Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature amplifies the effect of high CO2 on the photosynthesis, respiration, and calcification of the coralline algae Phymatolithon lusitanicum

Abstract The combination of ocean acidification (OA) and global warming is expected to have a significant effect on the diversity and functioning of marine ecosystems, particularly on calcifying algae such as rhodoliths (maërl) that form extensive beds worldwide, from polar to tropical regions. In addition, the increasing frequency of extreme events, such as heat waves, threatens coastal ecosystems and may affect their capacity to fix blue carbon. The few studies where the simultaneous effects of both temperature and CO2 were investigated have revealed contradictory results. To assess the effect that high temperature spells can have on the maërl beds under OA, we tested the short‐time effects of temperature and CO2 on the net photosynthesis, respiration, and calcification of the recently described species Phymatolithon lusitanicum, the most common maërl species of southern Portugal. Photosynthesis, calcification, and respiration increased with temperature, and the differences among treatments were enhanced under high CO2. We found that in the short term, the metabolic rates of Phymatolithon lusitanicum will increase with CO2 and temperature as will the coupling between calcification and photosynthesis. However, under high CO2, this coupling will favor photosynthesis over calcification, which, in the long term, can have a negative effect on the blue carbon fixing capacity of the maërl beds from southern Portugal.
Root Pruning and Auxin Alter Root Morphology of Hickories

A reputation for coarse root systems with dominant taproots, and for slow shoot development among seedlings, limits use of hickory species (Carya Nutt.) that could increase diversity in managed landscapes. We examined effects of root pruning and application of auxin on root and shoot development of seedlings of several species of hickory. Our hypothesis was that pruning the radicle shortly after seed germination and subsequent treatment with auxin would increase root branching without curtailing development of the shoot. Germinated seeds of Carya aquatica (F. Michx.) Nutt. , Carya cordiformis (Wangenh.) K. Koch, Carya laciniosa (F. Michx.) Loudon, Carya ovata (Mill.) K. Koch, and Carya tomentosa (Lam.) Nutt. were treated by removing two-thirds of the length of the radicle with and without immediate application of 3000 mg·L−1 indole-3-butyric acid (IBA) via Hormex rooting powder #3 to the remaining one-third of radicle. Neither treatment altered stem height, stem caliper, or root dry weight. After 75 days, root-pruned seedlings of Carya ovata without auxin had 42% fewer fibrous first-order lateral roots than did unpruned controls. Root pruning plus auxin led to a 79% increase in the number of fibrous first-order lateral roots of C. laciniosa and an ≈50% increase in the shoot dry weight of C. aquatica. Both root pruning and root pruning plus auxin evoked formation of taproot branches for all species. Because species differed in responses of root and shoot systems to root pruning with and without auxin, the practice should be implemented cautiously based on the species.
A unifying mechanistic model of bacterial transcription with three interconnected pause states and non-diffusive backtrack recovery

SUMMARY Pausing by RNA polymerase (RNAp) facilitates the recruitment of regulatory factors, RNA folding, and other related processes. While backtracking and intra-structural isomerization have been proposed to trigger pausing, the mechanisms of pause formation and recovery remain debated. Using high-throughput magnetic tweezers with single-molecule sensitivity, we have examined the full temporal spectrum of Escherichia coli RNAp transcription dynamics. Together with probabilistic dwell-time analysis and modelling, this has identified three distinct states that compete with elongation: a short-lived elemental pause and two long-lived backtracked pause states. We demonstrate that recovery from backtracking is not governed by diffusional Brownian motion, but rather by intrinsic RNA cleavage, whereby RNAp conformational changes hinder cleavage in long-lived pause states. We further show that state switching underlies stochastic alterations in the frequency of short pauses. Based on these findings, we propose a consensus model of intrinsic pausing that unifies all key findings while resolving earlier contradictions.
Prevalence and Antifungal Susceptibility of the Emerging Fungal Species, Candida nivariensis, Isolated in a Teaching Hospital in Poland

