Miracle-dz/UniFAR-FTUs huggingface dataset:
Seroprevalence and Molecular Identification of Brucella spp. in Camels in Egypt

Brucellosis is one of the most important worldwide zoonoses of many countries including Egypt. Camel brucellosis has not gained much attention in Egypt yet. This study is focused on the three governorates with the highest camel populations and the largest camel markets in the country to determine the disease seroprevalence and identify the Brucella species in local camel holdings. In total, 381 serum samples were collected from male and female camels from Giza, Aswan, and Al-Bahr Al-Ahmar (the Red Sea) governorates. Samples were serologically examined using the Rose–Bengal plate test (RBPT), indirect ELISA (i-ELISA), competitive ELISA (c-ELISA) and complement fixation test (CFT). Brucella antibodies were detected in 59 (15.5%), 87 (22.8%), 77 (20.2%) and 118 (31.0%) of sera by RBPT, i-ELISA, c-ELISA and CFT, respectively. Using real-time PCR, Brucella DNA was amplified in 32 (8.4%) seropositive samples including Brucella abortus (25/32), Brucella suis (5/32) and Brucella melitensis (2/32), defining a complex epidemiological status. To the best of our knowledge, this is the first study reporting Brucella suis DNA in camel serum. The risk-associated factors including age, sex, breed and geographical distribution were statistically analyzed, showing non-significant association with seroprevalence. The results of this study will raise awareness for camel brucellosis and help develop effective control strategies.
Inter-rater reliability of a composite health promotion scoring system developed in Singapore.

INTRODUCTION In view of the important role that environment plays in improving population health, the implementation of health promotion programmes are recommended in living and working environments. Assessing the prevalence of such community health-promoting practices is important for identifying gaps and making continuous and tangible improvements to health-promoting environments. We aimed to evaluate the inter-rater reliability of a composite scorecard used to assess the prevalence of community health-promoting practices in Singapore. METHODS Inter-rater reliability for the use of the composite health promotion scorecards was evaluated in eight residential zones in the western region of Singapore. Three raters were involved in the assessment and each zone was evaluated by two raters. Health-promoting practices in residential zones were assessed based on 44 measurable elements under five domains - community support and resources, healthy behaviours, chronic conditions, mental health and common medical emergencies - in the composite scorecard using weighted kappa. The strength of agreement was determined based on Landis and Koch's classification method. RESULTS A high degree of agreement (almost perfect-to-perfect) was seen between both raters for the measurable elements from most domains and subdomains. An exception was observed for the community support and resources domain, where there was a lower degree of agreement between the raters for a couple of elements. CONCLUSION The composite scorecard demonstrated a high degree of reliability and yielded similar scores for the same residential zone, even when used by different raters.
Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle

Simple Summary Reproductive performance has direct economic implications on the beef cattle industry. The majority of Zebu breeds (e.g., Nellore; Bos taurus indicus) have poor reproductive performance compared to other cattle breeds. In this context, genetic progress can be achieved for fertility and reproduction through the use of genomic selection for indicator variables that efficiently assess the biological mechanisms underlying cattle fertility. Therefore, this study aimed to estimate genetic parameters (heritability and genetic correlations) and identify candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. Our findings indicate that measuring circulating AMH in Nellore cattle enables the identification of animals with high genetic merit for superovulatory responses, as well as early selection of the best oocyte donors for in vitro embryo production. Both traits are heritable and influenced by a large number of important genes. Therefore, AMH and AFP can be used as indicator traits to genetically improve fertility rates in Nellore cattle and to identify better oocyte donors. Abstract Reproductive efficiency plays a major role in the long-term sustainability of livestock industries and can be improved through genetic and genomic selection. This study aimed to estimate genetic parameters (heritability and genetic correlation) and identify genomic regions and candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. The datasets included phenotypic records for 1099 and 289 Nellore females for AFP and AMH, respectively, high-density single nucleotide polymorphism (SNP) genotypes for 944 animals, and 4129 individuals in the pedigree. The heritability estimates for AMH and AFP were 0.28 ± 0.07 and 0.30 ± 0.09, and the traits were highly and positively genetically correlated (rG = 0.81 ± 0.02). These findings indicated that these traits can be improved through selective breeding, and substantial indirect genetic gains are expected by selecting for only one of the two traits. A total of 31 genomic regions were shown to be associated with AMH or AFP, and two genomic regions located on BTA1 (64.9–65.0 Mb and 109.1–109.2 Mb) overlapped between the traits. Various candidate genes were identified to be potentially linked to important biological processes such as ovulation, tissue remodeling, and the immune system. Our findings support the use of AMH and AFP as indicator traits to genetically improve fertility rates in Nellore cattle and identify better oocyte donors.
Frost-tolerance genes Fr-A2 and Fr-B2 in Australian wheat and their effects on days to heading and grain yield in lower rainfall environments in southern Australia

