Miracle-dz/UniFAR-FTUs huggingface dataset:
Moderate-Throughput Identification and Comparison of Campylobacter-Infecting Bacteriophages

Campylobacter jejuni is a leading cause of foodborne infection due to its ability to asymptomatically colonize agricultural animals. In addition to its prevalence, Campylobacter is becoming increasingly resistant to the clinical antibiotics, azithromycin and ciprofloxacin. As a result, public health agencies have identified drug resistant Campylobacter as a serious threat to public health and have suggested combating the pathogen at the farm-level by reducing its burden within agricultural animal reservoirs. Due to antibiotic restrictions in agricultural animals, reducing Campylobacter burden on the farm requires the identification and development of novel approaches. To this end, our group employed a broad sampling strategy to isolate a diverse collection of bacteriophages that can predate Campylobacter. We successfully isolated 70 bacteriophages from these samples and subjected them to whole-genome sequencing and initial comparative genomic analysis. Following this analysis, we performed dose-response assays by adding increasing concentrations of bacteriophage to C. jejuni cultures. From this work, we were able to identify diverse phage groups from multiple sources that correlated with robust inhibition of C. jejuni growth. Lastly, we employed transmission electron microscopy to examine the morphology of these bacteriophages and were able to confirm that genetic diversity reflected morphological diversity in these bacteriophages. Importance Globally, Campylobacter jejuni is the most common cause of bacterial-derived gastroenteritis due to its ability to colonize agriculturally relevant animals. The increasing prevalence of antibiotic resistant C. jejuni strains necessitates the development of novel treatments to combat colonization of the animal host. In this study, we describe the isolation of 70 bacteriophages from various environmental sources that infect and kill C. jejuni. A robust analysis of the genetic diversity of these phage is described, and transmission electron microscopy is utilized to evaluate morphological differences. This study describes a novel prospecting strategy for isolating bacteriophage that infect C. jejuni from various environmental sources. In previous studies, bacteriophage that kill C. jejuni have been isolated from sewage and pig manure; however, the majority have been isolated from chickens, and have been relatively few in number. We postulate this study increases the likelihood of isolating bacteriophage efficacious at combating C. jejuni colonization of agricultural animal hosts at the farm-level or treating infected humans.
Effects of High Temperatures on Development and Fecundity of Aulacorthum solani （Homoptera: Aphididae）and Aphis glycines （Homoptera: Aphididae）

: Effects of high temperatures on development and fecundity were examined using Aulacorthum solani （ Kaltenbach ） and Aphis glycines Matsumura clones. Nymphs of all A. solani clones showed 100% mortality at 30 (cid:155) C. By contrast, all nymphs of three A. glycines clones out of four survived and became adults at 30 (cid:155) C. The numbers of nymphs produced by adult females of A. solani clones were higher at 20 (cid:155) C than at 28 (cid:155) C. Adult females of A. glycines clones produced more nymphs at 28 (cid:155) C than at 20 (cid:155) C. These results suggest that A. solani is more susceptible to high temperatures rather than A. glycines.
Genetic Constraints and the Evolution of Chemical Defenses in Multiple Tissues of Boechera stricta

Genetic Constraints and the Evolution of Chemical Defenses in Multiple Tissues of Boechera stricta by Rose Keith University Program in Genetics and Genomics Duke University Date: May 26, 2017 Approved: ___________________________ Storrs Mitchell-Olds, Supervisor ___________________________ John Willis, Chair ___________________________ Mark Rausher ___________________________ Kathleen Donohue An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Genetics and Genomics in the Graduate School of Duke University 2017 Copyright by Rose Keith 2017
Climate‐biomes, pedo‐biomes or pyro‐biomes: which world view explains the tropical forest–savanna boundary in South America?

