Miracle-dz/UniFAR-FTUs huggingface dataset:
Randomization and Monte Carlo Methods in Biology.

Part 1 Randomization tests and confidence intervals: the idea of a randomization test examples of a randomization test aspects of randomization testing raised by the examples confidence intervals from randomization. Part 2 Monte Carlo and other computer intensive methods: Monte Carlo tests jackknifing bootstrapping bootstrap tests of significance and confidence intervals. Part 3 Some general considerations: power determining how many randomizations are needed determining a randomization distribution exactly the computer generation of pseudo-random numbers generating random permutations. Part 4 One and two sample tests: the paired comparisons design the one sample randomization test the two sample randomization test the comparison of two samples on multiple measurements. Part 5 Analysis of variance: one factor analysis of variance Bartlett's test for constant variance examples of more complicated types of analysis of variance discussion computer program. Part 6 Regrssion analysis: simple regression testing for a non-zero beta value confidence limits for beta multiple linear regression randomizing X variable values. Part 7 Distance matrices and spatial data: testing for association between distance matrices Mantel's test determining significance by sampling randomization distribution confidence limits for a matrix regression coefficient problems involving more than two matrices. Part 8 Other analyses on spatial data: the study of spatial point patterns Mead's randomization test a test based on nearest neighbour distances testing for an association between two point patterns the Besag-Diggle test tests using distances between points. Part 9 Time series: randomization and time series randomization tests for serial correlation randomization tests for trend randomization tests for periodicity irregularly spaced series tests on times of occurence discussion of procedures for irregular series bootstrap and Monte Carlo tests. Part 10 Multivariate data: univariate and multivariate tests sample means and covariance matrices comparison on sample means vectors chi-squared analyses for count data principal component analysis and other one sample methods discriminate function analysis. Part 11 Ad hoc methods: the construction of tests in non-standard situations testing for randomness of species co-occurences on islands examining time change in niche ovelap probing multivariate data with random skewers other examples. Part 12 Conclusion: randomization methods bootstrap and Monte Carlo methods.
Mechanism of Riboswitch Regulatory Domains and Application for Developing Novel Biosensors

Ceres, Pablo (Ph.D., Biochemistry, University of Colorado, Boulder) Mechanism of Riboswitch Regulatory Domains and Application for Developing Novel Biosensors Thesis directed by Professor Robert T. Batey Riboswitches are structural elements of gene control located in the 5’untranslated region of some mRNAs capable of regulating the expression of important genes. The mode of regulation occurs by binding a cellular metabolite if its concentration excess a threshold and controlling genes involved in the biogenesis or transport of this ligand. A common riboswitch is composed of two functionally distinct units: i) the aptamer domain, which recognizes and binds the cellular metabolite and ii) an expression platform responsible for interaction with the cellular machinery and control of gene production. The aptamer domain of riboswitches confers high degree of affinity and specificity towards the correct ligand. This binding event rearranges the secondary structure of the expression platform, which in turn allows regulation of gene expression. Riboswitch genetic control is observed in the three domains of life. However, it is most important in bacteria. Previously, the characterization of riboswitches has focused on the biophysical study of different aptamer domains and the changes that occur when the ligand binds the RNA. These studies have revealed the intricate recognition of essentially every functional group of a diverse set of cellular metabolites by RNAs. However, the signal transduction from the aptamer domain to the expression platform remains uncharacterized. Most importantly, the secondary structural switch that an expression platform undergoes has been reduced to a simple variation of secondary interactions. In this dissertation, I have functionally characterized, both in vitro and in vivo, two different riboswitches in their entirety, demonstrating novel findings about the regulatory response of these riboregulators. The results show that small secondary structures formed within the expression platform are important for gene control and that the ability of the switching mechanism is innate within this domain (independent of ligand presence). The application of these learned principles of riboswitch regulation for the development of novel RNA-based biosensors has also been accomplished. To establish engineering strategies capable of developing general, reliable, and modular RNA devices, I mixed and matched natural and SELEX-derived (systematic evolution of ligands by exponential enrichment) aptamers with a variation of natural expression platforms. These engineered riboswitches are functional in vitro and in E. coli, and present a new avenue to control cellular regulation for different applications including synthetic biology.
The protective effect of Ginsenoside Rgl on nerves in the mice model of Parkinson＇s disease.