Abstract. FROST RESISTANCE 2 (FR2) genes of wheat are C-Repeat Binding Factor (CBF) genes with two major alleles known for both Fr-A2 (‘T’ and ‘S’) and Fr-B2 (‘WT’ and ‘DEL’). VERNALIZATION 1 (VRN1) genes have a regulatory role on CBF genes, with known epistatic interactions between Vrn-A1 and Fr-A2 for tolerance to freezing temperatures during vegetative growth. VRN1 genes were also known to affect days to heading and grain yield. Therefore, FR2 genes might also affect these traits. A wide range of cultivars was characterised for VRN1, Fr-A2 and Fr-B2 genes. A third allele of Fr-A2 was found in cvv Excalibur and Axe. The winter cultivar Norstar, which was known to have a high level of frost tolerance during vegetative growth, had the combination Vrn-A1w + Fr-A2T + Fr-B2WT, as did a spring landrace from Afghanistan that was known to have superior tolerance to frost during reproductive development. No Australian spring cultivar was found with this combination, but it could be selected from crosses between adapted cultivars. This would enable the role of VRN1 and FR2 alleles in reproductive frost tolerance to be evaluated in an adapted background. Using large, existing, plant-breeding datasets, the T allele of Fr-A2 delayed heading relative to the S allele, and the WT allele of Fr-B2 delayed heading relative to the DEL allele, but only in combination with particular alleles of the VRN1 genes. Fr-B2 affected grain yield, with the highest grain yields for spring lines produced by Fr-B2DEL in combination with the spring allele of Vrn-B1.
An investigation into the initiation of VSG switching in Trypanosoma brucei

Trypanosoma brucei, the eukaryotic parasite that causes human African trypanosomiasis in humans, evades the immune system through antigenic variation. T. brucei antigenic variation involves the periodic switching of the variant surface glycoprotein (VSG) coat to an antigenically distinct variant. A single VSG is expressed on the cell surface at any one time, but the T. brucei genome contains a vast number of silent VSGs. To be expressed, a VSG must be located in a specialised VSG blood stream form expression site (VSG BES). Silent VSGs are copied into VSG BES by homologous recombination. Several proteins have been demonstrated to be involved in this process but how VSG switching is initiated remains unclear. Four putative DNA repair factors were identified in T. brucei, whose eukaryotic homologues play a range of roles in DNA repair and other aspects of genome maintenance. These were two RecQ-like helicases, a Mus81 endonuclease and a Pif1 family helicase (PIF6). To examine whether these factors play a role in DNA repair and VSG switching, mutants were generated in blood stream form T. brucei cells. Analysis of RecQ1 by RNAi knockdown revealed it to be an essential gene in bloodstream form T. brucei, possibly involved in nuclear DNA replication. Phenotypic analysis of recq2 mutants suggests that RECQ2 is involved in the repair of a range of DNA damaging agents. Furthermore, analysis of survival following DSB induction suggests RECQ2 is involved in the repair of DNA DSBs, including those in the active VSG BES. VSG switching analysis showed that recq2-/- mutants have an elevated VSG switching rate and increase in recombination events upstream of the active VSG. These analyses suggest that RECQ2 suppresses VSG switching in T. brucei by suppressing recombination events near the active VSG. Analysis of mus81 mutants showed mus81-/- mutants to be sensitive to agents inducing replication stalling and DNA breaks, and that MUS81 is important in the repair of DSBs. PIF6 appears to be a complicated DNA repair factor, different from MUS81 and RECQ2. pif6+/- and pif6-/- mutants appear to be more resistant to MMS than wild type cells, though more sensitive to the replication stalling agent hydroxyurea. pif6 mutants do not appear to be more sensitive to DSBs than wild type cells and may even be more resistant. It is unclear whether PIF6 is involved in VSG switching and more work is required on this factor to attempt to understand its DNA repair and VSG switching function in T. brucei. These analyses shed light on the DNA repair functions of four previously uncharacterised T. brucei proteins. In particular, observations that RECQ2 is deficient in repairing DSBs upstream of the active VSG and mutants exhibit an elevated VSG switching rate cannot be reconciled with current thinking that direct formation of DSBs in this location initiates VSG switching. This suggests that the initiation of VSG switching is more complex than currently thought and requires careful further study and consideration of the relevance of using direct DSBs in this location to model VSG switching.
Effects of protocatechuic acid on ameliorating lipid profiles and cardio-protection against coronary artery disease in high fat and fructose diet fed in rats

