Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Ability and Variance Components for Yield and Quality Traits in Tomato (Solanum lycopersicum L.)

Tomato (Solanum lycopersicum L.) is one of the most widely grown and the most popular vegetable crops in the world. It belongs to family Solanaceae with chromosome number of 2n = 24. Primary centre of origin is South American region consisting of Peru, Bolivia Ecuador (11) and it is presumed to have been brought to India during the second half of the 16 th century through far eastern countries. Tomato ranks second in production after potato and in India it is being grown in an area of 8.79 lakh hectares with the annual production of 18.22 lakh tons with a productivity of 20.7 tons per hectare. It occupies 3 rd position in area, 2 nd in production and 3 rd in productivity among the vegetables International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 10 (2019) Journal homepage: http://www.ijcmas. com
Maximum likelihood estimation of natural selection and allele age from time series data of allele frequencies

Thanks to advances in ancient DNA preparation and sequencing techniques, time serial samples of segregating alleles are becoming more widely available in ancestral populations. Such time series data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. Here we develop a likelihood-based method for co-estimating the selection coefficient and the allele age from allele frequency time series data. Our method is built on the hidden Markov model incorporating the Wright-Fisher diffusion conditioned to survive until the time of the most recent sample, which circumvents the assumption required in existing methods that the allele is created by mutation at a certain small frequency. We calculate the likelihood by numerically solving the Kolmogorov backward equation resulting from the conditioned Wright-Fisher diffusion backwards in time and re-weighting the solution by the emission probabilities of the observation at each sampling time point, which allows for a reduction of the two-dimensional numerical search for the maximum of the likelihood surface for the selection coefficient and the allele age. We show through extensive simulations that our approach can produce unbiased estimates of the selection coefficient and the allele age, even if the samples are sparsely distributed in time with small uneven sizes. We illustrate the utility of our method on real data by re-analysing the ancient DNA data associated with horse coat colouration and show that grouping samples can significantly bias the results of inference.
OAT VS WHITE MUSTARD AS CATCH CROP

Background. The number of species suitable for late summer sowing as catch crops intended for mulching soil is insufficient. It has been hypothetically assumed that oat (Avena sativa L.) may be an alternative to white mustard (Sinapis alba L.) that is commonly grown for this purpose. The aim of this study was to compare the yield and nitrogen accumulation of oat and white mustard planted as catch crops at different late summer dates, and the effect of mulch from these plants on spring barley (Hordeum sativum L.) yield. Material and methods. In the period from 2011 to 2013, oat and white mustard were sown separately on August 15 and September 1 and 15. No nitrogen fertilization was used for the catch crops. At the end of October, dry matter accumulation and nitrogen accumulation were determined. Photographic documentation of the mulch coverage of the soil was made. Over a 3-year period (2012–2014), spring barley was grown after the oat and mustard mulch. Plant density and grain yield of the barley was determined. Results. Delaying the sowing date resulted in a decrease in catch crop dry matter accumulation, on average for both species, from 2.36 to 0.61 Mg·ha-1, and in nitrogen accumulation from 45.4 to 30.3 kg·ha-1. Differences in biomass and nitrogen accumulation, in favor of mustard, were associated with the earliest sowing date only. Oat plants did not lose leaves in winter and thus provided greater soil cover than mustard plants. These species cultivated as a catch crop and used for mulch did not differ in their effect on plant density or spring barley yield. Conclusion. In crop rotations with a large proportion of cruciferous plants, oat may replace white mustard to capture residual N and to mulch the soil, however its sowing date should not be later than the beginning of September.
Forest-Type Classification Using Time-Weighted Dynamic Time Warping Analysis in Mountain Areas: A Case Study in Southern China

