Miracle-dz/UniFAR-FTUs huggingface dataset:
Vocalizations of the sperm whale (Physeter macrocephalus) off the Galapagos Islands as related to behavioral and circumstantial variables.

The purpose of this study was to gain insight into the significance of sperm whale (Physeter macrocephalus) sounds by examining their relationship to behavioral and circumstantial variables. Whales were tracked continuously for periods totalling months, off the Galapagos Islands, Ecuador, and sperm whale vocalizations were recorded systematically. In addition to the usual clicks (long series with interclick intervals of about 0.5 s), creaks (clicks at high repetition rates), and codas (short, repetitive click patterns) previously reported in the literature, a new vocalization type was discovered--"slow clicks. " These were found to be produced by mature males and were distinctively different from the females' usual clicks. There was a strong correlation between behavior visible at the surface and rates at which different types of vocalizations were heard. Codas were given in social situations of large "clusters" (whales swimming together within 100 m of another), whereas usual clicks were associated with feeding behavior, when whales were diving deeply and dispersed in smaller clusters. Codas were relatively rare, and could be categorized into 23 discrete, almost non-overlapping types according to number of clicks and proportional lengths of interclick intervals. Codas overlapped or followed one another according to type in a non-random way, and coda type "5" tended to initiate coda exchanges. The rate of production of different coda types varied with behavioral and circumstantial variables such as identified group, month, maximum cluster size, presence of male, but the specific details of these relationships were not clear. It is hypothesized that usual clicks function as echolocation, slow clicks as a sign of male maturity and competitive ability, creaks as echolocation and communication, and codas as a means of social communication which serves to maintain social cohesion within stable groups of females following periods of dispersion during foraging.
Phytochemical Screening and Antioxidant Activity of Leaves and Stem Bark Extracts of Garcinia Imberti - An Endangered Plant

Garcinia imberti Bourd. a critically endangered tree belongs to the family Clusiaceae found only in India. The phytochemicals and antioxidant studies were carried out for the methanolic extracts of Garcinia imberti leaves and stem bark using DPPH and ABTS radical scavenging assay. Preliminary phytochemical screening of methanolic extracts of Garcinia imberti revealed the presence of various bioactive components like alkaloids, flavanoids, steroids, glycosides, phenols, saponins, terpenoids, resins, carbohydrates and tannins in both leaves and stem bark. The quantitative analysis of phytochemicals of the extracts showed the presence of high amount of tannins (0.92 ± 0.23mg/gm) and alkaloids (0.83 ± 0.48mg/gm) in leaf and high concentration of flavanoids (0.65±0.16mg/gm) and tannins (0.78±1.12mg/gm) in bark extract. The result of the present study concluded that the methanolic extracts of Garcinia imberti leaves and stem bark possess significant antioxidant activity due to the presence of significant amount of phenolic compounds which are the major contributors of antioxidant activity. The finding of this study suggests that the studied plant is a potential source of natural antioxidant that could have great importance as therapeutic agents in preventing or slowing the progress of oxidative stress related degenerative diseases.
Effect of the filling season on aquatic plants in Mediterranean temporary ponds

Aims Pond environmental conditions may differ among years with regards to the season in which ponds begin to fill. We experimentally evaluated how seedling emergence, plant growth and phenology differed among years in which filling occurred in winter, autumn or spring. Methods We collected sediments from a natural temporary pond and located them in aquariums. They were placed in a climatic chamber that simulated annual variation in field environmental temperatures and light conditions. Aquariums were assigned to one of three treatments, which differed in the date on which they were filled with water (autumn, winter and spring). We counted the number of seedlings of different species emerged and recorded data about the presence of flowers, seeds or spores every week. The experiment was finished in June, when we harvested the plants and estimated their biomass. Important Findings In most species, seedling emergences were primarily related to time after filling, and thus synchronized their life cycles with the unpredictably timed wet phase of the ponds. Autumn filling resulted in the highest numbers of seeds/spores. However, winter filling promoted plant growth the most. In the spring filling treatment, more terrestrial plant seedlings emerged and fewer seeds/spores were produced. When ponds are flooded earlier, plants may produce a higher number of propagules. However, in years when inundation is delayed to spring and hydroperiods are short, seedling emergence deplete the seed bank and there is little to no seed production, while terrestrial monocots are able to colonize pond basin.
Statistical optimization of fermentation conditions for the improved production of poly-β-hydroxybutyrate from Bacillus subtilis

