Miracle-dz/UniFAR-FTUs huggingface dataset:
Trends in fragmentation and connectivity of Paspalum quadrifarium grasslands in the Buenos Aires province, Argentina

Background Despite its wide distribution worldwide, only 4.6% of temperate grasslands are included within systems of protected areas. In Argentina, this situation is even more alarming: only 1.05% is protected. The study area (central area of the southern Salado River basin) has a large extent of grasslands of Paspalum quadrifarium (Pq) which has been target since the middle of the last century of a variety of agricultural management practices including fire burning for cattle grazing. Methods Five binary images of presence-absence data of Pq from a 42-year range (1974–2016) derived from a land cover change study were used as base data. Morphological Spatial Pattern Analysis (MSPA), Morphological Change Detection (MCD) and Network Connectivity Analysis (NCA) were performed to the data using Guidos Toolbox (GTB) for the estimation of habitat and connectivity dynamics of the Pq patches (fragments). Results A loss of the coverage area and habitat nuclei of this grassland was observed during the study period, with some temporal oscillation but no recovery to initial states. Additional drastic reduction in connectivity was also evident in resulting maps. The number of large Pq grassland fragments (>50 ha) decreased at beginning of the study period. Also, fragmentation measured as number of components (patches) was higher at the end of the study period. The Pq pajonal nuclei had their minimum representativeness in 2000, and recovered slightly in area in 2011, but with a significant percentage increase of smaller patches (=islets) and linear elements as bridges and branches. Large corridors (mainly edge of roads) could be observed at the end of the study period, while the total connectivity of the landscape pattern drops continuously. Statistics of links shows mean values decreasing from 1974 to 2016. On the other hand, maximum values of links decreased up to 19% in 2011, and recovered to a 54% of their original value in 2016. Discussion Pq fragmentation and habitat reduction could have an impact on the ecosystem functioning and the mobility of some species of native fauna. The connecting elements of the landscape were maintained and/or recovered in percentage in 2011 and 2016. This fact, although favoring the dispersion of the present diversity in the habitat nuclei could cause degradation by an edge effect. Part of the area has the potential to be taken as an area of research and as an example of livestock management, since it is the one that would most preserve the biodiversity of the Pq environment. On the methodological side, the use of a proved tool as GTB is useful for monitoring dynamics of a grassland-habitat fragmentation.
Tumor mutational profile of triple negative breast cancer patients in Thailand revealed distinctive genetic alteration in chromatin remodeling gene

Background Triple negative breast cancer (TNBC) is a breast cancer subtype characterized by absence of both hormonal receptors and human epithelial growth factor receptor 2 (HER2). TNBC accounts for 15–20% of breast cancer. TNBC is associated with more aggressive disease and worse clinical outcome. Though the underlying mechanism of TNBC is currently unclear, the heterogeneity of clinical characteristics in various population may relate to the difference in tumor mutational profile. There were studies on TNBC gene mutations in various ethnic groups but the tumor genome data on Thai TNBC patients is currently unknown. This study aims to investigate mutational profile of Thai TNBC. Methods The patients were Thai individuals who were diagnosed with primary breast carcinoma between 2014 and 2017. All surgically removed primary tumor tissues were carefully examined by pathologists and archived as formalin-fixed paraffin-embedded tumor. TNBC was defined by absence of hormonal receptors and HER2 by immunohistochemistry. Genomic DNA was extracted, enriched and sequenced of all exomes on the Illumina HiSeq. Genomic data were then processed through bioinformatics platform to identify genomic alterations and tumor mutational burden. Results A total of 116 TNBC patients were recruited. Genomic analysis of TNBC samples identified 81,460 variants, of which 5,906 variants were in cancer-associated genes. The result showed that Thai TNBC has higher tumor mutation burden than previously reported data. The most frequently mutated cancer-associated gene was TP53 similar to other TNBC cohorts. Meanwhile KMT2C was found to be more commonly mutated in Thai TNBC than previous studies. Mutational profile of Thai TNBC patients also revealed difference in many frequently mutated genes when compared to other Western TNBC cohorts. Conclusion This result supported that TNBC breast cancer patients from various ethnic background showed diverse genome alteration pattern. Although TP53 is the most commonly mutated gene across all cohorts, Thai TNBC showed different gene mutation frequencies, especially in KMT2C. In particular, the cancer gene mutations are more prevalent in Thai TNBC patients. This result provides important insight on diverse underlying genetic and epigenetic mechanisms of TNBC that could translate to a new treatment strategy for patients with this disease.
Effect of Applying Sunflower Residues as a Green Manure on Increasing Zn Concentration of Two Iranian Wheat Cultivars in a Pb and Cd Polluted Soil

