Miracle-dz/UniFAR-FTUs huggingface dataset:
Speciation in a biodiversity hotspot: phylogenetic relationships, species delimitation, and divergence times of the Patagonian ground frogs of Eupsophus roseus group (Alsodidae)

The alsodid ground frogs genus Eupsophus is divided into the roseus (2n=30) and vertebralis (2n=28) groups, distributed throughout the temperate Nothofagus forests of South America. Currently, the roseus group is composed by four species, while the vertebralis group consists of two. Phylogenetic relationships and species delimitation within each group are controversial. In fact, previous analyses considered that roseus group was composed between four to nine species. In this work, we evaluated phylogenetic relationships, diversification times, and species delimitation within roseus group using a multi-locus dataset. For this purpose, mitochondrial (D-loop, Cyt b, and COI) and nuclear (POMC and CRYBA1) partial sequences, were amplified from 164 individuals, representing all species. Maximum Likelihood (ML) and Bayesian approaches were used to reconstruct phylogenetic relationships. Species tree was estimated using BEAST and singular value decomposition scores for species quartets (SVDquartets). Species limits were evaluated with six coalescent approaches. Diversification times were estimated using mitochondrial and nuclear rates with LogNormal relaxed clock in BEAST. Nine well-supported monophyletic lineages were recovered in Bayesian, ML, and SVDquartets, including eight named species and a lineage composed by specimens from Villarrica population (Bootstrap: >90, PP:> 0.9). Single-locus species delimitation analyses overestimated the species number in E. migueli, E. calcaratus and E. roseus lineages, while multi-locus analyses recovered as species the nine lineages observed in phylogenetic analyses (>0.95). It is hypothesized that Eupsophus diversification occurred during Mid-Pleistocene (0.42-0.14 Mya), with most species originated after of the Last Southern Patagonian Glaciation (0.18 Mya). Our results revitalize the hypothesis that E. roseus group is composed by eight species and support to Villarrica lineage as a new putative species.
Foraging behaviour of Razorbills Alca torda during chick-rearing at the largest colony in the Baltic Sea

ABSTRACT Capsule: Foraging behaviour in the Razorbill Alca torda during breeding was similar to that found elsewhere, aside from dive shape. Aims: To investigate the foraging behaviour of Razorbills during the breeding season at the largest colony in the central Baltic Sea. Methods: A combination of global positioning system (GPS) and time-depth recorder (TDR) devices were used on Razorbills breeding on the island of Stora Karlsö, Baltic Sea, during the chick-rearing period. Results: Five GPS tracks and nine TDR logs were retrieved from 12 Razorbills, and 7399 dives were analysed. Razorbills foraged south and southwest of the colony. Maximum and mean (±sd) foraging range from the colony was 72.7 km and 13.1 ± 13.5 km, respectively. Mean dive depth (15.3 ± 2.4 m) and duration (53.1 ± 8.5 s) were similar to those of a more southern Baltic Sea Razorbill colony. Dive depth had a bimodal distribution, with 70% of dives deeper than 10 m and 30% shallower than 10 m. There was a clear diel foraging pattern with 89% of dives occurring during daytime and a higher proportion of shallow dives at night. Unexpectedly, dives were primarily U-shaped. The Razorbills spent 31% of their overall time activity budget flying or diving. Conclusion: Aside from dive shape, foraging behaviour was consistent with that reported at other colonies of Razorbills. Inconsistency in dive shape may be due to a bimodal foraging strategy, local prey behaviour or competition with the Common Guillemot Uria aalge.
The Relationship between Age, Neural Differentiation, and Memory Performance

