Miracle-dz/UniFAR-FTUs huggingface dataset:
Cereal rye cover crop and herbicide application method affect cotton stand, Palmer amaranth (Amaranthus palmeri) control, and cotton yield

Abstract Six on-farm studies determined the effects of a rolled rye cover crop, herbicide program, and planting technique on cotton stand, weed control, and cotton yield in Georgia. Treatments included: (1) rye drilled broadcast with 19-cm row spacing and a broadcast-herbicide program (2) rye drilled with a 25-cm rye-free zone in the cotton row and a broadcast-herbicide program (3) rye drilled with a 25-cm rye-free zone in the cotton row with PPI and PRE herbicides banded in the cotton planting row, and (4) no cover crop (i.e., weedy cover) with broadcast herbicides. At two locations, cotton stand was lowest with rye drilled broadcast; at these sites the rye-free zone maximized stand equal to the no-cover system. At a third location, cover crop systems resulted in greater stand, due to enhanced soil moisture preservation compared with the no-cover system. Treatments did not influence cotton stand at the other three locations and did not differ in the control of weeds other than Palmer amaranth at any location. Treatments controlled Palmer amaranth equally at three locations; however, differences were observed at the three locations having the greatest glyphosate-resistant plant densities. For these locations, when broadcasting herbicides, Palmer amaranth populations were reduced 82% to 86% in the broadcast rye and rye-free zone systems compared with the no-cover system at harvest. The system with banded herbicides was nearly 21 times less effective than the similar system broadcasting herbicides. At these locations, yields in the rye broadcast and rye-free zone systems with broadcast herbicides were increased 9% to 16% compared with systems with no cover or a rye-free zone with PPI and PRE herbicides banded. A rolled rye cover crop can lessen weed emergence and selection pressure while improving weed control and cotton yield, but herbicides should be broadcast in fields heavily infested with glyphosate-resistant Palmer amaranth. Nomenclature: cereal rye; Secale cereale L. ; Palmer amaranth; Amaranthus palmeri S. Watson AMAPA; cotton; Gossypium hirsutum L.
Factors associated with candidemia by non-albicans Candida group in midwest region of Brazil: Eight-year cross-sectional study

The alarming increase in the non-albicans Candida group (NAC) as the etiologic agent of bloodstream infections has made it necessary for the factors associated with candidemia caused by NAC to be elucidated. A cross-sectional retrospective study was conducted which included analysis of microbiological reports, medical records and hospital infection notifications in two tertiary hospitals (Mato Grosso, Brazil) over 8 years (2006 to 2014). Of 144 observed episodes of candidemia, the NAC group represented 64.6%. The prevalence of candidemia caused by NAC was equal to 1.10 × 1,000 admissions, which was statistically different (p<0.001) from and greater than the prevalence of Candida albicans (CA). Hospitalization in the intensive care unit (PR = 1.83; p = 0.05), length of stay ≥42 days (PR = 0.62; p = 0.01) and the use of H2 blockers (PR = 1.75; p = 0.03) were significantly associated with death in patients with candidemia caused by NAC, regardless of gender, use of central venous catheter, treatment with amphotericin B and mechanical ventilation. The incidence of candidemia caused by NAC was 34% higher in men and 40% higher in patients who remained hospitalized for ≥42 days, regardless of prematurity, neutropenia, catheter, mechanical ventilation and age. After 42 days of hospitalization, the chances of survival were 67.3% among patients with candidemia caused by NAC and 56.4% among patients with candidemia caused by CA. This study suggests a different behavior between CA and NAC groups, which should be especially considered for choice of treatment regimen with antifungals. Key words: Candidemia, nosocomial bloodstream infection, epidemiology, tertiary care centers.
Occurrence of powdery mildew disease of Gerbera in Kerala