Abstract The data on susceptibility to antifungals of new species within Candida glabrata complex are limited. Our study was to enrich a global knowledge of yeast epidemiology and drug resistance. The study was focused on the identification of species within clinical isolates of the C. glabrata complex and on the determination of their resistance to antifungals. Four hundred forty-five clinical C. glabrata sensu lato strains were isolated from different clinical samples at routine mycological exams at the Infant Jesus Teaching Hospital in Warsaw. The identification of the most of tested isolates to species complex level was performed using the ID 32 C system. The identification of C. nivariensis and C. bracarensis species within the C. glabrata complex was performed by DNA sequencing. The MICs of amphotericin B, fluconazole, itraconazole, posaconazole, voriconazole, caspofungin, anidulafungin, and micafungin were determined by E-test. Twenty-four isolates did not have an ITS-1 region, characteristic of C. glabrata sensu stricto and their D1/D2 regions of the 26S rRNA were 99% homologous to C. nivariensis 26S rRNA. No strains of C. bracarensis were recovered. C. nivariensis strains were very susceptible to amphotericin B, anidulafungin, micafungin, and caspofungin. Ninety-two percent of C. nivariensis were resistant to itraconazole. The halves of the strains was resistant to posaconazole. Eighty-three percent of C. nivariensis were susceptible to voriconazole. None of the tested strains were susceptible to fluconazole. In the present study, none of the C. nivariensis strains were simultaneously resistant to azoles and echinocandins. C. nivariensis should be recognized as an emerging pathogen, resistant to azoles.
Differences in molecular epidemiology of lung cancer among ethnicities (Asian vs. Caucasian)

Background Differences in carcinogenesis and therapeutic efficacy according to ethnicity have been reported for lung cancer, and understanding differences in genetic mutation profiles among ethnicities is important for interpreting the results of clinical trials, preventing carcinogenesis, and individualizing treatment. However, no studies have focused on differences in mutation profiles among different ethnicities using large-scale genomic analysis data with detailed information on smoking history, the main cause of lung cancer. Methods To clarify the differences in genetic mutation profiles between Caucasian and Japanese subjects, we compared data from The Cancer Genome Atlas, which mainly included Caucasians, with results from the Japan Molecular Epidemiology for lung cancer study, which is an epidemiological study only involving Japanese subjects. We divided the participants into four groups according to smoking status and performed comparative analysis by tissue type (lung adenocarcinoma and squamous cell lung cancer). Results In patients with lung adenocarcinoma, the frequency of EGFR mutations was lower in Caucasian subjects than in Japanese subjects (14.6% vs. 51.1%), whereas the frequencies of mutations in other genes, namely KRAS (32.9% vs. 9.3%), TP53 (45.2% vs. 20.7%), BRAF (9.6% vs. 1.3%), PIK3CA (5.9% vs. 2.6%), KEAP1 (17.8% vs. 0.5%), NF1 (10.9% vs. 0.5%), STK11 (17.8% vs. 0.7%), RBM10 (8.7% vs. 0.1%), and MET (7.8% vs. 0.1%), were higher in Caucasian subjects. Among patients with squamous cell carcinoma, TP53 (81.2% vs. 49.1%), PIK3CA (14.5% vs. 6.8%), KEAP1 (12.7% vs. 0.9%), and NFE2L2 mutations (15.8% vs. 13.6%) were more common in Caucasian subjects. Conclusions Ethnicity is an important and complex characteristic that must be recognized and considered, even in the era of precision medicine. We should collaborate to share data for different ethnicities and incorporate them into clinical practice and the design of global clinical studies. Carefully designed molecular epidemiological studies focusing on ethnic differences are warranted.
Serological and molecular characteristics of pea seed borne mosaic virus-PSbMV from lentil (Lens culinaris Medik L.) in Iran

Abstract During 2016 growing season, samples with leaf yellowing and mosaic like symptoms were collected from main lentil (Lens culinaris Medik L.) fields. Specific ELISA positive PSbMV samples were selected for RT-PCR. Using specific pair of primer towards CP gene region of the virus, PCR product of approx.235 bp was amplified. Based on the nucleotide sequences of the CP gene PSbMV isolates were classified in two major groups. In which, isolates in group I divided into two subgroups of Iranian isolates (B2) and (G1), along with Czech Republic, Australia, China, Greece, Pakistan and Egypt were placed in the subgroup-I. Isolate (V18) from Iran placed independently in group II. In the grouping based on the amino acid sequencing the isolates divided into two phylogenetic groups. Iranian isolates along with an isolate from Australia categorized in group-II, however world isolates were all clustered in group-I.
The Evolutionary Origin of Associative Learning

