Miracle-dz/UniFAR-FTUs huggingface dataset:
A case–control study on effects of the ATM, RAD51 and TP73 genetic variants on colorectal cancer risk

Abstract Aim ATM, RAD51 and TP73 are genes that take part in DNA repair pathways. The aim of this prospective case-control study was to determine the genotype and allele distributions of the ATM 5′-UTR G/A, RAD51 135 G/C and TP73 GC/AT polymorphisms and their relationship with clinical parameters in Turkish colorectal cancer (CRC) patients. Material and methods One hundred and four CRC patients and 113 healthy individuals were included in this study as control. The polymerase chain reaction-restriction fragment length polymorphism techniques were used. Results The ATM 5′-UTR G/A polymorphism GG (p = 0.001) and AA (p = 0.0001) genotypes were found higher in the patient group, while the GA genotype (p = 0.0001) and A allele (p = 0.001) were significantly higher in the control group. Moreover, the GG genotype (p = 0.042) was higher among patients with advanced-stage cancer and, while GA genotype (p = 0.047) was increased in patients without perineural invasion. The RAD51 135 G/C polymorphism GC genotype (p = 0.0001) and C allele (p = 0.0001) were significantly higher in the patient group, while CC genotype (p = 0.0001) was higher in the control group. No statistical significance was observed between the TP73 GC/AT polymorphism genotype and allele distribution and the clinical parameters. Conclusion In the Turkish population, the ATM 5′-UTR GG and AA genotypes, and the RAD51 135 G/C GC genotype and the C allele presence may be risk factors for CRC.
Feeding sows during the transition period—is a gestation diet, a simple transition diet, or a lactation diet the best choice?1

Abstract Three experiments were carried out to study whether a gestation diet, a simple transition diet, or a lactation diet is the best choice in late gestation and when sows preferably should be transferred to a high crude protein (CP) lactation diet. In experiment 1, 35 sows were fed either a gestation diet (12.1% CP), a lactation diet (15.9% CP), or a 50/50 mix (simple transition diet; 14.0% CP) from 6 d before parturition until parturition, to study the impact on farrowing and colostrum performance. In experiment 2, 90 sows were studied from 6 d before parturition until weaning at day 24 and they were fed one of five strategies: a gestation diet until day 3 or day 10 of lactation (strategy 1 and 2) and then lactation diet; a simple transition diet until day 3 or day 10 (strategy 3 and 4) and then lactation diet; or a lactation diet throughout the study (strategy 5). In experiment 3, 124 sows were fed strategy 1 or 5. Sows were weighed and back fat (BF) scanned when entering the farrowing unit and at day 2, 10, 17, and 24. Piglets were weighed at birth and after 24 h, and colostrum production was studied (experiment 1). Litter weight at day 2, 10, 17, and 24 was recorded, milk and blood samples were collected weekly and sow fat and protein mobilization, and balances of energy, N, and Lys were calculated from day 3 to 10 of lactation (experiment 2). Total- and live born piglets, and frequencies of stillbirth and piglet diarrhea were recorded (experiment 3). Feeding sows a gestation diet, a simple transition diet, or a lactation diet showed no evidence of effects on colostrum production or farrowing process (experiments 1 and 3) or lactation performance (experiments 2 and 3). Compared to previous studies, sows had a poor milk yield. Plasma urea was elevated (P < 0.001) indicating CP oversupply prior to parturition in sows fed the lactation diet as compared with the two other diets. According to calculated balances, all dietary strategies supplied insufficient amounts of N and Lys from day 3 to 10, indicating that the best choice is to feed sows with a high CP lactation diet from parturition and onwards. Primiparous sows had a higher plasma insulin concentration (P < 0.01), lower colostrum yield (P < 0.01), and higher frequency of piglet diarrhea (P < 0.001) than multiparous sows. In conclusion, in our conditions (high CP in gestation diet; poor milk yield; restricted feeding in early lactation), sow performance was not compromised by the dietary strategies, but results indicate that primiparous and multiparous sows should be fed differently.
Hotspot coevolution at protein-protein interfaces is a key identifier of native protein complexes

