Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted low cost strategies to combatSalmonella spp. in finisher pigs and in theslaughterhouse

Salmonella carriage in pigs is a significant food safety issue and low-cost control measures may provide a useful element in reducing the prevalence of Salmonella in pigs. This thesis aimed to investigate several pre-harvest Salmonella control strategies directed towards finishing pigs (35-110 kg). At farm level, two strategies focusing on dietary supplementation with feed additives: (1) sodium butyrate; and (2) an encapsulated blend of formic acid, citric acid, and essential oils (FormaXOL™) were investigated for their effectiveness to control Salmonella shedding and seroprevalence in pigs 28- and 63-days prior to slaughter. In the abattoir, two strategies: (3) cleaning and disinfection (C&D) of lairage pens with a quaternary ammonium chloride or chlorocresol-based disinfectant; and (4) misting pigs with a preoxygen disinfectant at 0.5% were evaluated for their ability to eliminate Salmonella in the lairage environment and to topically reduce Salmonella prior to slaughter, respectively. Supplementation with sodium butyrate and FormaXOL™ for 28-days prior to slaughter, not 63-days (for sodium butyrate only), was effective in reducing Salmonella shedding and seroprevalence but only in the absence of secondary infections. Both feed additives did not influence intestinal carriage, nor did they reduce seroprevalence to below the cut-off used for the high Salmonella risk category in Ireland (50%), or significantly improve growth performance. Treatment with sodium butyrate provided a benefit of €0.04/kg of live-weight gain; while supplementation with FormaXOL™ increased the feed cost/kg of live-weight gain by €0.08. In the abattoir, drying lairage pens after C&D with a chlorocresol-based disinfectant eliminated Salmonella. Additionally, misting with a preoxygen disinfectant might have a role in topical antisepsis for pigs contaminated with Salmonella prior to slaughter and as such warrants further investigation. The findings presented herein, are readily applicable to farmers, abattoirs and regulatory agencies; and have added novel findings to the field of Salmonella control in pigs.
Role of Galactose Specific Lectin 3 and CYP17A1 Gene Polymorphism in Breast Cancer

Background: Breast cancer (BC) is the most frequent malignant tumor and is considered the second leading cause of cancer related deaths among women worldwide. Galactose specific lectin 3 (Gal-3) is a β-galactoside-binding animal lectin that contains carbohydrate-recognition domains and displays multiple related functions. The human CYP17A1 gene, which encodes the enzyme cytochrome P450 17A1, plays a key role in sex steroid synthesis. Objective: The aim of this study was carried out to evaluate the role of serum Gal-3 as a diagnostic tumor marker in BC and to assess the potential association between the CYP17A1 gene polymorphism and BC. Subjects and Methods: The present study was conducted on 35 breast cancer females patients compared to a control group of 35 healthy females of matching ages. Estimation of Gal-3 in serum using enzyme linked immune-sorbent assay (ELISA) technique and detection of CYP17A1 gene polymorphism using polymerase chain reaction - restriction fragment length polymorphism technique (PCR – RFLP) were performed in all participants. Result and Conclusion: The results of this study suggest that the Gal-3 showed increase in breast cancer cases and could be used as a useful marker of BC. On the other hand there was no significant association between CYP17A1 gene polymorphism and BC.
Public attitudes predict community behaviours relevant to the pork industry

Concerns about livestock animal welfare are well documented worldwide. Public attitudes are often studied as indicators of risk for the livestock industries, but are less often studied in relation to behaviours that may affect the livestock industries. The present paper examines the relationships between public attitudes, opinion leadership and self-reported pork consumption and community behaviours that may have a negative impact on livestock industries by promulgating views that farming engages in unacceptable practices. To the extent that these attitudes and behaviours are based on a lack of knowledge or a lack of understanding about the actual relationship between current practices and animal welfare and farm productivity, care needs to be exercised to determine what industry practice change should occur or what should be done to inform the public. The results showed that in regard to consumption, being male and holding positive attitudes towards eating meat and livestock welfare explained 11% of the variance in pork consumption. Notably, however, information seeking and trust in information, attitudes related to animal welfare and the livestock industries, and membership to an animal-welfare group, accounted for 44% of the variance in community behaviours that express dissatisfaction with the livestock industries. Opinion leaders, that is, people in the community who indicate that they are used by others as a source of information about livestock animal welfare, tended to eat less pork and engaged in many more community behaviours, such as calling talkback radio or writing to politicians. Together, these results suggest that more needs to be done to identify the population segment of opinion leaders and to engage them in dialogue about pork production.
Core Proteome and Architecture of COPI Vesicles

