Miracle-dz/UniFAR-FTUs huggingface dataset:
Long‐term temporal changes of plant phenology in the Western Mediterranean

Plants are altering their life cycles in response to current climatic change around the globe. More than 200 000 records for six phenological events (leaf unfolding, flowering, fruit ripening, fruit harvesting, leaf falling and growing season) of 29 perennial species for the period 1943–2003 recorded throughout Spain provide the longest temporal and the broadest spatial assessment of plant phenology changes in the Mediterranean region. The overwhelming majority of the 118 studied phenophases shifted their dates in recent decades. Such changes differed among phenological events. Leaf unfolding, flowering and fruiting are markedly advancing (−0.48, −0.59 and −0.32 days yr−1, respectively), but only since the mid‐1970s. Anemophilous have advanced more days their flowering than entomophilous. However, some species have delayed and others have advanced their leaf falling dates and as a result only a weak shift was observed in this event for the whole of the studied species (+0.12 days yr−1). The growing season lengthened by 18 days, which implies an increase of 8% in the life of annual leaves. Such an increase was achieved mainly through the advance of leaf unfolding dates in the spring, one of the most productive times of year for vegetation in the Mediterranean. Shifts in the plant calendar were accompanied as well by long‐term changes in the range of onset dates in 39% of studied phenophases. Leaf unfolding, flowering and growing season tended to reduce spatial variability, reflecting a faster and more synchronized onset (or duration) of phenophases across the study area. Changes in spatial variability may aggravate calendar mismatching with other trophic levels resulting from changes in dates. Because temporal responses differed markedly among species, calendar guilds of plants have changed, which suggests alterations of interspecific relationships in plant communities from Mediterranean ecosystems.
A Review of Antimicrobial Resistance in Poultry Farming within Low-Resource Settings

Simple Summary Poultry production can function as an instrument for poverty alleviation and economic development. As low-income countries transition into higher incomes alongside growing urban populations, there will be an increasing demand for quality sources of animal products. Consequently, poultry production systems will continue to shift from subsidence agricultural practices to intensive food production that implies routine antimicrobial usage. Promotion of intensive poultry production could increase antimicrobial resistance (AMR) within resource-limited settings lacking in effective biosafety and biosecurity measures. Bacterial resistance lessens the portfolio of antimicrobials available in poultry husbandry and potentially human medicine. This issue requires a systems framework in order to evaluate the various social and biological factors driving the emergence of resistance within the context of intensive poultry production. Abstract The emergence, spread, and persistence of antimicrobial resistance (AMR) remain a pressing global health issue. Animal husbandry, in particular poultry, makes up a substantial portion of the global antimicrobial use. Despite the growing body of research evaluating the AMR within industrial farming systems, there is a gap in understanding the emergence of bacterial resistance originating from poultry within resource-limited environments. As countries continue to transition from low- to middle income countries (LMICs), there will be an increased demand for quality sources of animal protein. Further promotion of intensive poultry farming could address issues of food security, but it may also increase risks of AMR exposure to poultry, other domestic animals, wildlife, and human populations. Given that intensively raised poultry can function as animal reservoirs for AMR, surveillance is needed to evaluate the impacts on humans, other animals, and the environment. Here, we provide a comprehensive review of poultry production within low-resource settings in order to inform future small-scale poultry farming development. Future research is needed in order to understand the full extent of the epidemiology and ecology of AMR in poultry within low-resource settings.
Biofilm Formation and Antibiotic Resistance Phenotype of Helicobacter pylori Clinical Isolates