ABSTRACT Poly-β-hydroxybutyrate (PHB) has been an effective biodegradable plastic obtained by microbial fermentation. Batch fermentation of Bacillus subtilis features an attractive system for the production of PHB. Identification of appropriate media components and cultivation conditions are extremely important for the optimal production of biomass and/or PHB production. Statistical media design was utilized for the optimization of different fermentation variables (glucose, peptone, sodium chloride, K2HPO4, KH2PO4, ammonium sulfate, ammonium chloride, sodium sulfate, temperature, inoculum size, and pH). The optimized media predicted the optimal dry cell weight of 7.54 g L−1 and PHB production of 77.2 mg L−1 at 1 g L−1 of peptone, 1.46 g L−1 sodium sulfate, and pH 6.8 in 24 h. Glucose utilization, batch growth, and PHB production kinetics of B. subtilis were determined experimentally. The effect of substrate inhibition on specific growth rate was also determined experimentally for B. subtilis. The values of kinetic and substrate inhibition parameters obtained from this study shall be utilized to develop a mathematical model for PHB production for further improving the production of PHB.
Global effects of focal brain tumours on functional complexity and network robustness

Background Neurosurgical management of brain tumours has entered a new paradigm of supra-marginal resections that demands thorough understanding of their peri-tumoural functional effects. Historically the effects of tumours have been considered as local, and long-range effects have not been considered. This work tests the hypothesis that focal tumours affect the brain at a global level producing long-range gradients in cortical function. Methods Resting state functional (f)MRI data were acquired from 11 participants with glioblastoma and split into discovery and validation datasets. Fractal complexity was computed with a wavelet-based estimator of the Hurst exponent. Distance related effects of the tumours were tested with a tumour mask dilation technique and parcellation of the underlying Hurst maps. Functional connectivity networks were constructed and validated with different parcellation and statistical dependency methods prior to graph theory analysis. Results Fractal complexity, measured through the Hurst exponent and tumour mask dilation technique, demonstrates a penumbra of suppression in the peri-tumoural region. At a global level, as distance from the tumour increases, this initial suppression is balanced by a subsequent over-activity before finally normalizing. These effects were best fit by a quadratic model, and were consistent across different network construction pipelines. The Hurst exponent was significantly correlated with multiple graph theory measures of centrality including network robustness, but graph theory measures did not demonstrate distance dependent effects. Conclusions This work provides evidence to support the theory that focal brain tumours produce long-range and non-linear gradients in function. Consequently the effects of focal lesions, and the resultant clinical effects, need to be interpreted in terms of the global changes on whole brain functional complexity and network architecture rather than purely in terms of functional localisation. Determining whether the peri-tumoural changes represent adaption or potential plasticity, for example, may facilitate extended resection of the tumour without functional cost.
ARMS-PCR Based SNP Analysis of MTHFR C677T Allele Using Syber Green in Pancreatic Tumour

