Miracle-dz/UniFAR-FTUs huggingface dataset:
Can genomic data enable genetic evaluation with phenotypes recorded on smallholder farms

The huge increases in dairy cattle milk yield in advanced economies over the past century is a powerful example of the role of breeding in improving livestock productivity. However, breeding practices have had poor efficacy and penetrance in smallholder farming systems in regions such as East Africa. Therefore, to meet the­­ continually growing expectations of a more discerning global population for a more varied and nutritious diet, effective dairy cattle breeding programmes need to reach smallholder dairy producers. In advanced economies, large data sets from commercial farms with modest to large herd sizes (e.g. 20 to several thousand cows) and widespread use of AI have provided sufficient animals within each herd and sufficient genetic connectedness between herds. This has enabled the genetic and environmental components of an individual animal’s phenotype to be accurately separated, thus providing accurate genetic evaluations with pedigree information. Typically, herds are neither large nor have high genetic connectedness in smallholder farming systems, such as in East Africa, which limits genetic evaluation with pedigree information. Genomic information keeps track of shared haplotypes rather than animals. This information could capture and strengthen connectedness between herds and through this may enable genetic evaluations based on phenotypes recorded on smallholder dairy farms. The objective of this study was to use simulation to quantify the power of genomic information to enable genetic evaluation under such conditions. The results show; (i) GBLUP produced higher accuracies than PBLUP at all population sizes and herd sizes, (ii) Models with herd fitted as a random effect produced equal or higher accuracies than the model with herd fitted as a fixed effect across all herd size scenarios, (iii) At low levels of genetic connectedness, with four offspring per sire and one to two animals per herd, GBLUP produced EBV accuracies greater than 0.5. Generally, a decrease in the number of sires mated showed consistently higher accuracies compared to when more sires were used. These results suggest that effective breeding programs that use data recorded on smallholder dairy farms in East Africa are possible.
Determining the Accuracy of Blood Pressure to Height Ratio as a Screening Tool for Hypertension among Egyptian Children

Background: Hypertension diagnosis in children is difficult because of the multiple sex, age, and height-specific thresholds to define elevated blood pressure (BP). Blood pressureto-height ratio (BPHR) has been used to facilitate the identification of elevated BP in children. Methods: From January to June 2017, a cross-sectional study was conducted for 830 adolescents aged 12 to 15 years in Abu Kabir city, Sharkia governorate, Egypt. Blood pressure tables from the National High Blood Pressure Education Program (NHBPEP) Working Group on High Blood Pressure in Children and Adolescents were used as our standard of comparison. Sex-specific systolic and diastolic blood pressure-to-height ratios (SBPHR and DBPHR) were calculated. Receiver operating Characteristic (ROC) curve analyses were performed to assess the accuracy of BPHR for discriminating between hypertensive and non-hypertensive adolescents. Results: The prevalence of prehypertension and hypertension were 8.4% and 4.9% respectively. Optimal SBPHR and DBPHR thresholds for defining elevated BP were 0.741 and 0.475 in males, respectively, and 0.750 and 0.494 in females, respectively. The sensitivity of SBPHR and DBPHR in both sexes was all above 93%, and specificity in both sexes was above 94%. Positive predictive value for SBPHR and DBPHR was 76.4% for both in males; and 71.4% and 71.6% in females respectively; negative predictive values in both sexes were all above 98%. Conclusions: BPHR is a simple screening tool with high sensitivity and specificity for screening hypertension in adolescents.
A Survey on the Hypervolume Indicator in Evolutionary Multiobjective Optimization

Hypervolume is widely used as a performance indicator in the field of evolutionary multiobjective optimization (EMO). It is used not only for performance evaluation of EMO algorithms (EMOAs) but also in indicator-based EMOAs to guide the search. Since its initial proposal in the late 1990s, a wide variety of studies have been done on various topics, including hypervolume calculation, optimal $\mu $ -distribution, subset selection, hypervolume-based EMOAs, and extensions of the hypervolume indicator. However, currently there is no work to systematically survey the hypervolume indicator for these topics whereas it has been frequently used in the EMO field. This article aims to fill this gap and provide a comprehensive survey on the hypervolume indicator. We expect that this survey will help EMO researchers to understand the hypervolume indicator more deeply and thoroughly, and promote further utilization of the hypervolume indicator in the EMO field.
DLITE: Dynamic Local Intercellular Tension Estimation

