Miracle-dz/UniFAR-FTUs huggingface dataset:
Species relationship and genetic diversity in some Iranian Lamium L. species using ISSR markers

Abstract. Azimishad F, Sheidai M, Talebi SM, Noormohammadi Z. 2019. Species relationship and genetic diversity in some Iranian Lamium L. species using ISSR markers. Biodiversitas 20: 1963-1972. Lamium is a widespread and taxonomically complex genus of Lamiaceae which comprises of 16-38 species. This genus is represented in Iran by nine species. In the present study, we used morphological and molecular (ISSR, Cp DNA, and nrITS) data to evaluate species relationships, genetic diversity and population genetic structure of the genus. 27 morphological characteristics, including 13 qualitative and 14 quantitative, and ten ISSR markers were used for morphological and genetical evaluation of 73 accessions from eight taxa. In general, species relationships obtained from morphological and molecular data were largely congruent. In the morphological study, characteristics like the life form, leaf shape, absence/existence of bracts and shape of corolla, were distinctive traits and we did not encounter intermediate forms. Our findings indicated a very high efficiency of the ISSR markers in the identification and delimitation of Lamium species. These results confirmed the placement of L. galeobdolon in the genus Lamium and segregation of L. purpureum and L. garganicum in section Lamium. AMOVA analysis revealed that the species of this genus are genetically differentiated. Nm analysis showed very low value of gene flow among the studied species and mantel test indicated isolation by distance occurred among them.
A Review on Nutritional Value, Functional Properties and Pharmacological Application of Perilla (Perilla Frutescens L.)

Perilla frutescens is an annual herb belonging to the mint family (Lamiaceae). It is majorly produced in countries like China, Japan, India, Thailand and Korea. Recently, Perilla plant is gaining more attention because of its medicinal benefits and phytochemical contents. The major phytochemical compounds reported in this species are phenolic compounds (Rosmarinic acid, caffeic acid, ferulic acid), flavonoids (luteolin, apigenin), Phytosterols, Tocopherols, Policosanols and Fatty acid. Perilla seed oil is also a rich source of essential fatty acid such as α-linolenic acid (54-64%) and linoleic acid (14%). Perilla seeds and its oils have been widely used in traditional nutritional and medicinal formulations. Biological analysis of Perilla seeds revealed that it showed anticancer, ant-diabetic, antiasthma, antimicrobial, anti-inflammatory, antioxidant and cardioprotective effect. The aim of this review is to provide an update on the nutritional composition, phytochemical profile and pharmacological research of Perilla seed.
Biases from Poor Data Analyses

Non-statisticians with little knowledge in basic descriptive statistics tend to think that statistics field is limited to the content to which they are exposed. Many of them believe that a statistical package can augment the little Statistics knowledge they have. They often have a tendency to perform their own data analyses and do not even bounce it against Statistics experts for quality check. Many studies were concluded from data analyses performed by analysts who lack insight into statistical methods. Hence, results in some of their researches have flaws and distorted truths. The paper explains the defects in data analyses and research results that can be caused by influences in the data. Flawed research results may be caused when the data were not scanned for variations and other inconsistencies present in the data. Properly trained statisticians who also understand theories and methods of dealing with outliers can perform these analyses more effectively. However, many researchers fail to seek their advices. This study shows the extent of falsifications that contaminated data can produce and the massive loss to the factualness contained in the data.
Development new multiplex reverse transcription quantitative real time polymerase reaction to detect human norovirus genogroups I and II

Norovirus (NV) is considering a highly contagious virus due to the increase in the number of cases of the virus in recent years. Therefore, there is a need to develop rapid, specific and sensitive molecular detection and diagnosis methods. Using the data from the National Center of Bioinformatics Information (NCBI), the sequence of more than 1000 Norovirus genogroupII genome and 39 genome of geno group I were chosen to select a common conserve region for all genotypes within the first group and the second group suitable for the design of primers and probes. The design of the first area of the junction of Open Reading Frame one (ORF) and the open reading frame two (ORF2), and the primers and probes were tested on samples of compared to the primers and using one step reverse transcription real time PCR. The kit designed for multiplex reverse reaction possess no overlap or interaction in the components of primers and probes of the two genogroups, also it is superior on the monoplex mixture of the previous kit, Norovirus being diagnosed in 45% of samples by primers and probes designed in this study, 10% of the samples were belong to the genogroupI and 35% of the samples belong to the genogroupII in comparing with virus results that tested with monoplex previous primers and probes accounted 44% , the genogroupI represented 10% and genogroupII II represented 34% of the tested samples. The use of the multiplex kit contributes to shortening the time and the largest number of samples and reduce amount of the solutions used, more than the monoplex reaction, as it should be performed separately for each genetic group.
Brain functional connectivity dynamics in the aftermaths of affective and cognitive events