Learning is a widespread ability among animals and, like physical traits, is subject to evolution. But how did learning first arise? What selection pressures and phenotypic preconditions fostered its evolution? Neither the fossil record nor phylogenetic comparative studies provide answers to these questions. Here, we take a novel approach by studying digital organisms in environments that promote the evolution of navigation and associative learning. Starting with a nonlearning sessile ancestor, we evolve multiple populations in four different environments, each consisting of nutrient trails with various layouts. Trail nutrients cue organisms on which direction to follow, provided they evolve to acquire and use those cues. Thus, each organism is tested on how well it navigates a randomly selected trail before reproducing. We find that behavior evolves modularly and in a predictable sequence, where simpler behaviors are necessary precursors for more complex ones. Associative learning is only one of many successful behaviors to evolve, and its origin depends on the environment possessing certain information patterns that organisms can exploit. Environmental patterns that are stable across generations foster the evolution of reflexive behavior, while environmental patterns that vary across generations but remain consistent for periods within an organism’s lifetime foster the evolution of learning behavior. Both types of environmental patterns are necessary, since the prior evolution of simple reflexive behaviors provides the building blocks for learning to arise. Finally, we observe that an intrinsic value system evolves alongside behavior and supports associative learning by providing reinforcement for behavior conditioning.
Sêmen refrigerado e seu potencial de uso na inseminação artificial de búfalas ( Bubalus Bubalis )

A exploracao da bubalinocultura tem crescido constantemente nos ultimos anos. Neste contexto, o uso de biotecnicas da reproducao como a inseminacao artificial em tempo fixo (IATF), aspiracao folicular (OPU) e producao in vitro de embrioes (PIVE), tem se mostrado factiveis em bubalinos, embora ainda com uma eficiencia reduzida e com pouca aplicacao comercial comparado a outras especies animais. Isto se deve a caracteristicas particulares da especie, como dificuldade de identificacao do estro e a complicacao em condicionar touros para a coleta de semen com a vagina artificial, principalmente animais adultos. Somados a isto, mesmos os animais apos o condicionamento e coleta de semen, nao mantem uma constância na producao de ejaculados com qualidade, chegando mesmo a interromper a producao de semen sem um motivo aparente. Em parte, esses problemas foram solucionados com a elaboracao de protocolos que permitam o uso da IA sem a necessidade de deteccao do estro, ou seja, em tempo fixo (IATF). Ja o conhecimento da dinâmica folicular nessa especie possibilitou o desenvolvimento de protocolos para controlar as fases folicular e luteinica do ciclo estral e, por fim, a ovulacao. A combinacao destes tratamentos de sincronizacao da ovulacao permite o uso da inseminacao artificial durante todo o ano, possibilitando o ganho genetico e a distribuicao da concepcao e dos partos conforme a demanda do mercado. No entanto, a inseminacao artificial em bubalinos, que tem como base o uso do semen congelado, apresenta alguns gargalos como: a falta de semen no mercado nacional; touros com genetica superior, mas que nao resistem ao processo de congelamento; injurias causadas aos espermatozoides durante o processo de congelamento, que pode causar um decrescimo de ate 60% na viabilidade da populacao espermatica em bubalinos e a existencia de deficiencias basicas de manejo nas propriedades. Face ao exposto, esse estudo tem o objetivo de testar a eficacia do semen refrigerado e congelado na IATF nos periodos reprodutivos favoravel e desfavoravel, assim como na fertilizacao in vitro para melhorar as taxas de fertilidade, estudar a expressao dos comportamentos sexuais de touros bubalinos e, a aplicacao de tecnicas de manejo racional durante o periodo de coleta de semen com a vagina artificial, visando facilitar o condicionamento e coleta de semen, bem como desenvolver novos extensores para o semen de bufalos. Os resultados obtidos com as inseminacoes artificiais durante o periodo reprodutivo favoravel e desfavoravel mostraram taxa de prenhez superior para o semen refrigerado. Resultado este que tambem foi obtido com a PIVE. Quanto ao comportamento dos touros, verificou-se que estes animais sao passiveis de condicionamento para a coleta de semen com vagina artificial a campo. Apos diversos testes foi verificado que o diluidor TRIS com 10% de LDL, acrescido de 0,5% de lecitina de soja e com a adicao de 10 mM do antioxidante acetilcisteina apresentou os melhores resultados de longevidade e fertilidade in vitro.
Pairwise learning of MRI scans using a convolutional Siamese network for prediction of knee pain

