Miracle-dz/UniFAR-FTUs huggingface dataset:
Seed limitation in a Panamanian forest

1 The role of seed limitation in tropical forests remains uncertain owing to the scarcity of experimental evidence. We performed seed addition experiments to assess seed limitation for 32 shade‐tolerant tropical forest species and monitored the natural seed rain of 25 of these species for 17 years. 2 One, two or five seeds were sown into 0.0079‐m2 plots for large‐ (n = 5 species), medium‐ (n = 5) and small‐seeded species (n = 22), respectively. The experiment was replicated at 69 sites, placed in groups of three at 23 locations. Seedling establishment was evaluated after 1 and 2 years in paired seed addition and control plots. Natural seedling emergence and understorey plant density were also measured. 3 Median natural seed rain was 0.31 seeds m−2 year−1 per focal species. 4 Seed addition enhanced seedling establishment in 31 and 26 of the 32 species after 1 and 2 years, respectively. Mean number of focal species’ seedlings after 2 years was 0.002 seedlings in control plots and 0.12, 0.37 and 0.60 seedlings in seed addition plots for large‐, medium‐ and small‐seeded species, respectively. 5 A 25 seeds added treatment increased seedling establishment by ≥ 2.0‐fold over the five seeds added treatment after 2 years. 6 Community‐wide recruitment and understorey plant density were strongly seed‐limited. The natural density of understorey plants averaged 12 plants m−2 and was significantly less than for seedlings of the single focal species in plots with ≥ 2 seeds added 2 years earlier. 7 The number of established seedlings per seed added was independent of seed size. 8 Treatment (adding zero or five seeds), species identity and location all affected seedling establishment for the 11 small‐seeded species represented at all sites, with treatment and its interactions accounting for 86% of the explained variation. 9 Our results suggest that seed limitation plays a dominant role in seedling recruitment and understorey plant community assembly in tropical forests. Although strong seed limitation may set the stage for species‐neutral community assembly, the species differences in seedling establishment rate and its spatial variation demonstrate an important role for species‐specific processes.
Atmospheric net transport of water vapor and latent heat across 70°S

The annual net atmospheric transports of water vapor and latent heat poleward across 70oS are estimated using the latest compilation of surface mass balance for the Antarctic ice sheet and new estimates of precipitation and evaporation in sectors of the southern oceans and of seaward drifting snow transport in particular sectors of the ice sheet. The mass and energy exchange rates at the ice sheet-atmosphere and ocean-atmosphere interfaces are integrated strictly for areas within that latitude. The estimates of net southward water vapor transport (6.6 + 1.3 kg m -1 s -1) and latent heat transport (18.9 + 3.6 MJ m -1 s -1) are larger than reported in all preceding studies, based on atmospheric advection and moisture data collected at stations located between 66oS and 80oS, and are generally in agreement with those based on surface mass balance data and seaward drifting snow transport across the ice terminus which extends between 65oS and 79oS.
The ArgoNeuT Detector in the NuMI Low-Energy beam line at Fermilab

The ArgoNeuT liquid argon time projection chamber has collected thousands of neutrino and anti-neutrino events during an extended run period in the NuMI beam-line at Fermilab. This paper focuses on the main aspects of the detector layout and related technical features, including the cryogenic equipment, time projection chamber, read-out electronics, and off-line data treatment. The detector commissioning phase, physics run, and first neutrino event displays are also reported. The characterization of the main working parameters of the detector during data-taking, the ionization electron drift velocity and lifetime in liquid argon, as obtained from through-going muon data complete the present report.
Antibacterial peptide defensin is involved in midgut immunity of the soft tick, Ornithodoros moubata

