Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution patterns of tree, understorey, and detritus biomass in coniferous and broad-leaved forests of Western Himalaya, India

ABSTRACT Forest biomass pools are the major reservoirs of atmospheric carbon in both coniferous and broad-leaved forest ecosystems and thus play an important role in regulating the regional and global carbon cycle. In this study, we measured the biomass of trees, understorey, and detritus in temperate (coniferous and broad-leaved) forests of Kashmir Himalaya. Total ecosystem dry biomass averaged 234.2 t/ha (ranging from 99.5 to 305.2 t/ha) across all the forest stands, of which 223 t/ha (91.9–283.2 t/ha) were stored in above- and below-ground biomass of trees, 1.3 t/ha (0.18–3.3 t/ha) in understorey vegetation (shrubs and herbaceous), and 9.9 t/ha (4.8–20.9 t/ha) in detritus (including standing and fallen dead trees, and forest floor litter). Among all the forests, the highest tree, understorey, and detritus biomass were observed in mid-altitude Abies pindrow and Pinus wallichiana coniferous forests, whereas the lowest were observed in high-altitude Betula utilis broad-leaved forests. Basal area has showed significant positive relationship with biomass (R2 = 0.84–0.97, P < 0.001) and density (R2 = 0.49–0.87). The present study will improve our understanding of distribution of biomass (trees, understorey, and detritus) in coniferous and broad-leaved forests and can be used in forest management activities to enhance C sequestration.
Effect of alfalfa fodder supplementation on enteric methane emission measured by sulfur hexafluoride technique in Murrah buffaloes

Phyto-sources possessing different secondary metabolites are under investigation for the mitigation of enteric methane emission from livestock. Alfalfa (Medicago sativa) contains considerable saponin which is known for methane reduction through anti-protozoal action. Therefore, this study was undertaken to ascertain the effect of saponin containing alfalfa fodder (Medicago sativa; second cut) on enteric methane emission in Murrah buffaloes quantified using sulfur hexafluoride (SF6 ) technique. Twelve male Murrah buffalo calves were randomly divided into two groups of six animals each. Buffalo calves in control group were fed on wheat straw and concentrate based diet (R: C, 60:40), while animals in test group were supplemented with saponin containing alfalfa fodder (second cut, 30%) replacing wheat straw on w/w basis. Effect of alfalfa fodder supplementation on rumen fermentation characteristics, archaeal and protozoal population were also studied. Enteric methane emission in control and test group buffaloes was reported as 78.09 and 61.39 g/d, respectively. In this study, about 21% reduction in enteric methane emission was achieved on the feeding of saponin containing alfalfa fodder at 30% level of the diet. However, dry matter intake, pH, ammonia nitrogen and total volatile fatty acid production did not differ (p>0.05) among the groups. A significant (p<0.05) decrease in acetate production was also with concomitant increase in propionate production. Results revealed a nonsignificant change in archaeal population, while protozoal population were adversely affected and about 20% less numbers were observed in test group. From the study it may be concluded that saponin from natural feed resources like alfalfa fodder at a level of 6.0 g/kg DM can be used for the significant enteric methane reduction.
In vitro evaluation of fungicides against purple blotch of onion caused by Alternaria porri

The onion (Allium cepa L.) “Princess of vegetables”, is one of the important cultivated crops belonging to the genus Allium and family Alliaceae. Among the major diseases of onion, purple blotch caused by Alternaria porri is especially most destructive pathogen causing leaf blight of onion in Karnataka. The diseases cause yield loss up to 60 to 70 per cent under favourable weather condition. Hence, the present investigation was taken on for evaluation of effective fungicides under in vitro condition. The results revealed that out of twelve fungicide tested tebuconazole + trifloxystrobin and propiconazole were found to be most effective in inhibiting the mycelial growth of A. porri and completely inhibited the pathogen at 0.15% per cent.
Effects of sex and age of Luciobarbus kersin (Osteichthyes: Cyprinidae) on the parasitic nematode Rhabdochona kurdistanensis from Greater Zab River, Kurdistan Rgion, Iraq

