Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Residue Cultivation Timing Impact on Organic No-Till Soybean Weed Management

A cereal rye cover crop mulch can suppress summer annual weeds early in the soybean growing season. However, a multi-tactic weed management approach is required when annual weed seedbanks are large or perennial weeds are present. In such situations, the weed suppression from a cereal rye mulch can be supplemented with the use of high-residue cultivators which can prolong the weed-free period during soybean growth. Research trials were conducted to determine the optimum timing of high-residue cultivation for weed control in rolled-crimped cereal rye mulches. Treatments included three cultivation timings with a high-residue cultivator: early (3–4 wk after soybean planting (WAP)), intermediate (5–6 WAP), and late (7–8 WAP), a weed-free and no-cultivation control. Crop and weed measurement included cereal rye biomass, weed biomass, soybean population and biomass, and yield. Cereal rye biomass was 50% lower and weed biomass was three times greater in 2011 than in 2010 and 2012 due to 2011 being a dry year. There was no significant effect of cultivation timing on soybean population when compared to no-cultivation or hand-weeded treatments. While cultivation reduced weed biomass by 67% compared to no-cultivation, soybean yield was only improved by 12% in early and late cultivation treatments and 22% in intermediate cultivation treatment when compared to no-cultivation. Effective strategies for improving weed management by integrating the use of a high-residue cultivator in no-till organic systems could help existing organic field crop producers to reduce tillage while also encourage adoption of organic crop production by conventional growers who prefer reduced-tillage systems. Unlike traditional organic cultivation equipment, therefore, optimal timing of cultivation should be delayed several weeks in organic cover crop-based no-till planted soybean production as compared to the typical tillage-based approach to ensure both weed control and optimal yield. Nomenclature: Cereal rye, Secale cereale L. ; soybean, Glycine max L.
First Record of Norileca indica (Isopoda, Cymothoidae) Parasitic on Selar crumenophthalmus and Decapterus kurroides (Perciformes, Carangidae) in the Philippines

ABSTRACT: The cymothoid isopod Norileca indica is recorded from the branchial cavites of bigeye scad, Selar crumenophthalmus, and redtail scad, Decapterus kurroides (Perciformes: Carangidae), in the Panay Gulf, Province of Iloilo, the Philippines. The overall prevalence and mean intensity of N. indica were 40.7% and 1.05 for S. crumenophthalmus and 100% and 1.0 for D. kurroides. The majority of the specimens of N. indica from both host fishes were ovigerous females. This record represents the first report of N. indica from these carangids in the Philippines, and D. kurroides is a new host.
Biochemical and Immunocytochemical Characterization of Canine Corneal Cells Cultured in Two Different Media

The study purpose was to determine whether canine corneal cultures demonstrate superior growth when cultured in a fully defined epithelial selective medium, Epilife, compared to Dulbecco’s modification of Eagle’s medium (DMEM) with fetal bovine serum (FBS), and to characterize cultured canine corneal cells. Superficial keratectomies were performed on three dogs. Samples were trypsinized to separate cell layers. Posttrypsinization, immunohistochemistry confirmed that epithelial cells had been released from the stroma. Both cell populations (presumed epithelial cells and stromal tissues) were cultured in DMEM with FBS or Epilife. First passage cells were fixed for immunocytochemistry and prepared for PCR. Immunocytochemical staining for pancytokeratin, vimentin, and E-cadherin was evaluated, and immunofluorescence for zonula occludens-1 was attempted. Amplification of cytokeratin 5 (CK5) mRNA was assessed by PCR. Primary presumed epithelial cells grew faster when cultured in DMEM with FBS compared to Epilife. Stromal tissue segments in Epilife medium failed to adhere to culture plates, indicating that this medium may inhibit attachment and growth of non-epithelial tissues. Staining of corneal tissue segments confirmed that epithelial layers were pancytokeratin and E-cadherin positive, while stromal cells were vimentin positive. Immunocytochemistry of cultured cells revealed that epithelial cells stained positively for pancytokeratin, vimentin, and E-cadherin, while stromal cells remained only vimentin positive. Greater amplification of CK5 mRNA occurred from epithelial cells grown in Epilife compared to epithelial cells in DMEM with FBS or the stromal cells. Based on PCR results, Epilife medium may support retention of the epithelial characteristic of CK5 mRNA expression better than DMEM with FBS.
Efficacy of dietary vitamin D and its metabolites in poultry - review and implications of the recent studies

