Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of Isolated Probiotic Bacteria from Piglet Nostrils in Fattening Pigs

Probiotics applications in animal husbandry can increase feed intake, growth and immune responses. The aim of this study was to isolate the probiotic bacteria from piglet nostrils and test their efficacy in fattening pigs. Nasal swabs collected from 110 healthy piglets were processed on Man, Rogosa and Sharpe (MRS) agar plates for lactic acid bacteria isolation. The biochemical standard tests were used for identification of isolates organisms including: Gram staining, catalase production, tolerance to bile salts, acid and base and the utilization of proteins, starch and fat. The antimicrobial activity and resistance against antibiotics were also determined. Comparative 16S rRNA analysis confirmed the identity of selected strains as Enterococcus italicus . Thirty weaned piglets (mixed sex and 35-day old) were divided into three groups (five replicates with two animals) consisting of a control group, a positive control group fed with commercial feed and antibiotic, and an experimental group fed with commercial feed and probiotics. Porcine reproductive and respiratory syndrome (PRRS) vaccination were performed twice. Administration of Enterococcus italicus had no impact on average daily gain, whereas it affected feed intake and feed conversion ratio (p 0.05).
Synthesis of 5-Arylpyrrole-2-carboxylic Acids as Key Intermediates for NBD Series HIV-1 Entry Inhibitors

Abstract 5-Arylpyrrole-2-carboxylic acids are important key intermediates in the synthesis of HIV-1 entry inhibitors (such as NBD-11021 and NBD-14010). Here we present a general method for the synthesis of some 5-arylpyrrole-2-carboxylic acids in three steps starting from pyrrole. By this method, the compounds could be prepared on gram scale and without chromatographic purification.
Development of peptide inhibitor nanoparticles (PINPs) for treatment of Alzheimer’s Disease

Purpose: To investigate the best carrier technology for our β-amyloid (Aβ) aggregation inhibitors by developing three types of liposomes (a) plain liposomes, (b) MAL-PEG liposomes, and finally the combination of retro-inverted peptide RI-OR2- TAT (Ac-rGffvlkGrrrrqrrkkrGyc-NH2) attached onto the surface of MAL-PEG liposomes, creating Peptide Inhibitor Nanoparticles (PINPs) of three different sizes (50, 100 and 200 nm). In addition, these nanoliposomes (NLPs) (with particular focus on PINPs) were examined for their ability to affect Aβ aggregation, and to protect against Aβ cytotoxicity. Methods: The creation of NLPs was carried out by the use of a mini extruder, while the elution of PINPs from a size exclusion column was assessed by Dynamic Light Scattering (DLS). The quantification of peptide bound to liposomes was determined by bicinchoninic acid (BCA) assay, while phospholipid content was quantified by Wako phospholipid assay. The effects of the different types of liposomes on Aβ toxicity and viability of SHSY-5Y neuronal cells were examined by MTS assay, whereas effects on Aβ aggregation were determined by Thioflavin-T (Th-T) assay. In addition, a cell penetration assay was carried out in order to examine the ability of liposomes to penetrate into neuroblastoma SHSY-5Y cells. Results: Low concentrations of PINPs 0.1 μM inhibited Aβ aggregation and toxicity in vitro. MAL-PEG liposomes and PINPs were able to penetrate into neuroblastoma SHSY-5Y cells and were also more stable than simple liposomes. Stability means the ability of liposomes to keep their size and their shape stable for long time. In addition, the three types of liposomes were not toxic towards SHSY-5Y neuroblastoma cells. Cytotoxicity is the quality of being toxic to cells. So, none of the three types of our liposomes showed any negative effect on the viability towards SHSY-5Y neuroblastoma cells. Conclusion: NLPs are an ideal carrier for our aggregation inhibitors because they affect Aβ aggregation and toxicity at low doses, and according to other data generated by our group, can cross the Blood Brain Barrier (BBB).
Genetic Characterization of Self-incompatible Lines and Strategies for Heterosis Breeding in Cauliflower