soil organic fertilizers such as sewage sludge instead of chemical fertilizers the soil nutrient in Background: This research was investigated to evaluate effect of applying sunflower residues as a green manure on increasing zinc (Zn) concentration of two Iranian wheat cultivars in a Pb and cadmium (Cd) polluted soil. Methods: Treatments included the application of sunflower residuals grown in a Zn-polluted soil at two levels of 0 and 8 t/ha, two wheat cultivars in a soil contaminated with Pb (0, 400 and 800 mg Pb/kg soil) and Cd (0, 5 and 10 mg Cd/kg soil). After 7 months of the experiment. Plant Pb, Zn and Cd concentrations were measured using atomic absorption spectroscopy. Results: The highest root and shoot Zn concentration of wheat plant was belonged to the Back cross cultivar. Addition of 8 t/ha sunflower residues in soil without Pb and Cd pollution increased the root Zn concentration of Back Cross and Kavir cultivars by 12 and 16%, respectively. The highest and lowest Zn translocation factor of wheat plants was belonged to Back Cross and Kavir cultivars, respectively. Conclusion: Applying sunflower residues has a significant effect on increasing plant Zn concentration and can be useful as a suitable way to increase Zn concentration of wheat grown in Zn deficient and heavy metal polluted soils.
Nutrition Therapy in Managing Pregnant Women With Gestational Diabetes Mellitus: A Literature Review

Objective: Gestational diabetes mellitus is the most common metabolic and endocrine perinatal complication and is a growing health problem worldwide. Considering the fetal programming and its contribution as one of the evolutionary origins of human diseases, it is very important to improve the glucose metabolism in pregnant women, determination of other nutrients, preventing excessive accumulation of fetal fats, emphasis on weight loss measures before pregnancy, dietary intake with low-fat healthy food and prevention of abundant weight loss. In this paper, we have provided a brief review on dietary intake and dietary interventions in GDM from the perspective of nutrition science attending the physiopathology and etiology of the disease. Materials and methods: Electronic search for English and Persian articles has been perform in databases, including Google Scholar, PubMed ,Scopus, Cochrane central ,Science direct, ISC, SID, Magiran, Iran Medex, and Med Libby key words: gestational diabetes, gestational diabetes mellitus, nutrition, macronutrient, micronutrient, Diabetes. All available articles (cross-sectional, descriptive-analytic, and clinical studies with desirable design and review quality studies were used. Reference books including Krause's Food and the Nutrition Care, The Williams Obstetrics editions of the 14th (2017) and the 24th edition (2014) were also reviewed. Results: Nutrition therapy and physical activity are the initial treatment of GDM. Proper and flexible methods of nutrition therapy that successfully regulate maternal glycaemia while improving expected fetal growth have extensive concepts. Meanwhile, dietary supplements with proven beneficial effects can play an important role in improving deficiencies and improving the metabolic profile of patients. Conclusion: Nutritional management is the main treatment for gestational diabetes mellitus and overweight/obesity is the principal contest in patient counseling and interventions during pregnancy. Despite extensive researches carried out, this field is an active research area and requires more clinical research to minimize maternal and fetal complications.
A Case of Alveolar Bleeding from Clotting Abnormality by Cefmetazole