The shape of cell-cell interfaces and the forces resulting from actomyosin interactions, mem-brane tension, or cell-cell adhesion are closely coupled. For example, the tight junction protein, ZO-1, forms a link between the force-bearing actin cortex and the rest of the tight junction protein (TJP) complex, regulating epithelial cell differentiation and the flux of solutes across epithelia. Here we introduce a method for Dynamic Local Intercellular Tension Estimation (DLITE) to computationally infer the evolution of cell-cell forces from a mechanical model of collective cell behaviour. This builds upon prior work in the field (CellFIT, Brodland et al., PloS one 9.6 (2014): e99116). We validate our estimated forces against those predicted by Surface Evolver simulations. Inferred tensions of a cell colony rearranging over time correlate better with the ground truth for our method (DLITE) than for prior methods intended for single time-points. DLITE is robust to both skeletonization errors and topological changes. Finally, we used DLITE in WTC-11 human induced pluripotent stem (hIPS) cells endogenously expressing ZO-1 GFP to find that major topo-logical changes in cell connectivity, e.g. mitosis, can result in an increase in tension. This suggests a correlation between the dynamics of cell-cell forces and colony rearrangement.
Bibliometric analysis of journal articles indexed in TR Index published with a pediatric dentist author: A snapshot of 21th Century

Bibliometric profile of articles published by pediatric dentists from Turkey were investigated in this study. Records of articles written with a pediatric dentist author between 2000- 2019 indexed in TR-Index database were compiled. Recurrent records and articles without a pediatric dentist author were excluded. Abstracts and full texts of the articles were processed to gather data of; year published, language, article’s area of interest (AoI), study design (Sd) and citation counts. Keyword co-occurrences were analyzed using VOSVIEWER® software.Spearman correlation analysis was performed between the numbers of dental schools, and number of published articles. Frequencies of categorical data were compared using chi square test. Differences between groups for continuous variables were assessed using Mann Whitney U test. P< 0.05 determined statistical significance. 512 articles were included. There was a positive correlation between the number of articles published and the number of dental schoolswho had started education(r=0.79, p< 0.001). The number of articles published in Turkish were more than English (X2= 157.531, 1) (p< 0.001). 300 of the articles were featured as research, 119 were reviews and 93 were case reports. Overall most frequently studied AoI was dental materials (23.8 %), followed by cariology/preventive dentistry (14.8%) and dental anomalies (10.2%). Laboratory research was the most preferred (26%) Sd, followed by literature review (23%), case reports (18.2%). Articles published in English were cited more than articles in Turkish (p= 0.02). Occurrences of the keywords were mostly nonspecific terms. Number of articles with pediatric dentist authors have been increasing remarkably since 2000. The increase in both the number of dental journals and the number of dental schools might have attributed to this trend. The next step for the authors of this field might be to branch out to less studied areas of interest and study designs to provide higher levels of evidence.
Simultaneous proteomics and three PTMomics characterization of pro-inflammatory cytokines stimulated INS-1E cells using TiO2 enrichment strategy

Diverse protein post-translational modifications (PTMs) in proteins form complex combinatorial patterns to regulate the protein function and biological processes in a fine-tuning manner. Reversible phosphorylation, cysteines (Cys) modification, and N-linked glycosylation are essentially involved in cellular signaling pathways of pro-inflammatory cytokines, which can induce beta cell death and diabetes. Here we developed a novel mass spectrometry–based proteomic strategy (termed TiCPG) for the simultaneous comprehensive characterization of the proteome and three post-translational modifications (PTMomes) by applying TiO2 enrichment of peptides with reversibly modified Cysteine (rmCys), Phosphorylation, and sialylated N-linked (SAN-) Glycosylation from low amount of sample material with largely minimized sample loss. We applied this TiCPG strategy to quantitatively study the change of the three PTMs in β-cell-like INS-1E cells subject to pro-inflammatory cytokines stimulation. It enabled efficient enrichment and quantitative analysis of 8346 rmCys sites, 10321 phosphosites and 1906 SAN-glycosylation sites from 5853 proteins. Significant regulation was found on 100 proteins at the total protein level, while much higher degree of regulation was identified on 3025 peptides with PTMs from 1490 proteins. The three PTMs were co-regulated in proteins, but demonstrated differential spatial and temporal patterns related to protein cellular localization and function in the time course of cytokines stimulation, and they were extensively involved in essential signaling pathways related to pro-inflammatory cytokine mediated β-cell apoptosis, such as the inducible NO synthase (NOS2) signaling pathway, Overall, the TiCPG strategy is proved as a straight forward and powerful tool for multiple PTMomics studies.
Pérdida de semillas en fase de pre-dispersión en dos especies de Prosopis (Fabacea: Mimosoidea) del Desierto del Monte, Argentina

