Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant Growth Promoting Rhizobacteria (PGPR) Regulated Phyto and Microbial Beneficial Protein Interactions

Abstract Plant Growth Promoting Rhizobacteria (PGPR) influence plants’ physiological characteristics, metabolites, pathways and proteins via alteration of corresponding gene expression. In the current study, a total of 42 upregulated uncharacterized sorghum bicolor root proteins influenced by PGPR were subjected to different analyses: phylogenetic tree, protein functional network, sequences similarity network (SSN), Genome Neighborhood Network (GNN) and motif analysis. The screen for homologous bacterial proteins to uncover associated protein families and similar proteins in non-PGPRs was identified. The sorghum roots’ uncharacterized protein sequences analysis indicated the existence of two protein categories, the first being related to phytobeneficial protein family associated with DNA regulation such as Sulfatase, FGGY_C, Phosphodiesterase or stress tolerance such as HSP70. The second is associated with bacterial transcriptional regulators such as FtsZ, MreB_Mbl and DNA-binding transcriptional regulators, as well as the AcrR family, which existed in PGPR and non PGPR. Therefore, Plant Growth-Promoting Rhizobacteria (PGPR) regulated phytobeneficial traits through reciprocal protein stimulation via microbe plant interactions, both during and post colonization.
The Influence of Taxonomy and Environment on Leaf Trait Variation Along Tropical Abiotic Gradients

Deconstructing functional trait variation and co-variation across a wide range of environmental conditions is necessary to increase the mechanistic understanding of community assembly processes and improve current parameterization of dynamic vegetation models. Here, we present a study that deconstructs leaf trait variation and co-variation into within-species, taxonomic-, and plot-environment components along three tropical environmental gradients in Peru, Brazil, and Ghana. To do so, we measured photosynthetic, chemical, and structural leaf traits using a standardized sampling protocol for more than 1,000 individuals belonging to 367 species. Variation associated with the taxonomic component (species + genus + family) for most traits was relatively consistent across environmental gradients, but within-species variation and plot-environment variation was strongly dependent on the environmental gradient. Trait-trait co-variation was strongly linked to the environmental gradient where traits were measured, although some traits had consistent co-variation components irrespective of gradient. Our results demonstrate that filtering along these tropical gradients is mostly expressed through trait taxonomic variation, but that trait co-variation is strongly dependent on the local environment, and thus global trait co-variation relationships might not always apply at smaller scales and may quickly change under future climate scenarios.
Use of Phosphatase and Dehydrogenase Activities in the Assessment of Calcium Peroxide and Citric Acid Effects in Soil Contaminated with Petrol

Abstract The objective of the study was to compare the effect of calcium peroxide and citric acid on the activity of acid phosphatase (ACP), alkaline phosphatase (ALP), and dehydrogenases (DHA) in uncontaminated soil and soil contaminated with petrol. The experiment was carried out on samples of loamy sand under laboratory conditions. Petrol was introduced to soil samples at a dose of 0 and 50 g·kg 1 DM, as well as calcium peroxide or citric acid at a dose of 0, 50, 100, or 150 mg·kg 1 DM. The humidity of the samples was brought to 60% maximum water holding capacity, and the samples were incubated at 20°C for 8 weeks. Enzyme activity was determined on days 1, 14, 28, and 56. The obtained results demonstrated that the addition of calcium peroxide and citric acid did not result in significant changes in the activity of the determined enzymes in uncontaminated soil. However, it was observed that the application of calcium peroxide, particularly at the dose of 150 mg·kg 1 DM, largely alleviated the impact of petrol on the enzymatic activity of the soil contaminated with petrol. Moreover, among the determined enzymes, the activity of DHA was found to be the best indicator of the effect of calcium peroxide on the soil ecosystem.
Video-based person re-identification with parallel spatial–temporal attention module

