Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant invasions and extinction debts

Whether introduced species invasions pose a major threat to biodiversity is hotly debated. Much of this debate is fueled by recent findings that competition from introduced organisms has driven remarkably few plant species to extinction. Instead, native plant species in invaded ecosystems are often found in refugia: patchy, marginal habitats unsuitable to their nonnative competitors. However, whether the colonization and extinction dynamics of these refugia allow long-term native persistence is uncertain. Of particular concern is the possibility that invasive plants may induce an extinction debt in the native flora, where persistence over the short term masks deterministic extinction trajectories. We examined how invader impacts on landscape structure influence native plant persistence by combining recently developed quantitative techniques for evaluating metapopulation persistence with field measurements of an invaded plant community. We found that European grass invasion of an edaphically heterogeneous California landscape has greatly decreased the likelihood of the persistence of native metapopulations. It does so via two main pathways: (i) decreasing the size of native refugia, which reduces seed production and increases local extinction, and (ii) eroding the dispersal permeability of the matrix between refugia, which reduces their connectivity. Even when native plant extinction is the deterministic outcome of invasion, the time to extinction can be on the order of hundreds of years. We conclude that the relatively short time since invasion in many parts of the world is insufficient to observe the full impact of plant invasions on native biodiversity.
Buckling of an Elastic Rod with High Intrinsic Twist

Motivated by the application of modelling DNA by an elastic rod, we use the technique of two-scale homogenization on a two-point boundary value problem (BVP) involving buckling of a rod with a high intrinsic twist. The basic question is to understand the errors generated in replacing a rod with a high, but nite, intrinsic twist, by an e ective rod in the in nite intrinsic twist limit. For our buckling problem the e ective problem is isotropic. As a consequence there is a continuous family of buckled planar solutions. We show that the buckled con gurations of the rod with high intrinsic twist are close to certain special planar buckled con gurations of the isotropic rod that are selected from among all the solutions to the e ective problem. The selected planes are independent of the values of the (bending and twisting) sti nesses and of the load.
Global land surface phenology trends from GIMMS database

A double logistic function has been used to describe global inventory mapping and monitoring studies (GIMMS) normalized difference vegetation index (NDVI) yearly evolution for the 1981 to 2003 period, in order to estimate land surface phenology parameter. A principal component analysis on the resulting time series indicates that the first components explain 36, 53 and 37% of the variance for the start, end and length of growing season, respectively, and shows generally good spatial homogeneity. Mann–Kendall trend tests have been carried out, and trends were estimated by linear regression. Maps of these trends show a global advance in spring dates of 0.38 days per year, a global delay in autumn dates of 0.45 days per year and a global increase of 0.8 days per year in the growing seasons validated by comparison with previous works. Correlations between retrieved phenological parameters and climate indices generally showed a good spatial coherence.
The virtual multifrequency spectrometer: a new paradigm for spectroscopy

Ongoing developments of hardware and software are changing computational spectroscopy from a strongly specialized research area to a general tool in the inventory of most researchers. Increased interactions between experimentally oriented users and theoretically oriented developers of new methods and models would result in more robust, flexible and reliable tools, and studies for the systems of increasing complexity, which are of current scientific and technological interest. This is the philosophy behind this review, which presents the development of a so‐called virtual multifrequency spectrometer (VMS) including state‐of‐the‐art approaches in a user‐friendly frame. The current status of the VMS tool will be illustrated by a number of case studies with special reference to infrared and UV–vis regions of the electromagnetic spectrum including also chiral spectroscopies. Only the basic theoretical background will be provided avoiding explicit equations as far as possible, and pointing out the most recent advancements beyond the standard rigid‐rotor harmonic‐oscillator model coupled to vertical electronic excitation energies. WIREs Comput Mol Sci 2016, 6:86–110. doi: 10.1002/wcms.1238
Sozialstrukturelle Modernisierung: Stabilisierung oder Destruierung des Wohlfahrtstaates