Protein-protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the protein docking challenge of distinguishing a natively bound complex from non-native forms. In this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein-protein interfaces. For a benchmark set of 53 bound complexes, KFC-E identifies a near-native binding mode as the top-scoring pose in 38% and in the top 5 in 55% of the complexes. For a set of 17 unbound complexes, KFC-E identifies a near-native pose in the top 10 ranked poses in more than 50% of the cases. By contrast, a scoring function that incorporates information on coevolution at predicted non-hotspots performs poorly by comparison. Our study highlights the importance of coevolution at hotspot residues in forming natively bound complexes and suggests a novel approach for coevolutionary scoring in protein docking. Author Summary A fundamental problem in biology is to distinguish between the native and non-native bound forms of protein-protein complexes. Experimental methods are often used to detect the native bound forms of proteins but, are demanding in terms of time and resources. Computational approaches have proven to be a useful alternative; they sample the different binding configurations for a pair of interacting proteins and then use an heuristic or physical model to score them. In this study we propose a new scoring approach, KFC-E, which focuses on the evolutionary contributions from a subset of key interface residues (hotspots) to identify native bound complexes. KFC-E capitalizes on the wealth of information in protein sequence databases by incorporating residue-level conservation and coevolution of putative binding hotspots. As hotspot residues mediate the binding energetics of protein-protein interactions, we hypothesize that the knowledge of putative hotspots coupled with their evolutionary information should be helpful in the identification of native bound protein-protein complexes.
Mucoidy, a general mechanism for maintaining lytic phage in populations of bacteria

We present evidence that mucoidy provides a general answer to the longstanding question of how lytic phage are maintained in bacterial populations. In serial transfer culture, populations of mucoid E. coli MG1655 that appear to be broadly resistant to lytic phage with different receptors are capable of maintaining these phage with little effect on the total density of bacteria. Based on the results of our analysis of a mathematical model, we postulate that the maintenance of phage in populations dominated by mucoid cells can be attributed to high rates of transition from the effectively resistant mucoid states to susceptible non-mucoid states. Our test of this “leaky resistance” hypothesis with both population dynamic and single cell experiments are consistent with it. We discuss reasons for the generalized resistance of these mucoid E. coli, and the genetic and molecular mechanisms responsible for the high rate of transition from mucoid to sensitive states.
Differences in unity: the go/no-go and stop signal tasks rely on different inhibitory mechanisms

Response inhibition refers to the suppression of prepared or initiated actions. Typically, the go/no-go task (GNGT) or the stop signal task (SST) are used interchangeably to capture individual differences in response inhibition. Yet, there is some controversy if these tasks assess similar inhibitory processes. We extracted the time-courses of sensory, motor, attentional, and cognitive control networks by group independent component (G-ICA) analysis of electroencephalography (EEG) data from both tasks. Additionally, electromyography (EMG) from the responding effector muscles was recorded to detect the timing of response inhibition. The results indicated that inhibitory performance in the GNGT may be comparable to response selection mechanisms, reaching peripheral muscles at around 316 ms. In contrast, inhibitory performance in the SST is achieved via biasing of the sensory-motor system in preparation for stopping, followed by fast sensory, motor and frontal integration during outright stopping. Inhibition can be detected at the peripheral level at 140 ms after stop stimulus presentation. The GNGT and the SST therefore seem to recruit widely different neural dynamics, implying that the interchangeable use of superficially similar inhibition tasks in both basic and clinical research is unwarranted.
Predator–prey interactions and climate change

