Miracle-dz/UniFAR-FTUs huggingface dataset:
Comment on “A genetic signature of the evolution of loss of flight in the Galapagos cormorant”

Burga et al. could not identify gene regulatory regions which might contribute to flightlessness in the Galapagos cormorant. Using a bird-specific alignment we discover 48 limb enhancers showing strong accelerated evolution in P. harrisi, including enhancers of key cilia development, hedgehog signaling, and planar cell polarity genes, such as Prickle1, Twist2 and Ndk1, extending Burga's proposed mechanism into the non-coding genome.
Fermentation of Azolla sp. leaves and the utilization as a feed ingredient of tilapia Oreochromis sp.

ABSTRACT The objective of this study was to study the effect of incubation period on the nutritional content of Azolla sp. meal fermented by Trichoderma harzianum, and its optimum supplementation level in the feed of tilapia Oreochromis sp. In incubation period treatments, fermentation of Azolla meal was performed in two, six, eight, and ten days (AF2, AF6, AF8, AF10) using Trichoderma harzianum as the fermentor. The fish used in this study was tilapia Oreochromis sp. with an average weight of 10.59±1.29 g. The design of the feeding treatments was repeletting commercial feed with Azolla leaves by with different supplementation levels, i.e. 0% (A/control), 30% (B), 60% (C), and 90% (D). Faecal collection for digestibility measurement was conducted for 15 days and fish growth rate was observed for 40 days. Azolla meal fermented for two days (AF2) showed the best results among the other treatments with a crude fiber decrease of 37.19% and protein increase of 38.65%. The results of this study indicate that fermentation can increase the nutritional quality of Azolla meal and its most optimal supplementation level in the diet of tilapia is 30%. Keywords: crude fiber, Azolla sp. , tilapia ABSTRAK Penelitian ini bertujuan untuk mengetahui pengaruh lama waktu fermentasi daun mata lele Azolla sp. menggunakan kapang Trichoderma harzianum serta dosis optimal dalam pakan ikan nila Oreochromis sp. Proses fermentasi tepung daun mata lele dilakukan selama dua, enam, delapan, dan sepuluh hari (AF2, AF6, AF8, AF10). Ikan uji pada penelitian ini menggunakan ikan nila Oreochromis sp. dengan bobot rata-rata 10,59±1,29 g yang ditebar sebanyak 6 ekor/akuarium berukuran 50×45×30 cm3. Sebagai pakan perlakuan yakni repeletting daun mata lele dengan pakan komersil pada tingkat suplementasi 0% (A/kontrol), 30% (B), 60% (C), dan 90% (D). Pemeliharaan ikan uji dan pengumpulan data dilakukan dengan mengumpulkan feses ikan untuk uji ketercernaan selama 15 hari dan mengamati pertumbuhan ikan selama 40 hari. Tepung daun mata lele yang difermentasi selama dua hari (AF2) memiliki hasil yang paling baik di antara perlakuan lainnya yakni dengan penurunan serat kasar sebesar 37,19% dan peningkatan protein sebesar 38,65%. Hasil penelitian ini menunjukkan bahwa fermentasi dapat meningkatkan kualitas nutrisi daun mata lele serta dosis optimal pemanfaatan tepung daun mata lele fermentasi dalam pakan ikan nila adalah sebesar 30%. Kata kunci: serat kasar, Azolla sp. , ikan nila
Reactivation of neural patterns during memory reinstatement supports encoding specificity

Encoding specificity or transfer appropriate processing state that memory benefits when items are encoded and retrieved in the same modality compared to when encoding and retrieval is conducted in different modalities. In neural terms, these effects can be expressed by a resonance process between a memory cue and a stored engram; the more the two overlap the better memory performance. We here used temporal pattern analysis in MEG to tap into this resonance process. We predicted that reactivation of sensory patterns established during encoding has opposing effects depending on whether there is a match or mismatch between the memory cue and the encoding modality. To test this prediction items were presented either visually or aurally during encoding and in a recognition test to create match (e.g. “dog” presented aurally during encoding and recognition) and mismatch conditions (e.g. “dog” presented aurally during encoding and shown visually during recognition). Memory performance was better for items in the match compared to the mismatch condition. MEG results showed that memory benefitted from neural pattern reinstatement only in the match condition, but suffered from reinstatement in the mismatch condition. These behavioural and neural effects were asymmetric in that they were only obtained for aurally encoded words but not for visually encoded words. A simple computational model was generated in order to simulate these opposing effects of neural pattern reactivation on memory performance. We argue that these results suggest that reactivation of neural patterns established during encoding underlies encoding specificity or transfer appropriate processing.
BRIGHT ASTEROIDS IN THE RED SEA - AN EMERGING PATHOGEN CANDIDA HAEMOLUNII: ARE AZOLES THE TREATMENT OPTION?