Abstract. We propose a parallel network with spatial–temporal attention for video-based person re-identification. Many previous video-based person re-identification methods use two-dimensional convolutional neural networks to extract spatial features, then, temporal features are extracted by temporal pooling or recurrent neural networks. Unfortunately, these series networks will cause the loss of spatial information when extracting temporal information. Different from previous methods, our parallel network can extract temporal and spatial features simultaneously, which can effectively reduce the loss of space information. In addition, we design a global temporal attention module, which obtains the attention weight through the correlation between the current frame and all the frames in the sequence. At the same time, the temporal module can act on the information extraction of spatial module. In this way, we can increase the temporal and spatial constraints. Experiments show that our method can effectively improve the re-id accuracy, better than the state-of-the-art methods.
Additive Manufacturing - A Literature Review

In the present scenario, the industries are looking for creating the model quickly and making the prototype. Additive manufacturing (AM) is a rising technology for a hefty choice of applications. This route has plenty of advantages such as the availability of a wide range of materials, fabrication speed and resolution of the final components. The current paper deals with the review of the recent developments in additive manufacturing methods and their applications. Further, the discussion has been made about the various materials used for additive manufacturing such as ceramic, polymer, composites and biomaterials. The survey denotes that fused deposition modeling has received the widespread attention of the researchers. Finally, some of the gaps in the research are found and reported.
Beyond the Forest-Grassland Dichotomy: The Gradient-Like Organization of Habitats in Forest-Steppes

Featuring a transitional zone between closed forests and treeless steppes, forest-steppes cover vast areas and have outstanding conservation importance. The components of this mosaic ecosystem can conveniently be classified into two basic types, forests and grasslands. However, this dichotomic classification may not fit reality as habitat organization can be much more complex. In this study, our aim was to find out if the main habitat types can be grouped into two distinct habitat categories (which would support the dichotomic description), or a different paradigm better fits this complex ecosystem. We selected six main habitats of sandy forest-steppes, and, using 176 relevés, we compared their vegetation based on species composition (NMDS ordination, number of common species of the studied habitats), relative ecological indicator values (mean indicators for temperature, soil moisture, and light availability), and functional species groups (life-form categories, geoelement types, and phytosociological preference groups). According to the species composition, we found a well-defined gradient, with the following habitat order: large forest patches – medium forest patches – small forest patches – north-facing edges – south-facing edges – grasslands. A considerable number of species were shared among all habitats, while the number of species restricted to certain habitat types was also numerous, especially for north-facing edges. The total (i.e., pooled) number of species peaked near the middle of the gradient, in north-facing edges. The relative ecological indicator values and functional species groups showed mostly gradual changes from the large forest patches to the grasslands. Our results indicate that the widely used dichotomic categorization of forest-steppe habitats into forest and grassland patches is too simplistic, potentially resulting in a considerable loss of information. We suggest that forest-steppe vegetation better fits the gradient-based paradigm of landscape structure, which is able to reflect continuous variations.
Associations Between Positive and Negative Affect and the Way People Perceive Their Health Goals

Objective Why are people who suffer from depressive symptoms or chronic negative mood less likely to adopt a healthy lifestyle? We postulated that adoption of health goals (HGs) and health behaviors is impeded by negative affect (NA) and facilitated by positive affect (PA). Our aim was to assess the associations between NA and PA, measured as a state and as a trait, and perceptions of HGs and related means. In our studies we tested the relationship between perceptions of HGs and affect measured as a state and as a trait. Methods Participants in three online studies were asked to choose and evaluate a health goal (Studies 1–3) or a health goal and related means (Study 3). In Study 1 we used the personal project analysis to assess 10 dimensions of HGs, inter-goal interference, and inter-goal facilitation; in Studies 2 and 3 we used a specially designed questionnaire to assess the difficulty, attainability, controllability, and congruency with self-identity of HGs and related means. We used the Positive and Negative Affect Schedule to measure trait and state affect and the NEO PI-R to measure neuroticism and extraversion. Results Participants perceived their HGs and related means in mood-congruent ways. High NA participants perceived their HGs to be less controllable, less attainable, more difficult, and less congruent with their self-identity. They also perceived their related means to be more difficult and less congruent with their self-identity. In contrast, high PA participants perceived their HGs and related means to be more attainable and more congruent with their self-identity, and they evaluated their related means as less difficult. In addition, our results suggest that state affect is better associated with perceptions of HGs than trait affect. Conclusion The adoption and attainment of HGs is likely to be facilitated by PA but impeded by NA. PA and NA may also impact the adoption and maintenance of healthy lifestyles. These results help provide a better understanding of the reasons why people with depression or negative mood adhere to behaviors that compromise their health.
Interictal Epileptiform Discharges and the Quality of Human Intracranial Neurophysiology Data