Healthy aging is associated with decreased neural selectivity (dedifferentiation) in category-selective cortical regions. This finding has prompted the suggestion that dedifferentiation contributes to age-related cognitive decline. Consistent with this possibility, dedifferentiation has been reported to negatively correlate with fluid intelligence in older adults. Here, we examined whether dedifferentiation is associated with performance in another cognitive domain—episodic memory—that is also highly vulnerable to aging. Given the proposed role of dedifferentiation in age-related cognitive decline, we predicted there would be a stronger link between dedifferentiation and episodic memory performance in older than in younger adults. Young (18–30 years) and older (64–75 years) male and female humans underwent fMRI scanning while viewing images of objects and scenes before a subsequent recognition memory test. We computed a differentiation index in two regions of interest (ROIs): parahippocampal place area (PPA) and lateral occipital complex (LOC). This index quantified the selectivity of the BOLD response to preferred versus nonpreferred category of an ROI (scenes for PPA, objects for LOC). The differentiation index in the PPA, but not the LOC, was lower in older than in younger adults. Additionally, the PPA differentiation index predicted recognition memory performance for the studied items. This relationship was independent of and not moderated by age. The PPA differentiation index also predicted performance on a latent “fluency” factor derived from a neuropsychological test battery; this relationship was also age invariant. These findings suggest that two independent factors, one associated with age, and the other with cognitive performance, influence neural differentiation. SIGNIFICANCE STATEMENT Aging is associated with neural dedifferentiation—reduced neural selectivity in “category-selective” cortical brain regions—which has been proposed to contribute to cognitive aging. Here, we examined whether neural differentiation is predictive of episodic memory performance, and whether the relationship is moderated by age. A neural differentiation index was estimated for scene-selective (PPA) and object-selective (LOC) cortical regions while participants studied images for a subsequent memory test. Age-related reductions were observed for the PPA, but not for the LOC, differentiation index. Importantly, the PPA differentiation index demonstrated age-invariant correlations with subsequent memory performance and a fluency factor derived from a neuropsychological battery. Together, these findings suggest that neural differentiation is associated with two independent factors: age and cognitive performance.
Estimates of abundance and longevity of Bridled Quail-Doves (Geotrygon mystacea) on Guana Island, British Virgin Islands

ABSTRACT The Bridled Quail-Dove (Geotrygon mystacea) is a columbiform resident of the eastern Caribbean. It is a poorly studied species with a lack of quantitative data to assess population status, but perceived population declines have led to it being considered a species of conservation concern on many islands. I attempted to assess population size and survival of Bridled Quail-Doves on Guana Island, British Virgin Islands. Based on detection probability, density estimates for Guana Island ranged from 1.38 to 1.57 individuals/ha in 2014 and 2015, respectively. Densities varied among cover type, with an estimated 1.13 individuals/ha in dry forest (90% of the island) and 4.63 individuals/ha in ghaut forest (5% of the island). These values would translate to a pooled estimate of ∼429 individuals during the survey period. Of 36 Bridled Quail-Doves captured and marked, the naïve estimate of annual survival was 0.813, with 0.36 captured individuals surviving at least 1 year, and the average minimum age at last recapture was 4.9 years old. This report is the first quantitative based estimates of population size and longevity for the species and may serve as a starting point for longer-term studies on Guana Island, but also for comparison to populations on other islands.
Disinhibition as a canonical neural mechanism for flexible behavior

Flexibility is a hallmark of human and animal behavior, but the context-dependent neural computations that generate flexible behavior are poorly understood. Here, we use a biophysically-based cortical network model to explore the hypothesis that vasoactive intestinal polypeptide (VIP) expressing inhibitory interneurons control local circuit dynamics by targeting other classes of inhibitory interneuron, supporting context-dependent computations. Depending on the strength of this disinhibition (simulating VIP activity), network dynamics support multiple-item working memory (WM, strong disinhibition) or decision making (DM, weak disinhibition). Within these regimes, disinhibition controls WM capacity and speedaccuracy-trade-off in choice behavior. Our findings suggest that long-range trans-cortical VIP-mediated disinhibition is a canonical neural mechanism for the top-down control of flexible behavior.
G-Dash: A Genome Dashboard Integrating Modeling and Informatics

