Miracle-dz/UniFAR-FTUs huggingface dataset:
Photosynthetic acclimation of Chlorella saccharophila to heat stress

Photosynthesis is one of the most important metabolic processes of algae; which is altered as a stress response. During mass cultivation of algae, temperature rise and high light are major factors that affect biomass productivity. High temperature affects photosystem II (PSII) complex irreversibly, damaging intermolecular interactions in it. However, the impact of high temperature on photosynthesis is highly variable among different algal species, depending on the prior acclimation to environmental conditions they were exposed to. The acclimation plays an important role in combating high temperature stress via regulation of photosynthetic responses. Chlorophyll a fluorescence is a highly sensitive, non‐destructive and reliable tool for such measurements of photosynthetic parameters, which provides information about algal photosynthetic performance under given conditions. To understand the effect of heat stress on the responses of high light acclimated alga Chlorella saccharophila, chlorophyll a fluorescence transients were measured after heat exposure at 40°C. Our study demonstrates that rise in temperature for short duration; during open field cultivation reversibly affects the efficiency of PSII in light acclimated alga C. saccharophila. The effects of heat stress on chlorophyll a fluorescence in this alga, grown under high light (max‐1600 μmol photons m−2 s−1) are presented here; they are used to infer changes in photosynthetic process during its exposure to heat, as well as their recovery after 72 h. We speculate that heat resistance may have been acquired due to prior exposures to high light.
Limited dispersal prevents Quercus rubra invasion in a 14‐species common garden experiment

Information about the importance of propagule pressure and habitat invasibility in invasion success of dispersal‐limited species is scarce. We aimed to assess invasiveness of Quercus rubra within stands of 14 tree species, and the effects of distance from propagule source on invasion success, to highlight limiting factors for further application in nature conservation.
A STUDY OF RACE

T HE Executive Board has asked me to give my address on the subject of race, and, reluctantly and diffidently, I have agreed to do so. I am not a specialist on this subject. I have never done research on race, but I have taught it for a number of years. Discussion of the races of man seems to generate endless emotion and con­ fusion. I am under no illusion that this paper can do much to dispel the con­ fusion; it may add to the emotion. The latest information available supports the traditional findings of anthropologists and other social scientists-that there is no scientific basis of any kind for racial discrimination. I think that the way this conclusion has been reached needs to be restated. The continua­ tionof antiquated biological notions inanthropology and the oversimplification of facts weakens the anthropological position. We must realize that great changes have taken place in the study of race over the last 20 years and it is up to us to bring our profession into the forefront of the newer understandings, so that our statements will be authoritative and useful. This paper will be concerned with three topics-the modern concept of race, the interpretation of racial differences, and the social significances of race. And, again, I have no illusion that these things can be treated briefly; I shall merely say a few things which are on my mind and which you may amplify by turning to the literature, and especially to Dobzhansky's book, Mankind Evolving. This book states the relations between culture and genetics in a way which is useful to social scientists. In my opinion it is a great book which puts the interrelations of biology and culture in proper perspective and avoids the oversimplifications which come from overemphasis on either one alone. The races of man are the result of human evolution, of the evolution of our species. The races are open parts of the species, and the species is a closed system. If we look, then, upon long-term human evolution, our first problem must be the species and the things which have caused the evolution of all mankind, not the races, which are the results of local forces and which are minor in terms of the evolution of the whole species. (A contrary view has recently been expressed by Coon in The Origin of Races. I think that great antiquity of human races is supported neither by the record nor by evolution­ ary theory.) The evolution of races is due, according to modern genetics, to mutation, selection, migration, and genetic drift. It is easy to shift from this statement of genetic theory to complications of hemoglobin, blood groups or other technical information. But the point I want to stress is that the primary implication
The Impact of Microbiome Alterations in the NOD Mouse Model of Type 1 Diabetes