A purposive sampling survey on the hilly tracts of Wayanad, Kerala revealed the existence ofpowdery mildew disease in gerbera crops, grown under both protected and open field condition.Among the other fungal diseases of gerbera, powdery mildew disease causes decisive damageto the ornamental cut flower crop, thereby decline in the industrial value of the crop. Symptomof the disease include as white powdery mat on the upper surface of leaf lamina that graduallyturned pale yellow to brown. Powdery mildew existed in two locations of Wayanad viz.,Ambalavayal and Chulliyode where highest per cent disease severity (PDS) of 50.72 wasobserved at Chulliyode and 47.2 per cent was observed at Ambalavayal during November-December. In Ambalavayal, the disease was non-significant and no correlation existed betweenweather parameters and disease progress. But, in Chulliyode, correlation studies revealed thatit was significant with positive correlation to relative humidity and a reverse relation existedwith temperature and rainfall. The weather data clearly depicts that at a low rainfall of 96 mmand above average relative humidity of 80.27 per cent during November-December was thecongenial factor influencing the disease development. But during summer, decline in relativehumidity (78.37%) and rainfall (63.13 mm) caused a slight reduction in mean per cent diseaseseverity of 49.12 per cent and 33.6 per cent at Chulliyode and Ambalavayal respectively.Morohological and cultural characters of the pathogen depicts presence of two distinct organismviz. , Golovinomyces cichoracearum (Erysiphe cichoracearum) and Podosphaera sp. as thecausative organism of the disease. Golovinomyces cichoracearumproduced hyaline, septatemycelia with globose conidia with irregular peripheral end formed in a chain and Podosphaerasp. produced superficial, hyaline, coenocytic mycelium with oval or ellipsoidal, catenate conidiawith dimension ranging from 22.1-30.18 x 13.36-18. 08ìm formed in unbranched erectconidiophores.
Disease Specific Bacterial Communities in a Coralline Algae of the Northwestern Mediterranean Sea: A Combined Culture Dependent and -Independent Approach

Crustose coralline red algae (CCA) are important components of marine ecosystems thriving from tropical waters and up to the poles. They fulfill important ecological services including framework building and induction of larval settlement. Like other marine organisms, CCAs have not been spared by the increase in marine disease outbreaks. The white-band syndrome has been recently observed in corallines from the Mediterranean Sea indicating that the disease threat has extended from tropical to temperate waters. Here, we examined the microbiome and the pathobiome of healthy and diseased Neogoniolithon brassica-florida coralline algae in the Mediterranean Sea by combining culture-dependent and -independent approaches. The coralline white-band syndrome was associated with a distinct pathobiome compared to healthy tissues and showed similarities with the white-band syndrome described in the Caribbean Sea. A sequence related to the genus Hoeflea, order Rhizobiales, characterized the white-band disease pathobiome described by amplicon sequencing. No representative of this genus was isolated by culture. We, however, successfully isolated an abundant member of the healthy CCA microbiome, an Alphaproteobateria of the family Rhodobacteraceae. In conclusion, we did not identify a potential causative agent of the disease, but through the complementarity of culture dependent and independent approaches we characterized the healthy microbiome of the coralline and the possible opportunistic bacteria colonizing diseased tissues.
PTP-3(LAR PTPR) promotes intramolecular folding of SYD-2(liprin-α) to inactivate UNC-104(KIF1A) in neurons

This study aims to demonstrate how PTP-3 regulates SYD-2 to control UNC-104-mediated axonal transport. UNC-104 is the C. elegans homolog of kinesin-3 KIF-1A known for its fast shuttling of STVs (synaptic vesicle protein transport vesicles) in axons. SYD-2 is the homolog of liprin-α in C. elegans known to directly regulate UNC-104 as well as being a substrate of LAR PTPR (leukocyte common antigen-related (LAR) protein tyrosine phosphatase (PTP) transmembrane receptor) with PTP-3 as the closest homolog in C. elegans. CoIP assays revealed increased interaction between UNC-104 and SYD-2 in lysates from ptp-3 knockout worms. Intramolecular FRET analysis revealed that SYD-2 predominantly exists in an open conformation state in ptp-3 mutants. These assays also revealed that non-phosphorylatable SYD-2 (Y741F) exists predominately in folded conformations while phosphomimicking SYD-2 (Y741E) exists predominantly in open conformations. In ptp-3 mutants, SNB-1 cargo accumulates in soma while at the same time UNC-104 motors increasingly cluster along initial segments of axons. Interestingly, the unc-104 gene is downregulated in ptp-3 mutants that might explain the vesicle retention phenotype. More strikingly, the few visibly moving motors and STVs were overly active in neurons of these mutants. We propose a model in which the lack of PTP-3 promotes increased open conformations of SYD-2 that in turn facilitates UNC-104/SYD-2 interactions boosting motor and STVs moving speeds.
ISOLATION AND CHARACTERIZATION OF A GEMINIVIRUS ISOLATED FROM SUGAR BEET PLANTS IN EGYPT