Recent contributions on the future development of the welfare state postulate very contradictory trends. One position assumes that the welfare state is losing the social and political bases of legitimacy as a consequence of social structural changes. The other position expects that these processes of modernization of the social structure will stabilize the modern welfare state. After dicussing the central theoretical arguments of both positions empirical data are presented to evaluate those positions. The data do not support the thesis that the German Welfare state is losing ist social and political legitimacy.
Transition of Transient Channel Flow with High Reynolds Number Ratios

Large-eddy simulations of turbulent channel flow subjected to a step-like acceleration have been performed to investigate the effect of high Reynolds number ratios on the transient behaviour of turbulence. It is shown that the response of the flow exhibits the same fundamental characteristics described in He & Seddighi (J. Fluid Mech., vol. 715, 2013, pp. 60–102 and vol. 764, 2015, pp. 395–427)—a three-stage response resembling that of the bypass transition of boundary layer flows. The features of transition are seen to become more striking as the Re-ratio increases—the elongated streaks become stronger and longer, and the initial turbulent spot sites at the onset of transition become increasingly sparse. The critical Reynolds number of transition and the transition period Reynolds number for those cases are shown to deviate from the trends of He & Seddighi (2015). The high Re-ratio cases show double peaks in the transient response of streamwise fluctuation profiles shortly after the onset of transition. Conditionally-averaged turbulent statistics based on a λ_2-criterion are used to show that the two peaks in the fluctuation profiles are due to separate contributions of the active and inactive regions of turbulence generation. The peak closer to the wall is attributed to the generation of “new” turbulence in the active region, whereas the peak farther away from the wall is attributed to the elongated streaks in the inactive region. In the low Re-ratio cases, the peaks of these two regions are close to each other during the entire transient, resulting in a single peak in the domain-averaged profile.
The cellular and biochemical rules of lipid antigen presentation

The recognition of both protein and lipid antigens follows similar strategies that rely on different molecular mechanisms. APC present lipid antigens exploiting the same mechanisms implicated in lipid translocation, lipoprotein assembly and lipid degradation. An important issue is how the lipid structure contributes to antigenicity. Lipid hydrophobicity influences the modes of internalization by APC, the trafficking through different membrane compartments, the binding to CD1 molecules and the stability of antigenic complexes. Some glycolipids with large hydrophilic parts require processing of the sugar moieties exerted by lysosomal hydrolases. Finally, extraction of lipids from membranes, their solubilization and loading on CD1 molecules are facilitated by the same lysosomal lipid‐binding proteins that are also instrumental in lipid catabolism. More recent investigations reveal how lipid‐specific immunity is regulated during infections. In this review we describe the main cellular and biochemical rules of lipid antigen presentation and discuss their implications in anti‐microbial and autoimmune responses.
Effect of Standard Radiotherapy With Cisplatin vs Accelerated Radiotherapy With Panitumumab in Locoregionally Advanced Squamous Cell Head and Neck Carcinoma: A Randomized Clinical Trial

