Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Community Structure in Rhizosphere Soil and Roots of Different Genotypes of Jacobaea vulgaris

The microbial community nearby root system of the plant is selected from the microorganisms present in the bulk soil by the plant and other factors. Rhizodeposition and secretion of defence compounds may stimulate or suppress the success of decomposing soil microorganisms, pathogens and symbiotic microorganisms in the rhizosphere. The defensive role that compounds such as pyrrolizidine alkaloids (PAs) play in plant protection against root-infecting bacteria and fungi is not fully understood (Chapter 2). Here we report on the impact of plant genotype, differing in PA composition, on the community structure of general (1) fungi and (2) bacteria in the rhizosphere; (3) fungi and (4) bacteria in the roots; and (5) arbuscular mycorrhizal fungi in the roots. Four different Jacobaea vulgaris genotypes were used in this study differing in the PA composition. They were chosen based on the presence or absence of jacobine-like PAs and were grown on two different soil-types; löss and sand. The general microbial community structures in the roots and rhizosphere were characterized by using Denaturing Gradient Gel Electrophoresis (DGGE) and for AMF in the roots by using Terminal Restriction Fragment Length Polymorphism (T-RFLP). The fungal community in both, rhizosphere soil and plant roots was clearly genotype dependent. However, we found no indications that the genotype effect was related to the PA composition except for the fungal diversity in the roots. We found a significant negative correlation between erucifoline-like PAs and the fungal diversity in the roots of the plant. There were no overall significant differences in bacterial community structure in roots and rhizosphere among the genotypes. Soil-type affected the AMF community structure in the roots but plant genotype did not.There were no overall significant differences in bacterial community structure in roots and rhizosphere among the genotypes. Soiltype affected the AMF community structure in the roots but plant genotype did not.
BIOLOGICAL AND MOLECULAR CHARACTERIZATION OF DAHLIA MOSAIC CAULIMOVIRUS

The genome structure and organization of a new and distinct caulimovirus that is widespread in dahlia (Dahlia pinnata) was determined. The double stranded DNA genome was ca. 7.0 kb in size and shared many of the features of the members of the genus Caulimovirus such as the presence of genes potentially coding for the movement protein, the inclusion body protein, the reverse transcriptase, and an intergenic region consisting of a potential 35S promoter. However, the virus differed from known caulimoviruses in that the aphid transmission factor was absent and the coat protein was smaller than its counterpart in known Caulimovirus species. Sequence homology at the amino acid level with known caulimoviruses was low and ranged from 32-70%. The absence of an aphid transmission factor and the highly divergent nature of the genomic sequence are characteristics of this newly characterized caulimovirus that is widely associated with dahlia mosaic disease. INTRODUCTION Dahlia mosaic caulimovirus (DMV) is an important viral pathogen of dahlia (Dahlia 12 pinnata) in the US and several parts of the world. First reported from Germany in 1928, the virus is considered to be one of the most important disease constraints affecting dahlias. DMV is a member of the family Caulimoviridae, genus Caulimovirus with a circular double stranded-DNA genome of approximately 7 kb. The symptomatology, propagative hosts and the role of various aphid species in virus transmission were reported (Albouy, 1992; Brierley & Smith, 1950, Brunt, 1971). The most characteristic symptoms of the disease include mosaic and vein-banding accompanied by stunting and leaf distortion. Symptoms vary depending on the cultivar, and cultivars with few or no symptoms are common. The economic impact of the disease is due to its negative affect on the quality and quantity of flowers produced by diseased plants. The physical map of a caulimovirus (DMV-Portland) genome associated with dahlia mosaic was reported (Richins & Shepherd, 1983), and its genomic sequence representing six open reading frames is available in GenBank (GenBank accessions AY309480, AY309479, AY291588, AY291587, AY291586, and AY291585). However, our surveys of dahlias to determine the incidence of DMV revealed the overwhelming presence of another caulimovirus, designated DMV-D10 that was found to be distinct from DMV-Portland (Pahalawatta et al., 2005; Pahalawatta et al., 2007a; Pahalawatta et al., 2007b; Pappu et al., 2005). A partial sequence representing a D10-like sequence variant, DMV-Holland (Nicolaisen, 2003) has also been reported. To better understand the identity and taxonomic position of the caulimoviruses associated with dahlia mosaic, the genome structure and organization of DMV-D10 genome was deciphered and was compared to DMV-Portland and other members of the genus Caulimovirus.
A Review of the Sphaeropthalma uro Species-group (Hymenoptera: Mutillidae), with Taxonomic Changes