Epidemiological and experimental data suggest Type 1 Diabetes (T1D) and gut inflammatory disorders share genetic and environmental risk fact ors. Genetics and microbiome composition differentiate T1D-prone NOD mice and T1D-resistant NOR mice. In the first part of this study, we examined the possible protective effects of NORderived microbiome transplant in NOD mice. We report, despite quantifiable, durable chan ges in the gut microbiome of NOD recipients of NOR-derived microbiome transplant compared to NO D and NOR controls, these mice were not protected from T1D. Studies have also suggested that probiotic bacteria can have protective effects in T1D and gut inflammatory disorders. In the second part of this study, we examined the possible protective effects of treatment with probiotic microbes in the NOD mice. We report Protecflor probiotictreated NOD mice showed quantifiable, durable chang es in gut microbiome composition, and were protected from autoimmune infiltration of the isl ts compared to vehicle-treated controls.
A short manual for LFMM

1 Description We proposed an integrated framework based on population genetics, ecological modeling and machine learning techniques for screening genomes for signatures of local adaptation. We implemented fast algorithms using a hierarchical Bayesian mixed model based on a variant of principal component analysis in which residual population structure is introduced via unobserved factors. These algorithms can detect correlations between environmental and genetic variation at the same time as they infer the background levels of population structure. A description of the method is available in our paper:
Physiological and quality responses of Shishe-Kab pomegranates to short-term high CO2 treatment and modified atmosphere packaging

ABSTRACT The objective of this study was to monitor quality parameters and to reduce postharvest losses as well as to extend the storage life of pomegranate fruit using pre-storage high CO2 treatment and active packaging. Short-term high CO2 treated pomegranate fruits cv. Shishe-kab packed with nano-bags (MAP1 and MAP2) or remained unpacked and stored in cold storage at 5°C for 12 weeks. The results show that the fruit decay, chilling injury, and weight loss values were significantly decreased by short-term high CO2 treatment in both packed (MAP) and unpacked fruits compared to unpacked control. As a general trend, there were no significant differences in pH, TSS, and TA between treatments at the end of storage period. Slight decreases in aril colour, measured as a* and chroma values were found in packed fruit with MAP2, which was included with the 1-MCP sachet. In conclusion, the short-term high CO2 shock alone was effective to reduce weight loss, decay, and storage disorders on pomegranate fruit cv. Shishe-kab compared to control, suggesting high CO2 shock as an alternative treatment to control postharvest decay and also maintaining the postharvest quality of the pomegranate fruits during cold storage.
Comparative market supply of protein from livestock and fish in the selected urban areas of Rajshahi district in Bangladesh

The study was conducted with the objectives to determine the market availability of animal sourced foods (ASF) and fish, and their share in the supply of biomass and protein through visiting the wet markets of metropolitan and municipality areas of Rajshahi district, Bangladesh. A preset questionnaire was used for recording the biomass weight of different ASF and fish in every four days interval in March, 2016. It was found that the supply of ASF (beef, chevon, chicken and egg) and fish in the metropolitan markets (80.20 and 35.89 t/d, respectively) was significantly higher (P<0.05) than any municipality wet market in the district (7.66 and 3.03 t/d, respectively). The market supply of biomass and its protein value of ASF were 3.64 and 4.33 times higher than fish. The chicken shared the highest amount of protein (28.19 %) followed by fish (26.8%), beef (26.21%), eggs (11.46%) and chevon (7.34%) during the study period. However, this initial work does not include milk, and the wet market of ASF and fish may have seasonal variations which needs to be explored through further research. In addition to them, socioeconomic status of consumers and regional variations are important which needs to be studied for addressing resource base safe food production help the strategic reduction of food insecurity in the country by 2030. Res. Agric. , Livest. Fish.4(1): 29-36, April 2017
Digestibility of calcium and digestible calcium requirements in pigs