Objective To investigate possible mechanism of Ginsenoside Rgl on dopaminergic nigral neurons apoptosis of Parkinson＇s disease （PD} and its protective effect. Methods C57BL/6N mice were administrated with 1-Methy-4-phenyl-1,2,3,6-tetrahydropyri-dine （MPTP） to produce chronic PD model,PD mice were observed in behavioral changes. The expression levels of caspase-3 and TH in ventral midbrain were studied with immunohistochemistry and Western blotting. Apoptotic cell numbers were determined by TdT-mediated dUTP-biotin nick end labeling （ TUNEL ）. Results In group treated with Ginsenoside Rgl, the number of TH-positive neurons in SN was only decreased by 31% as compared with the control group（55% ） （P 〈 0.01 ） ,the expression of caspase-3 was apparently decreased and major expressed in the cytosol of nigral neurons and TUNEL positive cells in SN decreased （ P 〈 0.01）. Conclusion The neuroprotective effect of Ginsenoside Rgl on dopaminergic nigral neurons apoptosis of the mice model of Parkinson＇s disease induced by MPTP is significant, Decreased expression of Caspase-3 may be the major mechanism of Ginsenoside Rgl for antiapoptosis. Key words: Parkinson＇s disease ; Ginsenoside Rgl ; Apoptosis ; Dopamine
Crowding Affects Health, Growth, and Behavior in Headstart Pens for Agassiz's Desert Tortoise

Abstract Worldwide, scientists have headstarted threatened and endangered reptiles to augment depleted populations. Not all efforts have been successful. For the threatened Agassiz's desert tortoise (Gopherus agassizii), one challenge to recovery is poor recruitment of juveniles into adult populations, and this is being addressed through headstart programs. We evaluated 8 cohorts of juvenile desert tortoises from 1 to 8 yrs old in a headstart program at Edwards Air Force Base, California, for health, behavior, and growth. We also examined capacities of the headstart pens. Of 148 juveniles evaluated for health, 99.3% were below a prime condition index; 14.9% were lethargic and unresponsive; 59.5% had protruding spinal columns and associated concave scutes; 29.1% had evidence of ant bites; and 14.2% had moderate to severe injuries to limbs or shell. Lifetime growth rates for juveniles 1–8 yrs of age were approximately two times less than growth rates reported for wild populations. Tortoises in older cohorts had higher growth rates, and models indicated that high density in pens and burrow sharing negatively affected growth rates. Densities of tortoises in pens (205–2042/ha) were 350–3500 times higher than the average density recorded in the wild (< 1/ha) for tortoises of similar sizes. The predominant forage species available to juveniles were alien annual grasses, which are nutritionally inadequate for growth. We conclude that the headstart pens were of inadequate size, likely contained too few shelters, and lacked the necessary biomass of preferred forbs to sustain the existing population. Additional factors to consider for future reptilian headstart pens include vegetative cover, food sources, soil seed banks, and soil composition.
Effects of green tea powder supplementation on egg production and egg quality in laying hens