Sugar beet is one of the main sources for sugar manufacturing in Egypt, however its cultivation and growing can be severely hampered due to viral infection. In this study beet plants infected with geminivirus-like symptoms (VLS), such as leaf curling, leaf rolling, and stunting plants growth, were collected from different several locations and examined for the presence of geminivirus through indirect DAS ELISA using two antiserums, namely C4 antiserum specific for tomato yellow leaf curl virus (TYLCV), which gave negative results, and TYLCV polyclonal antiserum which is common for any white-bean gave negative result. Electron microscope examination showed virus-like particles scattered in the cells of positive plant. Additionally, significant cytopathological effects due to viral infection were observed in the nuclei and many other organelles. Furthermore, the typical geminivirus amplicons from rolling circle amplification (RCA) combined with restriction fragment digestion amplification, which were detected in those infected host plants. Our results demonstrated that the isolated virus from infected beet plants belongs to the whitefly-transmitted geminiviruses (WTGs). Based on transmission patterns, virus host range, and sequence analysis of C1 region of viral genome, we suggest that the virus presented in this study can be considered as a new isolate of Tomato yellow leaf curl virus (TYLCV).
Targeted Proteomics Allows Quantification of Ethylene Receptors and Reveals SlETR3 Accumulation in Never-Ripe Tomatoes

Ethylene regulates fruit ripening and several plant functions (germination, plant growth, plant-microbe interactions). Protein quantification of ethylene receptors (ETRs) is essential to study their functions, but is impaired by low resolution tools such as antibodies that are mostly nonspecific, or the lack of sensitivity of shotgun proteomic approaches. We developed a targeted proteomic method, to quantify low-abundance proteins such as ETRs, and coupled this to mRNAs analyses, in two tomato lines: Wild Type (WT) and Never-Ripe (NR) which is insensitive to ethylene because of a gain-of-function mutation in ETR3. We obtained mRNA and protein abundance profiles for each ETR over the fruit development period. Despite a limiting number of replicates, we propose Pearson correlations between mRNA and protein profiles as interesting indicators to discriminate the two genotypes: such correlations are mostly positive in the WT and are affected by the NR mutation. The influence of putative post-transcriptional and post-translational changes are discussed. In NR fruits, the observed accumulation of the mutated ETR3 protein between ripening stages (Mature Green and Breaker + 8 days) may be a cause of NR tomatoes to stay orange. The label-free quantitative proteomics analysis of membrane proteins, concomitant to Parallel Reaction Monitoring analysis, may be a resource to study changes over tomato fruit development. These results could lead to studies about ETR subfunctions and interconnections over fruit development. Variations of RNA-protein correlations may open new fields of research in ETR regulation. Finally, similar approaches may be developed to study ETRs in whole plant development and plant-microorganism interactions.
Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines

One of the main goals of the Cancer Dependency Map project is to systematically identify cancer vulnerabilities across cancer types to accelerate therapeutic discovery. Project Achilles serves this goal through the in vitro study of genetic dependencies in cancer cell lines using CRISPR/Cas9 (and, previously, RNAi) loss-of-function screens. The project is committed to the public release of its experimental results quarterly on the DepMap Portal (https://depmap.org), on a pre-publication basis. As the experiment has evolved, data processing procedures have changed. Here we present the current and projected Achilles processing pipeline, including recent improvements and the analyses that led us to adopt them, spanning data releases from early 2018 to the first quarter of 2020. Notable changes include quality control metrics, calculation of probabilities of dependency, and correction for screen quality and other biases. Developing and improving methods for extracting biologically-meaningful scores from Achilles experiments is an ongoing process, and we will continue to evaluate and revise data processing procedures to produce the best results.
A new species of Metaspathius (Hymenoptera: Braconidae: Mesostoinae) from New Zealand