Monthly samples of the cyprinid fish Luciobarbus kersin were collected from Greater Zab River, Kurdistan Region, Iraq, during the period from June 2014 till the end of May 2015. Fishes were infected with the nematode Rhabdochona kurdistanensis . The prevalence of infection was 26.1%. No significant differences were noticed between male and female fishes infected with this worm. There are a direct proportion between prevalence, mean intensity and abundance of infection with R. kurdistanensis with the fish length. Higher infection was during Spring and Summer (maximum peak in July, prevalence= 54.54), and low during Autumn and Winter (Minimum peak in January, prevalence= 5.26). Fully matured males and gravid females were noticed only during the late June and July.
Evolution transforms pushed waves into pulled waves

Understanding the dynamics of biological invasions is crucial for managing numerous phenomena, from invasive species to tumours. Despite the breadth of application, and substantial theoretical development, invasions have proven difficult to predict. This may partly be due to an underappreciation of the interaction between the Allee effect (where individuals in low-density populations suffer lowered fitness) and evolution during invasions. Since invasion fronts are regions of perpetually low population density, selection should favour vanguard invaders that are resistant to Allee effects. Evolution in response to this pressure could cause invasions to transition from pushed waves, propelled by dispersal from behind the invasion front, to pulled waves, driven by the invasion vanguard. To examine this possibility, we construct an individual-based model in which a trait that governs resistance to the Allee effect evolves during an invasion. We find that vanguard invaders rapidly evolve resistance to the Allee effect, causing invasions to accelerate. This also results in invasions transforming from pushed waves into pulled waves; an outcome with important consequences for the predictability of invasion speed. These findings underscore the importance of accounting for evolution in invasion forecasts, and suggest that it has the capacity to fundamentally alter broader invasion dynamics.
Polarization Of Cystic Fibrosis Macrophages Is Dysregulated

ACTIVATION OF CYSTIC FIBROSIS MACROPHAGES IS DYSREGULATED Evan J. Levy, Cristina Barone, Emanuela Bruscia, Marie E. Egan. Department of Pediatrics, Yale University School of Medicine, New Haven, CT. We hypothesize that intrinsic defects in cystic fibrosis (CF) macrophages affect their ability to adequately respond to extracellular stimuli, affecting their phenotypic response and contributing to a hyper-inflammatory state. Peripheral blood-derived monocytes from healthy donors (HD) (n=10) as well as CF subjects (n=10) were differentiated into macrophages using RPMI media with 50 ng/mL of MCSF for 10 days. Cells were treated with 100 ng/mL of LPS plus 20 ng/mL of INF-gamma to activate the M1 phenotype or 20 ng/mL of IL-4 to activate the M2 phenotype. Cells were treated for 24 hours in preparation for RNA isolation and 3 hours in preparation for protein isolation. RNA was isolated and reverse transcribed to cDNA in preparation for qualitative, reverse transcription polymerase chain reaction (qRT-PCR). qRT-PCR was performed using IL-6, IL-1B, and TNF-alpha primers as M1 markers and TGF-B1, MRC, PPAR-gamma as M2 markers. Expression levels were performed in seven experiments, each using a different set of HD and CF subjects, utilizing 8.0 x 10^5 to 1.0 x 10^6 cells per well, while three protein experiment were done using different sets of HD and CF subjects. Stimulation of CF macrophages induces greater phosphorylation of proteins that regulate macrophage activation, as compared to HD macrophages. When CF macrophages are challenged with LPS/INF-gamma, they show greater phosphorylation of STAT1 protein as compared to HD macrophages. Similarly, when CF macrophages are challenged with IL-4, they exhibit greater phosphorylation of STAT6 protein, as compared to HD macrophages. Finally, CF macrophages show greater phosphorylation of AKT protein as compared to HD macrophages when stimulated with both M1 and M2 cytokines. As expected, HD macrophages (n=7, experiments) demonstrated appropriate plasticity and polarization with increased expression of M1 markers and decreased expression of M2 markers in response to LPS/INF-gamma. Furthermore, they demonstrated modestly increased expression of M2 markers and decreased expression of M1 markers in response to IL-4. In marked contrast, when stimulated with LPS/INFgamma CF macrophages (n=7, experiments) demonstrated hyper-inflammation with dramatically increased expression levels of M1 markers as well as aberrant polarization as evidenced by increased expression levels of some M2 makers. Aberrant polarization was further characterized by increased expression of M1 markers in the presence of IL-4 in addition to increased expression of M2 markers. These data suggest that lack of functioning CFTR in macrophages leads to the inability of macrophages to adequately respond to environmental cues and activate into appropriate phenotypes suggesting there is an intrinsic cellular defect. Moreover, the mechanism(s) that underlie these aberrant responses likely involve altered intracellular signal transduction which is currently under investigation.
Potential role of microbial pathogens in control of red palm weevil (Rhynchophorus ferrugineus) ‐ A Review