ABSTRACT The aim of this study was to investigate the effects of green tea powder supplementation on egg production and egg quality in chickens. A total of 240 Xianju chickens (all aged 20 weeks) were randomly allotted to five treatments, control group T0, no diet supplements; test groups T1, T2 and T3 were supplemented with 1%, 2% and 3% green tea powder into basal diet, respectively; test group T4, 3% green tea powder and 1.5% peanut oil were added to the diet. After the rearing test, the eggs from each treatment were collected and later analysed for egg quality. Results suggest that 1% green tea powder supplementation had little effect on egg production and feed conversion, but high amounts of green tea powder (>2%) treatment significantly decreased the egg production performance. Green tea powder treatment had some beneficial effects on egg quality, especially in the albumen height and Haugh unit. Additionally, green tea powder treatment significantly changed the nutritional composition of eggs.
Comparisons of Modern U.S. and Canadian Malting Barley Cultivars with Those from Pre-Prohibition: II. Amylolytic Enzyme Activities and Thermostabilities

ABSTRACT Amylolytic enzyme activities and thermostabilities in North American pre-Prohibition and modern malting barley cultivars were compared throughout Congress mashing. The mean α-amylase activity was significantly higher in modern cultivars throughout mashing than in pre-Prohibition varieties, although the reverse was observed for mean thermostabilities, expressed as percent of initial activity. The mean limit dextrinase activity in modern cultivars was higher early in mashing than in pre-Prohibition varieties, but modern cultivar mean thermostability was less than in pre-Prohibition varieties at the end of mashing. There were no significant differences in population means for β-amylase or α-glucosidase activities during mashing although mean thermostabilities for both enzymes were greater in pre-Prohibition cultivars than in modern cultivars. A comparison of individual genotypes showed the four highest α-amylase activities were in modern cultivars, with Charles having the most thermostable (116%) and Tradition the least thermostable (21%). Among pre-Prohibition cultivars, Oderbrucker (132%) and Manchuria (127%) had the most thermostable α-amylases. Hanna and Manchuria had the highest β-amylase activities at 30 and 45 min of mashing. No cultivar had β-amylase activity beyond 45 min of mashing. At the end of mashing, Silver King, Hannchen and Oderbrucker had the highest α-glucosidase activities and thermostabilities (88, 52, and 53%, respectively). Among modern cultivars, highest α-glucosidase activities and thermostabilities were in Metcalfe (39%), Tradition (47%) and Charles (42%). The highest limit dextrinase activities, followed by their thermostabilities, at the end of mashing were in Manchuria (57%) and Hannchen (60%) followed by Tradition (44%), Metcalfe (26%) and Charles (37%).
Variations of salivary cortisol in dogs exposed to different cognitive and physical activities

Abstract Working dogs are gaining popularity for their ability to learn and perform tasks entertaining their human companions. For this reason, dogs are often subjected to various stimuli due to inter- and intra-specific interactions, environmental variations and effort required by different activities. In the present study, salivary cortisol was measured to monitor physiological response to different conditions. The first study was performed to assess the variability of salivary cortisol in dogs in usual environmental conditions. For this, salivary cortisol was measured in 10 dogs at home during three not consecutive days at three different times of the day and not significant variations between days and time of sampling were observed. In the second study, salivary cortisol was measured in dogs before and after Pointing Hunting (No. 5), Tracking for Ungulate Hunting (No. 6), Blood Tracking (No. 4), Agility Training (No. 6) and Animal Assisted Activities (AAA, No. 6). Salivary cortisol concentration significantly increased after the Pointing Hunting activity (p < .05), while salivary cortisol significantly decreased at the end of AAA session (p < .05). No significant differences in cortisol variations were observed for Tracking for Ungulate Hunting, Blood Tracking and Agility Training, before and after the activities. The response of cortisol suggests that the extent of hypothalamus–pituitary–adrenal axis activation varies between short high-intensity activities and endurance exercises. The measurement of salivary cortisol can support the trainers to evaluate the animal response to the stimulations.
Diverse Genotypes and Phenotypes of Three Novel Thyroid Hormone Receptor- (cid:2) Mutations

