Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of using plant extracts and a probiotic on performance, intestinal morphology, and microflora population in broilers

SUMMARY The effects of garlic (Allium sativum) and thyme (Thymus vulgaris) extracts and a probiotic on growth performance, intestinal tissue morphology, and microbial flora in broilers were investigated. A total of 240 Ross 308 male broilers were divided into 4 treatments, with 4 replicates of 15 birds. Treatments were 2 plant extracts (1,000 ppm) and the probiotic (1,000 ppm from 0 to 7 d, 500 ppm from 8 to 21 d, and 250 ppm from 22 to 42 d) added to drinking water, and a control group with no additives. Birds in different treatments received the same diets during the experimental period. Feed intake, BW gain, and FCR were not influenced by the treatments. The weight of the ileum in birds receiving garlic was significantly lower than that in birds receiving thyme. The villus width in the duodenum of birds receiving garlic was lower than that of birds in control group (P < 0.05). A smaller villus width in the ileum was seen in birds fed garlic and the probiotic compared with birds fed the control diet. However, villus height and crypt depth were not affected by the treatments. At 20 d, birds fed garlic had significantly higher lactobacillus and lower coliform counts compared with birds fed the probiotic. Chickens that received thyme had lower total aerobic bacterial counts in the ileum than did birds in the control group. At 40 d, birds receiving the probiotic had higher total aerobic bacteria and lactobacillus counts in the crop than did birds receiving the control diet. It was concluded that these plant extracts and the probiotic can be used as natural growth promoters for broilers. The beneficial effects of plant extracts and the probiotic should be further studied on commercial farms.
Induced resistance against spider mites in cotton: Field verification

Cotton plants that had been damaged by spider mites (Tetranychus spp.) or by mechanical abrasion at the cotyledon stage were less likely to develop infestations of spider mites compared to controls early in the season. These are the first field results to demonstrate that induced resistance can reduce pest populations in an agricultural system. Differences in mite populations early in the season caused by induced resistance did not translate into differences in plant growth or cotton yield at harvest.
Modelling the role of agriculture for the 20th century global terrestrial carbon balance

In order to better assess the role of agriculture within the global climate‐vegetation system, we present a model of the managed planetary land surface, Lund–Potsdam–Jena managed Land (LPJmL), which simulates biophysical and biogeochemical processes as well as productivity and yield of the most important crops worldwide, using a concept of crop functional types (CFTs). Based on the LPJ‐Dynamic Global Vegetation Model, LPJmL simulates the transient changes in carbon and water cycles due to land use, the specific phenology and seasonal CO2 fluxes of agricultural‐dominated areas, and the production of crops and grazing land. It uses 13 CFTs (11 arable crops and two managed grass types), with specific parameterizations of phenology connected to leaf area development. Carbon is allocated daily towards four carbon pools, one being the yield‐bearing storage organs. Management (irrigation, treatment of residues, intercropping) can be considered in order to capture their effect on productivity, on soil organic carbon and on carbon extracted from the ecosystem. For transient simulations for the 20th century, a global historical land use data set was developed, providing the annual cover fraction of the 13 CFTs, rain‐fed and/or irrigated, within 0.5° grid cells for the period 1901–2000, using published data on land use, crop distributions and irrigated areas. Several key results are compared with observations. The simulated spatial distribution of sowing dates for temperate cereals is comparable with the reported crop calendars. The simulated seasonal canopy development agrees better with satellite observations when actual cropland distribution is taken into account. Simulated yields for temperate cereals and maize compare well with FAO statistics. Monthly carbon fluxes measured at three agricultural sites also compare well with simulations. Global simulations indicate a ∼24% (respectively ∼10%) reduction in global vegetation (respectively soil) carbon due to agriculture, and 6–9 Pg C of yearly harvested biomass in the 1990s. In contrast to simulations of the potential natural vegetation showing the land biosphere to be an increasing carbon sink during the 20th century, LPJmL simulates a net carbon source until the 1970s (due to land use), and a small sink (mostly due to changing climate and CO2) after 1970. This is comparable with earlier LPJ simulations using a more simple land use scheme, and within the uncertainty range of estimates in the 1980s and 1990s. The fluxes attributed to land use change compare well with Houghton's estimates on the land use related fluxes until the 1970s, but then they begin to diverge, probably due to the different rates of deforestation considered. The simulated impacts of agriculture on the global water cycle for the 1990s are∼5% (respectively∼20%) reduction in transpiration (respectively interception), and∼44% increase in evaporation. Global runoff, which includes a simple irrigation scheme, is practically not affected.
Long-term tree ring chronologies from sympatric tropical dry-forest trees: individualistic responses to climatic variation

