Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-Genome Patterns Of Dna Variation In Maize

For those genomes low in repetitive DNA, hybridizing total genomic DNA to high-density expression arrays offers an effective strategy for scoring single feature polymorphisms (SFPs). Of the ~2.5 Gb that constitute the maize genome (Zea mays L.), only 10-20% are genic sequences, with large amounts of repetitive DNA intermixed throughout. Therefore, a target preparation method engineered to generate a high genic-to-repetitive DNA ratio is essential for SFP detection in maize. To that end, we tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip Maize Genome Array (“Maize GeneChip”). Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and AFLP methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Our results indicate that these particular target preparation methods offer only modest power to detect SFPs with the Maize GeneChip. Most notably, CF and MF are comparable in power, detecting more than 10,000 SFPs at a 20% false discovery rate. Although reducing sample complexity to ~125 Mb by AFLP improves SFP scoring accuracy over other methods, only a minimal number of SFPs are still detected. Our findings of residual repetitive DNA in labeled targets and other experimental errors call for improved gene-enrichment methods and custom array designs to more accurately array genotype 2 M. Gore, P. Bradbury, R. Hogers, M. Kirst, E. Verstege, J. van Oeveren, J. Peleman, E. Buckler, and M. van Eijk. 2007. Evaluation of Target Preparation Methods for Single Feature Polymorphism Detection in Large Complex Plant Genomes. The Plant Genome S2: S-135-S-148.
Simulation and Experimental Validation of Novel Trajectory Planning Strategy to Reduce Vibrations and Improve Productivity of Robotic Manipulator

This paper aims at investigating vibrational behaviors of the industrial manipulator Racer 7-1.4, designed and manufactured by COMAU S.p.A. , with the target of new trajectory planning strategies to improve productivity rate without any loss of positioning accuracy. Starting from the analysis of a 9DoF multi-body system with lumped parameter, the first natural frequency of the robot was calculated in seven reference positions. Then, static and dynamic simulations were run by applying saturated ramp input and large motions to analyze the vibrational behavior of the manipulator. This research underlines that the optimal way to design the robot move is to set its duration at twice a period of free oscillation according to the first vibrational mode. Due to strong analogy of dynamic response of both 1DoF and 9DoF robot models, the closed-form solution of the 1DoF undamped system—featured by natural frequency equal to the first frequency of the 9DoF system—may be successfully adopted by the real-time trajectory planning process to predict residual vibration at move end-condition. This strategy was confirmed by experimental tests, allowing either residual vibration decrease and execution time reduction as well.
The Correlation of Career Adaptation and Career Preparation Behavior: The Mediating Role of Career Decision Self-Efficacy

Career preparation is important for students. Therefore, it is important to consider the factors that influence it, namely career adaptation and career decision self-efficacy. The online data on demographics, career preparation behavior, career adaptation, and career decision self-efficacy were collected from 241 university students. This study found that career decision self-efficacy can mediate the relationship between career adaptation and career preparation behavior. The results show that the indirect effects of career adaptation indirect effects and career preparation behavior through career decision self efficacy are significant (ß = 0.1308; SE=0.0256; 95% Cl = 0.0877, 0.1892). The total effect was significant (ß = 1700; SE = 0.0228; p=0,000). These results indicate that the proposed mediation model is acceptable. So, educational institutions need to pay attention to the character of their students, especially in self-efficacy in making career decisions that will be taken, so that they can support them in achieving optimal career preparation.
When Algorithms Go Shopping: Analyzing Business Models for Highly Autonomous Consumer Buying Agents

Consumer buying agents (CBAs) are software programs that automate tasks in the consumer buying process (e.g., product search and evaluation). Recently, CBAs have the ability to nearly automate the whole buying process, executing transactions with only minimal human involvement. With the rise of such highly autonomous CBAs, updates to business models (BM) of involved parties are expected (e.g., adding a sales channel and increasing customer value). However, our understanding of BMs for highly autonomous CBAs remains limited. In this work we aim to close this gap. We investigate 23 cases and develop a BM taxonomy for highly autonomous CBAs. We further encode these cases into the taxonomy and derive BM patterns. Our work contributes to research by setting a foundation for the conceptual understanding of BMs for highly autonomous CBAs. Practitioners can use our taxonomy and patterns for strategic guidance and to support BM innovation.
Prognostic Value of KI6 Biomarker to Predict Short Term Prognosis of Low Grade Cervical Intraepithelial Neoplasia in Human Papilloma Virus Negative and Positive Patients