Two defensin genes A and B were previously demonstrated to be up‐regulated by blood feeding in the soft tick, Ornithodoros moubata[ Nakajima et al. (2001) Two isoforms of a member of the arthropod defensin family from the soft tick, Ornithodoros moubata (Acari: Argasidae). Insect Biochem Mol Biol 31: 747–751]. In this study, two defensin isoforms C and D similar to defensins A and B were newly cloned. A total of four defensins have been identified in O. moubata. All four Ornithodoros defensins are coded as prepro‐defensins. Ornithodoros defensin genes consist of four exons and three introns, an organization reported in mussel defensins but not insect defensins. Ornithodoros defensin C and D genes are predominantly expressed in the midgut and up‐regulated in response to blood feeding. The mature peptide of the previously cloned Ornithodoros defensin A was purified from the midgut lumen, indicating defensin is secreted into the midgut. These findings confirm the involvement of Ornithodoros defensin in midgut immunity.
Cellular Immunity as a Potential Cause of Local Reactions to Booster Vaccination With Diphtheria and Tetanus Toxoids and Acellular Pertussis Antigens

Background: Booster doses of diphtheria-tetanus-acellular pertussis (DTaP) vaccines restore waning serum antibody values but frequently cause local inflammation. Cell-mediated immunity (CMI) develops after primary DTaP vaccination and might contribute to local reactions to booster doses, a possibility explored in this study. Methods: Healthy 4 to 5-year-old children were bled before DTaP.IPV booster vaccination. Peripheral blood mononuclear cells were tested for proliferative responses to D toxoid (DT), T toxoid, pertussis toxoid, pertactin, filamentous hemagglutinin and fimbriae (FIM) types 2, 3, and cytokine release patterns assessed. Proliferative responses were examined in relation to prebooster serum antibody concentrations and local reaction rates, previously reported. Results: Among 167 subjects tested, proliferative response rates were: filamentous hemagglutinin 95%, pertussis toxoid 90%, T toxoid 84%, pertactin 67%, DT 41%, and FIM 31%. Responses were present to 3 to 6 antigens in 87% of subjects and absent altogether in 2%. Subjects without residual pertussis antibodies often had CMI to pertussis antigens. Subjects with CMI had higher corresponding serum antibody concentrations before the booster, compared with CMI-negative subjects. CMI responses were mixed TH1/TH2 type by cytokine profile for all antigens. Injection site erythema (≥5 mm) was twice as frequent in those with than without CMI to DT (P = 0.009) or FIM (P = 0.042, Fisher exact test), the only antigens evaluable. Conclusion: CMI to vaccine antigens was often detectable in children before preschool booster vaccination and preliminary evidence suggests a role for CMI in local reactions to this dose.
Cryptic variation in butterfly eyespot development: the importance of sample size in gene expression studies

SUMMARY Previous studies have shown that development can be robust to variation in parameters such as the timing or level of gene expression. This leads to the prediction that natural populations should be able to host developmental variation that has little phenotypic effect. Cryptic variation is of particular interest because it can result in selectable phenotypes when “released” by environmental or genetic factors. Currently, however, we have little idea of how variation is distributed between genes or over time in pattern formation processes. Here we survey expression of Notch (N), Spalt (Sal), and Engrailed (En) during butterfly eyespot determination to better understand how pattern formation may vary within a population. We observed substantial heterochronic variance in the progress of spatial expression patterns for all three proteins, suggesting some degree of developmental buffering in eyespot development. Peak variance for different proteins was found at both early and late stages of development, contrasting with previous models suggesting that the distribution of variance should be more temporally focused during pattern formation. We speculate that our observations are representative of a standing reservoir of cryptic variation that may contribute to phenotypic evolution under certain circumstances. Our results also provide a strong cautionary message that gene expression studies with limited sample sizes can be positively misleading in terms of inferring expression pattern time series, as well as for making cross‐species phylogenetic comparisons.
Prevalence of antibody to Legionella pneumophila in middle-aged and elderly Americans.