Retrieval of escaped ER-residents and intra-Golgi transport is facilitated by coat protein complex I (COPI)-coated vesicles. Their formation requires the activated small GTPase ADP-ribosylation factor (Arf) and the coat complex coatomer. Here we assess the protein composition of COPI vesicles by combining stable isotope labeling with amino acids in cell culture (SILAC) with in vitro reconstitution of COPI vesicles from semi-intact cells (SIC) using the minimal set of recombinant coat proteins. This approach yields an unbiased picture of the proteome of these carriers. We define a set of ~40 proteins common to COPI vesicles produced from different human as well as murine cell lines. Almost all bona fide COPI vesicle proteins are either ER-Golgi cycling proteins or Golgi-residents, while only a minor portion of secreted proteins was found. Moreover, we have investigated a putative role of γ- and ζ-COP as well as Arf isoforms in sorting and recruitment of specific proteins into COPI vesicles. As opposed to the related COPII system, all isoforms of coatomer and all COPI-forming isoforms of the small GTPase Arf produce COPI-coated vesicles with strikingly similar protein compositions. We present a model for the core architecture of COPI vesicles.
MERS-CoV NSP16 necessary for IFN resistance and viral pathogenesis

Coronaviruses encode a mix of highly conserved and novel genes as well as genetic elements necessary for infection and pathogenesis, raising the possibility for common targets for attenuation and therapeutic design. In this study, we focus on the highly conserved nonstructural protein (NSP) 16, a viral 2’O methyl-transferase (MTase) that encodes critical functions in immune modulation and infection. Using reverse genetics, we disrupted a key motif in the conserved KDKE motif of MERS NSP16 (D130A) and evaluated the effect on viral infection and pathogenesis. While the absence of 2’O MTase activity had only marginal impact on propagation and replication in Vero cells, the MERS dNSP16 mutant demonstrated significant attenuation relative to control both in primary human airway cultures and in vivo. Further examination indicated the MERS dNSP16 mutant had a type I IFN based attenuation and was partially restored in the absence of IFIT molecules. Importantly, the robust attenuation permitted use of MERS dNSP16 as a live attenuated vaccine platform protecting from challenge with a mouse adapted MERS-CoV strain. These studies demonstrate the importance of the conserved 2’O MTase activity for CoV pathogenesis and highlight NSP16 as a conserved universal target for rapid live attenuated vaccine design in an expanding CoV outbreak setting. Significance Coronavirus emergence in both human and livestock represents a significant threat to global public health, as evidenced by the sudden emergence of SARS-CoV, MERS-CoV, PEDV and swine delta coronavirus in the 21st century. These studies describe an approach that effectively targets the highly conserved 2’O methyl-transferase activity of coronaviruses for attenuation. With clear understanding of the IFN/IFIT based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform as well as therapeutic development for both current and future emergent CoV strains. Importantly, other approaches targeting other conserved pan-coronavirus functions have not yet proven effective against MERS-CoV, illustrating the broad applicability of targeting viral 2’O MTase function across coronaviruses.
Knockdown surface expression of p75 neurotrophin receptor with ER retained intrabody in mammalian cells