Background: Screening of cervical cancer is the most common gynecologic cancer in developing countries. Despite being preventable, but we have still some problems in the screening of this cancer. Recently, many studies have been done on immunohistochemistry to improve screening of cervical intraepithelial neoplasia (CIN) as precancerous lesion. But, majority of the studies are based on cytological samples. The objective of this study was to analyze the correlation KI-67 biomarker and HPV infection in predict short time prognosis in CIN as an alternative or auxiliary method to current screening method in a different geographic population. Methods: This descriptive cohort prospective study included 40 patients with diagnosis of CIN based on cervical punch biopsy samples after colposcopy examination. They were referred to the department of gynecology and oncology of an academic hospital, Mashhad University of 2016 to 2017. All samples were investigated for HR- HPV DNA with Cobas test and immunostaining for KI-67 biomarker. Finally, after one year follow up, prognosis for all patients was evaluated. Data were analyzed by SPSS software program version 23.0 and Mann-Whitney U test and Fisher's exact test. P-value< 0.05 was considered significant. Results: significant difference was found between HR-HPV positive and negative tests in KI-67 expression (P<0.001), but no significant difference was observed in reactivity level (P=0.5), also no significant difference was found in KI-67 expression in metaplastic and non-metaplastic epithelium (P=0.88),. Conclusion : KI-67 biomarker is recommended as complementary screening tests not alternative for differentiating in high risks patients with CIN1. The patients with low KI-67 / HR-HPV positive could be offer for a less aggressive follow-up protocol.
COVID-19: A Drug Repurposing and Biomarker Identification by Using Comprehensive Gene-Disease Associations through Protein-Protein Interaction Network Analysis

COVID-19 (2019-nCoV) is a pandemic disease with an estimated mortality rate of 3.4% (estimated by the WHO as of March 3, 2020). Until now there is no antiviral drug and vaccine for COVID-19. The current overwhelming situation by COVID-19 patients in hospitals is likely to increase in the next few months. About 15 percent of patients with serious disease in COVID-19 require immediate health services. Rather than waiting for new anti-viral drugs or vaccines that take a few months to years to develop and test, several researchers and public health agencies are attempting to repurpose medicines that are already approved for another similar disease and have proved to be fairly effective. This study aims to identify FDA approved drugs that can be used for drug repurposing and identify biomarkers among high- risk and asymptomatic groups. In this study gene-disease association related to COVID-19 reported mild, severe symptoms and clinical outcomes were determined. The high-risk group was studied related to SARS-CoV-2 viral entry and life cycle by using Disgenet and compared with curated COVID-19 gene data sets from the CTD database. The overlapped gene sets were enriched and the selected genes were constructed for protein-protein interaction networks. Through interactome, key genes were identified for COVID-19 and also for high risk and asymptomatic groups. The key hub genes involved in COVID-19 were VEGFA, TNF, IL-6, CXCL8, IL10, CCL2, IL1B, TLR4, ICAM1, MMP9. The identified key genes were used for drug-gene interaction for drug repurposing. The chloroquine, lenalidomide, pentoxifylline, thalidome, sorafenib, pacitaxel, rapamycin, cortisol, statins were proposed to be probable drug repurposing candidates for the treatment of COVID-19. However, these predicted drug candidates need to be validated through randomized clinical trials. Also, a key gene involved in high risk and the asymptomatic group were identified, which can be used as probable biomarkers for early identification.
Complete mitochondrial genome characterization of Cirrhinus mrigala from the Three Gorges Reservoir in China