ABSTRACT Cauliflower (Brassica oleracea var. botrytis L.) is a thermosensitive crop grown almost all year-round in North Indian plains due to development of genotypes for production under different temperature regimes. Comparatively, varieties of early and mid-maturity group cauliflowers exhibit low yield compared to that of late maturing snowball types. Despite the presence of a higher level of heterosis in Indian cauliflower, development of hybrids in India is lacking due to nonavailability of strong self-incompatibility-based hybrids suitable for different seasons. To identify diverse parental lines for breeding in early and mid-maturity Indian cauliflower, genetic characterization of self-incompatible inbred lines was carried out based on quantitative and molecular analyses. To study heterotic performance of these lines in relation to divergence, 80 and 54 F1 hybrids of early and mid-maturity groups, respectively, were developed into a Line × Tester mating design and evaluated for yield and related traits. The mid-maturity group had higher diversity compared to that of early maturity group. Of 32 random amplified polymorphic DNA (RAPD) and 38 simple sequence repeat (SSR) primers, 25 RAPD and 3 SSRs exhibited polymorphism and generated a total of 164 reproducible amplicons, of which 37 were polymorphic. The average number of amplicons per primer was 6.71 and the maximum number of polymorphic amplicons (three) was obtained from RAPD primer SK-14. In SSR markers, the average number of polymorphic amplicons was 1.48 per primer. The SSR marker BoREM-1b indicated heterozygosity in the self-incompatible lines ccm-8 and cc-35L and further inbreeding may produce homozygosity in these lines. Lines cc-32E (early) and cc-22 (mid-maturity) had the most heterotic crosses for marketable curd weight and moderate diversity at the molecular level could be utilized for heterosis breeding. The molecular makers with quantitative analysis may be utilized for assessment of genetic diversity, testing of hybrid purity, and protection of superior lines and hybrids.
Bovine semen preservation under epididymal conditions and assessment of sperm quality by means of a sperm-oviduct binding assay

In this study, environmental conditions mimicking those prevailing in the epididymis were used for storing ejaculated bull spermatozoa in vitro during 4 days at room temperature (RT). These conditions were low pH, high osmolarity, high sperm concentration and low oxygen tension. Hepes-TALP was used as basic storage medium. Ejaculated spermatozoa were stored at a concentration of 10 x 10 spermatozoa/ml in Hepes-TALP of different pH (4, 5, 6, 7 or 8) and osmolarity (100, 300, 400, 500, 600 or 800 mOsm) and under different atmospheric conditions (nitrogen-gassed or aerobic). Spermatozoa were also stored undiluted or at different concentrations: 10 x 10, 100 x 10, 500 x 10 or 1 x 10 spermatozoa/ml. Sperm parameters such as membrane integrity, motility, mitochondrial membrane potential or DNA fragmentation were used to assess semen quality after storage. Adjustment of the pH of Hepes-TALP to pH 6 yielded significantly better results than storage at all other pH values. Isotonic Hepes-TALP had a less detrimental effect on spermatozoa than the hypoand hyperosmotic versions. No differences in sperm parameters were observed when spermatozoa were incubated under aerobic or under nitrogen-gassed storage conditions. Optimal sperm concentration in vitro is 10 x 10 spermatozoa/ml. This is in contrast with the in vivo situation, where spermatozoa are stored at a high concentration. Better results at high sperm concentrations were obtained when spermatozoa were diluted for less than 5 minutes in Triladyl-diluent supplemented with egg yolk and glycerol immediately after ejaculation. In vitro survival of bovine spermatozoa stored under epididymal conditions 51
Assessment of possible diel and sex-related differences in round goby (Neogobius melanostomus) diet