We evaluated biofilm formation of clinical Helicobacter pylori isolates from Indonesia and its relation to antibiotic resistance. We determined the minimum inhibition concentration (MIC) of amoxicillin, clarithromycin, levofloxacin, metronidazole and tetracycline by the Etest to measure the planktonic susceptibility of 101 H. pylori strains. Biofilms were quantified by the crystal violet method. The minimum biofilm eradication concentration (MBEC) was obtained by measuring the survival of bacteria in a biofilm after exposure to antibiotics. The majority of the strains formed a biofilm (93.1% (94/101)), including weak (75.5%) and strong (24.5%) biofilm-formers. Planktonic resistant and sensitive strains produced relatively equal amounts of biofilms. The resistance proportion, shown by the MBEC measurement, was higher in the strong biofilm group for all antibiotics compared to the weak biofilm group, especially for clarithromycin (p = 0.002). Several cases showed sensitivity by the MIC measurement, but resistance according to the MBEC measurements (amoxicillin, 47.6%; tetracycline, 57.1%; clarithromycin, 19.0%; levofloxacin, 38.1%; and metronidazole 38.1%). Thus, biofilm formation may increase the survival of H. pylori and its resistance to antibiotics. Biofilm-related antibiotic resistance should be evaluated with antibiotic susceptibility.
Multiple site-specific infrared dichroism of CD3-ζ, a transmembrane helix bundle

The structure of the transmembrane domain of CD3-ζ a component of the T-cell receptor involved in signal transduction, has been studied in its native state (a lipid bilayer) by multiple site-specific infrared dichroism. For the first time, the transmembrane domain has been labelled at multiple positions along the sequence, representing a total of 11 samples, each labelled at a different residue with an isotopically modified carbonyl group, 13C18O. A strategy is outlined that, based on the above data, can yield the rotational orientation and the local helix tilt for each labelled residue, giving a detailed description of helix geometry. The results obtained indicate that the transmembrane segment is in an α-helical conformation throughout, with an average helix tilt of 12 °. The N-terminal side of the helix is more tilted than the C-terminal. In an accompanying paper we describe the implementation of the infrared data in a model-building study of the CD3-ζ transmembrane complex. The model obtained is entirely consistent with results based on evolutionary conservation data. Taken together, this study represents the first step towards elucidation of the backbone structure of a transmembrane α-helical bundle by infrared spectroscopy.
Enhancement of Gonad Production in the Sea Urchin Loxechinus albus in Chile Fed Extruded Feeds

Loxechinus albus were fed algae (Macrocystis pyrifera and Ulva sp.) and two feeds prepared by extrusion (one containing kelp). Results were the same for individuals maintained in suspended cages in the sea and in aquaria on land. Gonads increased in size in individuals fed extruded feeds and decreased in individuals fed algae during the spawning season. Gonads increased ca. four-fold in size in individuals fed the extruded feeds during the post-spawning season, much greater than those fed algae. Individuals fed extruded feeds had a lower feeding rate than individuals fed algae on a wet-weight but not on a dry-weight basis. The extruded feed supports gonadal growth more than natural food and has potential for use for aquaculture of sea urchins.
Non-Thermal Plasma Couples Oxidative Stress to TRAIL Sensitization through DR5 Upregulation

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces apoptosis in various tumor cells without affecting most normal cells. Despite being in clinical testing, novel strategies to induce TRAIL-mediated apoptosis are in need to overcome cancer cell unresponsiveness and resistance. Plasma-activated medium (PAM) markedly stimulates reactive oxygen/nitrogen species (ROS/RNS)-dependent apoptosis in cancer cells. We investigate the capability of PAM and TRAIL (PAM/TRAIL) combination therapy to overcome TRAIL resistance and improve the anticancer efficacy of TRAIL. The combinatorial treatment of PAM and TRAIL shows synergistic effects on growth inhibition in TRAIL-resistant cancer cells via augmented apoptosis by two attributes. DR5 (TRAIL-R2) transcription by CHOP is upregulated in a PAM-generated ROS/RNS-dependent manner, and PAM itself upregulates PTEN expression mediated by suppression of miR-425 which is involved in Akt inactivation, leading to increased apoptosis induction. Treatment of cancer cell lines with the antioxidant N-acetylcysteine reduces the extent of membrane dysfunction and the expression of both CHOP-DR5 and miR-425-PTEN axes, attenuating PAM/TRAIL-induced cancer cell apoptosis. These data suggest that PAM/TRAIL treatment is a novel approach to sensitizing cancer cells to TRAIL-induced apoptosis and overcoming TRAIL resistance. PAM is a promising candidate for further investigations as a chemotherapeutic sensitizer in the treatment of cancer.
Bioactive peptides in dairy products