The influence of local precipitation and temperature on long-term growth dynamics in two species of seasonally dry tropical forest trees were investigated. Growth records were extracted from tree rings in Guanacaste province, Costa Rica. These chronologies provide a long-term (c. 85-y) record of tree growth for two species with contrasting phenologies. Annual growth, in both species, was dependent on annual and/or monthly variation in local precipitation but less so on temperature. For each species, however, patterns of growth reflected unique degrees of sensitivity to monthly rainfall and rainfall during previous years. It is hypothesized that such differences were due to the rooting depth of these species. A review of the literature also indicated similar diverse cambial growth responses by tropical trees to variation in annual and monthly climate. Lastly, it was shown that variation in longer term fluctuations in the Pacific and Atlantic oceans, as measured by the El Niño Southern Oscillation (ENSO) and North Atlantic Oscillation (NAO), significantly influenced local precipitation in Guanacaste only during the wettest portion of the wet season. Such temporal sensitivity may have differentially influenced the longer-term growth of some tropical tree species but not others. Together, these results support the hypothesis that tropical tree species respond individualistically to variation in local and regional climate and that some tropical assemblages may in fact be structured by species-specific differences in soil water-use.
Plankton Production and its Control

Vertical hauls between surface and 45 metres depth were made with a measuring net, throughout 1934, at a position 5 miles S.W. of Plymouth Breakwater in circa 50 metres depth of water. The phytoplankton organisms were counted and also assessed from their content of plant pigments. A close relation was found between numbers of diatoms and their pigment contents after making allowance for the small size of three species. The phosphorus content of the phytoplankton was estimated on several occasions. The zooplankton organisms per cubic metre of sea were counted and estimations were made of their phosphorus content. The diatom population differed from that found in 1933, in which year the spring outburst was shorter but more intense, the sporadic summer outbursts were more intense, the autumn one lasted longer; and more phosphate was utilised by the plants during the first half of the year.
Micromelia in Little Penguins (Eudyptula minor)

ABSTRACT Two cases of unilateral micromelia are described in wild juvenile little penguins (Eudyptula minor). The first bird was found at San Remo, Phillip Island, Victoria, Australia. The bird's left flipper was reduced in length, and radiography demonstrated severe shortening and dysplasia of the humerus. The second bird was found having difficulty swimming off the coast near Fremantle, Western Australia. Clinical examination revealed that the bird was underweight (0.55 kg) but otherwise in good condition with subadult plumage and had probably only recently fledged from nearby Garden or Penguin Islands. The left wing was markedly reduced in size and had limited range of elbow and carpal joint movement but sensation and motor control were normal. Radiography demonstrated a severe reduction in size and distortion of the humerus and shortening and fusion of the ulna, radius, metacarpals, and phalanges. The furcula was asymmetrical because the left clavicle was slightly thinner and more radiolucent than the right and was also slightly deviated to the right side. Necropsy results of histopathologic examination revealed no other significant external abnormalities other than a mild focal heterophilic ulcerative proventriculitis from a mild burden of Contracaecum eudyptulae. Concentrations of heavy metals in kidney, liver, and brain were: cadmium, <6 mg/kg; mercury, <0.05 mg/kg; lead, <2 mg/kg; and selenium, 1.30 mg/kg. Possible causes of unilateral micromelia in these penguins are discussed.
Incidence of acute kidney injury and its association with mortality in patients with COVID-19: a meta-analysis