ABSTRACT Objectives It remains difficult to characterize the source of pain in knee joints either using radiographs or magnetic resonance imaging (MRI). We sought to determine if advanced machine learning methods such as deep neural networks could distinguish knees with pain from those without it and identify the structural features that are associated with knee pain. Methods We constructed a convolutional Siamese network to associate MRI scans obtained on subjects from the Osteoarthritis Initiative (OAI) with frequent unilateral knee pain (n=1,529) comparing the knee with frequent pain to the contralateral knee without pain. The Siamese network architecture enabled pairwise learning of information from two-dimensional (2D) sagittal intermediate-weighted turbo spin echo slices obtained from similar locations on both knees. Class activation mapping (CAM) was utilized to create saliency maps, which highlighted the regions most associated with knee pain. The MRI scans and the CAMs of each subject were reviewed by an expert radiologist to identify the presence of abnormalities within the model-predicted regions of high association. Results Using 10-fold cross validation, our model achieved an area under curve (AUC) value of 0.808. When individuals whose knee WOMAC pain scores were not discordant were excluded, model performance increased to 0.853. The radiologist review revealed that about 86% of the cases that were predicted correctly had effusion-synovitis within the regions that were most associated with pain. Conclusions This study demonstrates a proof of principle that deep learning can be applied to assess knee pain from MRI scans.
Antimicrobial Potency and Bioactive Ingredients of Different Extracts of Prosopis africana against Some Selected Human Pathogenic Microbes: An In-vitro Approach

Background: The resistance to conventional drugs by microbes is at alarming rate and poses extra challenges in the field of medical and pharmaceutical industries. This study was aimed to determine the active ingredients and assess the antimicrobial potency of Prosopis africana leave extract using system of different solvents as aqueous, ethylacetate and n-hexane. Methodology: The plant specimen was collected, identified, prepared and cold macerated using aqueous, ethylacetate and n-hexane as solvent. The resulted crude extracts were further assayed for anti-infective potency; adopting agar well diffusion protocol against some selected human pathogenic isolates viz Streptococcus pyogenes, Klebsiella pneumoniae, Salmonella typhi, Methicillin-Resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa and Candida albicans. The Minimum Inhibitory Concentration (MIC), Minimum Bactericidal Concentration (MBC) and Minimum Fungicidal Concentration (MFC) were ascertained using the standard protocol of microdilution assay. Results: The antimicrobial screening of the crude extracts showcased that P. africana leave is susceptible against all the tested microbial stains by exhibiting significant degrees of inhibition zone of diameter (0 to 25 mm). The positive controls likewise were observed to be vulnerable to the tested isolates while P. aeruginosa was resistant. The MIC was observed at 50.0 to 12.5 mg/mL and MBC at 50.0 mg/mL against some bacteria strains. P. aeruginosa and C. albicans has no bactericidal and fungicidal properties. The phytochemical analysis led to the isolation of anthraquinones, carbohydrates, saponins, terpenes, steroids and cardiac glycosides as the active constituents of the plant part. Conclusion: This finding provides a logical justification to the traditional healers for the utilization of the plant in the management of different ailments caused by the tested microbes.
Gas6/TAM Signaling Components as Novel Biomarkers of Liver Fibrosis

