Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic divergence analysis in chickpea germplasm

A total of 434 germplasm lines of chickpea were assessed for 13 quantitative traits during rabi 2015-16 at JNKVV, Jabalpur. Genotypes were grouped into fourteen clusters. Clusters II and cluster XIV and cluster XII and cluster XIV, had maximum inter cluster distance. The characters viz.,effective pods per plant followed by biological yield per plant, plant height and 100-seed weight were main contribution to total divergence. Cluster XIV and cluster XIII had highest mean values for maximum number of characters. Based on the result IC 83812, EC 198729, EC 490027, IC 53245, IC 83827and IC 83889 are recommended for hybridization, as these genotypes showed good per se performance for seed yield and belong to the highly diverse clusters.
Inappropriate Total Oxidant/Antioxidant Status, Nitric Oxide Oxidation End Products and Trace Element Levels in Patients with Inflammatory Bowel Disease

Background: This study aimed at evaluating oxidant and antioxidant markers (including nitrite, nitrate, total antioxidant capacity (TAC), malondialdehyde (MDA), iron, selenium, glutathione peroxidase (GPx), and glutathione reductase (GR) in patients with inflammatory bowel disease (IBD) and compare them with healthy controls. Methods: Serum samples were obtained from 35 patients (19 ulcerative colitis (UC) and 16 Crohn’s disease (CD) in the active phase of the disease) and 30 healthy controls. Serum levels of nitrite and nitrate, TAC, MDA, iron, selenium, glutathione peroxidase, and glutathione reductase were measured. The results were compared between the two groups using independent t-student test. The Pearson’s correlation coefficient (for continuous data) was performed using the SPSS software. Results: Serum levels of nitrite, nitrate, and MDA were significantly higher (P = 0.001) in patients with IBD, while the levels of TAC, trace elements, glutathione peroxidase (GPx), and Glutathione Reductase (GR) levels were lower (P < 0.05) in patients with IBD. However, when females were considered separately, Gpx and GR activities were not significantly different in those with and without IBD. The present results showed that nitrite, MDA, GPx, GR, and Se: MDA ratio had the strongest correlation with disease activity
Coarse Woody Debris Following Silviculture Treatments in Southwest Mixed-Conifer Forest

Coarse woody debris (CWD) is an important component in the structure and function of southwestern mixed-conifer forest ecosystems. However, fire suppression and exclusion policies have changed the structure and fuel loads, including CWD, during the last 130 years. Consequently, managers are faced with the threat of stand replacement fires over large spatial areas and are seeking solutions to these challenges using silvicultural techniques. Our paper presents CWD characteristics based on 100-h and 1000-h time-lag fuels before (2006) and after (2016) silvicultural treatments including harvest, prescribed fire, and no treatment (control) on mixed-conifer forests in southcentral New Mexico, USA. Results indicated late-season broadcast burns characterized by mild fire behavior reduced 100-h CWD (Mg ha−1) and potentially 1000-h CWD. However, because control sites also saw reduced 1000-h CWD, this result was confounded. Harvest treatments maintained 1000-h CWD, which could be considered a compensatory response given the decrease in CWD on adjacent control sites over the same time period. This was supported by an increase in 1000-h logs per 75 m transect on harvest sites as compared to control sites. Silvicultural prescriptions including prescribed fire are useful tools to increase or decrease CWD to meet management objectives.
Abundance, biomass and community structure of epipelagic zooplankton in the Canada Basin

Changing environmental conditions such as decreasing sea ice cover impact Arctic zooplankton. In the Canada Basin, zooplankton surveys have seldom been done due to its traditionally thick, year-round ice cover. Here, we describe the zooplankton community of the Canada Basin before the two recent sea ice minima (2007 and 2012). Zooplankton were sampled from the upper 100 m during August and September of the years 2003–2006 using a 150-μm mesh net to determine species composition, abundance and biomass. To describe the zooplankton community and its relation to the environment, we used Bray–Curtis similarity, and then applied hierarchical clustering, non-parametric multidimensional scaling and the BEST BIO-ENV routine. The most abundant zooplankton species in all years were smaller copepods such as Oithona similis and Microcalanus pygmaeus. Biomass was dominated by larger copepod species such as Calanus hyperboreus and Calanus glacialis. For the non-copepod zooplankton, the pteropod Limacina helicina and the larvacean Fritillaria borealis were typically the most abundant species. The non-copepod biomass was dominated by the chaetognath Eukrohnia hamata and L. helicina, while F. borealis contributed relatively little to the overall biomass despite its high numbers. Zooplankton communities differed between shelf/slope and basin stations. We found no obvious interannual changes in community structure over our short 4-year observation period, with community structure influenced to a small degree by environmental factors.
An analysis of apoptotic and autophagic genes in novel Drosophila models of Parkinson disease