Efficient methodologies for mapping forest types in complicated mountain areas are essential for the implementation of sustainable forest management practices and monitoring. Existing solutions dedicated to forest-type mapping are primarily focused on supervised machine learning algorithms (MLAs) using remote sensing time-series images. However, MLAs are challenged by complex and problematic forest type compositions, lack of training data, loss of temporal data caused by clouds obscuration, and selection of input feature sets for mountainous areas. The time-weighted dynamic time warping (TWDTW) is a supervised classifier, an adaptation of the dynamic time warping method for time series analysis for land cover classification. This study evaluates the performance of the TWDTW method that uses a combination of Sentinel-2 and Landsat-8 time-series images when applied to complicated mountain forest-type classifications in southern China with complex topographic conditions and forest-type compositions. The classification outputs were compared to those produced by MLAs, including random forest (RF) and support vector machine (SVM). The results presented that the three forest-type maps obtained by TWDTW, RF, and SVM have high consistency in spatial distribution. TWDTW outperformed SVM and RF with mean overall accuracy and mean kappa coefficient of 93.81% and 0.93, respectively, followed by RF and SVM. Compared with MLAs, TWDTW method achieved the higher classification accuracy than RF and SVM, with even less training data. This proved the robustness and less sensitivities to training samples of the TWDTW method when applied to mountain forest-type classifications.
Effects of plant density and fertiliser rates on sugarcane (Saccharum officinarum L) growth, sucrose yield and quality in Swaziland.

Sugarcane growers are currently having difficulties producing and maintaining high sugarcane yields due to poor crop stand establishment in their plant cane and subsequent ratoons. Yields from sugarcane are dropping and farmers are reluctant to invest in sugarcane cultivation due to the increased cost of production and decrease in profits. The industry statistics as presented by Swaziland Sugar Association (SSA, 2016) showed that, despite an increase in the area planted from 2012 to 2016 of about 4000 ha, there has been a decline in cane yield from 105 to 88 tons/ha (SSA, 2016). This has consequently reduced the sugar yield per area from 12.3 to 10.5 tons cane/ha harvested (SSA, 2018). There is thus a need to increase productivity in Swaziland using various agronomic practices that reduce the cost of production and improve yields. This has necessitated that researchers come up with solutions to increase plant population so that yield decline is minimised. One of the strategies has been to increase the number of sugarcane plants per unit area. The innovation of planting three lines in a single row as opposed to the conventional single or tram line, has sparked a debate on whether there is a need to also increase the fertiliser rates (Figure 1). This research project investigated the effects of plant density and fertiliser rates on growth (i.e. canopy cover, plant diameter and height, number of leaves and plant population), sucrose yield (tons sucrose per hectare), sugarcane yield (tons cane per hectare) and quality (brix, fibre, moisture, purity, sucrose per cent) of sugarcane.
Visualization of the HIV-1 Env glycan shield across scales

Significance The HIV-1 Env “glycan shield” masks the surface of the protein from immune recognition, yet intrinsic heterogeneity defies a typical structure–function description. Using an integrated approach of cryo-EM, computational modeling, and mass spectrometry, we visualized the glycan shield structure in a new light. Our approach facilitated development of cryo-EM analysis methods and allowed for validation of models against experiment. Comparison of Env expressed in different cell lines revealed how subtle differences in composition impact glycan shield structure and affect the accessibility of epitopes on the surface, providing insights for vaccine design. Finally, time-resolved cryo-EM experiments uncovered how highly connected glycan clusters help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion. The dense array of N-linked glycans on the HIV-1 envelope glycoprotein (Env), known as the “glycan shield,” is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure–function analysis. Here, we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of interglycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same cell line used for vaccine production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner, we found that highly connected glycan clusters are resistant to digestion and help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion.
Acute viral bronchiolitis in South Africa : viral aetiology and clinical epidemiology