Abstract The subgenera Micromutilla Ashmead, 1899, Photopsioides Schuster, 1958, Photopsis Blake, 1886, Physetapsis Schuster, 1958, and Xenophotopsis Schuster, 1958 are junior synonyms of Sphaeropthalma Blake 1871. The single species previously placed in the subgenus Xenophotopsis is placed into the Sphaeropthalma orestes species-group. Species previously placed in the subgenus Physetapsis are placed into the Sphaeropthalma clara species-group. Species previously placed in the subgenera Sphaeropthalma and Photopsioides are placed into the Sphaeropthalma pensylvanica species-group and Sphaeropthalma uro species-group, respectively. A review of the males of Sphaeropthalma uro species-group is given. The females of Sphaeropthalma abdominalis (Blake) and S. amphion (Fox) are described. Forty-seven new host records and current distributional data are presented for the species of the Sphaeropthalma uro species-group. A key and illustrations are given for the males and known females of the Sphaeropthalma uro species-group.
A novel micro-groove impedance sensor for 3D cell viability monitoring and high-throughput drug screening

Drug screening is traditionally based on the pharmacodynamic models from 2D cell culture or animal experiments. Recently, three-dimensional (3D) tumor cell models have attracted increasing interest due to their great advantages in simulating more accurately the heterogeneous tumor behavior in vivo. Drug screening based on 3D cells can provide more accurate efficacy results. However, it is difficult to realize real-time and label-free monitoring of 3D cell viability by common imaging techniques. To solve this technical difficulty, a novel micro-groove impedance sensor (MGIS) was specially developed for 3D cell viability real-time monitoring. Precultured 3D spheroids cells are trapped in the micro-cavity with opposite gold electrodes for the in-situ impedance measurement. The presence of 3D spheroid cells will lead to the change of electron transfer efficiency on the electrode surface, which will lead to the change of impedance. When antitumor drugs act on the spheroid cells, the spheroids will cleave and the impedance will decrease. In order to verify the accuracy of MGIS chip, we adopted standard live/dead fluorescence staining to validate the activity of 3D cells. Furthermore, anti-tumor drug sensitivity tests were conducted to validate the drug screening ability of MGIS plat-form. All the results demonstrate that the MGIS is able to monitoring 3D cell viability and drug screening.
Responses of CaCl2 on Photosynthesis and antioxidative enzymes of Zea Mays under NaCl stress

An attempt was made to reclamation the sodium chloride stressed plants with calcium chloride. For this work, Zea mays Var. Co-24 was cultivated in control, 10 mM NaCl alone, and in combined salt (10 mM NaCl + 5 mM CaCl2). NaCl stressed plants showed decreased the photosynthetic pigments. When NaCl treatment was combined with CaCl2, it significantly improved the photosynthetic pigments such as chlorophyll and carotenoids. The antioxidant enzymes such as catalase, peroxidase and superoxide dismutase activities were increased in NaCl stressed plants while it is decreased in combined salt treated plants. In conclusion, NaCl treated plants significantly decreased the plants growth and photosynthetic pigments while increased the proline and antioxidant enzymes in Zea mays. However, calcium chloride treated with NaCl stressed plants it significantly improved the variables affected by NaCl salinity. The addition of calcium chloride plays a significant role in mitigating the deleterious effect of NaCl salinity.
Assessment of preclinical effect of (+)‐catechin hydrate on sexual function: An in silico and in vivo study