Pre-dispersal flters imposed on the seed stage can alter the likelihood of seed dispersal. We evaluate pre-dispersal seed loss due to predation by insects and abortion in Prosopis ﬂexuosa and P. chilensis . This study was conducted in two protected areas in the Monte Desert. We collected P. ﬂexuosa and P. chilensis fruits from diﬀerent trees, from two plots and two years. Samples were maintained for 50 days in translucent PVC boles stored in a laboratory under stable temperature (25 °C) and natural photoperiod, awaiting the emergence of insects. Then we opened the fruits and individually examined all seeds to determine their condition. We found that total pre-dispersal seed loss was 32% in P. ﬂexuosa and 21% in P. chilensis . Seed predation by insects was the major source of pre dispersal seed loss (19% in P. ﬂexuosa and 14% in P. chilensis ). The main seed predator was the apionid weevil (Brentidae: Apioninae) in P. ﬂexuosa , and bruchid beetles (Chrysomelidae: Bruchinae) in P. chilensis . Some bruchid beetles prey upon seeds, completing their life cycle, whereas others remain inside seeds (41% in P. ﬂexuosa and 49% in P. chilensis , of total seed damaged by bruchid beetles). Seed abortion was another important source of seed loss, especially for P. ﬂexuosa , but its cause still remains unknown. We show and discuss the extent of a proposed methodology to account for pre-dispersal seed predation that includes the immature stages of non-emergent bruchid. Pre-dispersal seed loss by insects and abortion represent an ecological flter that limits the amount of seeds available for dispersal and establishment of these species. Understanding seed loss process may contribute to know and predict Prosopis population dynamics, revealing the natural regeneration mechanisms to forest recovery. https://doi.org/10.25260/EA.18. 28.2. 0.576
Viruses rule over adaptation in conserved human proteins

Adaptive evolution often involves fast-evolving proteins, and the fastest-evolving proteins in primates include antiviral proteins engaged in an arms race with viruses 1-3. Even though fast-evolving antiviral proteins are the most studied cases of primate host adaptation against viruses, viruses predominantly interact with host proteins that are broadly conserved between distant species in order to complete their replication cycle 4. Broadly conserved proteins are generally viewed as playing a negligible role in adaptive evolution. Here, we used a dataset of ~4,500 human proteins known to physically interact with viruses (VIPs for Virus-Interacting Proteins), to test the involvement of broadly conserved proteins in adaptive evolution against viruses. We found that VIPs conserved between animals and fungi have experienced not only high rates of adaption, but also strong adaptive events. Broadly conserved proteins that do not interact with viruses experienced very little adaptation. As a result, the arms race with viruses explains more than 75% of adaptation in the most phylogenetically conserved subset of the human proteome. Our results imply that broadly conserved proteins have played a significant role in adaptation, and that viruses were likely one of very few selective pressures that were able to force the conserved, central pillars of host cellular functions to adapt during evolution.
Fiscal space in the euro area before Covid-19

Numerical simulations of fiscal space in the euro area, based on 12 different situations, point to the large uncertainty surrounding the capacity of Member States to pay back their public debts. Debt sustainability appears to depend crucially on long-term nominal interest rate being lower than nominal growth for a long period. Only in this case do major European countries experience some additional fiscal space. Although the analytics behind this exercise is common knowledge among macroeconomists, it gives an order of the magnitude of fiscal space in the euro area and it confirms that interactions between the ECB and governments are key to escape the public finances consequences of an exogenous global shock like Covid-19.
ASSESSMENT OF ACUTE METALS TOXICITY IN Catla catla THROUGH HEMATOLOGICAL AND BIOCHEMICAL BLOOD MARKERS