A coronary heart disease leads to increase in obesity and metabolic dysfunction. Protocatechuic acid (PCA), due to its antioxidant, anti-inflammatory, neuro protective activities was found efficient as cardio-protective in coronary heart disease. Our study investigated hypolipidemic and cardioprotective effects of protocatechuic acid in the coronary artery disease induced by high fat and fructose diet (HFD) rat models. A diet rich in fat and fructose was fed to male Wistar rats prior to the start of experimental procedures. Serum lipid levels and hepatic triglycerides (TG) and total cholesterol (TC) levels were examined and analyzed. Both in vitro an in vivo pancreatic lipase activity was determined as well. Histopathological examination was performed and their results were noted. Noteworthy reduction of serum lipid levels and hepatic TG and TC levels was seen in groups treated with simvastatin (SIM; 20 mg/kg) and PCA (50 and 100 mg/kg) in comparison to HFD groups. Pancreatic lipase activity was reduced in the SIM group and the group treated with doses of PCA (50 and 100 mg/kg). A marked increase in gain in body weight per week (P<0.05) was achieved in HFD group. Coronary risk index (CRI) and Atherogenic index of plasma (AIP) showed decreased index values after treatments with SIM and PCA (50 and 100 mg/kg), respectively. Our findings confirmed the efficacious cardio-protective and hypolipidaemic activities of protocatechuic acid in coronary artery disease induced in rats with fat and fructose rich diet.
A novel interspecies recombinant enterovirus (Enterovirus A120) isolated from a case of acute flaccid paralysis in China

ABSTRACT EV-A120 is a recently identified serotype of the enterovirus A species. Only one full-length genomic sequence is currently available in GenBank, and very few studies have been conducted on EV-A120 globally. Thus, additional information and research on EV-A120 are needed to explore its genetic characteristics, phylogeny, and relationship with enteroviral disease. In this study, we report the phylogenetic characteristics of a EV-A120 strain (Q0082/XZ/CHN/2000) from Tibet, China. The amino acid sequence similarity and nucleotide sequence similarity of the full-length genomic sequence of this EV-A120 strain and the EV-A120 prototype strain were 96.3% and 79.9%, respectively, showing an evolutionary trend. Recombination analysis found intraspecies recombination in the 5′ -UTR, 2B, 2C, and 3D regions. Serum neutralization testing of the EV-A120 (Q0082) strain was also carried out. Low serum-positive rates and geometric mean titres (GMTs) indicated that the extent of EV-A120 transmission and exposure in the population was very limited compared with that in the outbreaks of EV-A71 and CV-A16 in China since 2008. The EV-A120 strain (Q0082) is non-temperature sensitive, indicating its potential to spread in the population. In summary, this study reports the full-length genomic sequence of EV-A120 and provides important information for its global molecular epidemiology.
A New Late Triassic Traversodontid Cynodont (Therapsida, Eucynodontia) from India