An indirect fluorescent antibody (IFA) test was used to establish the background prevalence of antibody to Legionella pneumophila in single serum specimens from 1,143 persons. The serum specimens had been obtained from volunteers 46 years of age and older who were not acutely ill and who resided in the areas of Atlanta, Georgia; Washington, D.C.; Houston, Texas; and Rochester, New York. The overall prevalence of seropositivity (reciprocal titer, greater than or equal to 64) was 1.7%. The prevalence of seropositivity did not vary with age, sex, or geographic location. Groups of persons in which the prevalence of reciprocal titers of greater than or equal to 64 is significantly higher than 1.7% may have unusually great exposure to L. pneumophila. In the population tested, a reciprocal IFA titer of greater than or equal to 64 would have a specificity of 98.3% in the diagnosis of an acute illness as Legonnnaires' disease.
Mesenchymal Stem Cells Upregulate the Expression of PD-L1 But Not VDR in Dendritic Cells

ABSTRACT Objective: Mesenchymal stem cells (MSCs) show immunomodulatory functions. But the exact mechanism underlying these activities of MSCs is still not completely understood. There have been a few studies which have assessed the effects of these cells on dendritic cells (DCs) function. Given the importance of programmed cell death receptor-1 (PD-L1) and vitamin D receptor (VDR) expression in induction of tolerance in DCs, we were encouraged to investigate if one of the immunomodulatory functions of MSCs could be inducing upregulation of PD-L1 and VDR on DCs or not. Methods: DCs were co-cultured with MSCs or treated with them in transwell plates in the presence or absence of Lipopolysaccharide (LPS). Expression of PD-L1 and VDR mRNA and proteins in treated DCs were assessed by Real-time PCR and Western blot techniques. Furthermore, treated DCs were co-cultured with allogeneic T-cells, and T-cell proliferation and cytokine secretions in co-culture supernatants were assessed. Results: The results showed that PD-L1 but not VDR expression is significantly upregulated in the DCs co-cultured with MSCs. Furthermore, cell-to-cell contact and also presence of maturation inducers like LPS is necessary for this function. Moreover, our results indicated that MSCs could induce tolerogenic DCs (TolDCs) which could decrease the secretion of IL-2 by T-cells and inhibit T-cell proliferation as well as increase secretion of IL-10. Conclusions: Overall, our results show that MSCs may have several suppressive effects on immune responses by induction of TolDCs expressing more PD-L1 immunomodulatory molecule and change the cytokines profile of DCs and T-cells.
Prognostic power of abnormal cytogenetics for multiple myeloma: a multicenter study in China.

BACKGROUND Chromosomal abnormalities have been shown to play an important prognostic role in multiple myeloma (MM). Interphase fluorescence in situ hybridization (i-FISH) has been much more effective to identify cytogenetic aberrations in MM than conventional cytogenetic technique (CC). To clearly determine the cytogenetic features of Chinese MM patients and identify their prognostic implications, we designed a multicenter study based on i-FISH including 672 patients from 52 hospitals in China. METHODS All 672 patients were systematically screened for the following genomic aberrations: del(13q), IgH rearrangement, del(p53) and 1q21 amplifications. RESULTS The analysis showed that the chromosomal changes were detected in 22.1% patients by CC and in 82.3% patients by i-FISH. The most common abnormalities by CC were chromosome 1 aberrations (48.4%), -13/13q- (37.6%), hyperdiploidy (36.6%), hypodiploidy (30.1%) and IgH rearrangements (23.7%). The most frequent abnormalities by FISH was del(13q), which was found in 60.4% patients, whereas IgH rearrangement, 1q21 amplification and p53 deletions were detected in 57.6%, 49.0% and 34.7% cases, respectively. By statistical analysis, -13/13q- by CC was associated with low level of platelet (P = 0.015), hyperdiploidy was associated with low level of serum albumin (P = 0.028), and IgH rearrangement by FISH was associated with high level of β2 microglobulin (P = 0.019). Moreover, 1q21 amplification and del(p53) by FISH conferred a high incidence of progressive disease (PD) after initial therapy. Metaphase detection of IgH rearrangements and chromosome 1 aberrations concurrently was associated with a short progression free survival (PFS) (P = 0.036). No significant prognostic implications of other cytogenetic abnormalities were found associated with overall survival and PFS. CONCLUSIONS Chinese MM patients had similar cytogenetic abnormalities compared with the previous reported studies. However, the prognostic significance of FISH aberrations were not clearly determined and further study is required.
Identification and Tracing of Bifidobacterium Species by Use of Enterobacterial Repetitive Intergenic Consensus Sequences