Intracranial electroencephalography (IEEG) involves recording from electrodes placed directly onto the cortical surface or deep brain locations. It is performed on patients with medically refractory epilepsy, undergoing pre-surgical seizure localization. IEEG recordings, combined with advancements in computational capacity and analysis tools, have accelerated cognitive neuroscience. This Perspective describes a potential pitfall latent in many of these recordings by virtue of the subject population—namely interictal epileptiform discharges (IEDs), which can cause spurious results due to the contamination of normal neurophysiological signals by pathological waveforms related to epilepsy. We first discuss the nature of IED hazards, and why they deserve the attention of neurophysiology researchers. We then describe four general strategies used when handling IEDs (manual identification, automated identification, manual-automated hybrids, and ignoring by leaving them in the data), and discuss their pros, cons, and contextual factors. Finally, we describe current practices of human neurophysiology researchers worldwide based on a cross-sectional literature review and a voluntary survey. We put these results in the context of the listed strategies and make suggestions on improving awareness and clarity of reporting to enrich both data quality and communication in the field.
A comparative study of an anaerobic-oxic (AO) system and a sequencing batch biofilm reactor (SBBR) in coating wastewater treatment and their microbial communities

Abstract Coating wastewater from paper mills has been characterized by a high chemical oxygen demand (COD), high total suspended solids (TSS) and a high degree of color. In this paper, a sequencing batch biofilm reactor (SBBR) and an anaerobic-oxic (AO) system that consisted of a hydrolytic acidification reactor and an activated sludge reactor (HAASR) were implemented to treat coagulated coating wastewater from a paper mill. The COD, color and TSS removal efficiencies of the SBBR were 87.7 %, 33.5 %, and 41.4 %, and those of the HAASR were 85.3 %, 22.5 % and 19.4 %, respectively. It is proposed that more recalcitrant compounds were removed by the SBBR than by the HAASR. The microbial communities of the SBBR sludge and the HAASR sludge were evaluated and indicated that the SBBR sludge had lower microbial richness and diversity than the HAASR sludge. Moreover, Proteobacteria and Bacteroidetes were the dominant bacteria in both the HAASR and SBBR sludges.
Long Non-coding RNA Gas5 Is Associated With Preeclampsia and Regulates Biological Behaviors of Trophoblast via MicroRNA-21

Preeclampsia is a lethal pregnancy specific hypertensive disorder involving multisystem. Despite extensive studies to investigate the causes of preeclampsia, the pathogenesis still remains largely unknown. Long non-coding RNAs (lncRNAs) are a diverse class of non-translated RNAs which play a crucial part in various biological phenomena. Although lncRNA Growth Arrest-Specific 5 (GAS5) aberrantly expressed in multiple cancer tissues and is implicated in multiple biological processes of tumor cells, little is known about its role in preeclampsia. In this study, 40 patients with preeclampsia and 32 gestational age matched normotension pregnant women were recruited. Using quantitative real-time polymerase chain reaction (qRT-PCR), we found higher expression of GAS5 in placenta of preclamsia affected women. The level of GAS5 existed strongly in correlation with Thrombin Time indicating coagulation function and other clinical parameters by Pearson correlation analysis. Then we constructed the GAS5 lentivirus expression vectors and transfected into human trophoblast cell lines HTR-8/SVneo and JEG-3. Using in vitro cell culture studies, we found an inhibited effect of GAS5 on proliferative ability, migratory ability and invasive ability however; no effect on apoptosis was detected. Further mechanistic analysis found that GAS5 modulated microRNA-21 (miR-21) in an opposite variation tendency by qRT-PCR and rescue experiment. In addition, inhibition of GAS5 promoted the activation of PI3K/AKT signaling pathway and its downstream proteins covering MMP-9 and TP53 as evident from our qRT-PCR and western blot analyses. Thus, we suggested that GAS5 might involve in pregnancy with preeclampsia by influencing the biological functions of trophoblast cells through the regulation of miR-21 and activation of PI3K/AKT signaling pathway and its downstream targets, which may contribute to reveal the nature of preeclampsia.
White Hop Shoot Production in Slovenia: Total Phenolic, Microelement and Pesticide Residue Content in Five Commercial Cultivars