Context: Recentlyseveralpatientswithresistancetothyroidhormone(RTH)- (cid:2) duetoT 3 receptor- (cid:2) (TR (cid:2) ) mutations were identified. The phenotype of these patients consists of varying degrees of growth impairment, delayed bone, mental and motor development, constipation, macrocephaly, and near-normal thyroid function tests. Objective: The objective of the study was to describe the clinical phenotype of three new families with RTH (cid:2) and thereby gain more detailed knowledge on this novel syndrome. Design, Setting, and Participants: RTH (cid:2) was suspected in three index patients from different families. Detailed clinical and biochemical assessment and imaging and genetic analyses were performed in the patients and their relatives. In addition, functional consequences of TR (cid:2) mutations were investigated in vitro. Results: Westudied22individualsfromthreefamiliesandidentified10patientswithheterozygous TR (cid:2) mutations: C380fs387X, R384H, and A263S, respectively. The frame-shift mutation completely inactivated TR (cid:2) , whereas the missense mutations produced milder defects. These mutations were associatedwithdecreasingseverityoftheclinicalphenotype:thepatientinfamily1showedsevere defectsingrowth,mental,andmotordevelopment,whereasthesevenpatientsinfamily3hadonly mild clinical features. The most frequent abnormalities were anemia, constipation, and a delay in at least one of the developmental milestones. Serum free T 3 ranged from high-normal to high and serum free T 4 and rT 3 from normal to low. TSH levels were normal in all patients. Conclusions: This large case series underlines the variation in the clinical phenotype of RTH (cid:2) patients. RTH (cid:2) should be suspected in subjects when even mild clinical and laboratory features of hypothyroidism are present along with high/high-normal free T 3 , low/normal free T 4 , and normal TSH. Clin Endocrinol Metab 2945–2954,
Responses of Two Litter-Based Invertebrate Communities to Changes in Canopy Cover in a Forest Subject to Hurricanes

Tropical forests are subject to seasonal hurricanes resulting in cycles of canopy opening and deposition of litter, followed by periods of recovery and canopy closure. Herein, we review two studies of litter-based communities in Puerto Rico; (i) a survey of bromeliad invertebrates in three montane forest types along an elevational gradient in 1993–1997, during a period of canopy recovery after two severe hurricanes, and the results compared with those from a resurvey in 2010, and (ii) a large scale canopy trimming experiment in the lower montane (Tabonuco) forest designed to simulate an hurricane event, and to separate the effects of canopy opening from debris deposition. Measurements of changes in invertebrate community parameters and decay rates of litter were made in a litter bag experiment as part of this major experiment. As the canopy closed, during the periods of study, bromeliad density reduced, especially in the Tabonuco forest. This was associated with a decline in both alpha and gamma invertebrate diversity, which appears to have involved the loss of rarer species. In the Tabonuco forest, two endemic bromeliad specialists were not found during resampling in 2010, though the most common species were remarkably stable over the two decades. Canopy opening significantly altered the diversity, biomass, and composition of litter communities, irrespective of litter deposition. It particularly reduced organisms responsible for comminution of litter and increased the activity of fungivores and microbiovores. Both studies showed that canopy disturbance, either indirectly or directly, adversely affects invertebrate diversity and detrital processing.
GENDER-SPECIFIC INFLUENCE OF Aу MUTATION ON PROGENY METABOLIC PHENOTYPE, FETAL GROWTH AND PLACENTAL GENE EXPRESSION IN MICE