ABSTRACT Metaspathius gorgasoma Quicke & Ward sp. n. is described from specimens collected from litter samples. It is mainly characterised by the mesoscutum being strongly declivous anteriorly, a derived morphological feature not found in congeners. Wing structure of the new species including shape and loss of posterior longitudinal flexion lines (claval furrows) of both fore and hind wings indicate its close relationship with M. hemipterus Belokobylskij from which it is distinguished.
Growth, Yield and Phenology of Sesame (Sesamum indicum L.) as Affected by Sowing Method, Variety and Seed Rate in the Sudan Savanna of Nigeria

An experiment on the effect of sowing method, variety and seed rate on the growth and phenology of sesame (Sesamum indicum L.) was conducted at Teaching and Research Farm of Bayero University, Kano (11058'N and 8025'E) and Dutse Jigawa State (11045'N and 9020'E), Nigeria during the 2009 rainy season. The treatments consisted of three sowing methods (Broadcasting, Dibbling and Drilling), two varieties (Ex-Sudan and E8) and four seed rates (2.5, 5.0, 7.5 and 10.0 kg ha-1). A split-split plot design was used such that sowing method was allocated to main plot, variety to the sub plot and the seed rate was assigned to the sub-sub plot and replicated three times. Results showed that at Dutse, the different sowing methods had no significant effects on plant height at 4 and 10 weeks after sowing. At Kano however, significantly taller plants were recorded with broadcasting method while drilling and dibbling remained at par with shorter plants. Broadcasting also produced plants with significantly higher number of leaves, branches and capsules at both locations. Variety E8 produced plants that are significantly taller, with more leaves and flowers and but produced the lowest yield at both locations. Variety Ex-Sudan flowered and matured earlier and also produced higher grain yield than variety E8. The different seed rates had no significant effect on number of days to flowering and maturity. But with respect to grain yield, planting 5 kg of seeds per hectare produced significantly higher grain yields at both locations, while drilling and dibbling methods produced statistically similar grain yields, although both were significantly higer than dibbling method. A linear decrease in number of leaves and capsules was observed with every increase in seed rate. Key words: Growth, Phenology, Yield, Variety, Sowing date, Seed rate
Effect of Dietary Garlic Powder and Feeding Systems on Productive Performance of Broiler Chickens

This study was conducted to investigate the effect of supplemented diets with garlic powder as a natural growth promoter and feeding systems on productive performance of broiler chicks. A total number of five hundred one day cobb broiler chicks of a nearly similar body weight were used in this study Chicks were randomly divided into equal ten experimental groups, each group of 50 chick. Birds of the 1ˢᵗ group were fed ad-libitum (ADL) on starter and grower basal diets and considered as a control group, chicks of the 2ⁿᵈ, 3 and 4 group were fed basal diets supplemented with GP at a level of 0 mg/kg diet with feeding systems of provided chicks feed every day except for 24-hrs removal periods at 7 and 14 days of age (SKD2), at 7,14,21,and 28 days of age (SKD4) and at 7,14,21,28,35,and 42 days of age (SKD6) for the 2ⁿᵈ, 3 and 4 group, respectively, chicks of the 5 , 6 and 7 groups were fed basal diets supplemented with garlic powder at a level of 100 mg/kg diet with feeding systems of (SKD2) , (SKD4) and (SKD6), respectively. While, chicks of the 8 , 9 and 10 groups were fed basal diets supplemented with garlic powder at a level of 200 mg/kg diet with feeding systems of (SKD2), (SKD4) and (SKD6), respectively. Results obtained showed that chicks of control group (ADL) showed the highest LBW, BWG, GR and FI followed by chicks exposed to SKD2, SKD4 and SKD6, respectively. Chicks exposed to SKD6 showed the best feed conversion, followed by chicks exposed to SKD4, SKD2 and control group (ADL), respectively during the period from 0-6 weeks of bird's age. The lowest averages of mortality rate were observed in control group (ADL), then by birds fed diet supplemented with garlic powder at a level of 200 and 100 mg/kg diet, respectively. Significant variations were found on absolute and relative weights of carcass, giblets and total edible meat due to treatments applied, except absolute weight of carcass and total edible parts due to GP levels only. Chicks fed diet supplemented with GP at levels of 200, 100and 0mg/kg diet, respectively significantly increased protein and ash percentage and significantly decreased moisture percentage of meat samples. Chicks exposed to SKD6 and SKD4 had significantly the highest averages of overall score of sensory characterizations, followed by chicks exposed to SKD2 and the control group, respectively. It could be recommended that SKD4, SKD2 and SKD6 and the interaction between G0 and each of SKD4 or SKD6, respectively seemed to be adequate to achive the favorable results and its being recommended from the economic point of view
Lexical semantic variation and cross-language interaction in categorization