Climate change is likely to impact all trophic levels, although the response of communities and ecosystems to it has only recently received considerable attention. Further, it is expected to affect the magnitude of species interactions themselves. In this chapter, we summarize why and how climate change could affect predator–prey interactions, then review the literature about its impact on predator–prey relationships in birds, and provide prospects for future studies. Expected effects on prey or predators may include changes in the following: distribution, phenology, population density, behaviour, morphology, or physiology. We review the currently available information concerning particular key topics: top-down versus bottom-up control, specialist versus generalist predators, functional versus numerical responses, trophic cascades and regime shifts, and lastly adaptation and selection. Finally, we focus our review on two well-studied bird examples: seabirds and raptors. Key future topics include long-term studies, modelling and experimental studies, evolutionary questions, and conservation issues.
Factors affecting local, regional, and global scale cyanobacterial dominance and secondary metabolite occurrence

iii Acknowledgements . iv List of Tables . viii List of Figures . ix List of Appendices . x Introduction . 1 Chapter 1. Predicting cyanobacterial abundance, microcystin, and geosmin in a eutrophic drinking-water reservoir using a 14 year dataset . 5 Abstract . 6 Introduction . 7 Methods. 9 Results . 13 Discussion . 18 Figures and Figure legends . 27 Tables . 37 Chapter 2. Combined effects of nitrogen to phosphorus and nitrate to ammonia ratios on cyanobacterial metabolite concentrations in eutrophic Midwestern USA reservoirs . 39 Abstract . 40 Introduction . 41 Methods. 44 Results . 48 Discussion . 50 Figures and Figure legends . 55
Metabolic labeling of RNA uncovers the contribution of transcription and decay rates on hypoxia-induced changes in RNA levels

Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. However, most transcriptomic studies do not distinguish the relative contribution of transcription, RNA processing, and RNA degradation processes to cellular homeostasis. Here we used metabolic labeling followed by massive parallel sequencing of newly transcribed and preexisting RNA fractions to simultaneously analyze RNA synthesis and decay in primary endothelial cells exposed to low oxygen tension. We found that changes in transcription rates induced by hypoxia are the major determinant of changes in RNA levels. However, degradation rates also had a significant contribution, accounting for 24% of the observed variability in total mRNA. In addition, our results indicated that hypoxia led to a reduction of the overall mRNA stability from a median half-life in normoxia of 8.7 h, to 5.7 h in hypoxia. Analysis of RNA content per cell confirmed a decrease of both mRNA and total RNA in hypoxic samples and that this effect is dependent on the EGLN/HIF/TSC2 axis. This effect could potentially contribute to fundamental global responses such as inhibition of translation in hypoxia. In summary, our study provides a quantitative analysis of the contribution of RNA synthesis and stability to the transcriptional response to hypoxia and uncovers an unexpected effect on the latter.
Prospects for predictive modeling of transition cow diseases

Abstract Transition cow diseases can negatively impact animal welfare and reduce dairy herd profitability. Transition cow disease incidence has remained relatively stable over time despite monitoring and management efforts aimed to reduce the risk of developing diseases. Dairy cattle disease risk is monitored by assessing multiple factors, including certain biomarker test results, health records, feed intake, body condition score, and milk production. However, these factors, which are used to make herd management decisions, are often reviewed separately without considering the correlation between them. In addition, the biomarkers that are currently used for monitoring may not be representative of the complex physiological changes that occur during the transition period. Predictive modeling, which uses data to predict future or current outcomes, is a method that can be used to combine the most predictive variables and their interactions efficiently. The use of an effective predictive model with relevant predictors for transition cow diseases will result in better targeted interventions, and therefore lower disease incidence. This review will discuss predictive modeling methods and candidate variables in the context of transition cow diseases. The next step is to investigate novel biomarkers and statistical methods that are best suited for the prediction of transition cow diseases.
Transcription Profiles of Age-at-Maturity-Associated Genes Suggest Cell Fate Commitment Regulation as a Key Factor in the Atlantic Salmon Maturation Process