Bioactive peptides are hydrolysates with specific amino acid sequences that exert a positive physiological influence on the body. They are inert within the native protein, but once cleaved from the native protein by microbial or added enzymes and/or gastrointestinal enzymes during the digestive process, they apply their beneficial traits. Dairy products, particularly fermented products, are potential sources of bioactive peptides: several of them possess extra-nutritional physiological functions that qualify them to be classified under the ‘Functional Foods’ label. Biological peptides in milk, the methods of their generation and their prevalence in dairy products are reviewed along with the reported health benefits and safety aspects.
p27Kip1 induction and inhibition of proliferation by the intracellular Ah receptor in developing thymus and hepatoma cells

The Ah receptor (AhR), a bHLH/PAS transcription factor, mediates dioxin toxicity in the immune system, skin, testis and liver. Toxic phenomena are associated with altered cell proliferation or differentiation, but signaling pathways of AhR in cell cycle regulation are poorly understood. Here we show that AhR induces the p27Kip1 cyclin/cdk inhibitor by altering Kip1 transcription in a direct mode without the need for ongoing protein synthesis or cell proliferation. This is the first example of Kip1 being a direct transcriptional target of a toxic agent that affects cell proliferation. Kip1 causes dioxin-induced suppression of 5L hepatoma cell proliferation because Kip1 antisense-expressing cells are resistant to dioxins. Kip1 is also induced by dioxins in cultures of fetal thymus glands concomitant with inhibition of proliferation and severe reduction of thymocyte recovery. Kip1 expression is likely to mediate these effects as thymic glands of Kip1-deficient mice (Kip1Δ51) are largely, though not completely, resistant.
Development of the methodology for selecting the optimal type of pedestrian crossing

: The World Health Organization in its agenda on sustainable development 2030 sets a goal to reduce the number of traffic-related accidents by 50%. According to the trend toward reducing the number of traffic-related accidents and the latest statistics report by SIA Bitola, we have found that this is a great challenge for our city and a very high goal which we could try to reach. Namely, we have started a pedestrian safety initiative by trying to provide infrastructural facilities and elements that are planned and designed according to the security principles and which correspond to the projected speed and road function as well as safe infrastructure for pedestrians, the elderly and persons with disabilities. The main objective of this paper is to develop a case study methodology regarding the selection of pedestrian crossing types on the case study location example. Namely, the VISSIM simulation model for the studied location has been introduced, and the general conclusions have been adopted based on the multi-criteria decision-making process analysis. The most important aim is directed towards obtaining pedestrian safety while bearing in mind the role of pedestrian safety within the current safety goals.
Antioxidant Therapies and Oxidative Stress in Friedreich’s Ataxia: The Right Path or Just a Diversion?

Friedreich’s ataxia is the commonest autosomal recessive ataxia among population of European descent. Despite the huge advances performed in the last decades, a cure still remains elusive. One of the most studied hallmarks of the disease is the increased production of oxidative stress markers in patients and models. This feature has been the motivation to develop treatments that aim to counteract such boost of free radicals and to enhance the production of antioxidant defenses. In this work, we present and critically review those “antioxidant” drugs that went beyond the disease’s models and were approved for its application in clinical trials. The evaluation of these trials highlights some crucial aspects of the FRDA research. On the one hand, the analysis contributes to elucidate whether oxidative stress plays a central role or whether it is only an epiphenomenon. On the other hand, it comments on some limitations in the current trials that complicate the analysis and interpretation of their outcome. We also include some suggestions that will be interesting to implement in future studies and clinical trials.
Effect of Food with Low Enrichment of N-3 Fatty Acids in a Two-Month Diet on the Fatty Acid Content in the Plasma and Erythrocytes and on Cardiovascular Risk Markers in Healthy Young Men