Although p75 neurotrophin receptor (p75NTR) is the first neurotrophin receptor isolated, its precise functions in physiology and underlying signaling have remained elusive for many years. In this study, endoplasmic reticulum retained intrabody (ER-intrabody) technology was applied to knockdown p75NTR surface expression in mammalian cells. By fusing with the C-terminal ER retention signal KDEL, ER-intrabody impedes target receptor protein from secretory trafficking. Monoclonal recombinant scFvs against p75NTR were isolated by phage display. These scFvs bound to p75NTR with nanomolar affinities and were used to generate p75NTR-specific ER-intrabodies. In neuron-like cell lines PC12 and NSC19, p75NTR surface expression was significantly suppressed by the p75NTR-specific ER-intrabody construct SH325-G7-KDEL. The effect of this ER-intrabody on p75NTR surface knockdown could be maintained over a period of more than eight days without obviously activating unfolded protein response (UPR). Finally, the downregulation of p75NTR surface expression was determined in mouse hippocampal primary cultures using the ER-intrabody SH325-G7-KDEL. Sholl analysis showed that dendritic complexity of neurons was significantly increased if the p75NTR expressions were reduced on their surfaces by the ER-intrabody. In conclusion, the novel ER-intrabody SH325-G7-KDEL inhibits the surface translocation of p75NTR and ER-intrabody knockdown technology may become a powerful tool to investigate molecular mechanisms of target neuronal receptors.
Aspects of the Design and Interpretation of Competition (Interference) Experiments

The design and analysis of competition experiments should be based on an unambiguous objective. Recent criticisms of particular designs have been made without reference to objectives and may be misleading. Three common designs are discussed: additive, replacement series, and response surface. Additive designs are well suited to agronomic objectives; replacement series are useful for comparing pairs of species; response surface designs can be used for most objectives but may be unnecessarily complex. The published criticisms of additive and replacement series designs are argued to be acceptable limitations within the bounds of the objectives for which they are used. Concerns about these designs confounding density and proportion are irrelevant to the objectives for which they are most suited. The continued use of multiple comparison tests is argued to be illogical. Regression approaches to analysis are more relevant, many non-linear equations are now easy to fit to data and these can be used without the need for linearization. However, there are various pitfalls not adequately reported to date. In particular, error structures need to be checked carefully and over-elaborate equations should be avoided.
Soil and vegetation features determine the nested pattern of ant-plant networks in a tropical rainforest

Recently, several studies have focused on structural properties of ant-plant networks. However, little is known about the role of abiotic factors on these networks. 2. As a result of different abiotic factors that can affect the patterns of ant-plant interactions, it was tested whether soil pH and canopy cover contribute to variation in the nestedness of mutualistic (plants with extrafloral nectar-EFN) and neutral (plants without EFN) ant-plant networks. 3. It was shown that only mutualistic networks were affected by soil pH. It was suggested that this may occur because the variation in soil pH directly influences the secreted nectar, and as there is a preference for nectar composition by ants, this could change the patterns of interaction in mutualistic networks. As prey availability is possibly the main factor influencing ants' presence on plants without EFN, soil pH should have little or no influence on the patterns of interaction in neutral networks. 4. On the other hand, nestedness was not affected by canopy cover in mutualistic and neutral networks. In spite of that canopy cover (light availability) is directly related to the amount of nectar secreted, the volume of nectar may not be important for the structure of the networks. However, canopy cover varied little in this study site. This small variation could not be enough to change the nested pattern in mutualistic and neutral networks. 5. In short, the present results show that the abiotic factors that affect the availability and quality of food resources may have important effects on the structure of trophic interactions in non-symbiotic ant-plant networks.
Association of vitamin D with tuberculosis patients of Sargodha, Pakistan