Abstract Cirrhinus mrigala is a fish introduced from India to the south China in 1980s, and a large number of this species is found in the Three Gorges Reservoir of the upper Yangtze River now, which might pose a great threat to the indigenous fish. In this study, we sequenced and characterized the complete mitochondrial genome of C. mrigala from the Three Gorges Reservoir. The complete mitochondrial genome was 16,595 bp in length and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA) and one non-coding control region (D-loop). The overall nucleotide composition was 32.05% (A), 24.48% (T), 15.49% (G) and 27.98% (C). The phylogenetic tree indicated that C. mrigala was related to Sinilabeo rendahli, Abbottina rivularis and Pseudogyrinocheilus prochilus. The results can provide basic genetic information for subsequent population genetic and phylogenetic researches, which will be helpful for understanding the genetic resource dynamic of C. mrigala in areas outside of its native distribution.
Effects of Exogenous Spermidine on Root Metabolism of Cucumber Seedlings under Salt Stress by GC-MS

To investigate the effects of exogenous spermidine (Spd) on metabolism changes under salt stress in cucumber roots, a gas chromatography-mass spectrometry (GC-MS) was performed. The results showed that most of the 142 metabolites responded to salt stress or exogenous Spd treatment. Salt stress reduced carbon consumption, resulted in the transformation of glycolysis and the tricarboxylic acid (TCA) cycle to the pentose phosphate pathway (PPP), and meanwhile increased salicylic acid (SA) and ethylene synthesis, and, thus, inhibited the growth of seedlings. However, exogenous Spd further improved the utilization of carbon, the energy-saving pattern of amino acid accumulation, and the control of hydroxyl radicals. In conclusion, Spd could promote energy metabolism and inhibit SA and ethylene synthesis in favor of root growth that contributes to higher salt tolerance. This study provides insight that may facilitate a better understanding of the salt resistance by Spd in cucumber seedlings.
Plant growth promoter collection of Gluconacetobacter diazotrophicus from northern coast of Peru

The application of plant growth promoting bacteria (PGPB) represents a friendly alternative to the environment, in contrast to the use of chemical fertilizers. Endophytic bacteria can develop inside the plant tissues and directly benefit the plant. Gluconacetobacter diazotrophicus is a versatile bacterium that has been isolated from different plants and possesses different physiological properties that would serve to improve plant development. In this research, five cultures of G. diazotrophicus were isolated from sugarcane samples from the northern coast of Peru. The isolates showed the ability to solubilize phosphates and zinc, produce IAA, and resist salt stress (NaCl 1%). Antagonism evaluations showed that they can inhibit up to 75%, 57%, 40%, 49% and 17% of the development of Fusarium sp. , Alternaria sp. , Roselinia sp. , Lasiodiplodia sp. , and Sclerotinia sp. , respectively. Inoculation plant experiments were developed by inoculating individual and bacteria mixture. All treatments showed plant growth promotion in sugarcane, but mixture of G. diazotrophicus LASFB 1573, Klebsiella sp. LASFBP 086 and Enterobacter sp. LASFB 009 increased up to 84% and 89% in fresh and dry plant weight, respectively. The results show that the isolates have a high potential as PGPB and could be used later to improve the development of different crops.
Potential sources of Frankliniella spp. (Thysanoptera: Thripidae) in Iowa.

In Iowa, two possible sources of phytophagous Frankliniella spp. infesting strawberry fields in spring are individuals that overwinter in fields or migrate into fields. In April 2001 and March 2002, soil samples taken to a depth of 5 cm from three strawberry fields in central Iowa were dried in Berlese funnels to determine whether thrips overwintered in these strawberry fields. In 2001, one Frankliniella spp. second instar was collected from 39 soil samples; in 2002, five Frankliniella occidentalis (Pergande) adults were collected from 72 samples. To determine whether thrips were flying into fields, 13 yellow and 13 blue sticky cards (8 × 13 cm) were placed in each of three strawberry fields in central Iowa from April to June 2001 and from March to June 2002. Thrips were first captured on sticky cards during the third week of April 2001 and 2002. In 2001, yellow sticky cards caught significantly higher numbers of thrips in strawberry fields compared with blue sticky cards, whereas in 2002, more thrips were captured on blue sticky cards. On the basis of this field study, we conclude that F. occidentalis overwinters in relatively low numbers in the soil in Iowa strawberry fields. Frankliniella tritici (Fitch) was the most common thrips found on the sticky cards during both years. Pest managers may use sticky cards to monitor early colonization of strawberry fields by F. tritici before flowers start appearing.
StemNet - Knowledge Management for Hematopoietic Stem Cell Transplantation