Heavy metals constitute a major group of aquatic contaminants and their large amount accumulates in aquatic ecosystems as a consequence of land based activities (Vutukuru, 2003). Among metals, cadmium (Cd), one of the most dangerous environmental pollutant because of its tendency to bio-accumulate in living organisms raises environmental concern (Liao et al., 2011; Sfakianakis et al., 2015). The use of Cd containing agricultural chemicals, pesticides, fertilizers and sewage sludge in farm land, might also enhance to the water contamination (ATSDR, 2003). Survival rate of aquatic organisms is affected due to the exposure to Cd and leads to a gradual extinction of their generations in polluted water (Sridhara et al., 2008). Although copper (Cu) is essential to the health of all living organisms as it is involved in several fundamental biological processes however, it proves disastrous to aquatic organisms when it surpasses the normal limits. Its toxicity to aquatic organisms had previously been described by several workers (Paquin et al., 2002; Dhanapakiam et al., 2006; Ketpadung and Tangkrock-Olan, 2006; Isani et al., 2013). Copper sulphate (CuSO4) is generally used as an algaecide as well as an herbicide in aquatic weed control (Carbonell and Tarazona, 1993). Fishes are the animals that cannot escape from the negative effects of these contaminants and prove as good bioindicators of aquatic pollution (Pandey, 2013). Fish blood is being studied increasingly in environmental monitoring and toxicological research as a potential indicator of pathological and physiological changes in disease investigations and fishery management (Remyla et al., 2008). Numerous studies have showed that metals, for instance cadmium and copper induce changes in blood parameters of fish (Kotsanis et al., 2000; Mazon et al., 2003; Ajani and Akpoilih, 2010; AlGhanim, 2011; Sayed and Shokr, 2015). Numerous hematological indices, for instance hemoglobin, hematocrit, white blood cells, red blood cells, mean cell volume, mean cell hemoglobin and mean cell hemoglobin concentration have been used as indicators of metal contamination in the aquatic ecosystem (Kavitha et al., 2010). Measurement of serum biochemical parameters such as aspartate aminotransferase, alanine aminotransferase, ions, total protein and glucose is valuable to ascertain the toxicity of target organs along with the overall health status of animals (Kori-Siakpere et al., 2012). In fisheries management program hematology and serum biochemistry data are of great importance to monitor the health status of aquatic animals (Skjervold et al., 2001). Accordingly, the objective of this study was to investigate the effects of acute cadmium and copper exposure for varying durations on hematological and serum biochemical parameters as sensitive indices for the evaluation of fish Pak. J. Agri. Sci., Vol. 55(2), 449-454; 2018 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: 10.21162/PAKJAS/18.6002 http://www.pakjas. com.pk
Determination of the treatment period of banana seedlings with rhizobacteria in the control of Meloidogyne javanica

Abstract The introduction of rhizobacteria to the soil can be done via treatment of propagating materials. The aim of this work was to evaluate in greenhouse the influence of immersion periods of micropropagated ‘Prata-Anã’ banana seedling roots in suspension of different rhizobacterial isolates on the growth of seedlings and control of Meloidogyne javanica. The experiment was set up in greenhouse in a randomized block design in a 10 x 2 factorial scheme (rhizobacteria isolates) x (immersion periods: 60 and 120 minutes) with 10 replicates. The additional treatment (control) was composed of seedlings without any treatment infected with M. javanica. Treated seedlings were planted in pots containing soil: previously autoclaved sand. After twenty-four hours, suspension containing 3,000 M. javanica eggs was added to the soil. At 60 days, number of galls, egg mass and eggs per root system, number of second-stage juveniles (J2) per 100 cm3 of soil were evaluated and the reproduction factor was calculated. Shoot dry matter mass was also evaluated. Of the four rhizobacteria that reduced the reproductive capacity of the nematode, three were more efficient when seedlings were treated for 120 minutes. The treatment period of banana seedlings did not affect the shoot dry matter yield and all rhizobacteria increased the dry matter weight of seedlings infected with Meloidogyne javanica. It could be concluded that rhizobacteria have different treatment time requirements for seedlings to control the nematode, but do not interfere with the development of seedlings.
Fission product data for thermal reactors. Part II. Yields