Considering dopamine‐enhancing effect of (+)‐catechin, the present study was designed to evaluate dopamine‐2 (D2) receptor agonistic and phosphodiesterase‐5 (PDE5) enzyme inhibitory effects in in silico and effect on male sexual function of Sprague Dawley rats in vivo. (+)‐Catechin and standard (sildenafil and bromocriptine) were docked using Autodock Vina 1.1. 2 and visualised by UCSF Chimera 1.14. Significant interactions in terms of binding energies were observed for catechin with both proteins. In in vivo study, the rats were dosed orally for 54 days with (+)‐catechin hydrate (50 mg/kg), sildenafil citrate (standard, 4 mg/kg) and carboxymethylcellulose (vehicle, 0.25% w/v). The aphrodisiac effects were evaluated on the day 14, 28, 42 and 54 using the behavioural parameters of mounting and intromission. After the study, animals were sacrificed and testes and spermatozoa were assessed for safety profile. Results showed a significant increase in mount and intromission frequencies and a significant reduction in mount and intromission latencies in the catechin group on all tested days when compared to vehicle control. (+)‐Catechin was found to be safe on histology of testes, sperm count, sperm motility and sperm morphology parameters. In conclusion, catechin demonstrated an enhancement in sexual behaviour without eliciting toxicity on the male reproductive system in rats.
Semantic Priming in Mild Cognitive Impairment and Healthy Subjects: Effect of Different Time of Presentation of Word-Pairs

Introduction: Semantic memory is impaired in mild cognitive impairment (MCI). Two main hypotheses about this finding are debated and refer to the degradation of stored knowledge versus the impairment of semantic access mechanisms. The aim of our study is to evaluate semantic impairment in MCI versus healthy subjects (HS) by an experiment evaluating semantic priming. Methods: We enrolled 27 MCI and 20 HS. MCI group were divided, according to follow up, into converters-MCI and non converters-MCI. The semantic task consisted of 108 pairs of words, 54 of which were semantically associated. Stimuli were presented 250 or 900 ms later the appearance of the target in a randomized manner. Data were analyzed using factorial ANOVA. Results: Both HS and MCI answered more quickly for word than for non-word at both stimulus onset asynchrony (SOA) intervals. At 250 ms, both MCI and HS experienced a shorter time of response for related-word than for unrelated words (priming effect), while only the converters-MCI subgroup lost the priming effect. Further, we observed a rather larger Cohen’s d effect size in non converters-MCI than in converters-MCI. Conclusion: Our data, and in particular the absence of a semantic priming effect in converters-MCI, could reflect the impairment of semantic knowledge rather than the accessibility of semantic stores in MCI individuals that progress to dementia.
ROLE OF MYELOPEROXIDASE MEDIATED OXIDATIVE MODIFICATION AND APOLIPOPROTEIN COMPOSITION IN HIGH DENSITY LIPOPROTEIN FUNCTION

by ARUNDHATI UNDURTI High levels of high density lipoprotein (HDL) are associated with a decreased risk of cardiovascular disease (CVD). The atheroprotective function of HDL has been attributed to its key role in the reverse cholesterol transport (RCT) pathway. However, recent evidence suggests that HDL can be rendered “dysfunctional”, impairing its ability to promote RCT. The work described here suggests two mechanisms that can render HDL “dysfunctional. ” The first mechanism involves oxidation of HDL by the enzyme myeloperoxidase (MPO). Recent studies demonstrate that MPO binds to HDL in vivo, selectively targeting HDL for oxidative modification. We now show that (patho) physiologically relevant levels of MPO-catalyzed oxidation result in loss of non cholesterol efflux activities of HDL including anti-apoptotic and anti-inflammatory functions. One mechanism responsible is shown to involve loss of oxidized HDL binding to the HDL receptor, scavenger receptor B1, and concurrent acquisition of binding to a novel unknown receptor independent of scavenger receptors CD36 and SR-A1. HDL modification by MPO is further shown to confer pro-inflammatory gain of function activities as monitored by NFactivation and surface vascular cell adhesion molecule (VCAM-1) levels on aortic endothelial cells. Multiple site-directed mutagenesis studies of HDL suggest that the pro-inflammatory activity does not involve methionine, tyrosine,
Technical Note: plan-delivery-time constrained inverse optimization method with minimum-MU-per-energy-layer (MMPEL) for efficient pencil beam scanning proton therapy.