Genomics is a sequence based informatics science and a structure based molecular material science. There are few tools available that unite these approaches in a scientifically robust manner. Here we describe G-Dash, a web based prototype of a genomics dashboard, specifically designed to integrate informatics and 3D material studies of chromatin. G-Dash unites our Interactive Chromatin Modeling(ICM) tools with the Biodalliance genome browser and the JSMol molecular viewer to rapidly fold any DNA sequence into atomic or coarse-grained models of DNA, nucleosomes or chromatin. As a chromatin modeling tool, G-Dash enables users to specify nucleosome positions from various experimental or theoretical sources, interactively manipulate nucleosomes, and assign different conformational states to each nucleosome. As an informatics tool, data associated with 3D structures are displayed as tracks in a genome browser. The exchange of data between informatics and structure is bi-directional so any informatics track can inform a molecular structure (e.g. color by function) and structure features can be displayed as informatics tracks in a genome browser(e.g. Roll, Slide, or Twist). As a sample application, models of the CHA1 promoter based on experimentally determined nucleosome positions are explored with G-Dash. Steric clashes and DNA knotting are observed but can be resolved with G-Dash’s minimal coarse-grained model without significant variation in structure. Results raise questions about the interpretation of nucleosome positioning data and promoter structures. In this regard, G-Dash is a novel tool for investigating structure-function relationships for regions of the genome ranging from base pairs to chromosomes and for generating, validating and testing mechanistic hypotheses. http://dna.engr. latech.edu/∼gdash/GDash-landing-page
A study of ethnobotany in Kumluca (Antalya)

Kumluca’yi da icine alan Akdeniz bolgesi, bitki cesitliligi bakimindan zengin bir bolgedir. Geleneksel olarak, bu bolgedeki bitkilerin cogu, bircok kullanim alanina sahiptir. Bu calisma Kumluca (Antalya) 'daki bitkilerin etnobotanik ozelliklerini belirlemek icin Haziran 2014'ten Mayis 2015'e kadar gerceklestirilmistir. Bu bolgeden 255 kisi ile yuz yuze gorusmeler yapilarak bitkilerin kullanim alanlari hakkinda bilgi edinilmistir. Anketlerde yas, cinsiyet, medeni durum, egitim durumu, meslek, sosyal guvenlik, ankete katilanlarin gelir duzeyleri gibi bilgiler kaydedilmistir. Ayrica bitkilerin (tibbi, gida, baharat, yem, dini inanc vb.) kullanim alanlari kullanim talimatlari ile birlikte kaydedilmistir. Arastirmada katilimcilarindan bilgi toplarken, dogadaki canli ornekler katilimcilara gosterilmis ve bitkilerin kullanim alanlarina iliskin aciklama istenmistir. Arastirma, 51 aileye ait 89 yerel taksonun etnobotanik ozelliklere sahip oldugunu ortaya koymustur. Yaygin olarak kullanilan ailelerin Lamiaceae (9 takson), Fabaceae (6 takson), Rosaceae (6 takson), Asteraceae (5 takson) ve Anacardiaceae (4 takson) oldugu saptanmistir. Bu 89 taksonun 132 farkli kullanimi belirlenmis ve bunlar asagidaki gibidir; 37 (gida), 38 (tibbi), 27 (cay), 13 (esya), 8 (yem), 5 (sus) ve 4 (baharat). Bu taksonlarin yaygin olarak kullanilan kisimlari soyle bulunmustur; toprak ustu kisim (39), meyve (18), cicek (10), yaprak (9) ve kozalak (4). Bu tur calismalar yapildiginda ve literaturdeki eksiklikler tamamlandiginda, insanlik icin yararli olan bitkiler tanimlanabilir ve gelecek nesillere aktarilabilir.
Estabilidade e adaptabilidade para volume de madeira na seleção de Eucalyptus saligna em três ambientes

The objective of this work was to evaluate the genotype x environment (GxE) interaction in open-pollinated Eucalyptus saligna progenies for simultaneous selection for greater stability and adaptability for wood volume, as well as to compare the selection strategies through combined and individual analyses in three environments. Three experiments were conducted in a randomized complete block design, with four replicates and six plants per plot, with 102 to 122 progenies. Three years after planting, survival rate and wood volume were evaluated. The genetic parameters were estimated by the maximum restricted likelihood and best linear unbiased prediction (REML/Blup) methods, and the stability and adaptability analysis was conducted using the harmonic mean of the relative performance of genetic values (HMRPGV). The highest survival rate (82%) was observed in Sabinopolis and the highest volume (120 m³ ha -1 ) in Lencois Paulista. The mean heritability of progenies for the two analyzed variables was considered high, and the genetic correlations between survival rate and volume were weak for all sites. The G×E interaction was significant and of the complex type, with genotype correlation between sites of 47%, indicating that the ranking of the best progenies differed in each studied environment. The analysis of stability and adaptability indicated the possibility of selecting progenies with good performance in the three environments; however, to improve the quality of the evaluated characteristics, it is necessary to select specific progenies for each environment.
PENGEMBANGAN KOMIK FISIKA BERBASIS ANDROID SEBAGAI SUPLEMEN POKOK BAHASAN RADIOAKTIVITAS UNTUK SEKOLAH MENENGAH ATAS