This is a case study of a 15-year-old female who on chemotherapy and central line catheter-related bloodstream candidemia presented with recurrent episodes of candidemia, was febrile and breathless. She was diagnosed of Candida haemulonii fungemia. Echinocandins was started as this species of Candida is usually resistant to the commonly used antifungal agents. On treatment, the patient was afebrile and discharged. Keywords : Candida haemulonii, Candidemia, Case report, Emerging pathogen
Response of soybean genotypes against armyworm, Spodoptera litura based on no-choice test

Armyworm is important polyphagous pest causing economic losses in many agricultural crops including soybean. In Indonesia, there are no soybean varieties which indicated had a resistance against armyworm. The experiment was conducted in Laboratory of Entomology and Green House of Indonesian Legumes and Tuber Crops Research Institute from March to April 2016. The experiment was arranged using randomized block design with a total of 18 soybean genotypes as a treatment in three replicates. The results showed that the difference of soybean genotypes had a significant effect on the leaf damaged intensity. Based on no-choice test and the leaves damaged intensity compared with resistant check genotypes, there was no genotype indicated resistant against S. litura. Most of the tested genotype showed moderately resistant and others showed susceptible to highly susceptible. Genotypes that indicated as moderately resistant are G 511 H/Anjs-1-1, G 511 H/Arg//Arg///Arg-30-7, G 511 H/Kaba//Kaba///-4-4, G 511 H/Kaba//Kaba///Kaba////Kaba-16-2, G 511 H/Anjs/Anjs///Anjs-3-3, G 511 H/Anjs/Anjs-1-2, G 511 H/Anjs/Anjs-5-5, G 511 H/Anjs/Anjs///Anjs-6-11, and Argomulyo. In conclusion, those nine genotypes indicated have antixenosis resistance against armyworm and can be considered as a source of gene for improving the soybean resistance to armyworm.
Health risk assessment of heavy metals content in cocoa and chocolate products sold in Saudi Arabia

Abstract The study was carried out to assess the level of 10 heavy metals in 27 representative samples of cocoa and chocolate products sold in Saudi Arabia markets using Inductively Coupled Plasma-Mass Spectrometer (ICP-MS). The mean levels of heavy metals were in the range of 0.033–0.123; 0.001–0.080; 0.010–0.046; 0.013–0.070; 0.61–9.74; 0.27–3.17; 0.02–0.67; 1.11–14.22; 0.18–0.66; and 11.38–72.12 µg/g for Pb, Cd, As, Hg, Cu, Ni, Co, Mn, Cr, and Al, respectively. These values were used to determine the estimated daily intake (EDI), target hazard quotient (THQ), hazard index (HI), and target cancer risk (TCR) associated with dietary exposure to these potentially toxic elements. The EDI values did account for 0.027–0.077; 0.002–0.032; 0.014–0.023; 0.013–0.069; 0.85–5.92; 0.27–1.85; 0.018–0.069; 1.37–8.68; 0.164–0.290; and 10.80–40.75 µg/kg/d for Pb, Cd, As, Hg, Cu, Ni, Co, Mn, Cr, and Al, respectively. They were below the tolerable intake limits in all foodstuffs analyzed, except in cocoa product where Al exceeded the permissible limit. The THQ and HI values were also lower than the safe standard 1 for all foodstuffs analyzed, except for cocoa products where the HI value was 1.909. This high value of HI indicates that consumption of more amounts of cocoa products frequently may result in adverse non-carcinogenic health effect in consumers in future. The THQ of cobalt in cocoa products was 0.806 which enhanced the GTHQ to be 1.196 and thus cobalt contributing 34.08% to the HI explaining that the risk was mainly contributed by cobalt. The TCR values did not exceed the limit, except for Ni in cocoa products which exceed the limit for acceptable risk of developing cancer indicating some concern.
Genotype × management strategies to stabilise the flowering time of wheat in the south-eastern Australian wheatbelt