Parkinson disease (PD) is the most common neurodegenerative movement disorder in humans and is strongly associated with the selective loss of dopaminergic (DA) neurons. The clinical features include motor dysfunction, resting tremor and in some cases non-motor features such as autonomic, cognitive and psychiatric disorders. The neuropathologic hallmarks are Lewy bodies and Lewy neurites in surviving neurons which are composed of proteinaceous inclusions comprised of α-synuclein, ubiquitin and other proteins. Pathological mechanisms implicated in PD include aberrant protein aggregation, mitochondrial dysfunction, oxidative stress, and failed cellular processes such as apoptosis, autophagy, proteasomal pathway, and several cellular stressors. To analyse the implication and contribution of some of these cellular processes, we altered the expression of the; classical apoptotic genes namely Buffy and Debcl; autophagy genes Atg6 and Pi3K59F; the antiapoptotic transmembrane Bax inhibitor-1 containing motif (TMBIM) family Bax inhibitor-1, Lifeguard and GHITM; mitochondrial genes such as HtrA2, MICU1, porin/VDAC, Pink1 and parkin; and an increased disease risk gene pyridoxal kinase in DA neurons and in the developing eye. We show that the altered expression of key genes can either be detrimental or beneficial to the health of DA neurons as determined by lifespan and locomotor function, in addition to supportive results obtained from biometric analysis of phenotypes from the neuron rich eye. We found that the overexpression of Buffy, the sole pro-survival Bcl-2 homologue in Drosophila could suppress the loss of function-induced phenotypes.
Product and Residue Biomass Equations for Individual Trees in Rotation Age Pinus radiata Stands under Three Thinning Regimes in New South Wales, Australia

Using data from 239 trees that were destructively sampled and completely weighed in the field, four systems of nonlinear additive equations were developed for the estimation of product and residue fresh and dry weight of individual trees in rotation age (28 to 42 years) Pinus radiata stands under three thinning regimes: unthinned (T0), one thinning (T1) and two thinnings (T2). To cater for all practical applications, the four systems of equations included diameter at breast height overbark (DBHOB) as the only independent variable or both DBHOB and total tree height as predictors either with or without the incorporation of dummy variables for stand types. For all systems, the property of additivity was guaranteed by placing constraints on the structural parameters of the system equations. The parameter estimates were obtained by the generalized methods of moments (GMM) following a comparison with weighted nonlinear seemingly unrelated regression (WNSUR). Based on the predicted values from the system that had DBHOB as the predictor and dummy variables for stand types, the percentage of total tree fresh weight accounted for by residues increased from 14.8% to 20.5%, from 15.6% to 22.2% and from 13.9% to 18.7% for trees in the T0, T1 and T2 stands, respectively, as DBHOB increased from 15 to 70 cm. The corresponding changes in the percentage of residue dry weight were from 15.1% to 16.1%, from 15.7% to 17.1% and from 14.9% to 15.8% for the three stand types. In addition, two systems of allocative equations were developed to allocate the predicted product and residue biomass to their respective subcomponents. The system of allocative equations for product biomass predicted that sawlogs with bark accounted for 83% to 85% of product fresh weight and 82% to 87% of product dry weight over the same range of DBHOB. The predicted allocation of total residue dry weight to stump changed little, between 12% and 13%, over the same diameter range, but it was slightly higher for trees with DBHOB between 30 and 45 cm. The predicted allocation of total residue biomass to branches increased from 18% to 65% in fresh weight and from 18% to 57% in dry weight and that to waste decreased from 71% to 27% in fresh weight and from 70% to 32% in dry weight as DBHOB increased from 15 to 70 cm. Among the five biomass components, prediction accuracy was the lowest for pulpwood and waste. The systems of additive and allocative biomass equations developed in this study provided the first example of how the two approaches could be used together for the estimation of total tree, major and sub-component biomass. They will provide forest management with an enhanced capacity to more accurately estimate product and residue biomass of rotation age trees and thus to include the production of biomass for renewable energy generation in their management systems for P. radiata plantations.
Determination of Feeding Performance of Mustard Aphid, Lipaphis Erysimi (Kalt) on different Mustard Varieties at Water Stress Condition -