Deficiency of vitamin D (25-hydroxycholecalciferol) has long been concerned in activation of tuberculosis (TB). Pakistan stands fifth among 22 countries that have the highest TB incidence. Vitamin D influences the immune response to tuberculosis and vitamin D deficiency has been associated with increased risk of tuberculosis in different populations. This study was designed to show the relationship between vitamin D level (deficiency) and risk of tuberculosis. Eighty five blood samples of tuberculosis patients were taken from District Head Quarter (DHQ) Hospital, Sargodha. ORGENTEC ELISA Kit was used for vitamin D quantification. Mean vitamin D level were 13.9± 1.68 ng/mL in control and 9.3 ±1.38 ng/mL in TB patients. Out of 85 patients 82 patients showed vitamin D level less than 12 ng/mL. Vitamin D deficiency was seen in almost 96% of patients as compared to control. Female patients (9.05±1.55 ng/mL) also have significantly lower vitamin D level as compare to male patients (9.79±1.34 ng/mL). These findings warrant further studies that the vitamin D supplementation may have the role in the treatment and prevention of tuberculosis.
Effect of Spray Volume and Pressure on Postemergence Johnsongrass (Sorghum halepense) Control

Fenoxaprop, fluazifop/fluazifop-P, haloxyfop, and quizalofop at 0.14 kg ai ha−1 and sethoxydim at 0.28 kg ai ha−1 were applied broadcast over-the-top in spray volumes of 94 and 374 L ha−1, each at 138 and 345 kPa, to control johnsongrass in soybeans over a 5-yr period. The two spray volumes provided equal control, but control was better when treatments were applied at 345 kPa than at 138 kPa. There were no significant interactions among herbicides, spray volumes, or spray pressures. Most of the spray was deposited on the upper surface of the plant canopy. Less than 10% of the herbicide spray applied penetrated into the canopy onto water-sensitive spray cards located 10, 20, 30, or 40 cm above the ground.
Combining ability analysis for yield and yield components in sesame (Sesamum indicum L.) genotypes

Combining ability was estimated among nine parents for yield and its contributing traits in sesame. Both per se performance and gca effects were considered for judging the genotypes as best parent. The genotypes TMV 6, TMV (Sv) 7, TVS 0603 and ORM 21 recorded significant gca effect for single plant yield, number of capsules per plant, branches per plant, dry matter production. Hence these genotypes were categorized as good combiners. The cross TMV 3 x ORM 21 registered significant sca effect for single plant yield, dry matter production, plant height and branches per plant. While TMV6 x ORM 21 exhibited significant sca effect for single plant yield, dry matter production, plant height and branches per plant. The former cross involves parents with good combiners. Hence, pedigree breeding method could be adopted to isolate desirable recombinants. However, the late cross involved parents with poor combiners. Hence biparental mating followed by selection is recommended for the identification of desirable recombinants.
White‐tailed deer as the last megafauna dispersing seeds in Neotropical dry forests: the role of fruit and seed traits

Endozoochory is a prominent form of seed dispersal in tropical dry forests. Most extant megafauna that perform such seed dispersal are ungulates, which can also be seed predators. White‐tailed deer (Odocoileus virginianus) is one of the last extant megafauna of Neotropical dry forests, but whether it serves as a legitimate seed disperser is poorly understood. We studied seed dispersal patterns and germination after white‐tailed deer gut passage in a tropical dry forest in southwest Ecuador. Over 23 mo, we recorded ca 2000 seeds of 11 species in 385 fecal samples. Most seeds belonged to four species of Fabaceae: Chloroleucon mangense, Senna mollissima, Piptadenia flava, and Caesalpinia glabrata. Seeds from eight of the 11 species dispersed by white‐tailed deer germinated under controlled conditions. Ingestion did not affect germination of C. mangense and S. mollissima, whereas C. glabrata showed reduced germination. Nevertheless, the removal of fruit pulp resulting from ingestion by white‐tailed deer could have a deinhibition effect on germination due to seed release. Thus, white‐tailed deer play an important role as legitimate seed dispersers of woody species formerly considered autochorous. Our results suggest that more research is needed to fully understand the ecological and evolutionary effects of the remaining extant megafauna on plant regeneration dynamics in the dry Neotropics.
Organoleptic Evaluation of the High-Protein Yoghurt containing the Edible Insect Oxya chinensis sinuosa (Grasshopper): A Preliminary Study