Neuroimaging studies have shown carry-over effects on brain activity and connectivity following both emotional and cognitive events, persisting even during subsequent rest. Here, we investigate the functional dynamics of such effects by identifying recurring co-activation patterns (CAPs). Using the precuneus as seed region, we compare carrying-over effects on brain-wide CAPs and their modulation after both affective and cognitive challenges. Female volunteers (n=19) underwent fMRI scanning during emotional induction with sad movie clips, and executive control tasks, each followed by resting periods. Several CAPs, overlapping the default mode, salience, attention, and social cognition networks were impacted by both the preceding events (movie or task) and their valence (neutral or negative), with differential fluctuations over time. Specifically, a modulation of CAPs in posterior cingulate and ventromedial prefrontal cortex was observed after exposure to negatively valenced emotional content and predicted changes in subjective affect. Additionally, CAPs in anterior cingulate cortex and dorsal fronto-parietal areas were induced by cognitive control in a negative, but not neutral context, and amplified by the task difficulty. These findings provide new insights on the anatomical organization and temporal inertia of intrinsic functional brain networks, engaged by transient emotions and presumably involved in subsequent adaptive homeostatic processes.
Model-based decoupling of evoked and spontaneous neural activity in calcium imaging data

The pattern of neural activity evoked by a stimulus can be substantially affected by ongoing spontaneous activity. Separating these two types of activity is particularly important for calcium imaging data given the slow temporal dynamics of calcium indicators. Here we present a statistical model that decouples stimulus-driven activity from low dimensional spontaneous activity in this case. The model identifies hidden factors giving rise to spontaneous activity while jointly estimating stimulus tuning properties that account for the confounding effects that these factors introduce. By applying our model to data from zebrafish optic tectum and mouse visual cortex, we obtain quantitative measurements of the extent that neurons in each case are driven by evoked activity, spontaneous activity, and their interaction. This broadly applicable model brings new insight into population-level neural activity in single trials without averaging away potentially important information encoded in spontaneous activity.
Nucleolin Interacts and Co-Localizes with Components of Pre-Catalytic Spliceosome Complexes

Nucleolin is an RNA binding protein that is involved in many post-transcriptional regulation steps of messenger RNAs in addition to its nucleolar role in ribosomal RNA transcription and assembly in pre-ribosomes. Acetylated nucleolin was found to be associated with nuclear speckles and to co-localize with the splicing factor SC35. Previous nuclear pull down of nucleolin identified several splicing components and factors involved in RNA polymerase II transcription associated with nucleolin. In this report, we show that these splicing components are specifics of the pre-catalytic A and B spliceosomes, while proteins recruited in the Bact, C and P complexes are absent from the nucleolin interacting proteins. Furthermore, we show that acetylated nucleolin co-localized with P-SF3B1, a marker of co-transcriptional active spliceosomes. P-SF3B1 complexes can be pulled down with nucleolin specific antibodies. Interestingly, the alternative splicing of Fibronectin at the IIICS and EDB sites was affected by nucleolin depletion. These data are consistent with a model where nucleolin could be a factor bridging RNA polymerase II transcription and assembly of pre-catalytic spliceosome similarly to its function in the co-transcriptional maturation of pre-rRNA.
Cross-comparison of Digital and Digitized Physical Evidence

In forensics, investigations comprise diverse types of evidence. For example digital evidence in form of electronic documents and physical evidence, e.g. printed paper documents. One major challenge is to efficiently and accurately link digital evidence and physical evidence together. In particular, a computational method is needed to deal with the huge amount of data available in a forensic investigation and to reduce the time spent on linking and analyzing the different types of evidence. The thesis aims to improve the efficiency and effectiveness of this process by using computational methods such as plain text search (String search), approximate string matching and OCR (optical character recognition), and to incorporate these in a proof-of-concept tool. The tool is used for an experimental setup for testing of linking accuracy between similar and dissimilar documents. A dataset was created and used for testing, based on feedback from Økokrim1. The thesis seeks to answer how OCR affects evidence linking, characteristics of a forensics dataset, characteristics that enables linking and how it is possible to increase efficiency in evidence linking. The proof-of-concept tool, contains five methods for comparison, four text comparison methods; Levenshtein distance, Word frequency, Cosine similarity and W-shingles. And one image-to-image comparison; a pixel-to-pixel similarity. It uses Optical Character Recognition for text generation from scanned documents. Text extraction from digital documents are done through Java libraries. The results shows that W-shingles is the best performing algorithm for matching documents in this setting, and that text sanitation does not have any practical influence on W-shingles, whereas it does increase the matching accuracy for the remaining methods. Characteristics that enables evidence linking was found to be shingles and frequency of unique words used in Cosine similarity. Characteristics in a dataset consisting of DOCX documents are bold font style, and the combination of font size 11 and font type Calibri, which is the default combination for Microsoft Word R © 2007, 2010 and 2013. The efficiency and accuracy of OCR can be increased by using ensemble voting and decreasing runtime. As for OCR error rate in a forensics environment it is a nonissue since it is not used to recreate evidence, but for matching and locating evidence. 1The Norwegian National Authority for Investigation and Prosecution of Economic and Environmental Crime
Morphologic, Palynologic, and Phylogenetic Relationships of Acantholimon Species (Plumbaginaceae) Sharing Similar Habitats