Vitamin D plays many important functions in the animal, as it is necessary for proper calcium (Ca) absorption and use in different biological processes. The aim of several recent experiments with poultry was to evaluate the efficacy of different forms and levels of vitamin D3 in the diets for broiler chickens and laying hens. The results of these studies are presented and discussed in this review paper. Based on these results, the modern high-performing poultry requirement for supplemental vitamin D to maximise mineral digestibility, performance and immunity indices, bone health, and eggshell quality is about 3,000 IU/kg, i.e. much higher than NRC (1994) recommendations. The results of several recent poultry studies have shown that 25-hydroxycholecalciferol (25-OH-D3) is more efficient in commercial poultry nutrition than the basic form of vitamin D3 (cholecalciferol).
Laboratory cage studies on the efficacy of some medicinal plant essential oils for controlling varroosis in Apis mellifera (Hym.: Apidae)

Abstract Varroosis is a disease of Apis mellifera L. caused by the mite Varroa destructor Anderson and Trueman. Essential oils and their chemical constituents offer a safe alternative to synthetic acaricides for the control of this mite in bee hives. The present study was conducted to evaluate anti-parasitic activity of essential oils from Thymus kotschyanus Bioss & Hohen. , Mentha longifolia L. , Eucalyptus camaldulensis Dehnh. , and Ferula gummosa L. at concentrations of 1, 2.5, 4, and 5.5 μl/l air for 5 and 10 h. Findings indicated that mite mortality increased as oils concentration and exposure time increased. T. kotschyanus oil at 5.5 μl/l air caused a mite mortality rate of 54.4% and 84.43% after 5 and 10 h fumigation, respectively. At the same concentration and exposure time, the honey bee mortality was 0% and 7.2%, respectively. Application of M. longifolia and E. camaldulensis oils at 5.5 μl/l air resulted in 65.53% and 71.06% mortality in Varroa mites and 10.13% and 12% mortality in honey bees after 10 h exposure. Despite moderate acaricidal activity of F. gummosa oil against Varroa mite (49.69%), it was highly toxic to honey bee (30%). Also, GC/MS analysis of the oils showed that carvacrol (47.99%) and thymol (30.61%) in T. kotschyanus oil, piperitenone (36.86%), piperitenone oxide (27.53%),Cispiperitone epoxide (22.21%), and pulegone (8.38%) in M. longifoliaoil, 1,8-cineol (74.7%) and α-pinene (8.35%) in E. camaldulensis oil, and β-pinene (87.29%) in F. gummosa oil were the main chemical constituents. Collectively, our results led to a conclusion that T. kotschyanus, M. longifolia, and E. camaldulensis oils have enough potential to play an important role in integrated control programs of varroosis in apiaries.
Mécanismes régulant l'utilisation périphérique du glucose chez l'oiseau : focus sur le transport de glucose

Le metabolisme glucidique de l’oiseau est important pour maitriser la croissance de l’animal et la qualite de la viande. Nous avons etudie l’utilisation peripherique du glucose chez le poulet au niveau musculaire en identifiant et en caracterisant les principaux acteurs impliques. Nous avons identifie et caracterise un nouveau transporteur de glucose chez les oiseaux, GLUT12. Il est exprime dans les muscles, son expression est regulee in vivo par l’insuline et il peut etre enrichi dans les membranes plasmiques des cellules suite a une stimulation insulinique. In vitro, une augmentation du transport de glucose est mesuree sur le meme pas de temps que la translocation de GLUT12. Comme pour GLUT4 chez les mammiferes, la PI3K est impliquee dans la translocation de GLUT12. L’expression des GLUTs musculaires varie avec l’âge des animaux mais aussi avec leur etat physiologique, le type metabolique et/ou la fonction du muscle. L’ensemble de nos resultats explique en partie le metabolisme glucidique atypique des oiseaux et laisse entrevoir le developpement de nouvelles strategies d’elevage pour repondre a une demande croissante de produits avicoles de qualite.
Redescription of Psocus flavonimbatus Rostock (Psocoptera: Psocidae) from Finland