PURPOSE This work aims to reduce dose delivery time of pencil beam scanning (PBS) proton plans, which is the dominant factor of total plan delivery time. A proton PBS system, such as Varian ProBeam proton therapy system, can be equipped with the proton dose rate that is linearly proportional to the minimum monitor unit (MU) (i.e., number of protons) of PBS spots before saturation. Thus dose delivery time can be potentially reduced by increasing the MU threshold. However, commercially available treatment planning systems and current methods only allow for a single MU threshold globally for all PBS spots (i.e., all energy layers), and consequently the room to increase this minimum MU for reducing dose delivery time is very limited since higher minimum MU can greatly degrade treatment plan quality. METHODS Two major innovations of this work are the proposal of using variable MU thresholds locally adaptive to each energy layer, i.e., minimum-MU-per-energy-layer (MMPEL), for reducing dose delivery time, and the joint optimization of plan delivery time and plan quality. MMPEL is formulated as a constrained optimization problem with objectives of dose-volume-histogram based planning constraints and plan delivery time, and minimum-MU constraints per energy layer for deliverable PBS spots. MMPEL is solved by iterative convex relaxations via alternating direction method of multipliers. RESULTS Representative prostate, lung, brain, head-and-neck, breast, liver and pancreas cases were used to validate MMPEL. MMPEL reduced dose delivery time to 53%, 67%, 67%, 53%, 54%, 32%, and 14% respectively while maintaining the similar plan quality. Accepting a slightly degraded plan quality that still met all physician planning constraints, the treatment time could be further reduced to 26%, 35%, 41%, 34%, 32%, 16%, and 11% respectively, or in another word MMPEL accelerated the PBS plan delivery by 2-10 fold. CONCLUSIONS A new proton PBS treatment planning method MMPEL with variable energy-adaptive MU thresholds is developed to optimize dose delivery time jointly with plan quality. The preliminary results suggest that MMPEL could substantially reduce dose delivery time.
Plant functional types and climate in a southern African savanna

A system of easily defined plant functional types for a dry savanna is presented and related to climate data. To predict possible changes of vegetation in response to climate change, a system of functional attributes is developed. The attributes are based on both structural and functional charac- teristics and are chosen to be related to climatic conditions. plant functional types are defined as assemblages of plant species having similar combinations of plant functional at- tributes. Direct and indirect gradient analyses of a test data set show that the plant functional types as well as the vegetation described from them are strongly associated with total annual precipitation, precipitation of the wettest month and a mois- ture index (all related to soil moisture) and with temperature of the coldest month.
Chagas Disease Infection Reactivation after Heart Transplant

Chagas disease, caused by a Trypanosona cruzi infection, is one of the main causes of heart failure in Latin America. It was originally a health problem endemic to South America, predominantly affecting residents of poor rural areas. With globalization and increasing migratory flows from these areas to large cities, the immigration of T. cruzi chronically-infected people to developed, non-endemic countries has occurred. This issue has emerged as an important consideration for heart transplant professionals. Currently, Chagas patients with end-stage heart failure may need a heart transplantation (HTx). This implies that in post-transplant immunosuppression therapy to avoid rejection in the recipient, there is the possibility of T. cruzi infection reactivation, increasing the morbidity and mortality rates. The management of heart transplant recipients due to Chagas disease requires awareness for early recognition and parasitic treatment of T. cruzi infection reactivation. This issue poses challenges for heart transplant professionals, especially regarding the differential diagnosis between rejection and reactivation episodes. The aim of this review is to discuss the complexity of the Chagas disease reactivation phenomenon in patients submitted to HTx for end-stage chagasic cardiomyopathy.
Phylogenetic analysis of Ascidae sensu lato and related groups (Acari: Mesostigmata: Gamasina) based on nuclear ribosomal DNA partial sequences