Importance The Canadian Cancer Trials Group study HN.6 is the largest randomized clinical trial to date comparing the concurrent administration of anti–epidermal growth factor receptor (EGFR) monoclonal antibodies with radiotherapy (RT) to standard chemoradiotherapy in locoregionally advanced squamous cell carcinoma of the head and neck (LA-SCCHN). Objective To compare progression-free survival (PFS) in patients with LA-SCCHN treated with standard-fractionation RT plus high-dose cisplatin vs accelerated-fractionation RT plus the anti-EGFR antibody panitumumab. Design, Setting, and Participants A randomized phase 3 clinical trial in 17 Canadian centers. A total of 320 patients were randomized between December 2008 and November 2011. Interventions Patients with TanyN+M0 or T3-4N0M0 LA-SCCHN were randomized 1:1 to receive standard-fractionation RT (70 Gy/35 over 7 weeks) plus cisplatin at 100 mg/m2 intravenous for 3 doses (arm A) vs accelerated-fractionation RT (70 Gy/35 over 6 weeks) plus panitumumab at 9 mg/kg intravenous for 3 doses (arm B). Main Outcomes and Measures Primary end point was PFS. Due to an observed declining event rate, the protocol was amended to a time-based analysis. Secondary end points included overall survival, local and regional PFS, distant metastasis-free survival, quality of life, adverse events, and safety. Results Of 320 patients randomized (268 [84%] male; median age, 56 years), 156 received arm A and 159 arm B. A total of 93 PFS events occurred. By intention-to-treat, 2-year PFS was 73% (95% CI, 65%-79%) in arm A and 76% (95% CI, 68%-82%) in arm B (hazard ratio [HR], 0.95; 95% CI, 0.60-1.50; P = .83). The upper bound of the HR 95% CI exceeded the prespecified noninferiority margin. Two-year overall survival was 85% (95% CI, 78%-90%) in arm A and 88% (95% CI, 82%-92%) in arm B (HR, 0.89; 95% CI, 0.54-1.48; P = .66). Incidence of any grade 3 to 5 nonhematologic adverse event was 88% in arm A and 92% in arm B (P = .25). Conclusions and Relevance With a median follow-up of 46 months, the PFS of panitumumab plus accelerated-fractionation RT was not superior to cisplatin plus standard-fractionation RT in LA-SCCHN and noninferiority was not proven. Despite having negative results, HN.6 has contributed important data regarding disease control and toxic effects of these treatment strategies. Trial Registration clinicaltrials.gov Identifier: NCT00820248
Quantification of Upper Limb Motor Recovery and EEG Power Changes after Robot-Assisted Bilateral Arm Training in Chronic Stroke Patients: A Prospective Pilot Study

Background Bilateral arm training (BAT) has shown promise in expediting progress toward upper limb recovery in chronic stroke patients, but its neural correlates are poorly understood. Objective To evaluate changes in upper limb function and EEG power after a robot-assisted BAT in chronic stroke patients. Methods In a within-subject design, seven right-handed chronic stroke patients with upper limb paresis received 21 sessions (3 days/week) of the robot-assisted BAT. The outcomes were changes in score on the upper limb section of the Fugl-Meyer assessment (FM), Motricity Index (MI), and Modified Ashworth Scale (MAS) evaluated at the baseline (T0), posttraining (T1), and 1-month follow-up (T2). Event-related desynchronization/synchronization were calculated in the upper alpha and the beta frequency ranges. Results Significant improvement in all outcomes was measured over the course of the study. Changes in FM were significant at T2, and in MAS at T1 and T2. After training, desynchronization on the ipsilesional sensorimotor areas increased during passive and active movement, as compared with T0. Conclusions A repetitive robotic-assisted BAT program may improve upper limb motor function and reduce spasticity in the chronically impaired paretic arm. Effects on spasticity were associated with EEG changes over the ipsilesional sensorimotor network.
Identification of the minimum inertial parameters of robots

A direct method is developed to determine the minimum set of inertial parameters of tree-structure robots giving complete information. The method makes it possible to classify most of the regrouped parameters by closed-form relations. A linear model for the identification of the minimum inertial parameters is also presented. The identification model is computationally simple; it is a function of the joint positions and velocities and does not need to calculate the joint accelerations. The identification model is based on the energy theorem, providing a model which is linear in the link parameters. <<ETX>>
Understanding D-Ribose and Mitochondrial Function

Mitochondria are important organelles referred to as cellular powerhouses for their unique properties of cellular energy production. With many pathologic conditions and aging, mitochondrial function declines, and there is a reduction in the production of adenosine triphosphate. The energy carrying molecule generated by cellular respiration and by pentose phosphate pathway, an alternative pathway of glucose metabolism. D-ribose is a naturally occurring monosaccharide found in the cells and particularly in the mitochondria is essential in energy production. Without sufficient energy, cells cannot maintain integrity and function. Supplemental D-ribose has been shown to improve cellular processes when there is mitochondrial dysfunction. When individuals take supplemental D-ribose, it can bypass part of the pentose pathway to produce D-ribose-5-phosphate for the production of energy. In this article, we review how energy is produced by cellular respiration, the pentose pathway, and the use of supplemental D-ribose.
IoTChain: A blockchain security architecture for the Internet of Things