It remains poorly understood why the position of the forest–savanna biome boundary, in a domain defined by precipitation and temperature, differs in South America, Africa and Australia. Process based Dynamic Global Vegetation Models (DGVMs) are a valuable tool to investigate the determinants of vegetation distributions; however, many DGVMs fail to predict the spatial distribution or indeed presence of the South American savanna biome. Evidence suggests that fire plays a significant role in mediating forest–savanna biome boundaries; however, fire alone appears to be insufficient to predict these boundaries in South America. We hypothesize that interactions between precipitation, constraints on tree rooting depth and fire affect the probability of savanna occurrence and the position of the savanna–forest boundary.
Identification of cold-stress responsive proteins in Anabasis aphylla seedlings via the iTRAQ proteomics technique

ABSTRACT Cold stress is one of the major environmental factors that affects plant growth, development, and species distributions. In order to study the molecular mechanism of cold-stress responses in Anabasis aphylla seedlings, we used the isobaric tags for relative and absolute quantification (iTRAQ) technique to identify differential protein expression under cold stress. In total, 211 differentially expressed proteins were identified, including 109 up-accumulated proteins and 102 down-accumulated proteins, these cold-stress response proteins were mainly identified as proteins involved in carbohydrate and energy metabolism, protein metabolism and translation, stress response, transcription-related, amino acid metabolism, signal transduction, and membrane and transport. GO and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses indicated that most of the proteins related to cold-stress response were involved in carbohydrate and energy metabolism, indicating A. aphylla seedlings adapted to cold conditions mainly through changes in energy metabolism pathways. Additionally, the correspondence between mRNA transcript levels and protein abundance levels for nine accumulated proteins were also tested by qRT-PCR, only one protein did not show consistent trends in mRNA and protein levels. These data clarify our current understandings of stress responses in seedlings of species such as A. aphylla and identify the molecular mechanisms of the cold-stress responses.
Allergenic Plantago (Plantain) Pollen Concentrations in Turkey

Objective: Pollen grains of the species belonging to Plantago genus cause some allergic diseases like allergic rhinitis, allergic conjunctivitis and allergic asthma on sensitive individuals. Materials and Methods: In this study, monthly variation and annual proportions of Plantago pollen investigated for 62 atmospheric pollen studies in Turkey, which carried out by using Lanzoni/Burkard sampler with volumetric method or by using Durham sampler with gravimetric method. Furthermore, researches evaluated about Plantago pollen sensitivities, performed in Europe and our country. Results: According to the atmospheric pollen studies, incidences of Plantago pollen grains are changing between 0.08 to 11.45% in respect of total pollen amount. Plantago pollen grains are seen in the atmosphere for a long period and present in high levels in may-june. Conclusion: In the regions, atmospheric pollen studies have been prepared, Plantago pollen grains detected in the air in small amounts but for a long period. It should be considered that, Plantago pollen, which have important allergic effects, may cause symptoms on sensitive individuals especially between may-june, also in the other months.
Influence of a cocktail of protease and xylanase in different energy densities of corn- and soybean-meal-based diet on growth performance, nutrient digestibility, carcass quality, and gas emission in broilers

Abstract: A total of 480 one-day-old male Ross 308 broilers with an average initial body weight (BW) of 42 ± 1 g was randomly divided into four treatments (8 replicates/treatment, 15 birds/replicate) by their BW to evaluate the influence of a cocktail of protease and xylanase in different energy density of corn- and soybean-meal-based diet on broilers. This experiment lasted for 35 d and there were two phases; starter (1–18 d) and finisher (19–35 d). The experiment was a 2 × 2 factorial arrangement with two levels of metabolizable energy and the cocktail enzyme with 200 mg of protease kg-1 diet and 100 FXU xylanase kg-1 diet. Both high-nutrient density and cocktail enzyme supplementation increased (P < 0.05) the body weight gain (BWG) during day 1–18 and day 1–35 as well as dry matter retention on day 35. Broilers fed the high-nutrient-density diets had higher (P < 0.05) energy retention on day 35 and relative breast muscle weight. Broilers fed the cocktail enzyme diets significantly increased nitrogen (N) retention and decreased the levels of ammonia (NH3) and hydrogen sulphide (H2S) emission. In conclusion, dietary supplementation of the cocktail enzyme component improved BWG, N retention, and reduced excreta noxious gas emission in broilers.
Cerebro-Cortical Surface Areas, Volumes, Lengths of Gyri and their Interdependence in Mammals, Including Man