Obesity during pregnancy increases the risk of obesity in offspring. To correct the offspring development in obese mothers, it is necessary to reveal the molecular mechanisms that mediate the influence of the maternal environment on the offspring ontogenesis. Leptin levels increase with obesity. In C57Bl mice, the Ау mutation is associated with elevated blood levels of leptin in pregnant females and exerts a gender-specific effect on the metabolic phenotype of mature offspring. Aim: to study the influence of Ау mutation on sensitivity to diet-induced obesity in male and female offspring, on fetal and placental weight and on the expression of genes in the placentas of the fetuses of different sexes. Body weight and food intake on a standard and an obesogenic diet, fetal and placental weights on pregnancy days 13 and 18, and gene expression of glucose transporters (GLUT1, GLUT3), neutral amino acid transporters (SNAT1, SNAT2, SNAT4), insulin-like growth factor 2 IGF2 and its receptor IGF2R were measured in male and female offspring of и ɑ/ɑ (control) and Ау/ɑ mothers. Ay mutation influenced the body weight only in male offspring, which consumed a standard diet, and did not influence obesity development in both male and female offspring. The weight of fetuses and placentas in Ау/ɑ as compared to ɑ/ɑ females was reduced on day 13 of pregnancy and was not different on day 18. On day 13 of pregnancy, the mRNA levels of the examined genes did not differ in placentas of male and female fetuses in ɑ/ɑ females. In Ау/ɑ females, the gene expression of GLUT1, GLUT3, SNAT1 and SNAT4 was reduced in female placentas compared to male placentas. The results suggest that the sex-specific transcription response of placentas to elevated leptin levels in pregnant Ау/ɑ females can mediate the gender-specific impact of Ау mutation on the offspring metabolism in postnatal life.
Comparison of genotyping by sequencing and microsatellite markers for unravelling population structure in the clonal fungus Verticillium dahliae

Microsatellite genotyping of a large sample of isolates of Verticillium dahliae from diverse locations recently identified seven distinct genotypic clusters. However, these clusters were not put in the context of phenotypes known to be correlated with clonal lineages in V. dahliae. The objective of this study was to compare clusters defined by microsatellite markers with clonal lineages defined by single-nucleotide polymorphisms (SNPs) and vegetative compatibility groups (VCGs). Genotyping isolates known to belong to specific clonal lineages (based on SNPs) with microsatellite markers determined the correspondence of clusters and lineages. All but one cluster corresponded to a known clonal lineage, allowing analysis of correlations of phenotypes with microsatellite genotypes from other studies. As shown previously, most race 1 isolates are in lineage 2A, and most isolates with the defoliating pathotype are in lineage 1A. Phylogenetic incompatibility was used to test for recombination or homoplasy caused by hypervariable microsatellite loci; incompatibility was highly correlated with the number of alleles per locus, suggesting that homoplasy caused by parallel evolution of microsatellite alleles is the cause of incompatibility. Microsatellite genotyping of lineage 1A isolates from cotton and olive in Spain over a 29-year period revealed remarkably little variation; these markers did not mutate enough to provide insight on the spatial and temporal expansion of this clone. Overall, this study showed that microsatellite genotyping can be used to identify clonal lineages in V. dahliae, which has predictive power for inferring phenotypes of phytopathological relevance such as race and pathotype.
Effect of Different Pressing Processes and Density on Dimensional Stability and Mechanical Properties of Bamboo Fiber-based Composites

1) In this study, the dimensional stability and mechanical properties of bamboo fiber-based composites (BFBCs) were studied at two pressing manufacturing processes, i.e., hotand coldpressing, and were compared with three density parameters (1.0, 1.1, and 1.2 kg/m). Width swelling ratio (WSR), thickness swelling ratio (TSR), and water absorption ratio (WAR) were calculated for water immersions of 4 and 28 h. WSR, TSR, and WAR for specimens immersed for 28 h were higher than those for 4 h treatment, which shows that the immersion time has a significant influence on the dimensional stabilities of BFBCs. Moreover, the positive linear relations between density and dimensional were observed at both the pressing ways, indicating that the WSR, TSR, and WAR decreased with an increase in the density of BFBCs. The compressive strength, shear strength, modulus of rupture (MOR), and modulus of elasticity (MOE) were determined. The compressive strength, MOR, and MOE of hot-pressed specimens were significantly higher than those for the cold-pressed specimens, which are also directly proportional to density. Moreover, the samples with the highest density of 1.2 kg/m performed high values on mechanical properties in both the manufacturing methods.