Abstract. Several aspects of invasive round goby (Neogobius melanostomus) biology are based on sporadic observations or anecdotal reports only, e.g. they are night feeders, they prey on eggs and larvae of native fish and male feeding ceases or is highly restricted during breeding due to nest-guarding. To test the general validity of such hypotheses, we assessed diel and inter-sex differences in diet and feeding intensity of 232 gobies (144 female [54 day:90 night] and 88 male [39 day:49 night]) caught during the breeding season. Gobies took primarily aquatic insect larvae and did not predate on eggs, larvae or juveniles of native fish. Unlike previous studies, we observed no diel difference in feeding intensity or diet composition; hence no universal diel pattern can be implied for round goby feeding. On the other hand, we observed significant inter-sex differences in both feeding intensity and diet composition, with males consuming less food than females, presumably due to restricted feeding activity during nest-guarding. Inter-sex shifts in both diet composition and amount of food were less than expected, however, suggesting that, under most conditions, there is no reason to expect a fatal decrease in male energy intake, as suggested by some earlier studies.
Microbial Carbon Substrate Utilization Differences among High- and Average-Yield Soybean Areas

Since soybean (Glycine max L. (Merr.)) yields greater than 6719 kg ha−1 have only recently and infrequently been achieved, little is known about the soil microbiological environment related to high-yield soybean production. Soil microbiological properties are often overlooked when assessing agronomic practices for optimal production. Therefore, a greater understanding is needed regarding how soil biological properties may differ between high- and average-yielding areas within fields. The objectives of this study were to (i) evaluate the effects of region on soil microbial carbon substrate utilization differences between high- (HY) and average-yield (AY) areas and (ii) assess the effect of yield area on selected microbiological property differences. Replicate soil samples were collected from the 0–10 cm depth from yield-contest-entered fields in close proximity that had both a HY and an AY area. Samples were collected immediately prior to or just after soybean harvest in 2014 and 2015 from each of seven geographic regions within Arkansas. Averaged across yield area, community-level carbon substrate utilization and Shannon’s and Simpson’s functional diversity and evenness were greater (p < 0.05) in Region 7 than all other regions. Averaged across regions, Shannon’s functional diversity and evenness were greater (p < 0.05) in HY than in AY areas. Principal component analysis demonstrated that a greater variety of carbon substrates were used in HY than AY areas. These results may help producers understand the soil microbiological environment in their own fields that contribute to or hinder achieving high-yielding soybeans; however, additional parameters may need to be assessed for a more comprehensive understanding of the soil environment that is associated with high-yielding soybean.
Ethanol production by co-fermentation of molasses and oil palm empty fruit bunch hydrolysate

Maximum ethanol production by co-fermentation of molasses (22%, w/v total sugar) and oil palm empty fruit bunch (OPEFB) hydrolysate was 61.60 g/l (0.38 g/g sugar) at 72 h, while maximum ethanol produced from the molasses was 53.89 g/l (0.34 g/g sugar). OPEFB slurry (the OPEFB hydrolysate which contained solid residue of pretreated OPEFB) gave maximum ethanol 68.77 g/l (0.44 g/g sugar) when it was co-fermented with the molasses. After fermentation, scanning electron micrograph of pretreated OPEFB in the OPEFB slurry revealed yeast cells adsorped to the pretreated OPEFB. The results indicated that ethanol production by co-fermentation of molasses and OPEFB hydrolysate was cumulative sum of ethanol produced from each raw material, and pretreated OPEFB suspended in OPEFB hydrolysate increased ethanol production in the co-fermentation of molasses and OPEFB hydrolysate.
Optimization of Culture Conditions for the Production of Protease from Bacillus megaterium

Abstract In this Study, Bacillus megaterium was used for protease production to examine the optimal condition for its maximum accumulation. Hence the production of enzyme was investigated at various pH, temperature, NaCl concentrations and different carbon and nitrogen sources. The medium amended with 3.0% NaCl, 1.0% gelatin, 0. 4% lactose, 0.5% peptone and pH 9, incubation at 40°C for 42 h were supported maximum protease production of 78.5 U/ml. --- Centre for Advanced studies in Botany, University of Madras, Guindy campus, Chennai- 600 025, India --- Please Cite This Article As: R. Rajkumar*, K. R. Jayappriyan, P. Ramesh Kannan, R. Rengasamy. 2010. Optimization of Culture Conditions for the Production of Protease from Bacillus megaterium . J. Ecobiotechnol. 2(4):40-46.
Long‐distance dispersal syndromes matter: diaspore–trait effect on shaping plant distribution across the Canary Islands