The more feeding of plant sap by aphid, the more secretion of honeydew. Determination of the amount of honeydew secreted by aphids in a specific crop variety is one of the best ways to assess the susceptibility of aphid infestation to the variety. An experiment was conducted in glass house and controlled growth room of Bangladesh Institute of Nuclear Agriculture (BINA) at 25°C, RH 65Â–70% and 12:12 hrs daylight on 15 November 2016. Six mustard varieties were evaluated to determine the intensity of honeydew excretion by aphids for assessing susceptibility of aphids in mustard varieties under different water stress condition likely 100% field capacity (control), 50% field capacity (moderate drought) and 30% field capacity (severe drought). Aphid feeding and honeydew secretion were remarkably negatively affected by water stress. Weight of honeydew secreted by a mustard aphid during 24hrs was reduced by 13% and 25% when subjected to moderate and extreme drought respectively compared to that at non-stressed control. The weight of honeydew secreted by a mustard aphid in 24hrs in the varieties of Brassica campestris, B. napus and B. juncea was measured ranging 7.65 to 8.85mg; 4.81 to 5.15mg and 8.87 to 9.17mg, respectively. It may be concluded that feeding performance of aphid and honeydew secretion were more in susceptible varieties and negatively affected by water stress. The varieties of B. napus are more resistant to aphid infestation.
Role of Probiotics in Immune Regulation

In the present era, the research has been more focused on the natural mechanisms for managing, treating and curing the human diseases due to the several side effects of the chemotherapeutic agents and synthetic drugs. One of such natural mechanisms has come up with the use of beneficial microbes called as ‘Probiotics’. These microorganisms normally prevent infection and have a positive effect on nutrition. According to ‘WHO’ probiotics are the live microorganisms, which when administered in adequate amounts, confer a health benefit on the host [1]. Evidence has accumulated that certain probiotic microorganisms offer considerable health benefits for humans (Figure 1). However, one of the most important characteristics of probiotics is regulation of host immune response by which they are able to manipulate the host immune response towards the infectious microbes and can be useful in treatment of infectious diarrhea and day care related illness, antibiotic associated diarrhea caused by Clostridium difficile, inflammatory bowel disease, traveler’s diarrhea, allergy, irritable Bowel Syndrome etc. Lactobacillus casei have been shown to augment total and pathogen-specific secretory IgA levels upon infection in mice by stimulating B cell class switching to IgA [19]. However, specific antibodies against L. casei were not produced, indicating the nonresponsiveness of the gut immune system to this beneficial bacterium. Moreover, in infant rabbits pretreated with L. casei, morbidity of subsequent EHEC (Entero-Hemorrhagic E. coli) infection was reduced due to increased mucosal levels of anti-EHEC and anti-Shiga toxin IgA antibodies compared with controls [20]. Further, L. casei down-regulated the transcription of a number of genes encoding pro-inflammatory effectors such as cytokines and chemokines and adherence molecules induced by invasive S. flexneri. This resulted in an anti-inflammatory effect that appeared mediated by the inhibition of the NF-κB pathway, particularly through stabilization of I-κBα [21].
Assessment of Parasitic Load in Goat through the Examination of Faecal Matter