An experiment was conducted to test the hypothesis that differences in the apparent total tract digestibility (ATTD) and standardized total tract digestibility (STTD) of Ca exist among Ca supplements and that inclusion of microbial phytase increases the ATTD and STTD of Ca. One hundred and four growing barrows (average initial BW of 17.73 ± 2.53 kg) were allotted to a randomized complete block design with 13 dietary treatments and 8 pigs per treatment. A basal diet containing corn, cornstarch, potato protein isolate, soybean oil, calcium carbonate, monosodium phosphate, vitamins, and minerals was formulated. Five additional diets were formulated by adding monocalcium phosphate (MCP), dicalcium phosphate (DCP), calcium carbonate, L. calcareum Ca, or a high-Ca sugar beet co-product to the basal diet at the expense of cornstarch. Six additional diets with 500 units per kilogram of microbial phytase were also formulated. A Ca-free diet was used to determine basal endogenous losses of Ca. Feces were collected using the marker-to-marker approach. Results indicated that regardless of inclusion of microbial phytase, MCP had the greatest (P < 0.05) ATTD and STTD of Ca. The ATTD and STTD of Ca in DCP were greater (P < 0.05) than in calcium carbonate, L. calcareum Ca, or in the sugar beet co-product, but no differences were observed among the ATTD and STTD of Ca in calcium carbonate, L. calcareum Ca, or sugar beet co-product. Inclusion of microbial phytase increased (P < 0.05) the ATTD and STTD of Ca in the diets, but this was not the case in the Ca supplements. Regardless of inclusion of microbial phytase, the ATTD of P was
Cryptic Sebastes norvegicus species in Greenland waters revealed by microsatellites

Cryptic Sebastes norvegicus species in Greenland waters revealed by microsatellites Atal Saha*, Lorenz Hauser, Rasmus Hedeholm, Benjamin Planque, Svein-Erik Fevolden, Jesper Boje, and Torild Johansen Institute of Marine Research, Tromsø Department, PO Box 6404, Tromsø 9294, Norway School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195-5020, USA Greenland Institute of Natural Resources, Kivioq 2, PO Box 570, Nuuk 3900, Greenland Hjort Centre for Marine Ecosystem Dynamics, Bergen 5817, Norway Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø 9037, Norway DTU Aqua – National Institute of Aquatic Resources, Charlottenlund DK 2920, Denmark *Corresponding author: tel: þ47 97959302; fax: þ47 55238531; e-mail: atal.saha@imr.no
The AusBeef model for beef production: II. sensitivity analysis

SUMMARY The present study evaluated the behaviour of the AusBeef model for beef production as part of a 2 × 2 study simulating performance on forage-based and concentrate-based diets from Oceania and North America for four methane (CH4)-relevant outputs of interest. Three sensitivity analysis methods, one local and two global, were conducted. Different patterns of sensitivity were observed between forage-based and concentrate-based diets, but patterns were consistent within diet types. For the local analysis, 36, 196, 47 and 8 out of 305 model parameters had normalized sensitivities of 0, >0, >0·01 and >0·1 across all diets and outputs, respectively. No parameters had a normalized local sensitivity >1 across all diets and outputs. However, daily CH4 production had the greatest number of parameters with normalized local sensitivities >1 for each individual diet. Parameters that were highly sensitive for global and local analyses across the range of diets and outputs examined included terms involved in microbial growth, volatile fatty acid (VFA) yields, maximum absorption rates and their inhibition due to pH effects and particle exit rates. Global sensitivity analysis I showed the high sensitivity of forage-based diets to lipid entering the rumen, which may be a result of the use of a feedlot-optimized model to represent high-forage diets and warrants further investigation. Global sensitivity analysis II showed that when all parameter values were simultaneously varied within ±10% of initial value, >96% of output values were within ±20% of the baseline, which decreased to >50% when parameter value boundaries were expanded to ±25% of their original values, giving a range for robustness of model outputs with regards to potential different ‘true’ parameter values. There were output-specific differences in sensitivity, where outputs that had greater maximum local sensitivities displayed greater degrees of non-linear interaction in global sensitivity analysis I and less variance in output values for global sensitivity analysis II. For outputs with less interaction, such as the acetate : propionate ratio and microbial protein production, the single most sensitive term in global sensitivity analysis I contributed more to the overall total-order sensitivity than for outputs with more interaction, with an average of 49, 33, 15 and 14% of total-order sensitivity for microbial protein production, acetate : propionate ratio, CH4 production and energy from absorbed VFAs, respectively. Future studies should include data collection for highly sensitive parameters reported in the present study to improve overall model accuracy.
In vitro reaction of the Majorana hortensis Moench species depending on the nature of the cytokinin and the explant.