The invasive Red Palm Weevil (RPW), Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae), is one of the most destructive pests of ornamental and economically important palms globally. It has been found in 50 % of date‐growing and 15 % of coconut‐producing countries in the world. Synthetic organic insecticides have been the default method to combat this pest, but they are clearly inefficient due to the secretive nature of the insect and there is concern about non‐target effects from blanket spraying. For this reason, there is increasing interest in biological control methods such as the possible use of microbial entomopathogens, which might be incorporated into IPM approaches. In this review we summarize research work on microbial control agents, their effectiveness against RPW and their integration with other control measures.
Running Head: Characterisation of Rht-1 dwarfing genes in wheat

The introduction of the Rht-B1b and Rht-D1b semi-dwarfing genes led to impressive increases in wheat yields during the ‘Green Revolution’. The reduction in stem elongation in varieties containing these alleles is caused by a limited response to the phytohormone, gibberellin (GA), resulting in improved resistance to stem lodging and yield benefits through an increase in grain number. Rht-B1 and Rht-D1 encode DELLA proteins, which act to repress GA-responsive growth, and their mutant alleles Rht-B1b and Rht-D1b are thought to confer dwarfism by producing more active forms of these growth repressors. Whilst no semi-dwarfing alleles of Rht-A1 have been identified, we show that this gene is expressed at comparable levels to the other homoeologues and represents a potential target for producing novel dwarfing alleles. In this study we have characterised additional dwarfing mutations in Rht-B1 and RhtD1. We show that the severe dwarfism conferred by Rht-B1c is caused by an intragenic insertion, which results in an in-frame 90 bp insertion in the transcript and a predicted 30-amino acid insertion within the highly conserved N-terminal DELLA domain. In contrast, the extreme dwarfism of Rht-D1c is due to over-expression of the semi-dwarfing Rht-D1b allele, caused by an increase in gene copy number. We show also that the semi-dwarfing alleles Rht-B1d and Rht-B1e introduce premature stop codons within the N-terminal coding region. Yeast two-hybrid assays indicate that these newly-characterised mutations in Rht-B1 and Rht-D1 confer ‘GA-insensitive’ dwarfism by producing DELLA proteins that do not bind the GA receptor, GID1, potentially compromising their targeted degradation.
Genetic and physiological characterization and ecological management of non-target site resistance in multiple herbicide resistant Avena fatua L.

Extensive herbicide usage has led to the evolution of resistant weed populations that cause substantial crop yield losses and increase production costs. The multiple herbicide resistant (MHR) Avena fatua L. populations utilized in this study are resistant to members of all selective herbicide families, across five modes of action, available for A. fatua control in U.S. small grain production, and thus pose significant agronomic and economic threats. Resistance to ALS and ACCase inhibitors is not conferred by target site mutations, indicating that non-target site resistance mechanisms are involved. To investigate the potential involvement of glutathione-related enzymes in the MHR phenotype, we used a combination of proteomic, biochemical, and immunological approaches to compare their constitutive activities in herbicide susceptible (HS1 and HS2) and MHR (MHR3 and MHR4) A. fatua plants. Proteomic analysis identified three tau and one phi glutathione S-transferases (GSTs) present at higher levels in MHR compared to HS plants, while Western analyses revealed elevated levels of lambda, phi, and tau GSTs. GST specific activity towards 1-chloro-2,4-dinitrobenzene was 1.2-fold higher in MHR4 than in HS1 plants and 1.3and 1.2-fold higher in MHR3 than in HS1 and HS2 plants, respectively. However, GST specific activities towards fenoxaprop-Pethyl and imazamethabenz-methyl were not different between untreated MHR and HS plants. Dehydroascorbate reductase specific activity was 1.4-fold higher in MHR than HS plants. Pretreatment with the GST inhibitor NBD-Cl did not affect MHR sensitivity to fenoxaprop-P-ethyl application, while the herbicide safener and GST inducer mefenpyr reduced the efficacy of low doses of fenoxaprop-P-ethyl on MHR4 but not MHR3 plants. 44 Mefenpyr treatment also partially reduced the efficacy of thiencarbazone-methyl or mesosulfuron-methyl on MHR3 or MHR4 plants, respectively. Overall, the GSTs described here are not directly involved in enhanced rates of fenoxaprop-P-ethyl or imazamethabenz-methyl metabolism in MHR A. fatua. Instead, we propose that the constitutively elevated GST proteins and related enzymes in MHR plants are representative of a larger, more global suite of abiotic stress-related changes.
PLACE: Proximity Learning of Articulation and Contact in 3D Environments