Livestock sector plays an important and vital role in providing nutritive food and in supplementing family incomes and generating gainful employment in the rural sector, particularly among the landless, small and marginal farmers. India with 135million goat population stands second after China. Goats are generally reared by landless or the resource poor farmers whose average agricultural holding is either very less or is not sufficient to devote for cultivation of crops (Kumar and Pant, 2003 and Singh et al., 2005). Goat sector provides subsidiary source of livelihood to the people especially to small and marginal farmers and landless labourers. Technological and management options are the only alternatives to accelerate growth in the productivity of goats, which is low in the traditional system of production. Parasites are a major constraint on animal productivity throughout the world. Small ruminant (goats and sheep) production systems worldwide are significantly constrained by gastrointestinal nematode (GIN) parasites, reducing meat, milk, and fibre production (Preston et al., 2014). Epidemiological studies are necessary to determine the potential impact of parasitic infections in particular areas (Chaparro et. al., 2016). Gastrointestinal nematodes are ubiquitous parasites of grazing ruminants and cause decreases in survival, live weight gain, wool and milk production and reproduction performance. These losses can be particularly severe in developing countries where control measures are less readily available. Correlation between faecal egg count of trichostrongylid eggs and worm burden, making faecal egg count a good estimate for affected animals (Rodriguez et al., 2015). Gastrointestinal parasitic infections in small ruminants are of considerable economic importance because small ruminants’ rearing has been a major source of income especially to the marginal farmers and labours of the country. Parasitic problems are a serious problem in goat. Parasitic infection do not show heavy rate of mortality, however there occurrence being chronic, most of the time leads to serious production losses. This leads to the major problem that goat farm produce below capacity. Keeping above point in view the study was planned to access the parasitic load and type of parasite infects the goats.
Marsupialia : Microbiotheriidae ) in Chile and its Phylogenetic Relationships

Members of the digenean genus Gyrabascus have been reported from bats and rodents in Europe, Southeast Asia, North America, and most recently from the marsupial, Monito del Monte (Dromiciops gliroides), in the Argentinian part of Patagonia. We have found digeneans belonging to Gyrabascus in a different species of Monito del Monte (Dromiciops bozinovici) from Chile. This is the first record of Gyrabascus from D. bozinovici and only the second report of Gyrabascus in a marsupial. Although these specimens are morphologically very similar to Gyrabascus dromiciops, we refrained from identifying our material as G. dromiciops due to insufficient specimen quality and the presence of some morphological differences, leaving open the possibility that the specimens from Chile may potentially represent a different, new species. Both morphological characteristics and molecular phylogenetic analysis using partial sequence of nuclear large ribosomal subunit gene (28S) confirmed the systematic position of these specimens and allowed us to discuss their phylogenetic relationships.
White matter microstructural properties in bipolar disorder and its relationship to the spatial distribution of lithium in the brain

Background Lithium treatment is associated with an increase in magnetic resonance imaging derived measures of white matter integrity, but the relationship between the spatial distribution of brain lithium and white matter integrity is unknown. Methods Euthymic patients with bipolar disorder receiving lithium treatment (n=12) and those on other medications but naïve to lithium (n=17) underwent diffusion imaging alongside matched healthy controls (n=16). Generalised fractional anisotropy (gFA) within white matter was compared between groups using a standard space white matter atlas. Lithium-treated patients also underwent novel multinuclear 3D lithium magnetic resonance imaging (7Li-MRI) to determine relative lithium concentration across the brain. The relationship between 7Li-MRI signal intensity and gFA was investigated at the resolution of the 7Li-MRI sequence in native space. Results The lithium-treated bipolar disorder and healthy control groups had higher mean gFA in white matter than the bipolar disorder group treated with other medications but naïve to lithium (t = 2.5, p < 0.05; t = 2.7, p < 0.03, respectively). No differences in gFA were found between patients taking lithium and healthy controls (t = 0.02, p = 1). These effects were seen consistently across most regions in the white matter atlas. In the lithium-treated group, a significant effect of the 7Li-MRI signal in predicting the gFA (p < 0.01) was identified in voxels containing over 50% white matter. Conclusions Lithium treatment of bipolar disorder is associated with higher gFA throughout brain white matter, and the spatial distribution of lithium is also positively associated with white matter gFA.
Prevalence and Characterization of Listeria Species from Raw Milk and Dairy Products from Çanakkale Province