Acute kidney injury (AKI) is a complication of COVID-19. However, the incidence of AKI in COVID-19 varies among studies. Thus, we aimed to evaluate the pooled incidence of AKI and its association with mortality in patients with COVID-19 using a meta-analysis. We search Ovid MEDLINE, EMBASE, and the Cochrane Library for eligible publications reporting the clinical characteristics of patients with COVID-19 without language restriction. Incidence of AKI and mortality were reported. Meta-regression was used to describe the association between outcomes. From 26 studies (n=5497), the pooled incidence of AKI in patients with COVID-19 was 8.4% (95% CI 6.0% to 11.7%) with a pooled incidence of renal replacement therapy of 3.6% (95% CI 1.8% to 7.1%). The incidence of AKI was higher in critically ill patients (19.9%) compared with hospitalized patients (7.3%). The pooled estimated odds ratio for mortality from AKI was 13.33 (95% CI 4.05 to 43.91). No potential publication bias was detected. By using meta-regression analyses, the incidence of AKI was positively associated with mortality after adjusted for age and sex (Q=26.18; p=0.02). Moreover, age (p<0.01), diabetes (p=0.02), hypertension (p<0.01) and baseline serum creatinine levels (p=0.04) were positively associated with AKI incidence in adjusted models. In conclusion, AKI is present in 8.3% of overall patients with COVID-19 and in 19.9% of critically ill patients with COVID-19. Presence of AKI is associated with 13-fold increased risk of mortality. Age, diabetes, hypertension, and baseline serum creatinine levels are associated with increased AKI incidence.
Multicentre, randomised, open-label, parallel-group study evaluating the efficacy and safety of ixekizumab versus adalimumab in patients with psoriatic arthritis naïve to biological disease-modifying antirheumatic drug: final results by week 52

Objectives SPIRIT head-to-head (H2H) is a 52-week (Wk) trial comparing ixekizumab (IXE) with adalimumab (ADA) for simultaneous American College of Rheumatology (ACR)50 and Psoriasis Area and Severity Index (PASI)100 responses in 566 patients (distributed evenly across both groups) with psoriatic arthritis (PsA). IXE was superior to ADA for this primary end point at Wk24. We aimed to determine the final efficacy and safety results through Wk52 including a prespecified subgroup analysis of concomitant conventional synthetic disease-modifying anti-rheumatic drugs (csDMARD) use. Methods SPIRIT-H2H is a Wk52 multicentre, open-label, blinded-assessor study comparing IXE and ADA in bionaïve patients with PsA. Patients were randomised 1:1 to IXE or ADA with stratification by concomitant csDMARD use and presence of moderate-to-severe plaque psoriasis. Prespecified end points at Wk24 and Wk52 included musculoskeletal, psoriasis, quality-of life outcomes, subgroup analyses and safety. Results A significantly higher proportion of patients treated with IXE versus ADA simultaneously achieved ACR50 and PASI100 (39% vs 26%, p<0.001), PASI100 (64% vs 41%, p<0.001) at Wk52. Efficacy of IXE and ADA was similar at Wk52 for ACR50 (49.8% vs 49.8%, p=0.924), treat-to-target outcomes, enthesitis and dactylitis resolution. Responses to IXE were consistent irrespective of concomitant csDMARD use. Significantly more patients on IXE monotherapy versus ADA monotherapy had simultaneous ACR50 and PASI100 (38% vs 19%, p=0.007), and PASI100 responses (66% vs 35%, p<0.001) at Wk52. There were no new safety findings for IXE or ADA. Conclusions IXE provided significantly greater simultaneous joint and skin improvement than ADA through Wk52 in bionaïve patients with PsA. IXE showed better efficacy on psoriasis and performed at least as well as ADA on musculoskeletal manifestations. IXE efficacy was consistent irrespective of concomitant csDMARD use. Trial registration number NCT03151551.
AN EXPERIMENTAL STUDY OF THE VERTICAL DISTRIBUTION OF LITTORAL MARINE DIATOMS1