The goal of the StemNet Project (http://www.stemnet.de) is to develop a knowledge management system for Hematopoietic Stem Cell Transplantation and Immunogenetics [1] in order to assist biomedical researchers and practitioners in finding relevant information. The evolving knowledge service goes beyond tradtional approaches in that enables a targeted and fine-grained search for relevant biomedical entities (e.g. various protein functions, different types of immune cells, various sorts of antigens, blood diseases, clinical outcomes, etc.) in unstructured biomedical free text, in particular PubMed abstracts. At the same time, this information is linked to relevant biological database and ontology entries, such as UniProt, Entrez Gene, dbSNP, the Gene Ontology, the Sequence Ontology, and the Cell Ontology (see http://obo.sourceforge.net). Thus, StemNet enables the linking of heterogenuous knowledge sources to which the user only had separate access before. Semantic search and retrieval requires linguistic and semantic processing of documents. For this purpose, we employ state-of-the-art text-mining technologies [2, 3, 4, 5] , both to annotate and recognize semantic entities as well as to link them to databases and ontologies. Documents and their semantic metadata are then presented to the user via the Lucene search engine (http://lucene.apache.org/java/docs/index. html). In order to target user queries, annotated semantic entities are kept in special indices.
A Graph-Based Author Name Disambiguation Method and Analysis via Information Theory

Name ambiguity, due to the fact that many people share an identical name, often deteriorates the performance of information integration, document retrieval and web search. In academic data analysis, author name ambiguity usually decreases the analysis performance. To solve this problem, an author name disambiguation task is designed to divide documents related to an author name reference into several parts and each part is associated with a real-life person. Existing methods usually use either attributes of documents or relationships between documents and co-authors. However, methods of feature extraction using attributes cause inflexibility of models while solutions based on relationship graph network ignore the information contained in the features. In this paper, we propose a novel name disambiguation model based on representation learning which incorporates attributes and relationships. Experiments on a public real dataset demonstrate the effectiveness of our model and experimental results demonstrate that our solution is superior to several state-of-the-art graph-based methods. We also increase the interpretability of our method through information theory and show that the analysis could be helpful for model selection and training progress.
Coastal Mapping Using DJI Phantom 4 RTK in Post-Processing Kinematic Mode

Topographic and geomorphological surveys of coastal areas usually require the aerial mapping of long and narrow sections of littoral. The georeferencing of photogrammetric models is generally based on the signalization and survey of Ground Control Points (GCPs), which are very time-consuming tasks. Direct georeferencing with high camera location accuracy due to on-board multi-frequency GNSS receivers can limit the need for GCPs. Recently, DJI has made available the Phantom 4 Real-Time Kinematic (RTK) (DJI-P4RTK), which combines the versatility and the ease of use of previous DJI Phantom models with the advantages of a multi-frequency on-board GNSS receiver. In this paper, we investigated the accuracy of both photogrammetric models and Digital Terrain Models (DTMs) generated in Agisoft Metashape from two different image datasets (nadiral and oblique) acquired by a DJI-P4RTK. Camera locations were computed with the Post-Processing Kinematic (PPK) of the Receiver Independent Exchange Format (RINEX) file recorded by the aircraft during flight missions. A Continuously Operating Reference Station (CORS) located at a 15 km distance from the site was used for this task. The results highlighted that the oblique dataset produced very similar results, with GCPs (3D RMSE = 0.025 m) and without (3D RMSE = 0.028 m), while the nadiral dataset was affected more by the position and number of the GCPs (3D RMSE from 0.034 to 0.075 m). The introduction of a few oblique images into the nadiral dataset without any GCP improved the vertical accuracy of the model (Up RMSE from 0.052 to 0.025 m) and can represent a solution to speed up the image acquisition of nadiral datasets for PPK with the DJI-P4RTK and no GCPs. Moreover, the results of this research are compared to those obtained in RTK mode for the same datasets. The novelty of this research is the combination of a multitude of aspects regarding the DJI Phantom 4 RTK aircraft and the subsequent data processing strategies for assessing the quality of photogrammetric models, DTMs, and cross-section profiles.
Association of Morphological, Ecological, and Genetic Diversity of Aerva javanica Populations Growing in the Eastern Desert of Egypt