The importance of brain size from the Standpoint of evolution and of "intelligence" has been emphasized by numerous authors. Good reviews of the subject are those by Blinkov and Glezer (1968) and by Holloway (1968). The major points of emphasis in the past have been the ratio of brain weight or brain volume to body weight and the line of evolution leading from the insectivores to man. Less easily accessible to measurement than weight and volume has been the surface area of the cerebral cortex and especially of the paleoand neocortex. This parameter is of great significance because together with measurements of cortical thickness, the number of possible synapses would depend on the cortical surface area and on cell density per volume (now being determined by Dr. Herbert Haug in Kiel). This surface area depends on the total volume of the telencephalon and its degree of folding. It seemed of interest to compare representatives of several, taxonomically far separated mammalian classes, rather than to confine ourselves to the customary approach of following a line of evolution within a restricted group of mammals.
THE EFFECT OF FISH AND PALM OIL ADDITION ON FATTY ACIDS CONTENT OF PIG TISSUES

Thirty-two piglets at the age of eight weeks were divided into two groups for 60 days of fattening. The experimental group (FO) was fed the basic feed mixture with addition of fish oil (2.5%) and the control group (PO) was fed basic feed mixture with addition of palm oil (2.5%). Fish oil is characterized by high proportion of n–3 polyunsaturated fatty acids. Palm oil has high level of palmitic, oleic and linoleic acids. At the end of fattening period, fatty acids content in the liver, muscle and adipose tissues were determined. FO-diet caused increase of PUFA n–3 in all observed tissues (P < 0.01). PO-diet had effect only in adipose tissue, where significant increase of palmitic, stearic and linoleic acids was found (P < 0.05).
Clock Genes in Depression

Data demonstrate that abnormal regulation of the circadian system can result in cardio- vascular disease, metabolic syndrome, obesity, immune dysfunction, increased risk for cancer, reproductive complications, etc. It is highly individual among depressed patients and may be expressed as a phase advance or phase delay of rhythms and/or increase or decrease in the amplitude. The stress-induced anhedonic-like state characterizes by hypo- thermia, hypercortisolemia, and hypermelatoninemia associated with disturbances in the circadian system. Mainly Per2 and Bmal1 demonstrate altered expression in the brain and liver: expression of Per2 is sensitive to stress and changes in Bmal1 mostly associated with depressive behavior. The Per1 expression is sustainable in maintaining the circadian rhythm. A normalization of the expression patterns is likely to be essential for the recov ery from the pathological state. Depression is a high prevalent disorder. The number of incidents is rising due to changes in lifestyle. The symptomatology is inconsistent and it is difficult to agree on one hypothesis. The disturbances of the 24 h circadian rhythm may be a factor in the development of major depressive disorder. The molecular biology underlying a causal relationship between circadian rhythm and mood disorders is slowly being unraveled. However, many questions still need to be answered.
Prediction of starter feed intake of preweaned dairy calves and effects of rumen undegradable protein on performance and digestive characteristics of dairy holstein heifers

vii RESUMO . xi GENERAL INTRODUCTION . 1 REFERENCES . 4 Paper 1 – Development of equations, based on milk intake, to predict starter feed intake of preweaned dairy calves . 8 Abstract . 9 Introduction . 10 Material and Methods . 11 Developmental Database . 11 Statistical Analysis . 12 Sensitivity Analysis . 13 Results and Discussion . 14 Conclusions . 16 References . 17 Paper 2 – Effects of rumen undegradable protein on intake, performance and mammary gland development in prepubertal and pubertal dairy heifers . 29 Abstract . 30 Introduction . 31 Material and Methods . 32 Animals, Treatments and Management . 32 Experimental Period, Collections and Sampling . 33 Laboratory Analysis and Calculations . 35 In situ degradability trial . 37 Statistical analysis . 38 Results . 38 Intake, Digestibility and Sorting Behavior . 38
Specificity of the Antibody Response of Human Beings to Strains of Influenza Virus