Polyunsaturated fatty acids of the n-3 series (n-3 PUFA) exhibit a number of favorable effects on the human organism and it is desirable to increase their intake in the diet. For this purpose, flaxseed oil was added to a chicken-feed mixture for the production of meat and eggs. The content of n-3 PUFA in the obtained meat was increased from 250 mg (reference value) to 900 mg in 100 g of meat and from 110 mg (reference value) to 190 mg in 100 g of whole egg; the enriched products are designated as omega-3 meat and omega-3 eggs. Omega-3 meat and eggs were subsequently fed for a period of eight weeks in an amount of 480 g of meat and four eggs (228 g netto) a week to a group of 14 healthy volunteers, whose body composition parameters were measured and blood was analyzed biochemically to determine blood lipids, coagulation parameters, plasma, and erythrocyte fatty acid spectrum composition. A control group of 14 volunteers was fed normal chicken and eggs in the same regime. The performed dietary intervention increases the intake of long-chain PUFA (LC-PUFA) by 37 mg per day, which represents 7–15% of the recommended daily dose. The performed tests demonstrated that the consumption of omega-3 enriched meat and eggs significantly increases the content of n-3 PUFA in the erythrocytes, which are a long-term indicator of fatty acid intake. This intervention has no demonstrable effect on the basic body parameters, such as body weight, fat content, Body Mass Index (BMI), and also on the plasma cholesterol level, high-density lipoprotein (HDL), low-density lipoprotein (LDL), blood clotting and inflammation markers, and omega-3 index.
Morphological and behavioral alterations induced by endocrine disrupters in amphibian tadpoles

Developmental toxicity effects of endocrine disrupter chemicals, acephate and cypermethrin were studied in Bufo melanostictus tadpoles. Thirty developing eggs of B. melanostictus were exposed to each concentration (0.01, 0.05, 0.1, 0.5, and 1 µg L−1) of acephate or cypermethrin in the laboratory (temperature: 23 ± 1°C; photoperiod: 11.5–12.5 h). Eggs maintained in conditioned water alone served as controls. After hatching, larvae were fed on boiled spinach until the completion of metamorphosis. In control group, larvae that hatched on 3rd day were heavily pigmented, voracious feeders, and active swimmers; in these tadpoles, hind limb and forelimb-buds emerged on 16th and 24th day and metamorphosis was complete on 32nd day. Eggs exposed to acephate also hatched on 3rd day but larvae exhibited deformities such as, (i) tail distortions, (ii) laterally crooked trunk, (iii) decreased pigmentation, (iv) inactivity, (v) peeling of the skin, and (vi) delay in emergence of limbs and completion of metamorphosis. Cypermethrin-exposed eggs exhibited a delay (4–8 days) in hatching, there was no mortality, deformities in tail, trunk and head region, delay in the emergence of limbs, and completion of metamorphosis were evident. The demonstrated data indicate that these pesticides interfere with amphibian development when present in the aquatic system.
The risk factors associated with treatment-related mortality in 16,073 kidney transplantation—A nationwide cohort study

Mortality at an early stage after kidney transplantation is a catastrophic event. Treatment-related mortality (TRM) within 1 or 3 months after kidney transplantation has been seldom reported. We designed a retrospective observational cohort study using a national population-based database, which included information about all kidney recipients between 2003 and 2016. A total of 16,073 patients who underwent kidney transplantation were included. The mortality rates 1 month (early TRM) and 3 months (TRM) after transplantation were 0.5% (n = 74) and 1.0% (n = 160), respectively. Based on a multivariate analysis, older age (hazard ratio [HR] = 1.06; P < 0.001), coronary artery disease (HR = 3.02; P = 0.002), and hemodialysis compared with pre-emptive kidney transplantation (HR = 2.53; P = 0.046) were the risk factors for early TRM. Older age (HR = 1.07; P < 0.001), coronary artery disease (HR = 2.88; P < 0.001), and hemodialysis (HR = 2.35; P = 0.004) were the common independent risk factors for TRM. In contrast, cardiac arrhythmia (HR = 1.98; P = 0.027) was associated only with early TRM, and fungal infection (HR = 2.61; P < 0.001), and epoch of transplantation (HR = 0.34; P < 0.001) were the factors associated with only TRM. The identified risk factors should be considered in patient counselling, selection, and management to prevent TRM.
Protective Effect of Astaxanthin on Blue Light Light-Emitting Diode-Induced Retinal Cell Damage via Free Radical Scavenging and Activation of PI3K/Akt/Nrf2 Pathway in 661W Cell Model