Language provides a finite set of labels (words) for an infinite set of possible objects that a speaker may encounter. Previous picture naming studies of language production have focused on highly familiar object stimuli that elicit uniform responses among native-speaker participants. By contrast, this dissertation explores picture naming responses to a broad range of object stimuli, from typical prototypes to unusual or unfamiliar examples of the same name. Drawing on research in lexical categorization, I document variation in native-speaker picture naming behavior and examine how this naming behavior and the underlying neural responses change as a result of language interaction in bilinguals. Behavioral studies (Chapter 2) measure differences in lexical categorization patterns (picture naming responses over many different examples of an object name) among monolingual and bilingual speakers of Chinese and English. Further, this inter-personal variation is explained in terms of speakers' unique language histories and norms of each linguistic community (native speakers of English and Chinese). I propose a statistical model which describes the role of these variables in each language in predicting categorization patterns in both the native language (L1) and second language (L2), identifying significant effects of cross-language interaction for bilinguals in both languages. Next, I introduce a new stimulus set of 407 objects sampled from several semantic domains (e.g., clothing and vehicles) and normed by native, monolingual speakers of English and Chinese (Chapter 3). This stimulus set demonstrates the extensive variation in picture naming responses among native speakers of each language and between languages. I use these norms to examine a few specific variables relating to native speaker norms identified in the previous chapter. In the final set of experiments (Chapters 4 and 5) I select a subset of 183 objects from the new stimulus set to test functional neural correlates of these categorization variables in native, iv monolingual speakers of each language and in Chinese-English bilinguals. Each categorization variable is associated with brain regions that uniquely respond to its variation, and activity in these regions confirms functional involvement of both L1 and L2 variables in bilinguals' L1 picture naming behavior. These findings are situated in the broader context of neurocognitive models of language production and offer a refined view of lexical semantic retrieval and selection, accounting for the variety of potential objects that speakers may encounter and variation among native speakers of a language.
Comparative Analysis of Peptidoglycans From Pseudomonas aeruginosa Isolates Recovered From Chronic and Acute Infections

Pseudomonas aeruginosa is one of the first causes of acute nosocomial and chronic infections in patients with underlying respiratory pathologies such as cystic fibrosis (CF). It has been proposed that P. aeruginosa accumulates mutations driving to peptidoglycan modifications throughout the development of the CF-associated infection, as a strategy to lower the immune detection hence ameliorating the chronic persistence. As well, some studies dealing with peptidoglycan modifications driving to a better survival within the host have been published in other gram-negatives. According to these facts, the gram-negative peptidoglycan could be considered as a pathogen-associated molecular pattern with very important implications regarding the host’s detection-response, worthy to dissect in detail. For this reason, in this work we characterized for the first time the peptidoglycans of three large collections [early CF, late CF and acute infection (bloodstream) P. aeruginosa strains] from qualitative (HPLC), quantitative and inflammatory capacity-related perspectives. The final goal was to identify composition trends potentially supporting the cited strategy of evasion/resistance to the immune system and providing information regarding the differential intrinsic adaptation depending on the type of infection. Although we found several punctual strain-specific particularities, our results indicated a high degree of inter-collection uniformity in the peptidoglycan-related features and the absence of trends amongst the strains studied here. These results suggest that the peptidoglycan of P. aeruginosa is a notably conserved structure in natural isolates regardless of transitory changes that some external conditions could force. Finally, the inverse correlation between the relative amount of stem pentapeptides within the murein sacculus and the resistance to immune lytic attacks against the peptidoglycan was also suggested by our results. Altogether, this work is a major step ahead to understand the biology of peptidoglycan from P. aeruginosa natural strains, hopefully useful in future for therapeutic alternatives design.