Oceanic islands emerge lifeless from the seafloor and are separated from continents by long stretches of sea. Consequently, all their species had to overcome this stringent dispersal filter, making these islands ideal systems to study the biogeographic implications of long-distance dispersal (LDD). It has long been established that the capacity of plants to reach new islands is determined by specific traits of their diaspores, historically called dispersal syndromes. However, recent work has questioned to what extent such dispersal-related traits effectively influence plant distribution between islands. Here we evaluated whether plants bearing dispersal syndromes related to LDD – i.e. anemochorous (structures that favour wind dispersal), thalassochorous (sea dispersal), endozoochorous (internal animal dispersal) and epizoochorous (external animal dispersal) syndromes – occupy a greater number of islands than those with unspecialized diaspores by virtue of their increased dispersal ability. We focused on the native flora of the lowland xeric communities of the Canary Islands (531 species) and on the archipelago distribution of the species. We controlled for several key factors likely to affect the role of LDD syndromes in inter-island colonization, namely: island geodynamic history, colonization time and phylogenetic relationships among species. Our results clearly show that species bearing LDD syndromes have a wider distribution than species with unspecialized diaspores. In particular, species with endozoochorous, epizoochorous and thalassochorous diaspore traits have significantly wider distributions across the Canary archipelago than species with unspecialized and anemochorous diaspores. All these findings offer strong support for a greater importance of LDD syndromes on shaping inter-island plant distribution in the Canary Islands than in some other archipelagos, such as Galapagos and Azores. This article is protected by copyright. All rights reserved.
Drug Development in Dengue Virus and Molecular Epidemiology of Malaria in Western

Drug Development in Dengue Virus and Molecular Epidemiology of Malaria in Western Kenya by Brandt Levitt Department of Molecular Genetics and Microbiology Duke University Date:_______________________ Approved: __________________________ Steve Taylor, Co-Supervisor __________________________ Jen Tsan Chi, Co-Supervisor __________________________ Micah Luftig __________________________ Andrew Alspaugh __________________________ Katharina Koelle An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Molecular Genetics and Microbiology in the Graduate School of Duke University 2017 Copyright by Brandt Levitt 2017
Estimating lion's prey species profile in an arid environment

Information on large carnivore diet composition is important when conservationists seek to address stressors such as habitat encroachment, bush meat trade and retribution killing on the persistence of populations. Detailed diet sampling approaches can contribute to effective conservation management. We compare different approaches including GPS cluster analysis, scat analysis and opportunistic observations and describe lion diet profiles in the Kgalagadi Transfrontier Park (KTP). We determined that a sample size of between 65–69 lion feeding events out of 278 found by GPS cluster analysis and 55–59 lion scats out of 189 samples can provide a representative description of lion diet in the KTP. Our opportunistic observations (n = 52) were found to be too few for robust deductions. Scat analysis yielded the highest prey diversity (n = 11) and best representation of prey <50 kg, but required 160 scats at ~ 263 km driven per scat collected. GPS cluster analysis provided good information for large prey, but underrepresented prey <50 kg. Kill remains were found at only 37% of the investigated GPS cluster points (n = 823). Even so, GPS cluster analysis yielded diet descriptions quicker than scat analyses. The use of GPS cluster and scat analysis in tandem is recommended for the estimation of lion diet in this arid environment.
Nanopore detection of bacterial DNA base modifications

The common bacterial base modification N6-methyladenine (m6A) is involved in many pathways related to an organism’s ability to survive and interact with its environment. Recent research has shown that nanopore sequencing can detect m5C with per-read accuracy of upwards of 80% but m6A with significantly lower accuracy. Here we use a binary classifier to improve m6A classification by marking adenines as methylated or unmethylated based on differences between measured and expected current values as each adenine travels through the nanopore. We also illustrate the importance of read quality for base modification detection and compare to PacBio methylation calls. With recent demonstrations of nanopore sequencing in Antarctica and onboard the International Space Station, the ability to reliably characterize m6A presents an opportunity to further examine the role of methylation in bacterial adaptation to extreme or very remote environments.
Asetadiptacus, a new genus; family Rhyncaphytoptidae (Acarina: Eriophyoidea)