SUMMARY Harvesting of white hop shoots might be justified if they can be shown to be beneficial to human health. The aim of the present study is to determine the effects of hop cultivars and year of production on total phenolics, antioxidant potential, microelements and pesticide residues. Biomass per plant was highly variable across the cultivars (3.1-7.1 g dry mass per plant) and depended on hop cultivar and year (2009-2011). Total phenolics as chlorogenic acid equivalents (CAE) on dry mass basis varied from 0.60 to 1.80 mg/g, and showed significant effects across hop cultivar and year. The radical scavenging activities of the samples collected in years 2010-2012 ranged from 11 to 19 µg CAE. Ferric reducing activity was <0.01, with significantly different effects across hop cultivars (pC≤0.05) and year (py≤0.05) observed only in 2012. Traces of microelements and potentially active compounds from the use of pesticides in white hop shoots of Humulus lupulus ‘Dana’ were analysed. The content of zinc in the hop shoots on dry mass basis was very low (4 mg/kg), and it was below the limit of detection in the soil. The content of copper in the hop shoots was also very low (2.3 mg/kg), while in the soil it was below the critical emission (100 vs 300 mg/kg, respectively). All 182 active ingredients from the residues of the previously used pesticides were below the limits of detection. It can be concluded that these white hop shoots are better antioxidants than hop cones and hop leaves, and that they do not contain any pesticide residues.
The Steps to Therapeutic Drug Monitoring: A Structured Approach Illustrated With Imatinib

Pharmacometric methods have hugely benefited from progress in analytical and computer sciences during the past decades, and play nowadays a central role in the clinical development of new medicinal drugs. It is time that these methods translate into patient care through therapeutic drug monitoring (TDM), due to become a mainstay of precision medicine no less than genomic approaches to control variability in drug response and improve the efficacy and safety of treatments. In this review, we make the case for structuring TDM development along five generic questions: 1) Is the concerned drug a candidate to TDM? 2) What is the normal range for the drug's concentration? 3) What is the therapeutic target for the drug's concentration? 4) How to adjust the dosage of the drug to drive concentrations close to target? 5) Does evidence support the usefulness of TDM for this drug? We exemplify this approach through an overview of our development of the TDM of imatinib, the very first targeted anticancer agent. We express our position that a similar story shall apply to other drugs in this class, as well as to a wide range of treatments critical for the control of various life-threatening conditions. Despite hurdles that still jeopardize progress in TDM, there is no doubt that upcoming technological advances will shape and foster many innovative therapeutic monitoring methods.
Beliefs and Risk Awareness on Medications Among Pregnant Women Attending the Antenatal Care Unit in Ethiopia University Hospital. Overestimating the Risks Is Another Dread