Thermal neutron cumulative fission yields from 3 3 u, 8 3 U, Pu and Pu are reviewed. Particular attention is given to mass spectrometric data which accounts for the greater fraction of the total yields. A three-step treatment of spectrometric data is used: first, the concentrations of isotopes of each fission product element are determined to define the local shape of the yield vs. mass curve; second, the relative numbers of atoms of each element formed in fission are derived from isotope dilution or isobaric coupling measurements thus linking together all the isotopic concentrations of both the light or heavy mass peaks to obtain the shape over the entire mass spectrometric range; third, the mass spectrometric data are normalized using isotope dilution measurements of the number of fissions and radiometric and interpolated fields. In general, the greatest source of uncertainty in the mass spectrometric range is the second step and appears to arise from systematic differences between the methods used in different laboratories. Manuscript prepared November 1972 Chalk River Nuclear Laboratories Chalk River, Ontario April 1973 AECL-3037 Part II Données sur les produits de fission pour les réacteurs thermiques Partie II Rendements
Evaluation of growth, yield and quality attributes of different okra genotypes under Nagaland condition

Field experiments on “Evaluation of growth, yield and quality attributes of 28 okra genotypes” were conducted during 2013 and 2014 at the Experimental Farm, Department of Horticulture, School of Agricultural Sciences and Rural Development, Medziphema Campus, Nagaland University to evaluate the performance of various genotypes of okra under foothill condition of Nagaland. Twenty eight genotypes of okra were evaluated in RBD design with three replications. Results revealed that all the genotypes exhibited significant variation in their performance in terms of growth, yield and quality attributes. Among the genotypes, IIVRO-SKY/DR/RS-66 recorded maximum plant height (176.23 cm) and IIVRO-SKY/DR/RS-107 recorded maximum number of branches plant-1 (2.45). Maximum number of leaves (44.06), size of leaf (680.17 cm2), cumulative leaf area (3.00 m2) and leaf area index (22.25) were recorded in genotype IIVRO-608-8-1 while genotype IIVRO-770 exhibited least number of days to first flowering (42.52 days), number of nodes for first flower (4.95), number of days for fruit setting (43.55 days) and maturity period (50.95 days). Genotype IIVRO-770 also exhibited maximum duration of flowering (62.48 days) and number of ridges fruit-1 (7.13) whereas genotype IC-117319 recorded earliest period from fruit set to harvest (5.35 days). The findings also indicate that genotype IIVRO-608-8-1 recorded maximum result in yield attributes such as number of fruits (18.42), weight of fruits (25.95 g), number of seeds fruit-1 (54.09), yield plant-1 (477.66 g), and pod yield hectare-1 (17.39 t). For quality attributes, it was observed that maximum protein content (4.89%) was observed in genotype IC-218844, maximum vitamin-C (22.30 mg 100g-1 of fruit) in Arka Anamika. Genotype IIVRO-599-8-1 was found to be highly resistant to blister beetle infestation whereas genotype IIVRO-307-10-1 II showed high resistance to yellow vein mosaic virus.
Performance Assessment of a Cavity on Source ChargePlasmaTFET-Based Biosensor

The promising candidate for designing a highly sensitive biosensor is the tunneling field effect transistor (TFET). In this work, for the first time the performance analysis of a cavity on source charge plasma tunneling field effect transistor (CS-CPTFET) based lable-free biosensor has been proposed. To design the device,charge plasma concept is adapted, where suitable metal workfunctions have been used to create the source and drain regions. The charge plasma technique reduces random dopant fluctuation, thermal budget and steps required for the fabrication. The significant advantage of the proposed device includes the creation of abrupt doping profile at the tunneling junction (source-channel). The achievement of abrupt doping profile at the tunneling junction is responsible for the enhanced sensitivity and suppression of negative conduction (ambipolar) since the cavity is created in the source oxide region of CS-CPTFET biosensor. The response of the proposed biosensor for various biomolecules has been analyzed in terms of band energy variation, electric field, surface potential and transfer characteristics by using Silvaco ATLAS device simulator. Various biomolecules such as uricase (k = 1.54), Glucose oxidase (k = 3.46), APTES (k = 3.57), bacteriophage T7 (k = 6.3), keratin (k = 8) and gelatin (k = 12) have been considered for examining the performance of proposed biosensor.