A new genus, Asetadiptacus, is proposed. The genotype of this new genus, Asetadiptacus emiliae n. sp. , is found on leaves of Ficus carica L. , in Oeiras, Portugal. This nevv genus differs from the close genus Diptacus by the absence of dorsal setae, by the absence of a strong sternal ridge as a separation of the forecoxae and the abdomen has no dorsal ridge. It is characterized by divided featherclaw, ali leg segments are present and the dorsal tubercles are present but no setae. Asetadiptacus n. g. goes into the family Rhyncaphytoptidae.
Beyond Consensus: Embracing Heterogeneity in Neuroimaging Meta-Analysis

Coordinate-based meta-analysis can provide important insights into mind-brain relationships. A popular meta-analytic approach is activation likelihood estimation (ALE), which identifies brain regions consistently activated across a selected set of experiments, such as within a functional domain or mental disorder. ALE can also be utilized in meta-analytic co-activation modeling (MACM) to identify brain regions consistently co-activated with a seed region. Therefore ALE aims to find consensus across experiments, treating heterogeneity across experiments as noise. However, heterogeneity within an ALE analysis of a functional domain might indicate the presence of functional sub-domains. Similarly, heterogeneity within a MACM analysis might indicate the involvement of a seed region in multiple co-activation patterns that are dependent on task contexts. Here we demonstrate the use of the author-topic model to automatically determine if heterogeneities within ALE-type meta-analyses can be robustly explained by a small number of latent patterns. In the first application, the author-topic modeling of experiments involving self-generated thought (N = 179) revealed two cognitive components fractionating the default network. In the second application, the author-topic model revealed that the inferior frontal junction (IFJ) participated in three co-activation patterns (N = 323), which are differentially expressed depending on cognitive demands of different tasks. Overall the results suggest that the author-topic model is a flexible tool for exploring heterogeneity in ALE-type meta-analyses that might arise from functional subdomains, mental disorder subtypes or task-dependent co-activation patterns. Code and data for this study are publicly available at GITHUB_LINK_TO_BE_ADDED.
Quantifying uncertainty in the inference of generalized coalescents

We develop inference methods for generalized coalescent models, such as the Λ- and Ξ-coalescents, which have recently been proposed for populations with broad offspring distributions, repeated selective sweeps, or strong selection. These are all populations that may not be adequately described by the usual Kingman coalescent. A roadblock to the application of such models has been the lack of effective tools for inferring an appropriate model, which stems from difficulties in evaluating the associated likelihoods. We overcome these difficulties by introducing estimators that are both computationally tractable and statistically efficient. We use these estimators to obtain point estimates and confidence intervals for the parameters of the coalescent models, and p-values for the hypothesis that the population is described by the Kingman coalescent. Our approach is based on the theory of unbiased estimating equations, which is more general than composite likelihood and may be applicable in other areas of statistical genetics. Our main focus is on inference from linked site-frequency spectra using parameterized families of Λ-coalescents. We show that useful inferences may be made from non-singleton data alone if singletons are suspect due to sequencing or data-cleaning errors, although the data requirements are greatly increased. We apply our method to mitochondrial sequence data from Gadus morhua, the Atlantic cod.
AN UNSUPERVISED LEARNING AND STATISTICAL APPROACH FOR ENGLISH PHRASE SEGMENTATION

: In this paper, we propose a method to: (i) segment english sentences into phrases by using probabilistic model, (ii) use unsupervised learning process to optimize probabilistic model. In this model, new phrases are recognized and their words are linked together. The word-linking process improves the accuracy of statistical functions and improves contrarily the new phrases recognition and the probabilistic model will converge to an optimum. Our experimented corpus is collected from wikipedia with 18.459. 094 articles, which consists of more than 200.000. 000 sentences. After preprocessing process, we created the corpus with approx. 24.035. 527 phrases and sentences used for probabilistic model.