About 120 years since its original description from Estonia (region of lake Peipus) the enigmatic species Psocus flavonimbatus Rostock, 1879 has been rediscovered in semi-natural spruce-dominated forests in Kuhmo, Central Finland. The species, which had tentatively been synonymized with Loensia variegata (Latreille, 1799), is here reinstated. Coloration and general morphology of both sexes and terminalia of females are described and illustrated. Unfortunately the few males available are all damaged, lacking abdomen. Without information on male terminalia it is impossible to assign the species to one of the modern genera of Psocidae. Therefore, it is here retained in the genus Psocus, pending further studies.
INVESTIGATIONS ON THE RESISTANCE OF COMMENSAL SWINE ESCHERICHIA COLI TO SOME AMINOGLYCOSIDES-AMINOCYCLITOLS

Th e aim of this study was to describe the prevalence of antibiotic resistance to some aminoglycosides, streptomycin, spectinomycin and gentamicin and three aminoglycosideresistance genes in Escherichia coli isolated from feces and lagoon manure in six swine farms in Republic of Bulgaria. A total of 274 E. coli isolates from 270 fecal samples and twelve samples from lagoon manure were tested by disk diff usion method to determine resistance patterns to 11 antimicrobial agents. Aminoglycosides resistance also was determined by E-test, agar dilution method, PCR and qPCR. Th e highest resistance observed to streptomycin (70.0%) and spectinomycin (65.5%). Multi-resistance patterns in studied E. coli strains showed that the resistance to streptomycin/spectinomycin was most frequently seen together with resistance to ampicillin, tetracycline, and sulfonamides (39.6%). Th e E. coli isolates resistant to streptomycin, spectinomycin were examined for the presence of strA/strB, aadA1 genes, and resistant isolates to gentamicin were evaluated for the presence of the aacC1 gene. Th e most common gene determining resistance to aminoglycosides was aadA1 which was found in 54.0% of swine isolates and lagoon manure isolates followed by straA/strB genes (32.3%). Th e aacC1gene was not identifi ed in E. coli isolates resistant to gentamicin.
Ultrastructural correlates of acoustic sensitivity in Baikal coregonid fishes

We investigated the ultrastructure of the sensory saccular and lagenar epithelia of the coregonid fishes: pelagic planktophage Baikal omul (Coregonus migratorius), benthophage lacustrine-riverine whitefish, or Baikal pidschian (C. pidschian), a typical inhabitant of the shallow water of the lake, and their hybrids of the first generation (F1). We made a few suggestions on the possible adaptive significance of ultrastructural specializations to acoustic sensitivity in different species of coregonid fishes. Unlike the shallow-water pidschian, both the pelagic omul and F1 hybrids possess higher morphological diversity of sensory cells. However, sensory cells of pidschian are characterised by sensory bundles with shorter stereocilia that presumably could perceive higher frequency sound oscillations. The saccular orientations are different from the earlier described ones in other whitefishes. The predominance of any direction in the morphological polarization of the sensory macula of different fish species is expected to be attributed to their ecology.
MVSE: An R‐package that estimates a climate‐driven mosquito‐borne viral suitability index

Viruses, such as dengue, Zika, yellow fever and chikungunya, depend on mosquitoes for transmission. Their epidemics typically present periodic patterns, linked to the underlying mosquito population dynamics, which are known to be driven by natural climate fluctuations. Understanding how climate dictates the timing and potential of viral transmission is essential for preparedness of public health systems and design of control strategies. While various alternative approaches have been proposed to estimate local transmission potential of such viruses, few open‐source, ready to use and freely available software tools exist. We developed the Mosquito‐borne Viral Suitability Estimator (MVSE) software package for the R programming environment. MVSE estimates the index P, a novel suitability index based on a climate‐driven mathematical expression for the basic reproductive number of mosquito‐borne viruses. By accounting for local humidity and temperature, as well as viral, vector and human priors, the index P can be estimated for specific host and viral species in different regions of the globe. We describe the background theory, empirical support and biological interpretation of the index P. Using real‐world examples spanning multiple epidemiological contexts, we further demonstrate MVSE's basic functionality, research and educational potentials.
Global analysis of alternative splicing in human cells of myeloid origin