Bronchiolitis is a viral-induced lower respiratory tract infection that occurs predominantly in children <2 years of age, particularly infants. Many viruses have been proven or attributed to cause bronchiolitis, including and most commonly the respiratory syncytial virus (RSV) and rhinovirus. RSV is responsible for more severe disease and complications (including hospitalisation) in bronchiolitis patients. Whereas bronchiolitis is exclusively due to respiratory viral infections, with little evidence of bacterial co-infection, the former could nevertheless predispose to superimposed bacterial infections. Although data support an interaction between RSV and pneumococcal superimposed infections, it should be noted that this specifically refers to children who are hospitalised with RSV-associated pneumonia, and not to children with bronchiolitis or milder outpatient RSV-associated illness. As such, empiric antibiotic treatment against pneumococcus in children with RSV-associated pneumonia is only warranted in cases of hospitalisation and when the clinical syndrome is more in keeping with pneumonia than uncomplicated bronchiolitis. In South Africa, the peak in the RSV season varies only slightly by province, with onset in February, and lasting until June. The important implication of these new seasonality findings is that where prophylaxis is possible, as in the case of RSV, it should be commenced in January of each year.
Nurturing forest resources in the Vhavenda community, South Africa: factors influencing non-compliance behaviour of local people to state conservation rules

This comparative study analysed the compliance behaviour of local communities towards culturally protected areas and state-protected indigenous forests. Interviews were conducted with 135 households from four villages. Data analysis was done using non-parametric tests. All villages did not significantly differ in the proportion of compliance behaviour in cultural protected areas (χ2(3) = 5.21; p = 0.15) and state-protected indigenous forests (χ2(3) = 5.10; p = 0.16). The majority of local people (76%) were compliers to the cultural protected areas. In contrast, the majority (73%) were non-compliers to the state-protected indigenous forests. Villages did not significantly differ in the distribution of perceived local values (χ2 = 6.77; df = 3; p = 0.08). On average, an individual holds about four perceived local values (x̅ = 3.89, SD = 2.35) out of the seven perceived local values. The highest motive for conservation were the need to protect forest and trees of outstanding utility values (79%), watershed protection (73%), cultural values (61%), endangered species (n = 78(58%), and wildlife habitat (51%). About 50% of local people perceived the decline of state-protected indigenous forest cover. About 90% showed a willingness to take part in conservation. There was no consensus on the strength of enforcement of rules over the last 20 years (χ2(1) = 0.67; p = 0.796). The regression model (χ2 = 50.304; df = 7, p = 0.00, R 2 = 45.5%) revealed that individuals who held fewer perceived local values, perceived negative impact and weaker rules were mostly likely to be non-compliers. People’s experiential knowledge might have triggered intention for conservation, but did not influence compliance behaviour. We suggest that state-protected indigenous forests become more vulnerable to non-compliance when the necessity of resources for rural livelihood arise due to misalignment of the rules to local values, social norms and taboos. This can be addressed through inclusive policy reviews to reconcile diverse values and norms and through genuine co-management arrangement.
Performance of NPK with Vermicompost and Boron on Growth and Quality Attributes of Brinjal (Solanum melongena L.)

Brinjal (Solanum melongena L.) is also known as egg plant or aubergine. The green leaves of plant are the main source of the supply of antiascorbic acid (vitaminC). It is used in Ayurveda as appetizer, “cardiotonic” and aphrodisiac and fruit exhibits laxative property and provides relief from inflammation. It has got much potential as raw material in pickle making and dehydration industry. The white brinjal is said to be good for diabetic patients. It can also cure toothache and liver complains (Chouhan, 1981). Brinjal is also used for the treatment of bronchitis, asthma, dysentery, etc. it is also helpful for decreasing the level of blood cholesterol. Brinjal is low in energy (30 kcal/100g), protein (1.4%) and vitamin C (5mg/100g), but is a very good source of dietary fiber, potassium, calcium, manganese, copper and vitamin A and B also possess antioxidant ability (Anonymous, 2012). The International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 09 (2019) Journal homepage: http://www.ijcmas. com
Individual Variance Component of Fresh Semen Quality in Bali Cattle (Bos javanicus) Bull