Acantholimon Boiss cinsi. Dunya genelinde yaklasik 200 tur ve 71 taksonla temsil edilir, bunlarin %56'si Turkiye icin endemiktir. Bu calismada Acantholimon anatolicum, A. ulicinum var. ulicinum , A. gemicianum , A. riyatguelii ve A. acerosum var. acerosum benzer habitatlari paylasmalari nedeniyle karsilastirilmistir. Acantholimon anatolicum, A. ulicinum var. ulicinum , A. gemicianum morfolojik ve taksonomik olarak birbirlerine cok benzerdir. Ancak A. riyatguelii ve A. acerosum var. acerosum diger turlerden skalalarininin 2-3 (4-5 degil) ve ciceklenme boylarinin yapraklardan uzun olusuyla farklidir. Bu taksonlarin iliskilerini anlamak icin morfolojik, palinolojik ve molekuler calismalar yapilmistir. Morfolojik karakterleri elde etmek icin hem isik hem de elektron mikroskopu kullanilmis ve taksonlarin molekuler ozellikleri icin ITS nukleer gen bolgesi calisilmistir. Morfolojik benzerlikler verilerine ek olarak palinolojik ve molekuler veriler de benzerlik gostermektedir.
Automated Detection Method for Clustered Microcalcification in Mammogram Image Based on Statistical Textural Features

Breast cancer is the most frightening cancer for women in the world. The current problem that closely related with this issue is how to deal with small calcification part inside the breast called micro calcification (MC). As a preventive way, a breast screening examination called mammogram is provided. Mammogram image with a considerable amount of MC has been a problem for the doctor and radiologist when they should determine correctly the region of interest, in this study is clustered MC. Therefore, we propose to develop an automated method to detect clustered MC utilizing two main methods, multi-branches standard deviation analysis for clustered MC detection and surrounding region dependence method for individual MC detection. Our proposed method was resulting in 70.8% of classification rate, then for the sensitivity and specificity obtained 79% and 87%, respectively. The gained results are adequately promising to be more developed in some areas.
Usability of Free and Open-Source Tools for Translator Training Omegat and Bitext2tmx

In Spanish universities, free and open-source software (FOSS) is widely used in technical areas because of its usability, adaptability and low cost. Conversely, the use of these tools in the field of translator training has been minimal despite the existence of suitable software specifically developed for translation activities, such as OmegaT, Anaphraseus, bitext2tmx, Sun Open Language Tools, ForeignDesk or Transolution. In this context, GETLT was created to promote the use of FOSS both in translator training and professional translation, and to acknowledge the effort made by FOSS localization teams. After a short overview of the phases and results of research project PGIDIT07PX1B302200PR, Creacín dunha plataforma docente GNU/Linux para a formacín de tradutores – localizadores de software – subtituladores, funded by the Galician Government, within the framework of programme Incite, this chapter describes a particular research effort focused on testing the usability and applicability to translation training of free and open-source translation memory managers and text aligners with different texts types and genres.
Invasion but not hybridisation is associated with ecological niche shift in monkeyflowers