Pre-mRNA splicing is one of the processing steps by which the genetic information flows in a biological system for functional gene expression. Alternative splicing plays an important role in the development of eukaryotic cells during which the activity of the splicing regulatory machinery changes dynamically. Perturbations in alternative splicing are at the basis of a wide spectrum of human diseases. Recent investigations have shown that alternative splicing plays a role in the homeostasis of lymphoid cells in order to mount an efficient adaptive immune response. However, a detailed characterization of the role of alternative splicing in myeloid cells during an innate immune response is lacking. The characterization of alternative splicing events in myeloid cells will provide a basis to study perturbations that occur in various human disorders such as allergies, autoimmune diseases and cancers. Thus, we performed two transcriptome studies by RNA-sequencing in the aforementioned cells. In the first study, we performed analysis of the human monocytes and various subtypes of macrophages derived from them, both in the THP-1 cell line and in primary human cells. We identified genes that changed mRNA expression and changes in alternative splicing during the differentiation from monocytes to macrophages and during their polarization to various macrophage subsets. We found that alternative splicing plays a major role in the differentiation process and in the polarization of M1 macrophages but likely less in the activation of the M2 macrophages to the various subsets. In the second study, we successfully knocked out by CRISPR the splicing factor PRPF40B in K562 cell line. We rescued the knock out cells by overexpressing PRPF40B as wild-type or as mutated by introducing in the wild-type gene two mutations of the factor found in myelodysplastic syndromes. We found that PRPF40B controls the alternative splicing of thousands of events, hundreds of which are cassette exons, mainly repressing their inclusion, and we proved that it occurs co-transcriptionally. In addition, we found an activation of a hypoxia gene signature in the KO cells thus showing that PRPF40B has a role in inhibiting hypoxia, in contrast to its homologue PRPF40A which instead promotes it. We found that when PRPF40B is mutated, no major changes in gene expression and alternative splicing are occurring thus showing that the two mutations might be just passengers. Unexpectedly, we found a possible contrasting role of PRPF40A and PRPF40B in regulating hypoxia in Acute Myeloid Leukemia which could lead to a potential therapeutic application to decrease chemoresistance.
Induction of T helper 2 cell responses against Schistosoma mansoni eggs in the murine intestine

T helper 2 (Th2) cell responses typify the immune response to parasitic organisms, which frequently invade the intestine. Dendritic cells (DCs) are considered vital for the induction of Th2 responses as they present parasite- derived antigens to naive T cells in draining lymph nodes. However, the identities of the DC populations responsible for priming Th2 cells in the intestine are still unclear. We developed an experimental immunization protocol to deliver Schistosoma mansoni eggs into the intestine. During live infection by the parasite, these eggs cause intestinal damage, granuloma formation, tissue fibrosis and strong type 2 immune responses. Many aspects of type 2 immunity are controlled by the transcription factor IRF4 and we observed that intestinal Th2 responses against Schistosoma mansoni eggs did not develop in the draining lymph nodes in the absence of IRF4+ DCs. IRF4f/f CD11c-cre positive mice had fewer CD11b-expessing migrating DCs, and fewer parasite antigen-carrying DCs were present in the mesenteric lymph nodes (MLNs) draining the small intestine and colon. However, transfer of antigen-loaded IRF4-deficient DCs directly into the MLN revealed that these cells could induce antigen-specific Th2 responses, suggesting that IRF4 controlled the migration of CD11b-expessing DCs rather than their Th2 inducing capacity. Furthermore, immature DCs from the intestinal lamina propria, and semi-mature DCs from lymph were sufficient to prime antigen-specific Th2 responses against egg antigens when transferred into naive recipient mice. This induction was dependent on MHCII expression but not on the production of IL-4 by the transferred DCs, indicating that conventional intestinal DCs are fully capable of inducing Th2 responses against S. mansoni egg antigens upon transfer. Further analysis of migratory small intestinal and colonic lymph DCs revealed that distinct subsets of CD11b-expressing DCs were sufficient for the induction of Th2 responses in the small intestine and colon. CD11b+CD103+ DCs transported parasite antigen from the small intestine, whereas CD11b+CD103- DCs performed this role in the colon. Of note, these same small intestinal and colonic DC subsets were also the populations that were most efficient at priming antigen-specific Th2 responses in vivo. Thus, we have not only identified that IRF4-dependent CD11b-expressing DCs are specialized to drive Th2 responses in the intestine but have also revealed that different DC subsets promote Th2 responses in the small intestine and colon. These findings not only advance our knowledge of intestinal Th2 responses against parasite antigens but also reveal a hitherto unappreciated functional heterogeneity among intestinal DCs, which could also be relevant for other tissue- specific intestinal conditions like Crohn’s disease, ulcerative colitis and celiac disease.
Agronomic response of arugula to green fertilization with rooster tree during two culture times