High fidelity digital 3D environments have been proposed in recent years, however, it remains extremely challenging to automatically equip such environment with realistic human bodies. Existing work utilizes images, depth or semantic maps to represent the scene, and parametric human models to represent 3D bodies. While being straightforward, their generated human-scene interactions are often lack of naturalness and physical plausibility. Our key observation is that humans interact with the world through body-scene contact. To synthesize realistic human-scene interactions, it is essential to effectively represent the physical contact and proximity between the body and the world. To that end, we propose a novel interaction generation method, named PLACE (Proximity Learning of Articulation and Contact in 3D Environments), which explicitly models the proximity between the human body and the 3D scene around it. Specifically, given a set of basis points on a scene mesh, we leverage a conditional variational autoencoder to synthesize the minimum distances from the basis points to the human body surface. The generated proximal relationship exhibits which region of the scene is in contact with the person. Furthermore, based on such synthesized proximity, we are able to effectively obtain expressive 3D human bodies that interact with the 3D scene naturally. Our perceptual study shows that PLACE significantly improves the state-of-the-art method, approaching the realism of real human-scene interaction. We believe our method makes an important step towards the fully automatic synthesis of realistic 3D human bodies in 3D scenes. The code and model are available for research at https://sanweiliti. github.io/PLACE/PLACE.html.
Characterization of Some Aromatic Farmers’ Varieties of Rice (Oryza sativa L.) from West Bengal and Adjoining States

The genetic variability was assayed in 35 aromatic Farmers’ Varieties (FVs). High magnitude of variability was observed for all the characters under study. High heritability was observed for days to 50% flowering, plant height, number of panicles per plant, panicle length, number of grains per panicle, 100-grain weight, grain length, grain breath and grain yield. The collective contribution of the yield contributing characters resulted in high yield for Rampha, Laldhyapa-1, A-1-1, Kauka, Kalakali and Joha Bora. Khasa, Radhunipagul, Mohanbhog, Gobindobhog, Kalojeera, Badshahbhog, Tulsibhog, Tulaipanji, Bora, Joha Bora, Silathia Bora, Jailung Lal Komal, Ghee Bora, Birai, Kabra, Rampha, Kolajoha-Big, Kolajoha-Small and Konkoni Joha were classified as the FVs having strong aroma. Grain yield showed highly significant positive association with number of panicles per plant, 100-grain weight and grain thickness. Positive direct effect on grain yield/plant was observed in number of panicles/plant, 100-grain weight, and grain length and breadth.
Effects of commercial chilling methods for reducing bacteria on pork carcasses NPB

Previous laboratory studies have demonstrated that snap/blast chilling is known to significantly reduce some bacterial populations on pork surfaces, including Salmonella, Campylobacter, E. coli, and coliforms. However, very little information exists as to whether reductions observed under commercial conditions can be attributed to chilling parameters. In this study, individual carcass sponge samples (n=386) were obtained from commercially processed warm pork carcasses (n=188) and chilled pork carcasses (n=198) subjected to snap/blast chilling or conventional chilling and evaluated for mesophilic aerobic plate counts (APC), generic E. coli (EC), coliforms (CF), as well as the presence/absence of Salmonella spp. , Campylobacter spp. , and Listeria monocytogenes. Carcass samples were obtained from one very small, three small, and three large pork processing establishments. Of these, three establishments used conventional chilling only and four establishments used snap/blast chilling, followed by conventional chilling. Overall, warm carcasses exhibited average APC of approximately 7.09 log10 CFU/300 cm, average EC counts of 1.93 log10 CFU/300 cm, and average CF counts of 2.23 log10 CFU/300 cm. Salmonella spp. , L. monocytogenes, and Campylobacter spp. were present on 2.1%, 1.2%, and 7.4% of the warm carcasses, respectively. Chilled carcasses exhibited average APC, EC, and CF of 5.21, 0.25, and 0.50 log10 CFU/300 cm, respectively. Pathogen prevalence on the chilled carcasses was 4.3% Salmonella spp. , 0.05% L. monocytogenes, and 0.0% Campylobacter spp. In addition to microbial populations, chilling parameters, and carcass surface temperature were collected. This study demonstrates that commercial chilling conditions may reduce most bacterial populations associated with pork carcasses. This information may provide processors with an additional means to control microbes in/on freshly slaughtered pork, thereby improving the microbiological safety of pork products.
Cultivo agroflorestal de Psychotria Ipecacuanha (Brot.) Stokes no Território do Baixo Sul da Bahia