Cephalosporins are one of the most commonly used first-line antibiotics. In this report, we describe the case of a patient who developed alveolar bleeding due to clotting abnormality following the use of cefmetazole, one of cephalosporins containing an N-methylthiotetrazole (NMTT) side chain. Compared to other antibiotics, cephalosporins with an NMTT side chain cause a higher degree of bleeding events. The bleeding tendency is caused by the depletion of vitamin K-dependent clotting factors via inhibition of the vitamin K epoxide reductase. This mechanism of action is the same as warfarin. Recent years have seen an increase in the number of patients using direct oral anticoagulants that do not require coagulation tests. As a consequence, there may be an increase in the number of bleeding events due to anticoagulant drugs and such antibiotics coprescription. Therefore, this case is an instructive lesson.
Unraveling the hidden universe of small proteins in bacterial genomes

Identification of small open reading frames (smORFs) encoding small proteins (≤ 100 amino acids; SEPs) is a challenge in the fields of genome annotation and protein discovery. Here, by combining a novel bioinformatics tool (RanSEPs) with “‐omics” approaches, we were able to describe 109 bacterial small ORFomes. Predictions were first validated by performing an exhaustive search of SEPs present in Mycoplasma pneumoniae proteome via mass spectrometry, which illustrated the limitations of shotgun approaches. Then, RanSEPs predictions were validated and compared with other tools using proteomic datasets from different bacterial species and SEPs from the literature. We found that up to 16 ± 9% of proteins in an organism could be classified as SEPs. Integration of RanSEPs predictions with transcriptomics data showed that some annotated non‐coding RNAs could in fact encode for SEPs. A functional study of SEPs highlighted an enrichment in the membrane, translation, metabolism, and nucleotide‐binding categories. Additionally, 9.7% of the SEPs included a N‐terminus predicted signal peptide. We envision RanSEPs as a tool to unmask the hidden universe of small bacterial proteins.
Interactive comment on “Light absorption properties of aerosols over Southern West Africa”

This paper describes the aerosol physical and optical properties observed during the DACCIWA campaign. The paper is based on in-situ measurements performed a-board the ATR-42. The paper is well written and the topic ﬁts the ACP’s scope. However, I have many remarks and some needs to be taken into account before this paper could be published in ACP.
Patient and disease characteristics of adult patients with type 1 diabetes in Germany: an analysis of the DPV and DIVE databases

Background: An understanding of the current status of patients with type 1 diabetes mellitus (T1DM) can help to provide appropriate treatment. Methods: This was a retrospective analysis of the DIabetes Versorgungs-Evaluation (DIVE) and the Diabetes-Patienten-Verlaufsdokumentation (DPV) databases for Germany. Results: The analysis included 56,250 people with T1DM (54.2% male), a median age of 36.8 years, and a median diabetes duration of 12.4 years. 15.3% were obese (body mass index ≥ 30kg/m2). Long-acting insulin analogs were used by 53.3%, short-acting analogs by 72.1%, and oral antidiabetic drugs by 4.7%. Patients had a median glycosylated hemoglobin (HbA1c) of 7.8%. There was a drop in HbA1c and an increase in the rate of hypertension, oral antidiabetic drug use, and in the rate of severe hypoglycemia (all p < 0.01) with age. Flash glucose monitoring (FGM) showed the best glucose values with fewer complications compared to other monitoring systems. HbA1c and FBG were lower in patients using a pump versus multiple daily injections (MDIs; 7.7 versus 7.9% and 7.8 versus 8.7 mmol/l; all adjusted p < 0.01). Patients had a lower risk of at least one severe hypoglycemic or DKA episode during the most recent treatment year with pump treatment compared to MDI (9.4% versus 10.5% and 4.7% versus 6.1%, both adjusted p < 0.01). Conclusion: The data demonstrated less-than-optimal glycemic control in the young, an increasing metabolic pattern in T1DM with increasing age, a benefit of FGM to improve HbA1c control and adverse effects, as well as benefits of pump treatment over MDIs.
In Vitro Assessment of Antiplasmodial Activity and Cytotoxicity of Polyalthia longifolia Leaf Extracts on Plasmodium falciparum Strain NF54