The objective of this study was to determine the prevalence of Listeria species, specifically Listeria monocytogenes, in raw milk, pasteurized milk, white cheese, and homemade cheese. A total of 200 food samples were collected and analyzed to examine the presence of Listeria spp. The EN ISO 11290-1 method was used for isolation of Listeria. API Listeria test kit was used for biochemically characterization. Listeria spp. were isolated in 25 of the 200 samples (12.5%). The largest number of Listeria spp. was detected in homemade cheese (24%), followed by raw milk (18%), and white cheese (8%). Listeria spp. were not isolated from the pasteurized milk. The most common species isolated were Listeria innocua (5.5%); the remaining Listeria isolates were Listeria ivanovi (3.5%), Listeria welshimeri (3%), and Listeria monocytogenes (0.5%). Listeria monocytogenes was detected in only raw milk.
Characterization of a Francisella pathogenicity island-encoded secretion system

Supervisory Committee Dr. Francis Nano, Supervisor (Department of Biochemistry and Microbiology) Dr. Caroline Cameron, Departmental Member (Department of Biochemistry and Microbiology) Dr. Alisdair Boraston, Departmental Member (Department of Biochemistry and Microbiology) Dr. John Taylor, Outside Member (Department of Biology)
2,4-D-Resistant Buckhorn Plantain (Plantago lanceolata) in Managed Turf

Abstract A population of buckhorn plantain with suspected resistance to 2,4-D was identified in central Indiana following 30 yr of 2,4-D-containing herbicide applications. Our objectives were to (1) confirm and quantify the level of herbicide resistance in the buckhorn plantain population using dose-response experiments and (2) find alternative herbicides that could be used to control this population. Greenhouse experiments were conducted to quantify the dose-response of resistant (R) and susceptible (S) biotypes of buckhorn plantain to both 2,4-D and triclopyr, two synthetic auxin herbicides from different chemical families. The R biotype was ≥6.2 times less sensitive to 2,4-D than the S biotype. The efficacy of triclopyr was similar on both the R and S biotypes of buckhorn plantain, suggesting the absence of cross-resistance to this herbicide. This is the first report of 2,4-D resistance in buckhorn plantain and the first report of 2,4-D resistance in turf. The resistance mechanism was limited to within a chemical family (phenoxycarboxylic acid) and did not occur across all WSSA Group 4 synthetic auxin herbicides, as the pyridinecarboxylic acid herbicides clopyralid and triclopyr and the arylpicolinate herbicide halauxifen-methyl provided control in our experiments. Nomenclature: 2,4-D, clopyralid, halauxifen-methyl, triclopyr, buckhorn plantain, Plantago lanceolata L. PLALA
Human milk AFM1, OTA, and DON evaluation by liquid chromatography tandem mass specrometry and their relation to the Southern Brazil nursing mothers' diet

The occurrence of aflatoxin M₁ (AFM₁), ochratoxin A (OTA), and deoxynivalenol (DON) in human milk and their correlation to the lactating donors dietary habits from Southern Brazil were investigated. Milk samples were collected from 86 nursing mothers who were also interviewed through a Food Frequency Questionnaire (FFQ). The occurrence of AFM₁, OTA, and DON in the human milk samples was evaluated by liquid chromatography tandem mass spectrometry (LC‐MS/MS) and correlated with the FFQ data. The analysis of the FFQs revealed a high intake of foods susceptible to mycotoxin contamination, such as wheat flour and its derivatives, bovine milk, and coffee which had habitual consumption reported by 71, 50, and 43% of the participants, respectively. AFM₁, OTA, and DON were not detected in any sample of human milk, even though the results obtained by LC‐MS/MS suggest a possible occurrence of DON in four samples (>LOD: 2.5 ng/mL; <LOQ: 5 ng/mL). PRACTICAL APPLICATIONS: These findings might be valuable for food safety of human milk, showing that besides well‐known benefits breastfeeding do not present undesirable contaminants. However, it is important emphasize that the monitoring food need to be performed constantly to ensure the milk quality and consumer safety and, in addition, the data obtained should be according to regulation.
Genetic diversity assessment of the Mexican Simmental population through pedigree analysis

ABSTRACT The purpose of this study was to examine the genetic variability of the Mexican Simmental. Inbreeding was calculated by year for animals born from 1985 to 2014. Proportion of ancestors known, average equivalent complete generations, generation interval, and effective size, as well as the effective numbers of founders, ancestors, and founder genomes were calculated for animals born in six periods (1985-1989, 1990-1994, 1995-1999, 2000-2004, 2005-2009, and 2010-2014). The year 1985 was selected as the initial year to form the [. ]