Abstract. Growers in the wheatbelt of south-eastern Australia need increases in water-limited potential yield (PYw) in order to remain competitive in a changing climate and with declining terms of trade. In drought-prone regions, flowering time is a critical determinant of yield for wheat (Triticum aestivum L.). Flowering time is a function of the interaction between management (M, establishment date), genotype (G, development rate) and prevailing seasonal conditions. Faced with increasing farm size and declining autumn rainfall, growers are now sowing current fast-developing spring wheat cultivars too early. In order to widen the sowing window and ensure optimum flowering dates for maximum yield, new G × M strategies need to be identified and implemented. This study examined the effect of manipulating genotype (winter vs spring wheat and long vs short coleoptile) and management (sowing date, fallow length and sowing depth) interventions on yield and flowering date in high-, medium- and low-rainfall zones in south-eastern Australia. Twelve strategies were simulated at nine sites over the period 1990–2016. At all sites, the highest yielding strategies involved winter wheats with long coleoptiles established on stored subsoil moisture from the previous rotation, and achieved a mean yield increase of 1200 kg/ha or 42% relative to the baseline strategy. The results show promise for winter wheats with long coleoptiles to widen the sowing window, remove the reliance on autumn rainfall for early establishment and thus stabilise flowering and maximise yield. This study predicts that G × M strategies that stabilise flowering may increase PYw.
Meningkatkan Kemampuan Berbahasa Anak Usia Dini Melalui Model Pembelajaran Audio Visual Berbasis Android

Language skills are the abilities, skills, wealth greeting human thoughts and feelings through sound arbitrator, used to work together, interact, and identify themselves in a good conversation. In this study a problem Is the Audio Visual Learning Model-Based Android can improve Proficiency in Early Childhood Group A. The purpose of this study was to determine the improvement of language skills of early childhood through audio visual media in group A . The design of this research is a Class Action Research with research subjects are 12 children in PAUD Nawakartika Beran village District of Ngawi in the academic year 2016/2017. Technique of collecting Data are used such as observation, documentation and questionnaires. Classroom action research on learners' class A, it can be concluded that the audio visual media can improve language skills, it is shown that indicator of increased mastery learning students is increasing from the first cycle (50%) and cycles II (83.3%). Improved performance indicators can be shown by the child is able to interact with their peers using the newly acquired language, liveliness children in participating in learning activities increased significantly, the atmosphere of teaching and learning activities are very conducive. Teacher is advised be able to develop audio-visual media more varied and fun for children.
Enzymatic hydrolysis of cobia (Rachycentron canadum) meat and wastes using different microbial enzymes.

Some proteins, beyond to their technological, functional and nutritional properties, exhibit biological activity, being one of them, the antioxidant activity, associated to bioactive peptides released after hydrolysis. The industrial processing wastes of fishes are a great source of proteins, and the cobia (Rachycentron canadum), that it is a large and easily adaptable to aquaculture emerges as an option to obtain peptides. Thus, the aim of this study was to obtain peptides by hydrolyzing meat and wastes of cobia with different enzymes. Six hydrolysates through the hydrolysis of the meat and wastes with Alcalase, Flavourzyme and Protamex were obtained, wherein the last one presented greater hydrolytic capacity for the substrates, reaching a DH of 27.94% in 760 min for meat and 33.14% in 580 min for wastes. The free tyrosine content varied depending on the substrate and the enzyme, and the highest values for the hydrolysate wastes by Alcalase (8.46%) and by Protamex (6.46%) and hydrolysate meat by Protamex (6.47%). Therefore, these results indicate the potential utilization of the hydrolysates from cobia meat and wastes in food formulations.
Effect of Phosphorus, Biofertilizers and Organic Manures on Root Nodulation and Productivity of Green Gram (Vigna radiata L.)