ABSTRACT A large traversodontid cynodont Ruberodon roychowdhurii, gen et. sp. nov., is described from the Late Triassic Tiki Formation of the Rewa Gondwana Basin, India, based on an ontogenetic series of five partial lower jaws. Ruberodon is characterized by a robust and deep dentary symphysis, lower dental formula of i3-c1-pc9, procumbent and hypertrophied first lower incisor, a large canine, long diastema between the lower canine and first postcanine, and a high coronoid process at 60° to the horizontal tooth row. With growth, the symphyseal region became relatively more slender with lengthening of the diastema. Phylogenetic analysis based on 19 taxa and 35 craniodental characters places Ruberodon within the clade containing Gomphodontosuchus, Menadon, Protuberum, Scalenodontoides, and the multispecific Exaeretodon. The new genus forms a sister taxon to E. statisticae and is more advanced than E. riograndensis and E. argentinus based on the presence of a strong coronoid ridge anterior to the masseteric fossa. Based on its tetrapod assemblage, the Tiki Formation may be globally correlated with other formations such as the lower part of the Maleri Formation of India, the Isalo II Beds of Madagascar, and the upper part of the Santa Maria Formation of Brazil. An early Carnian age is proposed for the Tiki Formation.
BARLEY GENETICS AND GENOMICS: A REVIEW

Summary: This article discusses some recent developments in the use of DNA molecular markers in barley. The progress made in DNA marker technology has been tremendous and exciting. These markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The importance of barley as a crop plant has prompted widespread genetic research onto this species. Genetic and physiological studies have been used to scan the components of primary gene pool of barley (wild, landraces and modern cultivars) for tolerance to various abiotic stresses. Landraces and particularly, wild barley genotypes exhibit huge variation of interest to breeders in improving the modern crop for specific traits. The introgression of this exotic variation into modern barley cultivars has been problematic in the past due to linkage drag (associated deleterious genes), difficulties in recognizing and testing for the presence of introgressed characters and background genetic effects. Molecular marker procedures now provide a means of overcoming these problems. This review provides an overview of current developments and looks into the application of these technologies for barley breeding.
On-farm diagnosis of contagious bovine pleuropneumonia in nomadic herds using latex agglutination test (LAT)

Three outbreaks of contagious bovine pleuropneumonia (CBPP) in Kafur Local Government Area of Katsina State, involving a total of 250 animals were reported. All the animals were examined thoroughly and based on the clinical signs exhibited, 120 (group A, n= 51, B, n=29 and C, n=40) animals were selected for latex agglutination test (LAT), using serum from each of the animal. The results indicate infection rates of 11.8% (6/51) in adult animals and 19.6% (10/51) in calves in farm A, while in farm B the infection rate were 27.6% (6/29) for the adult animals and 13.8% (4/29) for calves. While in farm C, 15.0% (6/40) of the adult animals and 17.5% (7/40) of the calves are positive, as demonstrated by strong (+++) agglutination in cell 1 (Plate 2). Overall infection rate of 16.7 and 17.5% was observed for adult and calves respectively. Although this diagnostic test LAT is not new, this is the first time it’s being conducted in the area of study for the diagnosis of CBPP. Key words: Mycoplasma mycoides sub sp. Mycoides, nomadic cattle, latex agglutination test.
Digeneans Parasitic in Freshwater Fishes (Osteichthyes) of Japan. I. Aporocotylidae, Bivesiculidae and Haploporidae

Adult digenetic trematodes (digeneans) parasitic in freshwater fishes (Osteichthyes) of Japan are reviewed in a series of several papers. The current knowledge of each of the digenean species is provided from the existing specimens and literature, including a morphological descrip- tion with figures, lists of its synonyms, hosts, localities and existing specimens, and a summary of its life cycle where known. The Aporocotylidae Odhner, 1912 (Sanguinicola ugui, Sanguinicola hasegawai sp. nov. and Sanguinicola sp.), Bivesiculidae Yamaguti, 1934 (Bivesicula sp.) and Hap- loporidae Nicoll, 1914 (Carassotrema koreanum) are reviewed. Sanguinicola hasegawai sp. nov. is described and figured on the basis of specimens found in the blood vessels and heart of Barbat- ula toni (Dybowski, 1869) (Nemacheilidae) from Hokkaido.
Effect of Moringa Extract on Growth and Yield of Maize and Common Beans