In human, carcinoma of pancreas, a rare disease and mortality rate is quite high in Indian population. Epidemiological studies support the hypothesis that folate metabolism regulate DNA stability and prevent cancer. Because folate have been linked to dietary supplement and defect in folate metabolism have been increase risk of developing cancer shows adverse effect on health conditions. In the present study we have assess methylene tetrahydrofolate reductase gene polymorphism (MTHFR) 677 C T using ARMS PCR based SNP analysis using Syber green in the cases of pancreatic tumour to determine the “risk factor”. Interestingly, our findings reveals that 33.0% frequency (one case) showing mutation of MTHFR 677 TT genotype (rare type) in homozygous condition with Tm value 82.50°C for mutant 677T allele shifted to 67 7C allele (83.50°C). Two cases (66%) showing CC (wild type) all ele and Tm value 82.83°C for 677C allele. In MTHFR 677TT is a rare mutation and individuals show very low enzymatic activity due to the substitution of alanine to valine. The study further continue to confirm the mutation by Short Communication Saxena et al.; BJMMR, 11(12): 1-6, 2016; Article no.BJMMR. 20599 2 visualization on agarose gel electrophoresis of the same PCR product, again showing (Lane2) the band of 50 kb of mutant 677TT allele in the same case, suggesting an relevant role of folate metabolism and subsequent impairment of aberrant DNA methylation during carcinogenesis with increasing “high risk” for the development of carcinoma due to allele TT mutation of MTHFR. However, large samples size is required to further confirm the association.
Complete mitochondrial genome of the Andean morphotype of Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae)

Abstract The South America fruit fly Anastrepha fraterculus s.l. is an important pest of fruits in Latin America and it is really a complex with at least eight cryptic species. In this work, we report the complete mitochondrial genome for the Andean morphotype of A. fraterculus. The mitochondrial genome is 16,739 nucleotides in size; includes 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis was performed using all the protein-coding genes with other 19 species from Tephritidae.
Molecular Mechanisms Involved in Insulin- and Leptin-mediated Regulation of Hypothalamic Proglucagon Gene Expression and Action of Glucagon-like Peptides on Hypothalamic Neuropeptides

The hypothalamus is a central regulator of energy homeostasis. Recently, proglucagonderived peptides have emerged as potential appetite regulators. The proglucagon gene is expressed in the periphery and also in selective hypothalamic neurons. The regulation of hypothalamic proglucagon by two key regulators of energy balance, insulin and leptin, remains unstudied. Central glucagon-like peptide (GLP)-1 receptor (GLP-1R) activation by exendin-4, a long-acting GLP-1R agonist, induces anorexia; however, the specific hypothalamic neuronal populations activated by exendin-4 remain largely unknown. The role of GLP-2 as a central appetite regulator is poorly understood. In this thesis, using murine hypothalamic cell lines and mice as experimental models, mechanisms involved in the direct regulation of proglucagon gene by insulin and leptin were studied, and the actions of exendin-4 and GLP-2 on hypothalamic neuropeptides were determined. It was found that insulin and leptin regulate hypothalamic proglucagon mRNA by activating Akt and signal transducer and activator of transcription 3, respectively. Insulin and leptin did not regulate human proglucagon promoter regions, but affected proglucagon mRNA stability. In mice, intracerebroventricular exendin-4 and GLP-2 induced anorexia, activated proopiomelanocortinand neuropeptide Y-expressing neurons in the arcuate nucleus and
Nifuratel-nysfungin soft capsule suppository and preparation method thereof

The invention discloses a nifuratel-nysfungin soft capsule suppository. The nifuratel-nysfungin soft capsule suppository comprises 500mg of nifuratel, 200000IU of nysfungin, 8mg of promestriene, 25mg of carbomer, 700mg of glycerinum, 6mg of ethylparaben, 294mg of triethanolamine, 800mg of ethyl alcohol and 7.5g of water. The invention also discloses a preparation method of the nifuratel-nysfungin soft capsule suppository. The nifuratel-nysfungin soft capsule suppository can kill bacteria, mould and trichomonad, effectively protect lactobacillus and promote vaginal flora to restore balance, thus realizing the purpose of 'ecological treatment'; and the soft capsule suppository has both the dosage form characteristic of soft capsule (good stability of capsule core, capsule skin and drug) and local drug delivery characteristic of suppository.
Influence of Herpes Simplex Virus Latency-Associated Transcript (LAT) on the Distribution of Latently Infected Neurons