The effect of various cytokinins, in combination with an auxin, was studied to determine the potential for in vitro regeneration and multiplication stimulation of the apex and the detached nodule in the Majorana hortensis Moench species, which is known for its richness in aromatic and phytopharmaceutical chemical compounds.The MS growth mediums used are: Mt (control) = MS; V1 = Mt + 1.0 mg/l 2iP + 0.5 mg/l AIB; V2 = Mt + 1.0 mg/l K + 0.5 mg/l AIB; V3 = Mt +1.0 mg/l BA + 0.5 mg/l AIB; V4 = Mt + 1.0mg/l TDZ + 0.5mg/l AIB; V5 = Mt + 6.0 mg/l 2,4D + 0.5mg/l BA. The study followed regeneration capacity (%), marjoram apex and nodule multiplication (differentiation from neoplant/explant) in the presence of the four cytokinins, but also the growth of callus on V5, noting the complete organization of the new plants depending on the nature of the cytokinin. After 45 days of in vitro culture, good and uniform evolution was found on the BA (V3) and 2iP (V1) mediums:90% apex regeneration (on V3) and 75% (on V1), with 4-5 neoplants/apex, well rooted. In vitro nodule reaction on the same two mediums was good, but inferior to apex: on V3 there was 80% nodule regeneration with cca. 3 neoplants 3 cm tall, rooted; on V1 regeneration was at 60% with the same number of neoplnts/nodule. Weak evolution of explants was found on V4, with TDZ, (50% of explants showing necrosis), and no in vitro reaction on V5: we believe that the small dosage of BA is incapable of generating callus tissue differentiation. Following these observations, we recommend: for callus production, increasing the dosage of BA or using other cytokinins alongside it (cca. 6 mg/l) in combination with 2,4D (6mg/l); for multiplication, we recommend BA and 2iP (1mg/l) with a small dosage of auxin (0.5mg/l) and removing TDZ, which inhibits in vitro explant evolution, a reaction we have so far only encountered in marjoram.
Biochemical Variation in Caribbean Sponges of the Genus Aplysina

Sponges are among the simplest multicellular organisms, consisting of groupings of cells with similar functions rather than true tissues. Nonetheless, sponges are ecologically significant in many marine environments, including coral reefs. They are sedentary organisms that feed by filtration from the water column, which contributes to the numerous roles they play on coral reefs, including upkeep of the reef, production of usable energy, and recycling of nutrients. Like all multicellular organisms, sponges are made up of biologically significant macromolecules. These macromolecules provide the energy for the sponge, and their relative concentrations determine how sponges can store and access the energy necessary to perform required functions. These macromolecules include proteins, which are often structural, lipids, which function in long-term storage of energy, and carbohydrates, which allow easy access to energetically favorable breakdown pathways. Anything not contained in these categories is considered energetically inert, but may serve other purposes within the sponge, such as providing physical structure. This study evaluated the distribution of these biochemical components within three distinct morphotypes of Caribbean sponges: Aplysina fulva, Aplysina cauliformis thick morph, and Aplysina cauliformis thin morph. It was hypothesized that these morphotypes within the same genus would present differently in terms of biochemical components. The study also assessed the distribution of these biochemical components within the morphotypes at differentially impacted sites from St. Thomas, US Virgin Islands, and the Bahamas. It was again hypothesized that sponges would vary in their biochemical constituents due to variability in water quality among these sites. Results showed that the distribution of these biochemical components varied significantly, but not consistently, between both sites and morphotypes. Protein and carbohydrates were present at high concentrations at the most environmentally impacted site, while protein and lipid were present at high concentrations at the least impacted site, suggesting a relationship between assimilation of nutrients into macromolecules and water quality. Sites with an intermediate level of impact had an inverse relationship between percent carbohydrates and percent lipids in A. cauliformis and a proportional relationship in A. fulva, suggesting that these two components could be related in a site with limited resources.
High-resolution repertoire analysis of Tfr and Tfh cells reveals unexpectedly high diversities indicating a bystander activation of follicular T cells