Aerva javanica is one of Egypt’s most important traditional medicinal plants used as antidiarrheal and anthelmintic medicine and recently as an anticancer agent. In this study, variations among ten populations of Aerva javanica in different sites in the Eastern Desert of Egypt were analyzed based on morphological and ecological attributes and molecular variation expressed by Inter-Simple Sequence Repeat (ISSR) markers. Morphological diversity was higher for populations in the Wadi El-Markh and Bir Abbady regions than others. The polymorphism revealed by ten ISSR primers was 79.4% among populations. Distance trees created using the results obtained from soil variables, morphological characterizations, and molecular data showed that the highest similarity was 0.974 between Populations 8 and 9, while the lowest similarity was 0.715 between Population 1 and Population 3 regions. In conclusion, the obtained data are important to design a plan for sustainable conservation of Aerva javanica as an important medicinal plant having a wide interspecific genetic variability within various populations.
The effect of self-control upon participation in voluntary pension schemes

DOI: 10.14254/2071789X.2020/13-1/1 ABSTRACT. Population ageing, together with the recent economic downturn and its aftermath, are giving considerable cause for concern as regards the future sustainability of public pension systems. Voluntary pension schemes emerge here as an alternative to supplement the public pension pillar, and therefore, understanding how individuals make their financial decisions when participating in voluntary pension schemes becomes a question of key importance. There is a growing literature aimed at analysing this issue, but few studies to date have analysed the effect of behavioural traits on participation in voluntary pension schemes. Particularly, an analysis of the effect of self-control on this financial decision will be the aim of this paper. Based on data from the International Survey of Adult Financial Literacy, this paper analyses, through probit regression models, the effect of financial self-control, besides other control variables, e.g., gender, on the holding of financial assets for retirement savings. Empirical evidence reveals that higher levels of financial self-control are positively associated with saving for retirement. Moreover, when this variable is considered, the statistically significant effect of other driving forces traditionally highlighted by previous literature disappears. Therefore, our empirical evidence supports the need to consider behavioural issues in explaining individuals’ financial decisions.
Long-Term Stability of Benefits of Cognitive Behavioral Therapy for Obsessive Compulsive Disorder Depends on Symptom Remission During Treatment

Background Cognitive behavioral therapy (CBT) is an effective treatment for obsessive-compulsive disorder (OCD) and may afford stable long-term improvements. It is not clear, however, how stability or symptom recurrence can be predicted at the time of termination of CBT. Method In a 1-year follow-up intention-to-treat study with 120 OCD patients receiving individual CBT at a university outpatient unit, we investigated the predictive value of international consensus criteria for response only (Y-BOCS score reduction by at least 35%) and remission status (Y-BOCS score ≤ 12). Secondly, we applied receiver-operating characteristic (ROC) curves in order to find an optimal cut-off score to classify for deterioration and for sustained gains. Results Response only at post-treatment increased the likelihood of deterioration at follow-up compared to remission at an odds ratio of 8.8. Moreover, ROC curves indicated that a post-treatment score of ≥ 13 differentiated optimally between patients with and without symptom deterioration at follow-up assessment. The optimal cut-off score to classify for any sustained gains (response, remission, or both) at follow-up relative to baseline was 12. Importantly, previous findings of generally high long-term symptom stability after treatment in OCD could be replicated. Conclusion The findings highlight the clinical importance of reaching remission during CBT, and suggest that a recently published expert consensus for defining remission has high utility.