Despite recent taxonomic diversification in studies linking genotype with phenotype, follow-up studies aimed at understanding the molecular processes of such genotype-phenotype associations remain rare. The age at which an individual reaches sexual maturity is an important fitness trait in many wild species. However, the molecular mechanisms regulating maturation timing processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) identified large-effect age-at-maturity-associated chromosomal regions including genes vgll3, akap11 and six6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon development and their potential molecular partners and pathways. Using Nanostring transcription profiling technology, we show development- and tissue-specific mRNA expression patterns for vgll3, akap11 and six6. Correlated expression levels of vgll3 and akap11, which have adjacent chromosomal location, suggests they may have shared regulation. Further, vgll3 correlating with arhgap6 and yap1, and akap11 with lats1 and yap1 suggests that Vgll3 and Akap11 take part in actin cytoskeleton regulation. Tissue-specific expression results indicate that vgll3 and akap11 paralogs have sex-dependent expression patterns in gonads. Moreover, six6 correlating with slc38a6 and rtn1, and Hippo signaling genes suggests that Six6 could have a broader role in the HPG neuroendrocrine and cell fate commitment regulation, respectively. We conclude that Vgll3, Akap11 and Six6 may influence Atlantic salmon maturation timing via affecting adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.
Catch‐up growth in the rhinoceros beetle Trypoxylus dichotomus (Coleoptera: Scarabaeidae): Smaller neonates gain relatively more body mass during larval development

Body size often varies among conspecific neonates. As larger adults generally have higher fitness than smaller conspecifics, it is adaptive for smaller neonates to subsequently gain relatively more size increments during larval development (catch‐up growth). Although catch‐up growth has been suggested in insects, inappropriate methods have been used to examine the size dependence of growth increments. Therefore, it remains unclear to what extent catch‐up growth is common among insects. The present study examined the size dependence of growth increments among larvae of Trypoxylus dichotomus using reduced major axis regression of final to initial body masses. Catch‐up growth was found consistently for larval instars. Furthermore, simulations of the size increments revealed that not only sexual divergence of the mean size, but also catch‐up growth within sexes plays a role in the development of sexual divergence in the body size distribution of T. dichotomus. The significance of catch‐up growth in body size evolution was discussed.
Response of Canino apricot trees to different sources of bio-organic fertilization

The present study was performed during the two successive seasons of 2014 and 2015 on "Canino" apricot (Prunus armenica) trees of ten years old grown in a new reclaimed sandy soil in a private orchard at El-Khtattba, El-Monofia Governorate. Evaluation to different sources of bio and organic fertilizers were performed through the shoot length, shoot diameter, number of leaves and chlorophyll content were following recorded. In addition to, some fruiting parameters i.e. number of flowers/spur, fruit set (%), fruit weight (g), yield/tree and TSS/acid ratio. Dehydrogenase activity, CO2 evolution, total nitrogen, available P and K in soil, the leaf contents N, P, K, Zn, Fe and Mn in dry matter of dry leaves were also determined. Results showed that organic fertilizer treatments used with recommended dose in this study improvement markedly both vegetative growth, fruit set, fruit weight, yield and fruit quality. Also, all sources of bio-organic fertilizers observed that storage studies on "Canino" apricot fruits showed that highest fruit ability for keeping quality for 30 days in cold storage at 0 °C and 90 % R.H. and 8 days of shelf life at room temperatures (20 -25 °C) was also studied. Algae treatment was the most effective one for increasing shoot length, diameter, leaf number and chlorophyll, chicken manure extract followed in descending order. Algae, chicken and cattle manure extract recorded the highest fruit set, yield and fruit weight. The results cleared that using different sources of bio-organic fertilizers improved TSS which was in parallel decreased acidity in fruit juice. All treatments improved storage properties under the shelf life (room temperature) during eight days, Nile fertile recorded the highest value of the weight loss. On the other hand, chicken manure and algae recorded the least fruit weight loss. The same results were noticed with fruit firmness. TSS % was differ among treatments and led to increase through storage eight days at shelf life but at cold storage (0°C) SSC increase gradually prolonged tell 20 days then reduction in SSC % occur at the last ten days in both seasons. Algae, chicken and cattle extract effectively were superior than all other treatments. Soil biological activity in rhizosphere (total bacteria counts, dehydrogenase as well as CO2 evolution showed a positive response with bio-organic fertilizers. Soil application of algae, compost tea and Nile fertile extract led to increase the soil WHC, organic matter (OM %), pH and TN and decrease EC compared to control.
Numerical Synthesis Algorithms and Antenna Designs for Next Generation Spaceborne Wind Scatterometer and CubeSat Antennas