Acute and convalescent sera from cases of influenza A have been tested for neutralizing antibodies to PR8, W.S. , and Melbourne strains of influenza A, the Lee strain of influenza B, and the swine influenza virus by the chicken-cell agglutination method. Considerable specificity was demonstrated between PR8 and W.S. and swine influenza. It was also indicated that the strain-specificity was not limited to those producing poor rises to PR8, but occurred in some cases producing good rises to PR8. Mouse neutralization tests on selected cases confirmed the results obtained by the agglutinative test. Persons vaccinated with influenza A vaccines whose sera were tested with the same virus strains were found to be somewhat more specific in their antibody response to strains PR8, W.S. , and swine than were the sera of infected individuals. This apparent increase of specificity may be due, in part at least, to the fact that the response to the vaccine was not as great as was the response to an attack of influenza A. Sera of several persons infected or vaccinated with influenza A showed also an output of antibodies to the Lee strain of influenza B. Some of these apparent increases in reactivity may have been due, however, to the partial destruction of antibodies by a contaminant in the preliminary serum specimens. A few individuals vaccinated with active Melbourne vaccine showed a better response to Melbourne than to PR8. Conversely, those vaccinated with PR8-distemper virus vaccine responded better to PR8 than to Melbourne.
Distribution and frequency of tomato ringspot virus (ToRSV) in different varieties of Rubus idaeus in the Maule Region, Chile - Distribución y frecuencia de tomato ringspot virus (ToRSV) en diferentes variedades de Rubus idaeus en la Región del Maule, Chile

The raspberry (Rubus idaeus) is one of the most important fruit for production in the Maule Region, Chile. Raspberries are affected by the tomato ringspot virus (ToRSV), which causes decreased yield and deformed fruit. The objective of this work is to study ToRSV spread in different raspberry varieties in the Maule Region, Chile. The virus was detected using the ELISA test and RT-PCR in the Heritage, Meeker, Chilliwack, Amity and Coho varieties. Bayesian analysis determined the relationship between the percentage of ToRSV incidence in the cultivated varieties and the locations in the different provinces of the Maule Region. It was observed that the Linares province showed the highest levels of the virus in the different varieties: Amity (70%), Meeker (39%) and Heritage (26%), compared to other provinces in the region. These results suggest a high spread of ToRSV through the Maule Region. Nei distance analysis suggests that 14 of the virus isolates coming from the Talca and Linares Provinces would show differences with the ToRSV accessions deposited in the global gene bank (NCBI).
Effects of Tree Species Composition and Foraging Effort on the Productivity of Golden-Cheeked Warblers

Effects of Tree Species Composition and Foraging Effort on the Productivity of GoldenCheeked Warblers. (May 2011) Michael E. Marshall, B.S., The University of Texas at Austin Chair of Advisory Committee: Dr. Michael L. Morrison The concept of habitat quality is fundamental to the study of ecology. Ecologists have long recognized the importance of vegetation structure and composition in the assessment of wildlife habitat. Vegetative characteristics affect productivity in birds for a variety of reasons (e.g., predator assemblages, nesting sites, song perches, food availability). This research investigated the relationship between habitat quality and prey availability and the effect these parameters have on reproductive success in goldencheeked warblers (Dendroica chrysoparia). The objectives were to: 1) Determine any differences in pairing and fledging success of warbler territories within two ecosites exhibiting two distinctive tree species composition, 2) Explore the relationship between tree species composition, arthropod density, and foraging effort, and the effect these parameters have on reproductive success in golden-cheeked warblers, and 3) Investigate the connection between preferred foraging substrates and changes in arthropod abundance within golden-cheeked warbler territories throughout the breeding season. Individual warbler territories were mapped out and searched for fledglings, foraging behavior observed, and arthropods collected, to determine productivity, foraging effort,
Pollination along an elevational gradient mediated both by floral scent and pollinator compatibility in the fig and fig‐wasp mutualism