Pokok bahasan fisika pada sekolah menengah atas seringkali mengandung konsep abstrak, seperti pokok bahasan radioaktivitas. Terlebih, pokok bahasan radioaktivitas berada di akhir semester 2 kelas 12 SMA membuat siswa kurang mendalami pokok bahasan tersebut. Konsep abstrak bisa diatasi dengan menggunakan gambar, gambar dikembangkan dalam bentuk komik agar tercipta suasana belajar yang lebih menyenangkan dan menarik. Penelitian ini mengembangkan komik fisika bersifat mobile untuk sistem operasi Android sebagai suatu suplemen pembelajaran. Kelayakan komik diuji menggunakan metode angket, dokumentasi, serta tes rumpang untuk mengetahui tingkat keterbacaan komik. Angket diberikan kepada responden, yakni siswa kelas 12 SMA, guru fisika, ahli media, serta ahli materi. Penelitian ini menghasilkan aplikasi komik fisika berbasis Android sebagai suplemen pokok bahasan radioaktivitas untuk sekolah menengah atas. Skor rata-rata data responden sebesar 77,91% atau berada dalam kriteria baik, maka aplikasi komik fisika berbasis Android layak digunakan sebagai suplemen pembelajaran pada pokok bahasan radioaktivitas untuk sekolah menengah atas. The subject of physics at high school often contain the abstract concept, such as the subject of radioactivity. Moreover, subject of radioactivity was in the end of the 2nd semester grade 12 High School make students less explore the subject of the. Abstract concept can be overcome by using images, images developed in the form of comics in order to create atmosphere of learning more fun and interesting. This study developed a comic physics is mobile for Android operating system as a supplement learning. Feasibility comics tested using the questionnaire method, documentation, as well as the test hiatus to determine the level of the legibility of comics. Questionnaire given to the respondents, namely grade students 12 High School, physics teacher, media experts, as well as the matter experts. This research result in the application comic physics based Android as a supplement the subject of radioactivity for high school. The mean score of respondents data is 77.91% or in a good criterion, it’s means that the application comic physics based Android worth used as a supplement learning on the subject of radioactivity for high school.
A Novel Idea: English as Foreign Language Reading via Virtual Literature Circles

To investigate the effects of virtual literature circle (VLC) on cultivating positive reading attitudes and enhancing general English proficiency and reading comprehension, a mixed-method study was conducted with 54 college students studying English as a foreign language. Analyses of multiple data sources revealed that during this year-long VLC-integrated English course, participants' English reading comprehension and general English proficiency have improved whereas their reading attitudes remained unchanged. VLCs could be an effective means to cultivate positive reading attitudes. Peer interactions within the VLCs not only help students see their peers reading but also provide audience with meaningful reading. Nevertheless, the lack of simultaneous communication and the language barrier were cited by the participants as the primary hindrance for them to benefit fully from VLCs. Merely hosting LCs online does not warrant the successful transfer of literary discussion from the face-to-face to the computer-mediated interaction. To bridge the gap between the face-to-face and the computer-mediated literary discussion, concrete modeling, linguistic support, and individual accountability for VLCs seem important.
Recent Advances by In Silico and In Vitro Studies of Amyloid-β 1-42 Fibril Depicted a S-Shape Conformation