ABSTRACT Eighty-nine Bifidobacterium strains from 26 species were identified and classified to the species level with an enterobacterial repetitive intergenic consensus (ERIC)-PCR approach. We demonstrated that ERIC-PCR is useful for a phylogenetic and taxonomical analysis but as well as for a species composition analysis of mixed bifidobacterial cultures isolated from dairy products and other environments.
Survey on scheduling in hybrid clouds

Cloud computing provides infinite access to on demand resources, this is true in case of public clouds but not in case of private clouds. As public cloud charges on usage basis, private clouds are owned by user. Composition of private and public cloud is known as hybrid cloud. In hybrid cloud task scheduling is a complex process as jobs can be allocated either in private cloud or public cloud. Deciding which resource should be taken on lease from public cloud into private cloud to complete the task is decided by number of scheduling algorithms. In this paper, we look at the various scheduling techniques and algorithms that are used in hybrid cloud and these are classified according to their optimization criteria and features provided by them. This paper is composed of five parts as introduction, scheduling process in hybrid clouds, types of scheduling techniques with their classification, execution cost parameter and conclusion is given in the end.
Glial fibrillar acidic protein in the cerebrospinal fluid of Alzheimer's disease, dementia with Lewy bodies, and frontotemporal lobar degeneration

Biomarkers in the cerebrospinal fluid (CSF) are currently regarded as indispensable indicators for accurate differential diagnosis of neurodegenerative disorders. Although high levels of astrocyte‐secreted glial fibrillar acidic protein (GFAP) in the CSF of patients with Alzheimer's disease (AD) have been reported, the levels of GFAP in the CSF have not been fully investigated in other neurological disorders that cause dementia, such as dementia with Lewy bodies (DLB) and frontotemporal lobar degeneration (FTLD). In this study, we determined the levels of GFAP in the CSF of healthy control subjects and AD, DLB, and FTLD patients to address two questions: (i) Do the levels of GFAP differ among these disorders? and (ii) Can GFAP be used as a biomarker for the differential diagnosis of these neurodegenerative disorders? The levels of GFAP in AD, DLB, and FTLD patients were significantly higher than those in the healthy control subjects. Although the levels of GFAP were not significantly different between AD and DLB patients, a higher level of GFAP was observed in FTLD patients than in AD and DLB patients. It is concluded that representative neurological disorders causing dementia were associated with higher levels of GFAP in the CSF.
Cloud and Shadow Detection in Satellite Imagery

In recent years there has been an enormous growth in the amount of publicly available satellite imagery and overall satellites launched, which has imposed a challenging data problem of how to label or classify objects on satellite imagery. This thesis reviews Fmask algorithm[1], a state of the art solution, of cloud and shadow detection, and explores a problem of synthesizing satellite data and a problem of semantic labelling of satellite imagery by designing, implementing and evaluating neural network. The resulting pipeline synthesizes image into clouds and background. The modelled clouds can be then combined with any other image creating a new or enhanced data. The main contribution of this thesis is the utilization of the dataset synthesis in learning of neural networks. We have achieved 94.3% accuracy on a real world dataset. Neural networks were created with a help of Caffe framework [2].
Neural Response Telemetry in 12- to 24-Month-Old Children