Abstract : Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are similar viruses with several notable differences. While both viruses establish latency in sensory ganglia and reactivate to cause recurrent disease, HSV-1 reactivates more efficiently from trigeminal ganglia to cause cold sores or keratitis and HSV-2 reactivates more efficiently from lumbosacral dorsal root ganglia (DRG) to cause genital herpes. Both viruses are capable of causing central nervous system (CNS) disease, but HSV-1 CNS infections typically manifest as severe necrotizing encephalitis while HSV-2 is more commonly associated with relatively benign meningitis. Potential mechanisms for type-specific differences between HSV-1 and HSV-2 have not been closely examined, although the latency associated transcript (LAT) of HSV plays a critical role in the establishment of latency and site-specific reactivation and may have regulatory influence over viral replication and spread
PROSPECTIVE USE OF BACTERIOPHAGES AS AGENTS TO COMBAT PHYTOPATHOGENIC BACTERIA OF POTATOES

Plant diseases caused by bacteria are a serious problem in the cultivation and storage of agricultural products. During the last years bacteriophages have attracted increased research interest as a realistic environmentally friendly means for controlling bacterial diseases. The main objective of the study was to characterize the bacteriophages that could be used in the search for and developing the antimicrobial agents based on bacterial viruses. Four isolates of bacteriophages specific to bacteria from Pseudomonas genus were isolated from potato samples with typical symptoms of bacterial disease. These phage isolates differed in terms of the morphology of their negative colonies. Slight variation in the morphology of studied phages was observed using electron microscopy. A group of phages was identified as Podoviridae family of Caudovirales order (icosahedral head without long tail, small size – head diameter 43 ± 1 nm, tail length 1 ± 0,5 nm). To identify host range/specificity of isolated phages, we analyzed the spectrum of lytic activity against 15 strains of phytopathogenic bacteria. Our research revealed that among four phage samples three expressed lytic activity against different strains of phytopathogenic bacteria. The aforementioned data enable us to conclude that these three isolates with broad spectrum of lytic activity can be used as perspective biologic agents in control of bacteriosis. Thereby phages from our collection could be of therapeutic interest, they have the potential to be used in future prospects for phage therapy research.
An ontogenetically stable sexual character in a montane agamid, Salea horsfieldii Gray, 1845 (Reptilia: Agamidae) from Nilgiris, India

ABSTRACT Many agamid lizards are known to show sexual dimorphism in body shape, colour and ornamentation or a combination of these traits. Adult males of Salea horsfieldii have a discontinuous dorsal crest at the nuchal region, which is a sexually dimorphic character. However, there is no information about the age or size at which this dimorphic ornamentation develops and if the species exhibits sexual shape dimorphism (SShD). The authors studied the morphology of S. horsfieldii and found that its ornamentation is an ontogenetically stable character present in all males, including juveniles. Seven morphological characters were measured to determine if they exhibited SShD at adult and juvenile stages. Analysis of covariance was used to identify differences in morphology between sexes. The results show that only adults exhibited SShD, but not juveniles. Adult males had larger head and foot lengths in comparison to females of the same size. Larger head length in adult males is a sexual fitness trait, which increases bite-force during intra-sexual combats. Although the presence of sexually dimorphic ornamentation right from the juvenile stage is rare in agamids, S. horsfieldii is an exception . The role of sexually dimorphic ornamentation at juvenile stages remains unknown and requires further investigation.
VenomKB v2.0: A knowledge repository for computational toxinology

Motivation Venom peptides comprise one of the richest sources of bioactive compounds available for drug discovery. However, venom data and knowledge are fragmentary and poorly structured, and fail to capitalize on the important characteristics of venoms that make them so interesting to the biomedical community. Results We present VenomKB v2.0, a new open-access resource for knowledge representation and retrieval of venom bioactivities, sequences, structures, and classifications. VenomKB provides a complete infrastructure for computational toxinology, with a focus on drug discovery and effects that venoms have on the human body. VenomKB is accompanied by a suite of tools for programmatic access, and, in this article, we highlight scenarios demonstrating its usefulness and novel contributions to toxinology, pharmacology, and informatics. Availability VenomKB can be accessed online at http://venomkb.org/, and the code can be found at https://github.com/tatonetti-lab/venomkb/. All code and data are available under open-source and open-access licenses.
Diversity of methanogens in the hindgut of grower and finisher pigs