Background Malaria is one of the most important life-threatening infectious diseases in the tropics. In spite of the effectiveness of artemisinin-based combination therapy, reports on reduced sensitivity of the parasite to artemisinin in Cambodia and Thailand warrants screening for new potential antimalarial drugs for future use. Ghanaian herbalists claim that Polyalthia longifolia has antimalarial activity. Therefore, antiplasmodial activity, cytotoxic effects, and antioxidant and phytochemical properties of P. longifolia leaf extract were investigated in this study. Methodology/Principal Findings Aqueous, 70% hydroethanolic and ethyl acetate leaf extracts were prepared using standard procedures. Antiplasmodial activity was assessed in vitro by using chloroquine-sensitive malaria parasite strain NF54. The SYBR® Green and tetrazolium-based calorimetric assays were used to measure parasite growth inhibition and cytotoxicity, respectively, after extract treatment. Total antioxidant activity was evaluated using a free radical scavenging assay. Results obtained showed that extracts protected red blood cells against Plasmodium falciparum mediated damage. Fifty percent inhibitory concentration (IC50) values were 24.0±1.08 μg/ml, 22.5±0.12 μg/ml, and 9.5±0.69 μg/ml for aqueous, hydroethanolic, and ethyl acetate extracts, respectively. Flavonoids, tannins, and saponins were present in the hydroethanolic extract, whereas only the latter was observed in the aqueous extract. Aqueous and hydroethanolic extracts showed stronger antioxidant activities compared to the ethyl acetate extract. Conclusions/Significance The extracts of P. longifolia have antiplasmodial properties and low toxicities to human red blood cells. The extracts could be developed as useful alternatives to antimalarial drugs. These results support claims of the herbalists that decoctions of P. longifolia are useful antimalarial agents.
Phenotypic plasticity closely linked to climate at origin and resulting in increased mortality under warming and frost stress in a common grass

Abstract Phenotypic plasticity is important for species responses to global change and species coexistence. Phenotypic plasticity differs among species and traits and changes across environments. Here, we investigated phenotypic plasticity of the widespread grass Arrhenatherum elatius in response to winter warming and frost stress by comparing phenotypic plasticity of 11 geographically and environmentally distinct populations of this species to phenotypic plasticity of populations of different species originating from a single environment. The variation in phenotypic plasticity was similar for populations of a single species from different locations compared to populations of functionally and taxonomically diverse species from one environment for the studied traits (leaf biomass production and root integrity after frost) across three indices of phenotypic plasticity (RDPI, PIN, slope of reaction norm). Phenotypic plasticity was not associated with neutral genetic diversity but closely linked to the climate of the populations’ origin. Populations originating from warmer and more variable climates showed higher phenotypic plasticity. This indicates that phenotypic plasticity can itself be considered as a trait subject to local adaptation to climate. Finally, our data emphasize that high phenotypic plasticity is not per se positive for adaptation to climate change, as differences in stress responses are resulting in high phenotypic plasticity as expressed by common plasticity indices, which is likely to be related to increased mortality under stress in more plastic populations.
Evaluation of metastasis and 5-year survival in oral squamous cell carcinoma patients in Isfahan (2001–2015)