T follicular helper (Tfh) and regulatory (Tfr) cells regulate B cell activation and ultimately antibody production. While concordant results show that Tfh cells are specific for the immunizing antigens, limited and even controversial results have been reported regarding the specificity of Tfr cells. Here we used high-throughput T cell receptor (TCR) sequencing to address this issue. We observed that although the Tfh- and Tfr-cell repertoires are less diverse than those of effector (Teff) and regulatory T (Treg) cells, they still represent thousands of clonotypes after immunization with a single antigen. T-cell receptor beta variable (TRBV) gene usage distinguishes both follicular T cells (Tfol) from non-Tfol cells, as well as helper (Teff and Tfh) vs. regulatory (Treg and Tfr) cells. Analysis of the sharing of clonotypes between samples revealed that a specific response to the immunizing antigen can only be detected in Tfh cells immunized with a non-self-antigen and Tfr cells immunized with a self-antigen. Finally, the Tfr TCR repertoire is more similar to that of Tregs than to that of Tfh or Teff cells. Altogether, our results highlight a bystander Tfol-cell activation during antigenic response in the germinal centres and support the Treg cell origin of Tfr cells. Significance Statement Follicular helper T (Tfh) cells promote high-affinity antibody production by B cells while follicular regulatory T (Tfr) cells represses it. The question of the specificity of follicular T (Tfol) cells is of utmost importance in the understanding of the antibody response specificity and our work is the first to analysed the global Tfol TCR repertoire in wild type mice. This allowed us not only to portray the overall global structure of these repertoires, but also to substantiate the fact that Tfr cells respond to self-antigen while Tfh cells respond to non self-antigen, a still controversial issue. Importantly, our work revealed an unexpected bystander activation of Tfol cells. We think and discuss that it has a general significance in immune responses and possibly immunopathologies.
Walkway on coastal dunes negatively affects mobility of the spiny–footed lizard Acanthodactylus erythrurus

espanolLos sistemas dunares son los ecosistemas mas degradados de toda la costa europea y la actividad humana ha causado una profunda transformacion en la costa mediterranea de Espana. En Torredembarra (Tarragona, Espana) habita una poblacion de lagartija colirroja Acanthodactylus erythrurus en algunas de las dunas naturales y parches de vegetacion que aun existen, donde la fauna silvestre coexiste con unas intensas actividades turisticas. Nuestro objetivo fue conocer si las pasarelas instaladas sobre las dunas estaban afectando a la movilidad de la lagartija colirroja. Se comparo la movilidad de lagartijas marcadas entre dos zonas con habitat similar, pero una con pasarelas y otra sin. Se observo que las pasarelas acortaron las distancias entre reavistamientos consecutivos y que afectaban mas a los juveniles de lagartija colirroja que a los adultos. Llegamos a la conclusion de que la pasarela puede estar afectando a las interacciones sociales naturales de la especie. EnglishDune systems are the most degraded ecosystems of the entire European coast, and human activity on the Mediterranean coast of Spain has caused dramatic transformation. In Torredembarra (Tarragona, Spain), a population of spiny–footed lizards Acanthodactylus erythrurus inhabits the few remaining natural dunes and vegetation patches where wildlife coexists with intensive tourism activities. Our aim was to know whether walkways installed across the dunes were affecting the mobility of the spiny–footed lizard. We compared the mobility of marked lizards in two areas with a similar habitat, one with and one without a walkway. We found that the walkway reduced the distances between consecutive resightings, affecting juveniles more than adults. We conclude that the walkway may affect social interactions in the species.