Abstract An analysis of the phylogeny of Ascidae sensu lato and related groups based on DNA data is presented. This group was recently separated in Ascidae sensu stricto, Melicharidae and Blattisociidae, retaining the first two families in Ascoidea and moving the third to Phytoseioidea. These changes were made based mainly on the morphology of the spermathecal apparatus. On the other hand, considerable morphological similarities exist between some genera of Ascidae s.l. and of Phytoseiidae and Rhodacaridae. This study uses partial sequences from the 18S and 28S regions of the nuclear ribosomal DNA to infer the phylogenetic relationships between Ascidae s.s. , Melicharidae and Blattisociidae as well as their relationships with Phytoseiidae and Rhodacaridae. Results obtained with the Bayesian and Maximum Likelihood methods supported the paraphyly of Ascidae s.l. , but did not support the recent assignment of their members into the recently conformed superfamilies. The results also suggested that Blattisociidae and Phytoseiidae constitute a monophyletic group and that Rhodacaridae is paraphyletic. Except for Protogamasellopsis posnaniensis Wiśniewski and Hirschmann, all rhodacaroid representatives considered in this analysis (Digamasellidae, Ologamasidae and Rhodacaridae), as well as Zygoseius Berlese (a genus currently of uncertain familial placement), were placed at the base of the constructed phylogenetic tree, constituting a sister group of the previously mentioned taxa. The phylogenetic hypothesis presented here suggests the need to reconsider the morphological structures presently used to characterize the families of Ascoidea, Phytoseioidea and Rhodacaroidea.
Virtual Screening of Solanine and its derivatives to analyze inhibitory activity towards Acetylcholinesterase for the treatment of Alzheimer's disease

Abstract: Alzheimer’s disease (AD) is most common form of dementia affecting elderly people, and sixth leading cause of death worldwide. The two abnormal structures formed in AD patient’s brain are beta -amyloid plaques and neurofibrillary. The beta-amyloid plaque formation is accelerated due to acetylcholinestarases. Treatment of AD has majorly dependent on inhibition of acetylcholinestarase. In the present study, acetylcholinesterase receptor is docked with solanine and its derivatives and with a commercially available drug. The lead 3 compounds, are selected based on minimum binding energy and interaction with the active site of the receptor, are much better compared to commercially available drug. Molecular interactions of the receptor complexes with lead solanine compounds are also found to be higher in number. By this it can be hypothesize that solanine derivatives can inhibit acetylcholinesterase more effectively, which controls rapid breaking of acetylcholine, a neurotransmitter to acetyl an
LineSpyX: A Power Line Inspection Robot Based on Digital Radiography

Most of the current power line inspection robots use cameras and LiDARs to inspect the power line surfaces and the surrounding environment. But it is still difficult to detect the internal defects of the power lines. In this letter, the design and implementation of LineSpyX, a novel power line inspection robot based on digital radiography (DR), is introduced to solve the problem of non-destructive testing (NDT) of the overhead Aluminum Conductor Composite Core (ACCC) wires. The proposed robot has a stable wrapped mechanical structure with a moving system, a live work system, and a NDT system. The wheeled moving system enables the robot to move on the wires and cross obstacles such as vibration dampers. The NDT system consists of a portable X-ray generator and a DR detection panel. When the robot performs the inspection task, the X-ray goes up through the ACCC wire to the panel, where the X-ray images of the internal carbon fiber cores are recorded. A deep learning based defect diagnosis method combined with manual diagnosis is proposed to detect potential defects. The main functionalities of the developed robot are verified by lab experiments and field tests.
A markerless system for gait analysis based on OpenPose library

The paper reports the performance of a low-cost markerless system for 3D human motion detection and tracking, consisting of the open-source library OpenPose, two webcams and a linear triangulation algorithm. OpenPose is able to identify anatomical landmarks with a commercial webcam, using Convolutional Neural Networks trained on data obtained from monocular images. When images from at least two different points of view are processed by OpenPose, 3D kinematic and spatiotemporal data of human gait can be also computed and assessed. Despite its potential, the accuracy of such a system in the estimation of kinematic parameters of human gait is currently unknown. With the aim to estimate OpenPose accuracy in 3D lower limb joint angle measurement during gait, two synchronized videos of a healthy subject were acquired, with two webcams, in a walking session on a treadmill at comfortable speed. 2-dimensional joint centers coordinates were assessed by OpenPose, and computed in 3D by triangulation algorithm. The resulting angular kinematics was, then, compared with inertial sensors outputs. Results showed that the system was generally able to track lower limbs motion, producing angular traces representative of normal gait similar to the ones computed by IMUs. However, OpenPose approach showed inaccuracy, mostly in the computation of maxima and minima joint angles, reaching error values up to 9.9°.