

There is an increasing incidence of knee pain and injury among the population, and increasing demand for higher knee function in total knee replacement designs. As a result, clinicians and implant manufacturers are interested in improving patient outcomes, and evaluation of knee mechanics is essential for better diagnosis and repair of knee pathologies. Common knee pathologies include osteoarthritis (degradation of the articulating surfaces), patellofemoral pain, and cruciate ligament injury and/or rupture. The complex behavior of knee motion presents unique challenges in the diagnosis of knee pathology and restoration of healthy knee function. Quantifying knee mechanics is essential for developing successful rehabilitation therapies and surgical treatments. Researchers have used in-vitro and in-vivo experiments to quantify joint kinematics and loading, but experiments can be costly and time-intensive, and contact and ligament mechanics can be difficult to measure directly. Computational modeling can complement experimental studies by providing cost-effective solutions for quantifying joint and soft tissue forces. Musculoskeletal models have been used to measure whole-body motion, and predict joint and muscle forces, but these models can lack detail and accuracy at the joint-level. Finite element modeling provides accurate solutions of the internal stress/strain behavior of bone and soft tissue using subject-specific geometry and complex contact and material representations. While previous FE modeling has been iii used to simulate injury and repair, models are commonly based on literature description or average knee behavior. The research presented in this dissertation focused on developing subject-specific representations of the TF and PF joints including calibration and validation to experimental data for healthy, pathological, and implanted knee conditions. A combination of in-vitro experiment and modeling was used to compare healthy and cruciate-deficient joint mechanics, and develop subject-specific computational representations. Insight from in-vitro testing supported in-vivo simulations of healthy and implanted subjects, in which PF mechanics were compared between two common patellar component designs and the impact of cruciate ligament variability on joint kinematics and loads was assessed. The suite of computational models developed in this dissertation can be used to investigate knee pathologies to better inform clinicians on the mechanisms surrounding injury, support the diagnosis of at-risk patients, explore rehabilitation and surgical techniques for repair, and support decisionmaking for new innovative implant designs.