An evaluation on the potential benefit of using Moringa oleifera leaf extract as a growth hormone on common beans (Phaseolus vulgaris ) and maize ( Zea mays ) was done. Trials were carried out in the greenhouse and field. In the greenhouse, five treatments were used: control (M0, only water applied), second control (ME, only ethanol applied), moringa extract (in 80% ethanol) applied (on leaves) once at 2 weeks from emergence (M1), moringa extract applied at 2 and 4 weeks from emergence (M2), and moringa extract applied every 2 weeks to maturity from two weeks from germination (M3). The same treatments were adopted in the field except ME, which was considered unnecessary after observing the results of the greenhouse experiment. Results showed that moringa extract increased growth and yield of beans in both greenhouse and field, and of maize in the field. However, the extract showed no significant effect on DM yield, root DM or plant height of maize in the greenhouse. The highest DM and root weight, height and crop yields in greenhouse and field experiments for beans, and for maize in the field only, were obtained at M3. The study recommends the application of extract at M3.
Utilization of the S-locus as a Genetic Marker in Cherry to Differentiate Among Different Pollen Donors

Fruit set in sweet (Prunus avium L.) and sour cherry (P. cerasus L.) is frequently less than adequate for profitable production despite the availability of compatible pollen and abundant flowers. When fruit set consistently falls below acceptable levels, growers may attempt to increase fruit set by increasing the availability of compatible pollen. We describe the use of the self-incompatibility locus (S-locus) as a genetic marker to quantify the relative contributions of competing pollen sources in achieving fruit set in 'Balaton™' sour cherry. Pollen race experiments were conducted to determine if nonself-pollen provided in a pollen mixture was more competitive than self-pollen in achieving fruit set in 'Balaton™'. We further investigated what pollen set the 'Balaton™' crop in two commercial 'Balaton™' orchards where multiple potential pollinators were planted in adjacent orchards. S-allele genotyping using DNA extracted from the seed was done to discriminate among the competing pollen sources. The results suggest that in certain environmental conditions, nonself-pollen may be more competitive in achieving fruit set in 'Balaton™' than self-pollen. These examples illustrate how seed genotyping can be used to further our understanding of the competitive abilities of different pollen sources in both controlled experiments and production orchards.
Displaced Abomasum and Ketosis in Dairy Cows

High producing dairy cows struggle to meet energy demands and handle various transitional changes in late gestation and early lactation. Negative energy balance in early lactation is inevitable and metabolic disorders may follow as a consequence of a deep negative energy balance. This thesis studies associations between blood profiles and body condition score (BCS) in dairy cows, and displaced abomasum (DA) or clinical ketosis, and investigates risk factors for the two diseases at the herd level. In study I, blood profiles of cows with and without DA were compared. In studies II and III, blood of cows was sampled to investigate how blood profiles differed among herds with a high incidence of DA or clinical ketosis, and between cows in high-incidence and low-incidence herds, respectively. In study IV, associations between high or low incidence and factors related to housing, feeding, management and milk yield were studied to identify herd-level risk factors for DA and ketosis. The blood profiles included parameters with which to assess energy metabolism, hepatic cell damage, inflammation, and a metabolic index (RQUICKI)used in humans to assess insulin sensitivity. The cows with DA displayed blood profiles indicating a severely altered energy metabolism (NEFA, BHB, insulin, cholesterol, RQUICKI), liver cell damage (AST, GD) and inflammatory responses (haptoglobin). At the herd level, energy markers (NEFA, insulin, glucose, cholesterol, RQUICKI) indicated altered metabolism in cows in high-incidence herds compared with cows in low-incidence herds. The markers of liver cell damage and inflammation were not different between highand low-incidence herds. Among high-incidence herds, BCS and change in BCS, and one metabolic marker (NEFA) were found most useful to pinpoint herd problems. Large herd size, high individual milk production level, keeping all dry cows in one group, and not cleaning the feeding platform daily, were found to be risk factors for a high incidence of DA or ketosis at the herd level. In conclusion, the studies confirm a difference in blood profiles between cows with DA and healthy herd mates as well as a difference at the herd level between cows in herds with high versus low incidence of DA and clinical ketosis.