Author(s): Budhu, Jordan | Advisor(s): Rahmat-Samii, Yahya | Abstract: Two novel aperture type antennas, both for next-generation space borne applications, are designed. The first is 3D printed, all-dielectric, inhomogeneous, shaped lens antenna designed to produce a conically scanned spinning spot beam. The electronic scan stems from a ring of feeds located along the ring focus designed into the azimuthally symmetric lens. The antenna is proposed for use in a space-borne scatterometer used to measure wind speeds upon the surface of the earth’s oceans. The design requires the advent of a complex code hybridizing the Computational Electromagnetics method of Geometrical Optics with the optimization strategy of Particle Swarm Optimization. This code and its mathematical formulations, the resultant designs, and the measurements validating the codes and obtained designs are presented in this dissertation. The second is a new novel dual reflector Gregorian antenna system designed to meet the stringent requirements of the newly proposed CubeSat satellite paradigm by folding the optics into one of the most compact dual reflectors to date. The design combines a high gain reflectarray main aperture with an ellipsoidal subreflector fed by a patch array feed. The system is coplanar with the CubeSat chassis, deploying only the subreflector and thus has no moving cables or RF parts. This antenna design also requires a complex computer code to design. The code implemented to design the reflectarrays applies several novel acceleration strategies to the spectral domain method of moments algorithm in order to speed up the calculations. The theory and mathematical formulations behind this algorithm are also presented, as well as the resultant designs and measurements. The accelerated codes are used to design several Ka-Band reflectarrays. Measured and simulated results are provided.
Impact of Foliar, Mineral Fertilization and some Plant Activators on Cucumber Growth and Productivity

Two field experiments were conducted during 2016 and 2017 summer seasons in a private farm near El-Mahalla ElKobra, El-Gharbia governrate to evaluate the effect of three NPK levels (100, 75 and 50 percentage of NPK recommended dose) and NPK foliar application (with or without foliar NPK spraying) with three foliar activators applications (chitosan, moringa leaf extract and lithovit) as well as tap water as a control and their interactions on vegetative growth characters, ion percentage, yield and its quality of cucumber plants cv. prince. Obtained data revealed that 100 % of recommended NPK (120 kg N, 50 kg P2O5, 100 kg K2O/fed.) and foliar application with NPK at 3 g/l combined to foliar application with chitosan at 3 g/l gave the highest values of yield and its components i.e. (number of fruits, fruit yield/ plant, early and total yield/fed.), while 75% NPK of recommended dose (90 kg N, 37.5 kg P2O5, 75 kg K2O/fed.) plus NPK foliar application with spraying moringa leaf extract at 10 ml/l gave the highest values of vegetative growth parameters i.e. (number of leaves/plant, shoot fresh and dry weight, plant height), also chitosan at 3 g/l combined with foliar NPK and 75% of NPK recommended dose as soil application gave superiority in N, P and K percentage in cucumber leaves, in addition, total sugar, TSS and total chlorophyll in cucumber fruits. Thus, it can be recommended that use 75% NPK from recommended dose plus foliar application NPK and foliar spray with moringa leaf extract applications to decrease mineral fertilization which reflected on reducing production costs and mitigate the environmental pollution and protect the human health.