Extensive covers of cpilithic diatoms seldom develop on intertidal substrates in southern Oregon in the prcscnce of grazing animals and macroscopic algae. If an area is cleared, however, a brown coating of diatoms often appears in 2 to 3 weeks, but the density depends on the season and the local conditions during tidal emergence. I have attempted to evaluate the effects of exposure on the vertical distribution of diatoms in the absence of grazers and macrophytes. The differences in exposure to insolation were emphasized. Vertical transects in the same block, facing north, east, west, and south (<all with the same wave exposure) were denuded and later sampled by analyzing the species composition and estimating the density of the coversometimes quantitatively as chlorophyll content. Daily tidal curves were calculated and records of the daylight hours of clear and overcast skies were made. The upper limit of the diatom cover, the vertical species pattern, and the species present depended principally on the time exposed to direct sunlight during emergence and, thcrefore, on the sky conditions and position of the sun during low water. The diatom cover on the shaded north transect invariably extended higher than on the other transects. This maximum was usually bctwecn mean lower high water and higher high water. Some species tolerated almost no indation-exposure, others up to about 2.5 hr in a single exposure, and a few up to 4.0 hr or longer. The tolerance was sometimes increased by a moisture-retaining carpet of barnacles or %a. The upper limit of the diatom cover was lowest on the east transect in spring and summer, since lower low water occurred in the morning, often during clear daylight hours. In the fall and winter, the limit was lowest on the west transect, since lower low water occurred after noon, often during clear daylight hours. The consequences of prolonged exposure to insolation, such as desiccation, high temperature, high light intensity, and ultraviolet radiation are discussed but were not isolated, The seasonal pcriodicity and tolerances of common diatom species are summarized.
Green Fluorescent Protein Targeted to the Nucleus, a Transgenic Phenotype Useful for Studies in Plant Biology

Abstract We present a characterization of transgenic Arabidopsis thaliana (L.) Heynh. plants expressing a chimeric gene comprising the Green Fluorescent Protein (GFP) and β-glucuronidase (GUS) coding sequences, fused to an efficient nuclear localization signal (NLS). The transgenic plants accumulate the fusion protein in their nuclei, and this provides a novel phenotype, that of green-fluorescent nuclei. The fluorescent nuclei are readily observed using conventional epifluorescence and laser scanning confocal microscopy. We describe the use of this phenotype for in vivo studies of nuclear shape and movement, cell division, and for analysis of the transcriptional activities of constitutive and tissue-specific promoters. We propose that the phenotype of fluorescent nuclei will prove particularly valuable in histological, physiological and developmental studies of higher plants that require the facile observation of nuclei within living cells and in the absence of fixation or external staining.
Nowhere to hide: pumas, black bears, and competition refuges

One hypothesis for how carnivores with overlapping ecology coexist in natural systems is through heterogeneous competition landscapes, in which subordinates utilize "competition refuges" to mitigate risks associated with dominant competitors. We tested for the effects of American black bear (Ursus americanus) kleptoparasitism on puma (Puma concolor) foraging in 2 systems in North America. We also tested whether partial prey consumption exhibited by pumas in the presence of bears was better explained by rules of optimal foraging or by kleptoparasitism by black bears, and whether pumas utilized spatial competition refuges to mitigate competition with bears over carcass remains. Puma kill rates in ungulates/wk were equivalent across study systems, but 48% greater in the bear season than the no-bear season. Our analyses of handling time did not support the notion that partial prey consumption exhibited by pumas followed patterns of optimal foraging. Rather, puma handling time and prey consumption were better explained by the presence of bears. Surprisingly, pumas did not utilize spatial competition refuges to mitigate competition with black bears, and instead our results suggested they increase their kill rates to compensate for losses. Our results linking high seasonal kill rates of a top predator with kleptoparasitism by a dominant competitor provide strong evidence that the effects of predation can only be understood within a community framework. In particular, we propose that future predation studies should differentiate between relative contributions of predators and competitors on prey dynamics. Further, our results suggest kleptoparasites may indirectly impact prey populations through their effects on top predators.
Response of water hyacinth manure on growth attributes and yield of Celosia argentea L (Lagos Spinach)