India is the largest producer of pulses in the world. Green gram is one of the most ancient and extensively grown leguminous crops of India. Green gram is an excellent source of high quality of protein. It also contains high quality of lysine (4600 mg/g N) and tryptophan (60 mg/g N) and consumed as whole grain or as well as in the form of dal for table purpose. Green gram is supposed to be easily digestible, hence preferred by patients. The sprouted seeds of green gram are rich in ascorbic acid (vitamin C), riboflavin and Thiamine (Dhakal et al., 2016). In India, green gram represents 18% (34.4 lakh hectares) of total pulse area and 11.48 % (514 lakh tonnes) of pulse production (CMIE, 2014-15). Despite occupying a greater position both in respect of area and production, the productivity of green gram is low compared to world average. One reason for this could be the imbalanced nutrient management.
Response of soil fungal diversity to nitrogen deposition in a Deyeuxia augustifolia wetland of Sanjiang Plain, Northeast, China

In order to understand the effects of nitrogen deposition on soil fungal diversity, a study was conducted with a Deyeuxia augustifolia wetland in the Sanjiang Plain, China, using an experimental setup simulating nitrogen deposition at different loads over a five-year period. Three conditions were investigated: N1 (no artificial deposits, control), N2 with low-level nitrogen deposition (4 g N·hm a) and N3 with high-level nitrogen deposition (8 g N·hm a). At the end of the experiment the soil physiochemical characteristics were determined and high-throughput sequencing was employed to monitor the soil fungal diversity. The addition of exogenous nitrogen to the soils changed the physicochemical properties of the soils and affected the fungal community composition and the relative abundance of species: low doses increased the diversity while high doses reduced the fungal diversity. In each of the three types of nitrogen-amended soils, the most predominant phyla were Ascomycota followed by Basidiomycota. The abundance of Basidiomycota decreased with nitrogen deposition, while Ascomycota changed in the opposite direction. A heatmap tree based on ITS rDNA sequences illustrated how different fungal communities responded differently to nitrogen deposition. The findings in the present study provide fundamental data and theoretical insights that can be employed to predict the effects of atmospheric nitrogen deposition on wetland soil fungi and wetland ecosystems in Sanjiang Plain. © 2017 Friends Science Publishers
Bio availability of iron from finger millet, pearl millet and rice (control) recipes

recipes’’ was conducted on four millet preparations namely dosa, idli, roti and rice (meal), using two millets namely finger millet, pearl millet. The iron content of millets was 3.65, 7.0mgin finger millet, pearl millet, respectively. Compared to rice all millets had high amount of protein, fat, ash and iron content, while the carbohydrate was low in millets compared to rice. Wheat had similar protein, fat and carbohydrates close to many types of millet.The total iron was good in all preparations.Finger millet idli had 4.57mg and meal had 4.58mg total iron without any significant difference between the two products.The dosa had a total iron of 5.04mg and roti had 5.55mg both of which differed significantly compared to each other and with other preparations (p<0.05). Per cent available iron was highest in finger millet dosa at 37.3% against 4.1% in idli, 12.3% in roti and 2.7% in meal with significant difference between each other (p<0.05). Per cent available iron was highest in pearl millet dosa at 62.4%against in 33.5% in idly, 44.0% in roti and 44.0% in meal. Total iron content was 7.9mg in rice dosa, which was highest, followed by 4.8mg in roti, 3.8mg in meal and 1.8mg in idli, with significant difference between preparations (p<0.05). Per cent available iron was least in roti at 5.2% against meal at 8.2%, idli at 6.59% and dosa at 25.6% with significant difference between each other. Percent available iron was least in roti at 5.2% against meal at 8.2%, idli at 6.59% and dosa at 25.6% with significant difference between each other. The in vitro availability of iron was high in dosa, probably due to fermentation and shallow fry on iron tawa, seems to low steamed cooking method of pearl millet idly compared to dry heat or roasted millet preparations.
Regeneration status of tree composition in the sacred groves of Mercara,Central Western Ghats

Sacred groves are pristine forest patches that are left untouched for centuries in the name of local deities, beliefs and taboos. They play an important role in conservation of biodiversity as they are abode of many endemic and threatened species. Tree species diversity, structure and their regeneration status was investigated in the eight sacred groves of Mercara, Central Western Ghats. A total of 170 tree species belonging to 110 genera and 49 families were recorded from them. Higher species richness was observed in the sacred groves which were bigger in size and moderately disturbed. Though, a good number of tree density, seedling and sapling density and basal area were observed in all the eight sacred groves, an inversely proportional relation was observed between degree of disturbances and tree density, seedling density, sapling density and basal area. Lesser similarity between adult and regenerating tree species and greater number of species with no regeneration status and reappearing status indicated a possible change in the tree species composition of these sacred groves in the near future. Hence it becomes crucial that efforts should be taken in a sustainable manner to protect these pristine forest patches for future generations.
Changes in excitability and ion channel expression in neurons of the major pelvic ganglion in female type II diabetic mice