This study examined the diversity of the methanogens in the hindgut of two different weight groups of pigs and correlated it with the amount of digested organic carbon (OC) and various components of dietary fiber. Five grower (58.9 ± 1.15 kg) and five finisher (89.4 ± 0.85 kg) Duroc × Landrace × Large Yorkshire female pigs were allocated into two groups and individually housed in cages. During the experiment, feed intake and fecal output were recorded for determination of apparent digestibility of OC, crude fiber (CF), neutral detergent fiber (NDF) and acid detergent fiber (ADF). At the end of the digestibility trial, pigs were sacrificed, and the contents of five segments of hindgut were sterilely collected to determine diversity of methanogens. Total microbial DNA of the hindgut contents was used as template for amplification of the methanogen16S rRNA gene, and the PCR products were further subjected to denaturing gradient gel electrophoresis (DGGE) analysis. Results show that the number of DGGE bands and Shannon diversity index for the 90 kg pigs were higher (P<0.05) than those for the 60 kg pigs. Methanogen communities did not alter along the different segments of the hindgut for the two weight groups. In addition, the amount of OC, CF, NDF and ADF digested (g/d) for the 90 kg pigs (1018.77, 23.11, 268.86 and 99.16, respectively) was higher (P<0.05) than the respective values for the 60 kg pigs (669.27, 13.77, 222.31 and 69.07), indicating that the higher diversity of methanogens in the former group was related to the higher quantity of fiber materials fermented in the hindgut. The positive correlation (p<0.05) between number of DGGE bands and Shannon diversity index with quantity of digested OC and ADF further reaffirmed the above suggestion. Key words : Methanogen, pig, Shannon diversity index, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE).
Milk intake and growth rate of Awassi lambs sucking ewes grazing on natural pasture in the semi-arid Negev

We determined milk intake and growth rate of fat-tailed Awassi ram lambs from birth to 30 days of age when sucking ewes that were grazing natural green pasture in the semi-arid Negev. The conversion of milk and energy intake to body mass and body solids gain in the lambs were calculated. Annual rainfall and, as a consequence, pasture availability were below average during the study. Body mass at birth was 4·22 (s.d. 0·71) kg and at 30 days was 12·10 (s.d.1·22) kg for an average daily gain of 256 (s.d.33) g/day. Of the 256 g/day, 100 (s.d.12·3) g/day were body solids, and for every unit body mass increase, proportionately 0·391 was body solids. Milk and energy intakes averaged 1·34 (s.d.0·23) l/day and 5·66 (s.d.0·97) MJ/day, respectively. The volume of milk intake per kg increase in body mass and body solids were 5·2 l and 13·4 l, respectively, whereas, the energy intake per kg increase in body mass and body solids were 22·1 MJ and 56·6 MJ, respectively. Of the total metabolizable milk energy intake, proportionately 0·46 was converted to body energy of the lamb. Although dry matter intake of the ewes was insufficient to prevent body mass loss, they produced sufficient milk to support a relatively high lamb growth rate, presumably by mobilizing fat reserves in the tail.
A neural network framework for the orbitofrontal cortex and model-based reinforcement learning

Model-based reinforcement learning (mbRL) has been widely used in explaining animal behavior. In mbRL, the model, or the structure of the task, is used to evaluate the associations between actions and outcomes. It has been proposed that the orbitofrontal cortex (OFC) encodes the model during mbRL. However, it is not well understood how the OFC acquires and stores model information. Here, we propose a neural network framework based on reservoir computing. Reservoir networks exhibit heterogeneous and dynamic activity patterns that are suitable to encode task states. The information can be extracted by a linear readout trained with reinforcement learning. We demonstrate how our framework acquires and stores the task state space. The framework exhibits mbRL behavior and its aspects resemble experimental findings of the OFC. Our study provides a theoretical explanation of how the OFC may contribute to mbRL and a new approach to understanding the neural mechanism underlying mbRL.