Background The ecological niche occupied by novel hybrids can influence their establishment as well as the potential to coexist with their parents. Hybridisation generates new phenotypic combinations, which, in some cases, may allow them to occupy ecological niches outside the environmental envelope of parental taxa. In other cases, hybrids may retain similar ecological niches to their parents, resulting in competition and affecting their coexistence. To date, few studies have quantitatively assessed niche shifts associated with hybridisation in recently introduced populations while simultaneously characterising the niche of parental species in both native and introduced ranges. Aims In this study, we compared the ecological niche of a novel hybrid plant with the niches of its two parental taxa in the non-native geographic range. We also characterised and compared the parental taxa’s ecological niche of native and introduced populations in order to assess potential niche changes during the invasion process independent of hybridisation. Methods We studied monkeyflowers (Mimulus spp., Phrymaceae) that were introduced from the Americas to Europe and New Zealand in the last 200 years. We focused on a novel hybrid, triploid, asexual taxon (M. × robertsii) that occurs only in the British Isles where its two parents (M. guttatus and M. luteus) come into secondary contact. We assembled more than 12,000 geo-referenced occurrence records and eight environmental variables of the three taxa across native and introduced ranges, and conducted ecological niche model analysis using maximum entropy, principal component and niche dynamics analysis. Results We found no evidence of niche shift in the hybrid, M. × robertsii compared to introduced populations of both of their parental taxa. The hybrid had a niche more similar to M. luteus, which is also the rarest of the parental taxa on the introduced range. Among parental monkeyflowers, M. guttatus showed niche conservatism in introduced populations in Europe, but a niche shift in New Zealand, while M. luteus showed a niche shift in Europe. However, the evidence of niche shift should be treated with caution due to the occurence of non-analog climatic conditions, small population size and unfilling niche dynamics. Conclusions Our results suggest that hybridisation in non-native monkyeflowers did not result in a shift in ecological niche. This niche conservation could create competition between parental and derived taxa, the outcome of which will depend on relative competitive abilities. Further work is needed to establish if the expansion of the hybrid in the introduced range is causally related to the apparent rarity of one of the parents (M.luteus). Finally, the comparison of native and non-native populations of parental taxa, suggest that whether invasions result in niche shifts or not depends on both taxon and geographic region, highlighting the idiosyncratic nature of biological invasions.
Colour polymorphism and protective coloration in coconut crabs

Phenotypic colour polymorphisms are common in nature but their adaptive significance is often difficult to interpret. Terrestrial coconut crabs Birgus latro have cohabiting distinct red and blue colour morphs and earlier research suggested that red morphs are more cryptic in open inland areas whereas blue morphs are more cryptic in nearshore closed environments, hinting that microhabitat specialization maintains the polymorphism. We used five independent methods to investigate this hypothesis. (i) Behavioural observations of crabs in the wild, and (ii) behaviour of wild-caught crabs exploring an arena revealed no differences in habitat-specific movement patterns between morphs. (iii) An experiment with red and blue plasticine covered model crabs placed out in the field uncovered no consistent differences in visitation rates by terrestrial hermit crabs or live coconut crabs based on the colour of the plasticine. (iv) An experiment involving people locating model crabs in the field generated inconclusive evidence that one morph was more cryptic than the other. (v) An updated large dataset comprising over 500 live crabs found that neither morph showed a preference for one habitat with different degrees of exposure. Our findings lend no support to the idea that red and blue crabs preferentially occupy different habitats to gain protective advantages, or that coloration influences visits by people or sympatric species, or that morphs behave differently in relation to habitat exposure. Colour polymorphism in this species is unlikely to be maintained by niche-specific protective coloration, and may be a neutral polymorphism although this requires investigation.
Screening and molecular identification of gelatinase-producing bacteria isolated from Indonesian mangrove ecosystem.

The objective of this research was to isolate and identify gelatinase-producing bacteria from several mangrove ecosystems in Indonesia. Soil samples were collected from seven coastal locations of mangrove ecosystem in 2017. The gelatinase-producing bacteria were screened by using screening and confirmation methods. The gelatinase-producing bacteria were further analyzed by using the 16s rDNA molecular method. Ten isolates were diagnosed to be gelatinase-producing bacteria, which belonged to three genera: Lysinibacilus sp, Enterobacter sp. and Proteus sp. The isolated bacteria can further be investigated for the possibility of gelatinase production.
Research of the properties of receptive field in handwritten Chinese character recognition based on DCNN model

For problem of influence of different size of receptive fields to DCNN modeling on offline handwritten Chinese character recognition (HCCR), the relationships of the receptive field, the number of parameter, the number of layer, the number of feature map and the size of the area occupied by the basic strokes of Chinese characters have been deeply researched and verified with experiment. With a Softmax classifier of output layer, GPU techniques are applied to accelerate model training and Drop-out method is adopted to prevent over-fitting. The research results of the theory and the experiment are important reference in the light of reasonable or effective selection of receptive field size for DCNN model in HCCR applications. It also provides a method for selecting the size of the receptive field for DCNN in HCCR.
Research of Static Detection Technology of Software Testability

The testability of program is a prediction of its ability to reveal faults and it is an important characteristic of software. This paper introduces academic models about the process of software fault detection and the RELAY model of error detection. It presents a whole process of software fault detection, which comprises executing process, infecting process and propagating process. It is able to analyze program structure, the errors originated in smallest expressions, the computing and information flow transfer of errors, etc. A solution of software testability detection using static analyzing method is provided. That is, the testability of a whole program can be obtained by averaging the testability of all sentences in the program.