Bladder cystopathy is a common urological complication of diabetes, and has been associated with changes in parasympathetic ganglionic transmission and some measures of neuronal excitability in male mice. To determine whether type II diabetes also impacts excitability of parasympathetic ganglionic neurons in females, we investigated neuronal excitability and firing properties, as well as underlying ion channel expression, in major pelvic ganglion (MPG) neurons in control, 10-week, and 21-week db/db mice. Type II diabetes in Leprdb/db animals caused a non-linear change in excitability and firing properties of MPG neurons. At 10 weeks, cells exhibited increased excitability as demonstrated by an increased likelihood of firing multiple spikes upon depolarization, decreased rebound spike latency, and overall narrower action potential half-widths as a result of increased depolarization and repolarization slopes. Conversely, at 21 weeks MPG neurons of db/db mice reversed these changes, with spiking patterns and action-potential properties largely returning to control levels. These changes are associated with numerous time-specific changes in calcium, sodium, and potassium channel subunit mRNA levels. However, Principal Components Analysis of channel expression patterns revealed that the rectification of excitability is not simply a return to control levels, but rather a distinct ion channel expression profile in 21-week db/db neurons. These data indicate that type II diabetes can impact the excitability of post-ganglionic, parasympathetic bladder-innervating neurons of female mice, and suggest that the non-linear progression of these properties with diabetes may be the result of compensatory changes in channel expression that act to rectify disrupted firing patterns of db/db MPG neurons.
Wild Bee Community Assemblages Across Agricultural Landscapes1

ABSTRACT Wild bees are essential to the functioning of both agricultural and natural ecosystems, yet these pollinator communities are declining worldwide. Agricultural intensification by means of habitat and floral resource loss is thought to be one of the leading causes of wild bee population deterioration. This study examined multiple agricultural land use systems in New Hampshire to determine how wild bee biodiversity and community interactions are affected by different land use practices. A total of 2292 wild bees were collected during these surveys, representing 112 species. A high species overlap was found at all land use systems, although all sites had some species exclusivity. Land use significantly affected species abundance and richness. The moderately managed sites supported both the greatest pollinator abundance and species richness, while the low management sites had the smallest abundance and the same level of richness as the high management sites. The findings of this study support the importance of floral landscape diversity in bee conservation efforts and suggest that not all agricultural practices negatively affect the pollinator community.
Excitable dynamics of Ras triggers self-organized PIP3 signaling for spontaneous cell migration

Spontaneous cell movement is underpinned by an asymmetric distribution of signaling molecules including small G proteins and phosphoinositides on the cell membrane. A fundamental question is the molecular mechanism for the spontaneous symmetry breaking. Here we report that GTP bound Ras (Ras-GTP) breaks the symmetry due to excitability even in the absence of extracellular spatial cues and cytoskeletal polarity as well as downstream signaling activities. A stochastic excitation of local and transient Ras activation induced PIP3 accumulation via direct interaction with PI3K, causing tightly coupled traveling waves propagating along the membrane. Comprehensive phase analysis of the waves of Ras-GTP and PIP3 metabolism-related molecules revealed the network structure of the excitable system including positive feedback regulation of Ras-GTP by PIP3. A mathematical model reconstituted a series of the observed symmetry breaking phenomena, illustrating an essential involvement of excitability in the cellular decision-making process. Author contributions S.F. conducted the experiments; all authors analyzed the data and wrote the manuscript. Abbreviations GAP Guanosine Triphosphate hydrolase activating protein GEF Guanine nucleotide exchange factor GFP Green fluorescent protein PHD Pleckstrin homology domain PI3K Phosphoinositide 3-kinase PIP2 Phosphatidylinositol (4,5)-bisphosphate PIP3 Phosphatidylinositol (3,4,5)-trisphosphate PKB&Akt Protein kinase B PLCδ1 Phospholipase C delta 1 PTEN Phosphatase and tensin homolog RBD Ras binding domain RFP Red fluorescent protein