A especie Psychotria ipecacuanha (Brot.) Stokes, conhecida popularmente como ipeca ou poaia, tem despertado interesse da industria farmaceutica a muitas decadas, devido a presenca dos alcaloides emetina e cefalina em suas raizes, que possuem propriedades expectorantes, emeticas e amebicidas. O risco de extincao e a dificuldade do cultivo convencional da especie, frente a grande demanda de mercado, fomentam estudos de metodos de cultivo que possibilitem a exploracao economica e, consequentemente, a criacao de novas cadeias produtivas em areas de floresta tropical. O presente trabalho foi realizado na Area de Preservacao Ambiental do Pratigi - APA do Pratigi – localizada no territorio do Baixo Sul da Bahia e teve como objetivos quantificar o crescimento e a producao de emetina em plantas de ipeca sob cultivo agroflorestal tipo cabruca, avaliando o efeito de diferentes condicoes de luminosidade, idade e fontes de adubacao. A quantificacao da emetina foi feita por meio de cromatografia liquida de alta eficiencia (CLAE) e os resultados experimentais foram submetidos a analise de variância, comparando-se as medias dos tratamentos por meio dos testes Tukey e Skot Knot. Os resultados experimentais demonstraram que as condicoes de luminosidade afetaram o crescimento das plantas de ipeca, sendo maior em ambientes com sombreamento acima de 90%. A ipeca apresentou rendimento medio de 207 kg Ha-1 de raiz fresca e 80 kg Ha-1 de raiz seca aos 16 meses de cultivo; e de 240 kg Ha-1 de raiz fresca e 93 kg Ha-1 aos 28 meses. Foi possivel obter teores de emetina, nas condicoes de cultivo agroflorestal tipo cabruca no territorio Baixo Sul da Bahia, equivalente aos teores obtidos de plantas coletadas extrativistamente nas demais regioes do pais. A idade afeta o teor de emetina nas condicoes de cultivo agroflorestal, com maiores teores em plantas mais jovens, aos 16 meses de cultivo. Considerando as fontes de adubacao, com e sem calagem, obteve-se maior altura de plantas e maior n° folhas/planta nos tratamentos que nao receberam calagem, entretanto, obteve-se melhores resultados para n° raizes/planta nas areas com calagem. Para o acumulo de massa seca de raiz, parte comercial da planta, os tratamentos com nitrogenio, com e sem calagem, promoveram as maiores medias. Os teores de emetina foram maiores nos tratamentos sem calagem e submetidas a adubacao com potassio.
How to routinely assess transition, adhesion and survival of probiotics into the gut: a case study on propionibacteria

Summary Two commercial promising probiotic strains (Propionibacterium jensenii and Propionibacterium freudenreichii) were studied to evaluate two basic probiotic requisites (adhesion and survival during the transit into the gut); two commercial starter cultures (Lactobacillus plantarum and Lactobacillus delbrueckii subsp. bulgaricus) were used as references. As an additional goal, the technological robustness was evaluated as growth as a function of pH, temperature and salt. Adhesion was studied as biofilm formation and hydrophobicity, whereas a simplified protocol was used to simulate the transit into the gut, along with the assessment of survival at pH 2.5 and in the presence of 0.3% bile salts. Propionibacteria were hydrophobic and form biofilm on glass slides, thus confirming the correlation of these properties and with the ability to adhere. None of the strains survived after the simulation of the transit into the gut, but this property could be induced in propionibacteria using a simple protocol of adaptive evolution. This paper suggests the possibility of using hydrophobicity as a screening tool to assess adhesion in propionibacteria and highlights the necessity of using a complete protocol of simulation of the gut to study the resistance to the conditions of stomach and intestine to avoid false-positive results.