Semen quality is an important factor influencing the success of a cattle breeding program, therefore an effort to continuously evaluate semen quality is needed. Indonesia has Bali cattle; it is indigenous, tropically adapted, robust, and has high fertility. Bali cattle need to be developed into meat producer by selecting best traits from bulls and disseminate their sperm through artificial insemination program. To obtain the desired improvement, semen quality became one of the keys to ensure. This study aimed to determine the factor (s) affecting fresh semen quality of Bali cattle bull. In total, 742 ejaculates were collected from nine bulls in 2016-2017 over a 12-month period. Semen was collected twice a week, followed with semen quality evaluation as semen volume (ml), sperm concentration (x106/ml), sperm motility (%), and pH. A linear model was built to obtain the significant fixed factor of season and/or age affecting sperm quality followed by mixed model procedure including individual bulls as random effect to estimate the variance components. The result showed that season didn’t give any effect (p>0.05) in all fresh semen quality observed, while there was a significant effect of age (p<0.05) on volume, sperm concentration and pH. There is no interaction (p>0.05) between season and age in this study. The variance component of individual bulls contributed 71.15, 67.92, 48.22, and 11.76% of the total variance of semen volume, sperm concentration, sperm motility, and pH respectively. This study shows that there is a wide variation of semen quality resulted due to the variation between individual of the Bali cattle bull, which mirroring the diverse of Bali cattle genetic. In bull’s selection as semen source, careful selection and the application of genetic standard need to be concerned.
Sequestered paralytic shellfish poisoning toxins mediate glaucous-winged gull predation on bivalve prey.

A•sllo, cr. --Glaucous-winged Gulls (Larus glaucescens) avoid paralytic shellfish poisoning by conditioned aversions developed after the regurgitation of contaminated bivalve prey. In feeding experiments with free-ranging Glaucous-winged Gull chicks, toxic (445 •g saxitoxin equivalents per 100 g) butter clams (Saxidomus giganteus) were regurgitated in <5 rain (n = 58), and nontoxic butter clams were never regurgitated (n = 30). Chicks that had ingested toxic S. giganteus then refused to eat either toxic or nontoxic butter clams offered later, but they accepted other bivalve prey. In feeding experiments with wild adult and juvenile L. glaucescens, gulls took significantly fewer butter clams at a site where S. giganteus has been chronically toxic for > 14 yr than they took at a nontoxic but otherwise comparable site. These preferences were species-specific and independent of prey toxicity or whether the live clams were intact or removed from their shells. The gulls showed no difference between sites in their preferences for three other bivalve species (Clinocardium nuttalli, Protothaca staminea, Tresus capax), all of which contained either no or very low levels of toxins at both sites. The aversion to intact but not to shucked butter clams was more strongly developed in adults than in juveniles. Most of the gulls that ate butter clams at the toxic site discarded the siphons (which account for the majority of the toxicity in contaminated butter clams) of both toxic and nontoxic butter clams, but they never discarded siphons of other bivalves. Gulls at the nontoxic site never discarded the siphons of bivalve prey. I suggest that avian predators generally are not at risk from paralytic shellfish poisoning toxin via bivalve vectors because they can detect and avoid toxic prey. Because of the apparent inability of gulls to discriminate between toxic and nontoxic individuals of the same prey species, avian predation pressure on some bivalve populations may be greatly reduced. Received 16 [uly 1990, accepted 8 November 1990.
Alpha-synuclein antisense oligonucleotides as a disease-modifying therapy for Parkinson’s disease