In this paper, we propose IoTChain, a combination of the OSCAR architecture [1] and the ACE authorization framework [2] to provide an E2E solution for the secure authorized access to IoT resources. IoTChain consists of two components, an authorization blockchain based on the ACE framework and the OSCAR object security model, extended with a group key scheme. The blockchain provides a flexible and trustless way to handle authorization while OSCAR uses the public ledger to set up multicast groups for authorized clients. To evaluate the feasibility of our architecture, we have implemented the authorization blockchain on top of a private Ethereum network. We report on several experiments that assess the performance of different architecture components.
Anti-Vascular Endothelial Growth Factor Targeting by Curcumin and Thalidomide in Acute Myeloid Leukemia Cells

Acute myeloid leukemias (AMLs) are blood disorders that exhibit uncontrolled growth and reduction of apoptosis rates. As with other malignancies, progression may be result of induction and formation of new blood vessels influenced by disease conditions. Cancer cells produce a variety of factors which play important roles in angiogenesis. Vascular endothelial growth factor (VEGF) is critical for many malignancies, including AMLs. Curcumin, as a natural compound, is able to enhance apoptosis via a mechanism affecting regulatory genes. As a new strategy we here evaluated anti-VEGF properties of curcumin, alone and in combination with thalidomide, in leukemic cell lines. Growth inhibitory effects were assessed by MTT assay and apoptosis was detected by annexin/PI staining in U937 and KG-1 cell lines. mRNA expression levels of VEGF isoforms were evaluated by qRT-PCR. Curcumin inhibited proliferation and induced apoptosis in both KG-1 and U937 cells and this effect was stronger in combination with thalidomide. In KG-1 cells, the level of VEGF (A, B, C and D) mRNA was decreased in curcumin-treated as compared to untreated cells. Maximum effects were obtained at the concentration of 40 μM curcumin in U937 cells. Taken together, the results indicate that the VEGF autocrine loop may have an impact on AML development and progression and could be considered as a therapeutic target. Thalidomide as a VEGF inhibitor in combination with curcumin appears to have a synergistic impact on inhibition of cell proliferation and promotion of apoptosis.
Occurrence and Diversity of Diazotrophic Cyanobacteria in Distillery Effluents

Cyanobacteria are unique and rare among the entire microbial community. A large number of Cyanobacterial strains are well known for their diazotrophic nature and significant for nitrogen economy of the soil, however being damaged by environmental contamination such as agrochemical and industrial effluents. In present study occurrence of diazotrophic Cyanobacteria exposing their diversity in distillery effluent was investigated. The physicochemical properties of effluents of two distillery industries situated in Bilaspur district were analyzed. Total 19 strains of diazotrophic Cyanobacteria were identified and isolated from distillery effluent flooded area, whereas Anabaena was found more abundant with 05 species followed by 04 species of Nostoc, 02 species of Calothrix, Gloeotrichia and Scytonaema while Aulosira, Cylindrospermum, Plectonema and Revularia were observed with single species. The abundance of Cyanobacteria in these effluents was due to favorable contents of oxidizable organic matter, rich Calcium, high Alkalinity and abundant nutrients such as nitrates, phosphate with less dissolved Oxygen. However various nondiazotrophic Cyanobacteria were also observed.
The ecological and genetic basis of convergent thick‐lipped phenotypes in cichlid fishes