Liver fibrosis consists in the accumulation of extracellular matrix components mainly derived from activated hepatic stellate cells. This is commonly the result of chronic liver injury repair and represents an important health concern. As liver biopsy is burdened with many drawbacks, not surprisingly there is great interest to find new reliable noninvasive methods. Among the many are new potential fibrosis biomarkers under study, some of the most promising represented by the growth arrest-specific gene 6 (Gas6) serum protein and its family of tyrosine kinase receptors, namely, Tyro3, Axl, and MERTK (TAM). Gas6/TAM system (mainly, Axl and MERTK) has in fact recently emerged as an important player in the progression of liver fibrosis. This review is aimed at giving an overall perspective of the roles played by these molecules in major chronic liver diseases. The most promising findings up to date acknowledge that both Gas6 and its receptor serum levels (such as sAxl and, probably, sMERTK) have been shown to potentially allow for easy and accurate measurement of hepatic fibrosis progression, also providing indicative parameters of hepatic dysfunction. Although most of the current scientific evidence is still preliminary and there are no in vivo validation studies on large patient series, it still looks very promising to imagine a possible future prognostic role for these biomarkers in the multidimensional assessment of a liver patient. One may also speculate on a potential role for this system targeting (e.g., with small molecule inhibitors against Axl) as a therapeutic strategy for liver fibrosis management, always bearing in mind that any such therapeutic approach might face toxicity.
Efficacy and Satisfaction Rate in Postpartum Intrauterine Contraceptive Device Insertion: A Prospective Study

Background Postpartum intrauterine contraceptive device (PPIUCD) reduces the rate of abortions and it is a cost-effective, reversible, and convenient choice of contraception. The objective of our study was to evaluate the efficacy and satisfaction rate in women with postpartum intrauterine contraceptive device insertion. Methods This prospective study of immediate PPIUCD insertion was conducted at our institute from March 2016 to February 2019. Approval from the Institutional Review Board (IRB) was taken before starting the study. A total of 372 women were enrolled in the study after taking informed consent. All the women were counseled regarding different methods of contraception and birth control during antenatal checkups, early labor and immediately postpartum (within 48 hours). All the enrolled women in the study were followed for three years to determine the satisfaction and success rate of PPIUCD continuation. We also kept the record of women who discontinued PPIUCD. Results After the exclusion criteria, 372 women were recruited in the study. The mean gestation age at the time of delivery was 38.5 weeks with a standard deviation (SD) of 1.45. All the women were followed for short-term and long-term complications and satisfaction rates. Out of 372, 51.07% of women (n = 190) had a spontaneous vaginal delivery, and 48.9% of women (n = 182) had a cesarean section but there was no significant long-term satisfaction outcome difference in both the groups. The highest success rate of the postpartum long-acting intrauterine contraceptive device was noted in patients who were counseled thoroughly in the antenatal and intrapartum period 61.5% as compared to those patients who were counseled either antenatally 42.2 %, intrapartum 35.4%, or immediate postpartum 22.4% alone. Conclusion PPIUCD insertion is an opportunity not to be missed. It allows women to obtain safe, long-acting, highly effective contraception while already within the medical system. More research data are needed in the literature with regard to counseling timings for PPIUCD insertion during the antenatal and postnatal period as it can affect the decision of women to prevent unplanned pregnancy. PPIUCD has one of the highest patient satisfaction rates among all the contraceptives.
Autumnal Cultivation of Energetic Plants in Agroecological No-tillage System in Southern Brazil

Cropping energetic plants could provide soil protection, additional incomes to farmers and suppress weed development without loss of food production. It also contributes to the development of no-tillage cultivation in agroecological farming system. Energetic plants such as: sunflower, crambe, canola and safflower were evaluated in no-tillage agroecological farming in autumnal planting, after soybean crop. Higher plant heights were observed in sunflower, flowering [46 days after emergency (dae)] and harvest (108 dae) was first observed in crambe plants. Intermediate earliness was observed in the sunflower (61 and 136 dae, respectively). Biomass was found greater in the sunflower compared to safflower or canola. Intermediate values were obtained for crambe plants. Greater grain and oil yields were found in descending order in sunflower, crambe, canola and cartamo. Despite the drought period occurred during crop development, sunflower and crambe yields were similar or even higher to means, than yields of these same crops in conventional fields in Brazil. Sunflower and crambe were the best options to take part in succession/rotation system after soybean spring/summer crop.