Water hyacinth Eichhornia crassipes (Pontederiaceae, Liliales) is a floating aquatic weed and the world most harmful weed because of its negative effects on waterways and people’s livelihood. Efforts made to combat the water hyacinth problems were not at all successful. It is against this backdrop that the experiment was conducted to evaluate the responses of water hyacinth manure (WHM) on the growth and yield of Celosia argentea (Lagos spinach) at the Teaching and Research Farms of Lagos State Polytechnic, Ikorodu in 2011 cropping season. There were 3 treatments replicated 3 times: 1.32kg/plot (30g/plant); 2.64 kg/plot (60g/plant) and control treatment with no water hyacinth manure application. Treatments were compared on the basis of number of leaves, plant height, stem girth before and 3 weeks after manure application and yield at maturation. The results revealed that application of water hyacinth manure significantly influenced the growth and yield of C. argentea and among the treatments water hyacinth manure (WHM) applied at the rate of 2.64kg/plot (60g/plant) performed best in all the parameters evaluated. From the study it can be concluded that water hyacinth is locally available, plentiful and cost free, its effective use as organic soil amendment would be an interesting method for soil restoration and would minimize partially and/ or totally the negative impacts of this weed on the aquatic ecosystem and socioeconomic activities.
High-Throughput Screen Identifies Host and Microbiota Regulators of Intestinal Barrier Function.

BACKGROUND & AIMS The intestinal barrier protects intestinal cells from microbes and antigens in the lumen-breaches can alter the composition of the intestinal microbiota, the enteric immune system, and metabolism. We performed a screen to identify molecules that disrupt and support the intestinal epithelial barrier and tested their effects in mice. METHODS We performed an imaging-based, quantitative, high-throughput screen (using CaCo-2 and T84 cells incubated with lipopolysaccharide; tumor necrosis factor; histamine; receptor antagonists; and libraries of secreted proteins, microbial metabolites, and drugs) to identify molecules that altered epithelial tight junction (TJ) and focal adhesion morphology. We then tested the effects of TJ stabilizers on these changes. Molecules we found to disrupt or stabilize TJs were administered mice with dextran sodium sulfate-induced colitis or Citrobacter rodentium-induced intestinal inflammation. Colon tissues were collected and analyzed by histology, fluorescence microscopy, and RNA sequencing. RESULTS The screen identified numerous compounds that disrupted or stabilized (after disruption) TJs and monolayers of epithelial cells. We associated distinct morphologic alterations with changes in barrier function, and identified a variety of cytokines, metabolites, and drugs (including inhibitors of actomyosin contractility) that prevent disruption of TJs and restore TJ integrity. One of these disruptors (putrescine) disrupted TJ integrity in ex vivo mouse colon tissues; administration to mice exacerbated colon inflammation, increased gut permeability, reduced colon transepithelial electrical resistance, increased pattern recognition receptor ligands in mesenteric lymph nodes, and decreased colon length and survival times. Putrescine also increased intestine levels and fecal shedding of viable C rodentium, increased bacterial attachment to the colonic epithelium, and increased levels of inflammatory cytokines in colon tissues. Colonic epithelial cells from mice given putrescine increased expression of genes that regulate metal binding, oxidative stress, and cytoskeletal organization and contractility. Co-administration of taurine with putrescine blocked disruption of TJs and the exacerbated inflammation. CONCLUSIONS We identified molecules that disrupt and stabilize intestinal epithelial TJs and barrier function and affect development of colon inflammation in mice. These agents might be developed for treatment of barrier intestinal impairment-associated and inflammatory disorders in patients, or avoided to prevent inflammation.
Phosphoinositides regulate force-independent interactions between talin, vinculin, and actin

Focal adhesions (FA) are large macromolecular assemblies which help transmit mechanical forces and regulatory signals between the extracellular matrix and an interacting cell. Two key proteins talin and vinculin connecting integrin to actomyosin networks in the cell. Both proteins bind to F-actin and each other, providing a foundation for network formation within FAs. However, the underlying mechanisms regulating their engagement remain unclear. Here, we report on the results of in vitro reconstitution of talin-vinculin-actin assemblies using synthetic membrane systems. We find that neither talin nor vinculin alone recruit actin filaments to the membrane. In contrast, phosphoinositide-rich membranes recruit and activate talin, and the membrane-bound talin then activates vinculin. Together, the two proteins then link actin to the membrane. Encapsulation of these components within vesicles reorganized actin into higher-order networks. Notably, these observations were made in the absence of applied force, whereby we infer that the initial assembly stage of FAs is force independent. Our findings demonstrate that the local membrane composition plays a key role in controlling the stepwise recruitment, activation, and engagement of proteins within FAs.