The evolution of convergent phenotypes is one of the most interesting outcomes of replicate adaptive radiations. Remarkable cases of convergence involve the thick‐lipped phenotype found across cichlid species flocks in the East African Great Lakes. Unlike most other convergent forms in cichlids, which are restricted to East Africa, the thick‐lipped phenotype also occurs elsewhere, for example in the Central American Midas Cichlid assemblage. Here, we use an ecological genomic approach to study the function, the evolution and the genetic basis of this phenotype in two independent cichlid adaptive radiations on two continents. We applied phylogenetic, demographic, geometric morphometric and stomach content analyses to an African (Lobochilotes labiatus) and a Central American (Amphilophus labiatus) thick‐lipped species. We found that similar morphological adaptations occur in both thick‐lipped species and that the ‘fleshy’ lips are associated with hard‐shelled prey in the form of molluscs and invertebrates. We then used comparative Illumina RNA sequencing of thick vs. normal lip tissue in East African cichlids and identified a set of 141 candidate genes that appear to be involved in the morphogenesis of this trait. A more detailed analysis of six of these genes led to three strong candidates: Actb, Cldn7 and Copb. The function of these genes can be linked to the loose connective tissue constituting the fleshy lips. Similar trends in gene expression between African and Central American thick‐lipped species appear to indicate that an overlapping set of genes was independently recruited to build this particular phenotype in both lineages.
Nutrients in soil layers under no-tillage after successive pig slurry applications

Successive applications of pig slurry to soils under no-tillage can increase the nutrient levels in the uppermost soil layers and part of the nutrients may be transferred to deeper layers. The objective was to evaluate the distribution of nutrients in the profile of a soil after 19 pig slurry applications under no-tillage for 93 months. The experiment was conducted from May 2000 to January 2008 in an experimental area of the Federal University of Santa Maria, southern Brazil, on a Typic Hapludalf. The treatments consisted of pig slurry applications (0, 20, 40 and 80 m3 ha-1) and at the end of the experiment, soil samples were collected (layers 0-2, 2-4, 4-6, 6-8, 8-10, 10-12, 12-14, 14-16, 16-18, 18-20, 20-25, 25-30, 30-35, 35-40, 40-50 and 50-60 cm). The levels of mineral N, available P and K and total N, P and K were evaluated. The 19 pig slurry applications in 93 months promoted migration of total N and P down to 30 cm and available P and K to the deepest layer analyzed. At the end of the experiment, no increase was observed in mineral N content in the deeper layers, but increased levels of available P and K, showing a transfer of N, P and K to layers below the sampled. This evidences undesirable environmental and economic consequences of the use of pig slurry and reinforces the need for a more rational use, i.e., applications of lower manure doses, combined with mineral fertilizers.
Evasion and Subversion of Interferon-Mediated Antiviral Immunity by Kaposi's Sarcoma-Associated Herpesvirus: an Overview

ABSTRACT Viral invasion of a host cell triggers immune responses with both innate and adaptive components. The innate immune response involving the induction of type I interferons (alpha and beta interferons [IFN-α and -β]) constitutes the first line of antiviral defenses. The type I IFNs signal the transcription of a group of antiviral effector proteins, the IFN-stimulated genes (ISGs), which target distinct viral components and distinct stages of the viral life cycle, aiming to eliminate invading viruses. In the case of Kaposi's sarcoma-associated herpesvirus (KSHV), the etiological agent of Kaposi's sarcoma (KS), a sudden upsurge of type I IFN-mediated innate antiviral signals is seen immediately following both primary de novo infection and viral lytic reactivation from latency. Potent subversion of these responses thus becomes mandatory for the successful establishment of a primary infection following viral entry as well as for efficient viral assembly and egress. This review gives a concise overview of the induction of the type I IFN signaling pathways in response to viral infection and provides a comprehensive understanding of the antagonizing effects exerted by KSHV on type I IFN pathways wielded at various stages of the viral life cycle. Information garnered from this review should result in a better understanding of KSHV biology essential for the development of immunotherapeutic strategies targeted toward KSHV-associated malignancies.