Background: Frequency analysis of metastasis in patients with oral squamous cell carcinoma (OSCC) helps to partly anticipate the upcoming chance of metastasis in the patients following primary diagnosis. This study was conducted to determine the evaluation of metastasis and 5-year survival in OSCC. Materials and Methods: This was a retrospective, descriptive study. A total of 96 OSCC patients were studied. Demographic data and clinical view of lesion as well as histopathological grade of patients were recorded in previously prepared forms of pathology centers. These findings were then evaluated in relation to the 5-year survival. The obtained data were fed into SPSS and analyzed by Chi-square test, t-test, one-way ANOVA, and Scheffé test. A significant level of α = 0.05 was used. Results: The 5-year survival of patients was 41.7%. From among the patients, 44% were found to have local recurrence and 36% were reported to have distant metastasis. There was no significant association between the 5-year survival rate and primary grade (P = 0.105). However, it revealed a significant relationship between the 5-year survival rate and distant metastasis (P = 0. 001). Conclusion: This study showed that the 5-year survival is dependent on the primary site of involvement, local recurrence, regional and distant metastasis, and mean age. However, gender (P = 0.89), grade (P = 0.105), and stage (P = 0.242) have no effect on the 5-year survival of patients.
The nectar report: quantitative review of nectar sugar concentrations offered by bee visited flowers in agricultural and non-agricultural landscapes

There is growing concern that some bee populations are in decline, potentially threatening pollination security in agricultural and non-agricultural landscapes. Among the numerous causes associated with this trend, nutritional stress resulting from a mismatch between bee nutritional needs and plant community provisioning has been suggested as one potential driver. To ease nutritional stress on bee populations in agricultural habitats, agri-environmental protection schemes aim to provide alternative nutritional resources for bee populations during times of need. However, such efforts have focused mainly on quantity (providing flowering plants) and timing (during flower-scarce periods), while largely ignoring the quality of the offered flower resources. In a first step to start addressing this information gap, we have used literature data to compile a comprehensive geographically explicit dataset on nectar quality (i.e., total sugar concentration), offered to bees both within fields (crop and weed species) as well as outside fields (wild species) around the globe. Social bees are particularly sensitive to nectar sugar concentrations, which directly impact calorie influx into the colony and consequently their fitness making it an important resource quality marker. We find that the total nectar sugar concentrations in general do not differ between the three plant communities studied. In contrast we find increased variability in nectar quality in the wild plant community compared to crop and weed community, which is likely explained by the increased phylogenetic diversity in this category of plants. In a second step we explore the influence of local habitat on nectar quality and its variability utilizing a detailed sunflower (Helianthus annuus L.) data set and find that geography has a small, but significant influence on these parameters. In a third step we identify crop groups (genera), which provide sub-optimal nectar resources for bees and suggest high quality alternatives as potential nectar supplements. In the long term this data set could serve as a starting point to systematically collect more quality characteristics of plant provided resources to bees, which ultimately can be utilized by scientist, regulators, NGOs and farmers to improve the flower resources offered to bees. We hope that ultimately this data will help to ease nutritional stress for bee populations and foster a data informed discussion about pollinator conservation in modern agricultural landscapes.
Comparison of Different Histone Deacetylase Inhibitors in Attenuating Inflammatory Pain in Rats

Histone deacetylase inhibitors (HDACIs), which interfere with the epigenetic process of histone acetylation, have shown analgesic effects in animal models of persistent pain. The HDAC family comprises 18 genes; however, the different effects of distinct classes of HDACIs on pain relief remain unclear. The aim of this study was to determine the efficacy of these HDACIs on attenuating thermal hyperalgesia in persistent inflammatory pain. Persistent inflammatory pain was induced by injecting Complete Freund's Adjuvant (CFA) into the left hind paw of rats. Then, HDACIs targeting class I (entinostat (MS-275)) and class IIa (sodium butyrate, valproic acid (VPA), and 4-phenylbutyric acid (4-PBA)), or class II (suberoylanilide hydoxamic acid (SAHA), trichostatin A (TSA), and dacinostat (LAQ824)) were administered intraperitoneally once daily for 3 or 4 days. We found that the injection of SAHA once a day for 3 days significantly attenuated CFA-induced thermal hyperalgesia from day 4 and lasted 7 days. In comparison with SAHA, suppression of hyperalgesia by 4-PBA peaked on day 2, whereas that by MS-275 occurred on days 5 and 6. Fatigue was a serious side effect seen with MS-275. These findings will be beneficial for optimizing the selection of specific HDACIs in medical fields such as pain medicine and neuropsychiatry.