The minimum age for cochlear implantation has been reduced to 12 months in an effort to provide auditory stimulation to children with hearing loss during early development. Because behavioral measures in such young children are limited, objective measures such as the electrically evoked compound action potential (EAP) from the auditory nerve are needed to facilitate measurement of stimulation level requirements. We assessed EAPs recorded by the Nucleus 24 neural response telemetry (NRT) system in children who underwent implantation between 12 and 24 months of age. We recorded EAPs in 37 such children (mean age at implantation, 18.1 ± 3.6 months). The EAPs were of large amplitude, and thresholds fell between behavioral T and C levels. A correction factor applied to EAP thresholds provided useful predictions of T levels. The EAPs can be used to ensure that even very young children receive auditory stimulation with their cochlear implants upon device activation.
Donor‐derived organ transplant transmission of coccidioidomycosis

Coccidioidomycosis in solid organ transplant recipients most often occurs as a result of primary infection or reactivation of latent infection. Herein, we report a series of cases of transplant‐related transmission of coccidioidomycosis from a single donor from a non‐endemic region whose organs were transplanted to 5 different recipients. In all, 3 of the 5 recipients developed evidence of Coccidioides infection, 2 of whom had disseminated disease. The degree of T‐cell immunosuppression and timing of antifungal therapy initiation likely contributed to development of disease and disease severity in these recipients. This case series highlights the importance of having a high index of suspicion for Coccidioides infection in solid organ transplant recipients, even if the donor does not have known exposure, given the difficulties of obtaining a detailed and accurate travel history from next‐of‐kin.
Polarity of Response to Transforming Growth Factor-β1 in Proximal Tubular Epithelial Cells Is Regulated by β-Catenin*

Transforming growth factor-β1 (TGF-β1)-mediated loss of proximal tubular epithelial cell-cell interaction is regulated in a polarized fashion. The aim of this study was to further explore the polarity of the TGF-β1 response and to determine the significance of R-Smad-β-catenin association previously demonstrated to accompany adherens junction disassembly. Smad3 signaling response to TGF-β1 was assessed by activity of the Smad3-responsive reporter gene construct (SBE)4-Lux and by immunoblotting for phospho-Smad proteins. Similar results were obtained with both methods. Apical application of TGF-β1 led to increased Smad3 signaling compared with basolateral stimulation. Association of Smad proteins with β-catenin was greater following basolateral TGFβ-1 stimulation, as was the expression of cytoplasmic Triton-soluble β-catenin. Inhibition of β-catenin expression by small interfering RNA augmented Smad3 signaling. Lithium chloride, a GSK-3 inhibitor, increased expression of β-catenin and attenuated TGF-β1-dependent Smad3 signaling. Lithium chloride did not influence degradation of Smad3 but resulted in decreased nuclear translocation. Smad2 activation as assessed by Western blot analysis and activity of the Smad2-responsive reporter constructs ARE/MF1 was also greater following apical as compared with basolateral TGFβ-1 stimulation, suggesting that this is a generally applicable mechanism for the regulation of TGF-β1-dependent R-Smads. Caco-2 cells are a colonic carcinoma cell line, with known resistance to the anti-proliferative effects of TGF-β1 and increased expression of β-catenin. We used this cell line to address the general applicability of our observations. Inhibition of β-catenin in this cell line by small interfering RNA resulted in increased TGF-β1-dependent Smad3 phosphorylation and restoration of TGF-β1 anti-proliferative effects.
A general approach for synchronisation of nonlinear networked systems with switching topology

This article investigates synchronisation of a nonlinear networked system with switching topology. By defining a common synchronisation manifold for each possible switching topology, exponential synchronisation of a nonlinear networked system can be assessed by the exponential stability of a reduced nonlinear system corresponding to the concerned system, wherein the communication graph can be directed and weighted and the inner-linking matrix might be singular. In particular, a synchronisation criterion consisting of the self-dynamics of isolated nodes and the consensus dynamics of a linear switched system is given. Two numerical simulations of synchronisation are presented to illustrate the effectiveness of the analytical results for the periodic and random switching cases.