The consumption of arugula is low compared to lettuce and coriander. However, it has been increasing, and there is a lack of information on fertilization and culture times. Growth and development characteristics of arugula were assessed. It was fertilized with different amounts of rooster tree biomass, at different times in the soil. It was cultured at two planting times (springsummer and fall), in the municipality of Serra Talhada, PE, Brazil. The experimental design was randomized block, with treatments arranged on a 4 × 4 factorial, with three replications. The first factor is the amounts of rooster tree biomass (5.4, 8.8, 12.2 and 15.6 Mg ha -1 on a dry base), and the second one is times of incorporating in the soil (0, 10, 20 and 30 days before the planting of arugula). The characteristics of arugula assessed were: Plant height, number of leafs per plant, yield of green and dry mass of the above-ground part. The maximum yield of arugula was obtained at a dose of 15.6 Mg ha -1 of green fertilizer. Some synchronicity between the supply of nutrients (green fertilizer) and the period of maximum demand by the arugula plants was observed when they were incorporated 20 days before planting. The culture increased the cycle of arugula during the fall, offering greater green and dry mass yields to the culture.
Lactoferrin Gene Polymorphism of Holstein Cows in Isfahan Province

A total of 404 Holstein cows from five dairy herds in Isfahan province were used to obtained polymorphism of bovine lactoferrin (LTF)gene for a possible genetic marker information. Two alleles A and B were found in the examined population. The frequency of A-allele ranged from 0.775 to 0.831, while frequency of B-allele 0.169 to 0.225. The alleles controlled the occurrence of two genotypes AA and AB,with frequency of 0.606 and 0.394 respectively.Statistical analysis showed that there was no Hardy-Weinberg equilibrium between the observed and expected distribution of LTF genotypes.It was found that polymorphism existed in intron 6 region of bovine LTF gene, which suggested that this polymorphism could be associated with somatic cell count (susceptibility/resistance mastitis).
A calcium-binding protein CAS regulates the CO2-concentrating mechanism in the green alga Chlamydomonas reinhardtii

Abbreviation Introduction.1 1. Inorganic carbon transport system.3 2. Carbonic anhydrases.7 3. Microcompartments containing Rubisco in aquatic photosynthetic organisms.9 4. CO2-concentrating mechanism in Chlamydomonas reinhardtii.11 5. Regulation of the CO2-concentrating mechanism.12 6. Calcium signaling and CO2-response in plants.14 Purpose.16 Materials and Methods.17 Results.30 1. Isolation and characterization of high-CO2-requiring mutants.30 2. Photosynthetic characteristics of the complemented strains of the CAS insertion mutant.37 3. CAS-dependent regulation of CO2-concentrating mechanism-related components.43 4. Subcellular localization of CAS in Chlamydomonas reinhardtii.50 5. CAS functions in protein complexes.54 6. Calcium-binding activity of Chlamydomonas CAS.55 7. Calcium-dependent regulation of the CO2-concentrating mechanism.56 8. Increased fluorescence signal of a calcium indicator in the pyrenoid in response to CO2 and light.58 Discussion.60 Conclusion.68 References.69 Acknowledgment.79
Apreliminary study for determination of the possibility of simultaneous selection for oil content and grain yield in maize

We investigated the genetic potential of six maize families for simultaneous selection of oil content and grain yield. Six generations of six families were generated in 2011 and 2012. These genotypes were tested in a field experi- ment, conducted in Dardanos Research and Application Center, Canakkale, Turkey, in 2013. Data were collected on oil content and grain yield per plant and then analyzed by using Generation Mean Analysis method to determine the appropriate families for simultanous selection studies. We also calculated genetic effect estimations for these traits in the investigated genotypes. Results showed that there were significant differences among the families and generations for oil content and grain yield. The variation in oil content in the families was mainly controlled by additive gene actions. Simultaneous selection did not seem feasible in the tested families, though there was a good chance for considerable enhance- ment in some genotypes if the investigated traits were taken into account singlehandedly. Three families (A680x- IHO, IHOxB73 and IHOxHYA) showed potential for selection to enhance oil content, while two others (IHOxMo17 and Mo17xIHO) were promising for grain yield. Estimated genetic gains were in the range of 0.4% to 4.1% per cycle for oil content, and 17.7 g to 60.7 g per cycle for grain yield.