Light-emitting diodes (LEDs) are widely used and energy-efficient light sources in modern life that emit higher levels of short-wavelength blue light. Excessive blue light exposure may damage the photoreceptor cells in our eyes. Astaxanthin, a xanthophyll that is abundantly available in seafood, is a potent free radical scavenger and anti-inflammatory agent. We used a 661W photoreceptor cell line to investigate the protective effect of astaxanthin on blue light LED-induced retinal injury. The cells were treated with various concentrations of astaxanthin and then exposed to blue light LED. Our results showed that pretreatment with astaxanthin inhibited blue light LED-induced cell apoptosis and prevented cell death. Moreover, the protective effect was concentration dependent. Astaxanthin suppressed the production of reactive oxygen species and oxidative stress biomarkers and diminished mitochondrial damage induced by blue light exposure. Western blot analysis confirmed that astaxanthin activated the PI3K/Akt pathway, induced the nuclear translocation of Nrf2, and increased the expression of phase II antioxidant enzymes. The expression of antioxidant enzymes and the suppression of apoptosis-related proteins eventually protected the 661W cells against blue light LED-induced cell damage. Thus, our results demonstrated that astaxanthin exerted a dose-dependent protective effect on photoreceptor cells against damage mediated by blue light LED exposure.
High Performance 2D-DCT Architecture for HEVC Encoder

— The revolutionary Ultra-High Definition (UHD) video has found its way to diverse rich multimedia applications. HEVC (H.265) standard is proposed as the gateway to increase the compression rate with no loss in video quality. Large integer DCT, with sizes 16x16 and 32x32, is one of the key new features of the H.265 standard. In this paper, we propose a new optimized architecture for integer DCT in HEVC encoder. The proposed architecture is a fully pipelined architecture with optimized adder-widths. Simulation results confirm the high performance of the optimized adder-width design. For 16-DCT, the proposed architecture increases the maximum clock frequency by 42.7% and decreases area by 3.1%. While for 32-DCT, the proposed design increases the maximum clock frequency by 64.8% with cost of increasing area by only 3%.
Sulfur-oxidizing bacteria as plant growth promoting rhizobacteria for canola

Canola (Brassica napus) has a high sulfur requirement during vegetative growth and exhibits symptoms of sulfur deficiency when cropped on Saskatchewan soils low in plant available sulfur. Elemental sulfur (S0) is frequently used as a fertilizer to alleviate this deficiency. The potential of sulfur-oxidizing microorganisms to enhance the growth of canola in S0 fertilized soils was assessed. Sulfur-oxidizing bacteria and fungi were isolated from the rhizosphere and rhizoplane of canola grown in four different Saskatchewan soils under growth chamber conditions. Of 273 bacterial isolates, 245 (89.7%) oxidized S0 to thiosulfate or tetrathionate in vitro, and 133 (48.7%) oxidized S0 to sulfate; 70 fungal isolates oxidized S0 to sulfate. Eighteen bacterial isolates demonstrating the highest in vitro sulfur oxidation were tested as seed inoculants under growth chamber conditions, with S0 as sulfur source. Fourteen isolates increased canola leaf size measured at the bud stage of growth, and seven isolates increase.
The impact of information quantity and strength of relationship between training set and validation set on accuracy of genomic estimated breeding values

Recent advances in genomic selection are a revolution in animal breeding. A genome consisting 10 chromosomes each with 100 cM in length with 100 equally spaced markers (1 cM) were simulated. After 50 generations of random mating in a finite population (Ne = 100) in order to create sufficient linkage disequilibrium, population was expanded to two different population sizes of 500 and 1000. This structure was conserved until generation 59. Only females of generations 51 to 58 had phenotypic records and were included in the training set. The generation 59 was assumed as juveniles without any phenotypic records (validation set). Two measures of heritability (h = 0.1 and h = 0.5) were considered. Each simulation was replicated 10 times and results were averaged across replications. The results showed that using individuals of more recent generations in training set led to higher accuracy of genomic estimated breeding values (GEBVs) than individuals from more distant generations. However, increase in the amount of phenotypic records in training set even from individuals of older generations will increase accuracy of GEBVs. Number of phenotypic records in training set was shown to have important role in accuracy of GEBVs especially for low heritability traits.