Background: Most studies on drug use during pregnancy were generally focused on potential teratogenic effects. However, beliefs and risk awareness of medications can also influence medication use and fetal well-being. Objective: This study aimed at assessing the risk awareness and beliefs on medication use among pregnant women attending antenatal care unit in an Ethiopian university hospital. Method: A cross-sectional study was employed in pregnant women who were attending for antenatal care service at Gondar University Referral Hospital from March 15, to April 15, 2016. A pretested structured interview questionnaire adopted from the Beliefs About Medicines Questionnaire (BMQ) was used for data collection. Chi-square test and binary logistic regression were used to identify possible predictors influencing the outcome variables. Result: Of the 423 women approached, 384 agreed to complete the questionnaire (90.8% response rate), and the mean age of the participants was 27.22 ± 5.5 years. More than two-thirds of the respondents had two to three (46.1%) or greater than three (25.8%) pregnancy histories. A third and nearly half (45.6%) of the respondents were on the first trimester and second trimester of their gestational age, respectively. The majority (70%) of pregnant women thought all drugs are harmful if taken during pregnancy. Only few (4.2%) of the participants did not mind taking drugs without professional advice. Most (90%) of the respondents were not willing to take drugs without professional advice. Pregnant women who came from rural areas had 25% less likelihood to self-medicate, with an adjusted odds ratio of 95% CI, 0.75 (0.37, 0.96). Conclusion: In this study, overestimated and exaggerated beliefs of medication risks during pregnancy are a concern, though cautious drug use is necessary and warranted. Adequate counseling has to be provided by physicians, pharmacists, and other healthcare professionals to change pregnant women's conservative attitudes and misinformed beliefs on medication risk.
The Hybrid Genome of a New Goldfish-Like Fish Lineage Provides Insights Into the Origin of the Goldfish

Distant hybridization leads to obvious changes in genotypes and phenotypes, giving rise to species with novel capabilities. However, the fusion of distinct genomes also polymerizes the DNA or gene variations that occur during the course of evolution. Knowledge of the early stages of post-hybridization evolution is particularly important. Here, we investigated the full-length (FL) transcriptomes and the sequences resulting from the genome resequencing of the red crucian carp-like homodiploid fish (RCC-L) and goldfish-like homodiploid fish (GF-L) derived from the interspecific hybridization of koi carp (KOC) and blunt snout bream (BSB) to provide molecular evidence for the hybrid origin of the goldfish (GF). We compared the orthologous genes in the transcriptomes of RCC-L and GF-L with those of KOC and BSB. We also mapped the orthologous genes to the common carp (CC) and BSB genomes and classified them into eight gene patterns in three categories (chimaera, mutant, and biparental origin genes). The results showed that 48.20% and 46.50% of the genes were chimaera and that 3.70% and 8.30% of the genes were mutations of orthologous genes in RCC-L and GF-L, respectively. In RCC-L and GF-L, 63.70% and 68.20% of the genetic materials were from KOC, and 12.30% and 11.90% of the genetic materials were from BSB. The sequences from the genome resequencing of RCC-L and GF-L were mapped to the genome sequences of CC and BSB, revealing that the similarities of both RCC-L and GF-L to the CC genome (92.52%, 90.18%) were obviously higher than to the BSB genome (50.33%, 49.18%), supporting the suggestion that the genomes of both RCC-L and GF-L were mainly inherited from KOC but had some DNA fragments from BSB. Overall, our results provide molecular biological evidence for the hybrid origin of red crucian carp (RCC) and GF.
The diversity of the Baikal lineage of Hydra oligactis Pallas, 1766: molecular and morphological evidence

Abstract In this paper, molecular analyses of Baikal hydras from the ‘oligactis group’, based on COI and ITS1–5.8S–ITS2, and morphological analysis of their holotrichous isorhizas, were performed. Low genetic diversity and shared haplotypes were found between Hydra oligactis Pallas, 1766 and Hydra baikalensis Swarczewsky, 1923 specimens, which is evidence of the mixing of these lineages. Genetic distances among all Baikal hydras (0.006) were less than the interspecific distances of other hydras. The size of hydras and proportions of their holotrichous isorhizas varied depending on microhabitat and environmental conditions. Our combined molecular and morphological approach proves that H. baikalensis is synonymous with H. oligactis