The amyloid-β 1-42 (Aβ1-42) peptide is produced by proteolytic cleavage of the amyloid precursor protein (APP) by sequential reactions that are catalyzed by γ and β secretases. Aβ1-42, together with the Tau protein are two principal hallmarks of Alzheimer’s disease (AD) that are related to disease genesis and progression. Aβ1-42 possesses a higher aggregation propensity, and it is able to form fibrils via nucleated fibril formation. To date, there are compounds available that prevent Aβ1-42 aggregation, but none have been successful in clinical trials, possibly because the Aβ1-42 structure and aggregation mechanisms are not thoroughly understood. New molecules have been designed, employing knowledge of the Aβ1-42 structure and are based on preventing or breaking the ionic interactions that have been proposed for formation of the Aβ1-42 fibril U-shaped structure. Recently, a new Aβ1-42 fibril S-shaped structure was reported that, together with its aggregation and catalytic properties, could be helpful in the design of new inhibitor molecules. Therefore, in silico and in vitro methods have been employed to analyze the Aβ1-42 fibril S-shaped structure and its aggregation to obtain more accurate Aβ1-42 oligomerization data for the design and evaluation of new molecules that can prevent the fibrillation process.
Effect of hairy vetch (Vicia villosa Roth.) and vetch-rye (Secale cereale L.) biculture cover crops and plastic mulching in high tunnel vegetable production under organic management

ABSTRACT Effects of cover crops on soil physical and chemical properties and yield of the following cash-crops were evaluated in an organic system in a high tunnel. The sequence of crops in the two-year study was: vetch or vetch-rye followed by zucchini (Cucurbita pepo) and then lettuce (Lactuca sativa L) in 2016 and celery (Apium graveolens L.) in 2017. In the plots with cover crops, two mulches (black and transparent polyethylene (PE) film) were used to cover the soil at the end of the first season during the winter period. The differences in the biomass between vetch grown on its own and the vetch-rye mixture were not significant, but the total amount of N accumulated in the biomass of the vetch (252 kg N ha−1) was greater than that of the vetch-rye mixture (174 kg N ha−1). The use of cover crops improved soil properties in the first season (2016), including water stable aggregate index and soil organic matter. In the second season (2017), the use of cover crops combined with PE mulching had a beneficial effect on soil the pH, the water-stable aggregate index, and the availability of Ca, Mg, B and Fe. Covering the soil with black PE mulch during the winter (in both the vetch and the vetch-rye treatments), increased celery yield, compared with the transparent PE mulch and the untreated soil. The use of black PE mulch in the vetch treatment and transparent PE mulch in the vetch-rye treatment reduced soil organic carbon.
Enation leaf curl virus (ELCV): A real threat in major okra production belts of India: A review

Production of okra is threatened by viral diseases. Okra enation leaf curl disease is an emerging serious disease in India. The disease was first reported from Karnataka in the early 1980s. Infection at early stages of crop growth may cause severe yield loss in okra. The disease is transmitted by insect vector, whitefly (Bemisia tabaci). Hot weather with little or no rainfall is conducive for virus disease development. Recently, associations of betasatellites and alphasatellites causing enation leaf curling disease in okra have been reported from India. There is no stable source of resistance to this disease in cultivated species. However, some wild species (Abelmoschus crinitus, A. ficulneus, A. angulosus and A. manihot) of okra have stable and reliable sources of resistance to ELCV. No attempts have been made in the past to study the genetics of resistance to ELCV disease in India. Moreover, the basis of resistance against this disease has not so far been studied in detail. In this background, this review deals with the advancements in ELCV disease, and special emphasis has been laid on the genetic and biochemical basis of this disease resistance for the development of resistant varieties.
Investigation of annotatorâ€™s behaviour using eye-tracking data

This paper presents an analysis of an annotator’s behaviour during her/his annotation process for eliciting useful information for natural language processing (NLP) tasks. Text annotation is essential for machine learning-based NLP where annotated texts are used for both training and evaluating supervised systems. Since an annotator’s behaviour during annotation can be seen as reflecting her/his cognitive process during her/his attempt to understand the text for annotation, analysing the process of text annotation has potential to reveal useful information for NLP tasks, in particular semantic and discourse processing that require deeper language understanding. We conducted an experiment for collecting annotator actions and eye gaze during the annotation of predicate-argument relations in Japanese texts. Our analysis of the collected data suggests that obtained insight into human annotation behaviour is useful for exploring effective linguistic features in machine learning-based approaches.