In the fig (Moraceae) and fig‐wasp (Agaonidae) mutualism, scent is believed to be of primary importance in pollinator attraction and maintenance of species specificity. Scent divergence between closely related Ficus species seems sufficient in promoting reproductive isolation through pollinator behaviour, starting the process of speciation. We investigated volatile organic compound (VOC) variation from figs in several Ficus species endemic to Papua New Guinea. Sister species of section Papuacyse and subspecies of Ficus trichocerasa substitute each other along the continuously forested Mt. Wilhelm elevational gradient. We placed these species in a phylogenetic context to draw conclusions of scent divergence between close relatives. In addition, pollinator response to VOCs emitted by figs of different species was tested. Volatile profiles differed significantly between focal species, although with a varying degree of overlap between (sub)species and elevations. Pollinators were generally attracted to VOCs emitted only by their hosts except in one case where pollinating fig wasps were also attracted to the sister species of its host. Wasp morphological traits, however, indicate that it is mechanically impossible for this species to oviposit in figs of this atypical encounter. Synthesis. This study demonstrates that while scent is an effective signal for partner recognition, there are multiple barriers which help maintain prepollination isolation in fig and pollinating fig‐wasp interactions. Speciation along this elevational gradient is reinforced by divergence in key reproductive isolation mechanisms on both sides of the mutualism.
DensityPath: a level-set algorithm to visualize and reconstruct cell developmental trajectories for large-scale single-cell RNAseq data

Cell fates are determined by transition-states which occur during complex biological pro-cesses such as proliferation and differentiation. The advance in single-cell RNA sequencing (scRNAseq) provides the snapshots of single cell transcriptomes, thus offering an essential opportunity to study such complex biological processes. Here, we introduce a novel algorithm, DensityPath, which visualizes and reconstructs the underlying cell developmental trajectories for large-scale scRNAseq data. DensityPath has three merits. Firstly, by adopting the nonlinear dimension reduction algorithm elastic embedding, DensityPath reveals the intrinsic structures of the data. Secondly, by applying the powerful level set clustering method, DensityPath extracts the separate high density clusters of representative cell states (RCSs) from the single cell multimodal density landscape of gene expression space, enabling it to handle the heterogeneous scRNAseq data elegantly and accurately. Thirdly, DensityPath constructs cell state-transition path by finding the geodesic minimum spanning tree of the RCSs on the surface of the density landscape, making it more computationally efficient and accurate for large-scale dataset. The cell state-transition path constructed by DensityPath has the physical interpretation as the minimum-transition-energy (least-cost) path. We demonstrate that DensityPath is capable of identifying complex cell development trajectories with bifurcating and trifurcating branches on the human preimplantation embryos. We demonstrate that DensityPath is robust and has high accuracy of pseudotime calculation and branch assignment on the real scRNAseq as well as simulated datasets.
Ethanolic Extract of Solanum melongena Linn Fruit Mitigated Monosodium Glutamate-Induced Oxidative Stress

Background/Aim: Monosodium glutamate (MSG), a flavour enhancing food additive generally regarded as safe by food regulatory Results: The determined vitamins in the sample were vitamin A (0.36 ± 0.02IU), vitamin B3 (9.03 ± 0.07 mg/100 g) and vitamin C (369.67± 7.54 mg/100 g) while the phytochemicals were alkaloids (1.13 ± 0.10 mg/100 g), saponins (5.54 ± 0.37 mg/100 g), tannins (11.87 ± 1.87 mg/100 g), cyanogenic glycogenic (6.21 ± 0.22 mg/100 g) and phytates (30.62 ± 1.54 mg/100 g). The MSG only fed group significantly (P =.05) increased malondialdehyde (MDA) concentration but decreased (P =.05) glutathione (GSH), catalase (CAT) and superoxide dismutase (SOD) activity compared to the control, suggesting induction and enhanced generation of reactive oxygen species (ROS) which compromised the antioxidant defense of the MSG-fed rats. Co-administration of MSG with ethanol extract of Solanum melongena Linn fruit significantly (P=.05) reduced the MDA concentration to a value non-significant (P=.05) compared to that of the control rats, and conversely, significantly (P=.05) increased GSH, CAT and SOD activities compared to the group 2 rats. Conclusion: The Solanum melongena Linn fruit contains the studied phytochemicals and vitamins while the ethanol extract of the fruit could significantly mitigate MSG-induced oxidative stress in the rats.