Parkinson’s disease (PD) is a prevalent neurodegenerative disease with no approved disease-modifying therapies. Multiplications, mutations, and single nucleotide polymorphisms in the SNCA gene, encoding alpha-synuclein protein (aSyn), either cause or increase risk for PD. Intracellular accumulations of aSyn are pathological hallmarks of PD. Taken together, reduction of aSyn production may provide a disease-modifying therapy for PD. We show that antisense oligonucleotides (ASOs) reduce production of aSyn in rodent pre-formed fibril (PFF) models of PD. Reduced aSyn production leads to prevention and removal of established aSyn pathology and prevents dopaminergic cell dysfunction. In addition, we address the translational potential of the approach through characterization of human SNCA targeting ASOs that efficiently suppress the human SNCA transcript in vivo. We demonstrate broad activity and distribution of the human SNCA ASOs throughout the non-human primate brain and a corresponding decrease in aSyn cerebral spinal fluid (CSF) levels. Taken together, these data suggest that by inhibiting production of aSyn it may be possible to reverse established pathology and thus supports the development of SNCA ASOs as a potentially disease modifying therapy for PD and related synucleinopathies. Summary Antisense oligonucleotides designed against SNCA, which are progressing to the clinic, have the potential to be a disease modifying therapeutic for Parkinson’s disease patients.
Neurocomputational mechanisms underlying immoral decisions benefiting self or others

Immoral behavior often consists of weighing transgression of a moral norm against maximizing personal profits. One important question is to understand why immoral behaviors vary based on who receives specific benefits and what are the neurocomputational mechanisms underlying such moral flexibility. Here, we used model-based fMRI to investigate how immoral behaviors change when benefiting oneself or someone else. Participants were presented with offers requiring a tradeoff between a moral cost (i.e., profiting a morally bad cause) and a benefit for either oneself or a charity. Participants were more willing to obtain ill-gotten profits for themselves than for a charity, driven by a devaluation of the moral cost when deciding for their own interests. The subjective value of an immoral offer, computed as a linear summation of the weighed monetary gain and moral cost, recruited the ventromedial prefrontal cortex regardless of beneficiaries. Moreover, paralleling the behavioral findings, this region enhanced its functional coupling with mentalizing-related regions while deciding whether to gain morally-tainted profits for oneself vs. charity. Finally, individual differences in moral preference differentially modulated choice-specific signals in the dorsolateral prefrontal cortex according to who benefited from the decisions. These findings provide insights for understanding the neurobiological basis of moral flexibility.
Recapitulating idiopathic pulmonary fibrosis related alveolar epithelial dysfunction in an iPSC-derived air-liquid interface model

An abnormal emergence of airway epithelial-like cells within the alveolar compartments of the lung, herein termed bronchiolization, is a process often observed in patients suffering from idiopathic pulmonary fibrosis (IPF), a fatal disease characterized by progressive fibrotic lung remodeling. However, the origin of this dysfunctional epithelium remains unknown. In this study, we aimed to investigate the effects of a pro-fibrotic milieu, similar to that found in an IPF lung, on human alveolar epithelial progenitor cell differentiation. We developed an induced pluripotent stem cell (iPSC)-derived air-liquid interface (ALI) model of alveolar type II (ATII)-like cell differentiation and stimulated it with an IPF-relevant cocktail (IPF-RC), composed of cytokines previously reported to be elevated in IPF lungs. iPSC-derived cultures express ATII markers and contain lamellar body-like structures. Stimulation with IPF-RC during the last two weeks of differentiation increases secretion of IPF biomarkers. Transcriptome analysis of IPF-RC treated cultures reveals significant overlap with human IPF data and enrichment of transcripts associated with extracellular matrix organization. IPF-RC stimulation further impairs ATII differentiation by driving a shift towards an airway epithelial-like expression signature. In conclusion, we show for the first time, the establishment of a human model system that recapitulates aspects of IPF-associated bronchiolization in vitro. Our findings reveal how aberrant alveolar epithelial progenitor cell differentiation in a pro-fibrotic environment could contribute to alveolar bronchiolization in the distal IPF lung. SOURCE OF SUPPORT The research was funded by Boehringer Ingelheim Pharma GmbH & Co. KG.