Hong-Seok Kim, Young-Ji Kim, Jung-Whan Chon, Dong-Hyeon Kim, Kwang-Young Song, Hyunsook Kim, and Kun-Ho Seo 1Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul, Korea 2National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA 3Dept. of Biological Engineering, Yanbian University of Science and Technology, Yanji, China 4Dept. of Food & Nutrition, College of Human Ecology, Hanyang University, Seoul, Korea
Phosphorus‐rich grasshoppers consume plants high in nitrogen and phosphorus

1. Insect herbivores choose their food according to its protein to carbohydrate ratio, but the reasons why different species have contrasting intake targets remain unclear. According to the growth rate hypothesis, P‐rich insects have higher growth rates. It is therefore expected that P‐rich insects will prefer plants that are high in protein (hence in nitrogen, N) and phosphorus (P).
Agromorphological diversity of South African sorghum genotypes assessed through quantitative and qualitative phenotypic traits

Knowledge of genetic diversity among sorghum genotypes is essential for their efficient utilisation in plant breeding schemes and effective conservation. The objective of this study was to assess the level of genetic diversity present among South African sorghum genotypes using phenotypic traits. Ninety-eight sorghum accessions were phenotyped at two sites during the 2012 growing season. Experiments were laid out in an alpha lattice design with three replications. Data were collected on eight quantitative and six qualitative traits, and subjected to principal component and hierarchal cluster analyses. A dendrogram was constructed using the unweighted pair group method with arithmetic mean. Grain yield showed a positive and significant association with plant height, panicle width and rachis number but was negatively associated with panicle exsertion. The principal component analysis revealed three important principal components that accounted for 88.0% of the total variation observed among genotypes across locations. Principal components 1, 2 and 3, respectively, correlated with plant height, grain yield and panicle weight. A dendrogram revealed three main clusters of genotypes. The most diverse accessions identified were 4277, 2934, 5097, 4909 and 4303, which are useful for breeding. The diversity observed among the sorghum genotypes could be useful in improvement of sorghum for various traits.
Comparative suppressive effect of some organic acids against Meloidogyne incognita infecting tomato

The comparative suppressive potential of some organic acids known as resistance inducing chemicals viz., salicylic acid (SA) and its two derivatives; acetylsalicylic acid (ASA) and 3,5-dinitrosalicylic acid (DNSA), along with Lascorbic acid (AA), oxalic acid (OA) and citric acid (CA) for managing Meloidogyne incognita infecting tomato plants was investigated under greenhouse conditions. The results showed that all tested organic acids as well as the application methods significantly reduced tomato root galls and 2 nd stage juvenile numbers in soil compared with control. Except DNSA and AA, foliar application of tested organic acids was more effective in reducing nematode galls than soil drench application. Foliar application of ASA caused superior effect in the reduction of J2 in soil (100 %) followed by AA (89.44 %), OA (88.25 %) and SA (70.69 %). CA (96.52 %) was tended to be the most effective chemicals in reducing J2 in soil when applied as soil drench. All treatments enhanced shoot and root length of tomato as well as shoot weight compared with the untreated check. Only SA and DNSA significantly increased the root weights. DNSA enhanced the growth indices of tomato plant when used as foliar spray more than soil drenching and opposite trend was observed for OA. These chemical activators have potential to suppress M. incognita infection through the stimulation of tomato tolerance.
Influence of abiotic and biotic factors on the seasonal incidence of major sucking pests of brinjal

Field trials were conducted to study the influence of abiotic and biotic factors on the seasonal incidence of major sucking pests of brinjal, whitefly (Bemisia tabaci) and leaf hopper (Amrasca devastans) during rabi 2010–11 and 2011–12. The incidence of whitefly population started from first week after transplanting in both the years and peak incidence was observed during the final week of October to first week of November and decreased gradually up to crop maturity. The leaf hopper incidence was also observed during first week after transplanting in both the years and population reached peak in fourth week of October. The major sucking pest incidence had a non-significant association with abiotic factors like maximum and minimum temperatures, relative humidity and rainfall. The incidence of sucking pests showed a positive and significant correlation with biotic factors like coccinellid beetles as well as spiders.