Miracle-dz/UniFAR-FTUs huggingface dataset:
CD154 Blockade Is TLR4 Independent Function in Transplant Recipients after T Regulatory Cell Induction and + CD4

Although the role of CD4 (cid:1) T regulatory cells (Treg) in transplantation tolerance has been established, putative mechanisms of Treg induction and function in vivo remain unclear. TLR4 signaling has been implicated in the regulation of CD4 (cid:1) CD25 (cid:1) Treg functions recently. In this study, we ﬁrst examined the role of recipient TLR4 in the acquisition of operational CD4 (cid:1) Treg following CD154 blockade in a murine cardiac transplant model. Then, we determined whether TLR4 activation in allograft tolerant recipients would reverse alloimmune suppression mediated by CD4 (cid:1) Treg. We document that donor-speciﬁc immune tolerance was readily induced in TLR4-deﬁcient recipients by a single dose of anti-CD154 mAb, similar to wild-type counterparts. The function and phenotype of CD4 (cid:1) Treg in both wild-type and TLR4 knockout long-term hosts was demonstrated by a series of depletion experiments examining their ability to suppress the rejection of secondary donor-type test skin grafts and to inhibit alloreactive CD8 (cid:1) T cell activation in vivo. Furthermore, TLR4 activation in tolerant recipients following exogenous LPS infusion in conjunction with donor-type skin graft challenge, failed to break Treg-mediated immune suppression. In conclusion, our data reveals a distinctive property of CD4 (cid:1) Treg in tolerant allograft recipients, whose induction and function are independent of TLR4 signaling. The Journal of Immunology, 2006, 176: 5988–5994.
Edinburgh Research Explorer Dark Energy Survey Year 1 Results

We perform a joint analysis of the auto and cross-correlations between three cosmic fields: the galaxy density field, the galaxy weak lensing shear field, and the cosmic microwave background (CMB) weak lensing convergence field. These three fields are measured using roughly 1300 sq. deg. of overlapping optical imaging data from first year observations of the Dark Energy Survey (DES) and millimeter-wave observations of the CMB from both the South Pole Telescope Sunyaev-Zel ’ dovich survey and Planck . We present cosmological constraints from the joint analysis of the two-point correlation functions between galaxy density and galaxy shear with CMB lensing. We test for consistency between these measurements and the DES-only two-point function measurements, finding no evidence for inconsistency in the context of flat Λ CDM cosmological models. Performing a joint analysis of five of the possible correlation functions between these fields (excluding only the CMB lensing autospectrum) yields S 8 ≡ σ 8
Gene Expression in T Cells Fas Ligand Participates in Regulation of The IFN Regulatory Factor Family

TCR engagement leads to the transcriptional activation of cytokine genes and activation-induced cell death. Activated T cells undergo apoptosis upon expression and ligation of Fas ligand (FasL) to Fas/APO-1 (CD95) receptor. FasL expression is under the transcriptional regulation of multiple factors. The present study demonstrates that TCR-inducible FasL expression is also under the direct inﬂuence of the IFN regulatory factor (IRF) transcription factor family. Deletion and mutagenesis of a putative IRF-1 binding site in the FasL promoter results in deﬁcient expression of FasL. EMSAs demonstrate speciﬁc FasL promoter binding by IRF-1 and IRF-2. Forced expression of either IRF-1 or IRF-2 leads to FasL promoter activation in T cells and FasL expression in heterologous cells. Finally, suppression of IRF-1 expression in T cells results in deﬁcient TCR-induced FasL expression. These results conﬁrm that the IRF family participates in the regulation of FasL gene expression. The Journal of Immunology, 2000, 164: 3512–3518. CMV promoter (pCMV-Bam) not FasL FasL in pCMV-IRF-1-transfected cells. FasL was in pCMV-IRF-2-transfected cells. Detection of similar intensities of b conﬁrmed equal amounts of RNA were used for the RT-PCR reaction. These results support the promoter analysis studies and demonstrate directly the involvement of IRF-1 and in the regulation of FasL expression.
patients with relapsed/

the development of novel agents for lymphoma, although few studies have combined these as a therapeutic strategy. We report unacceptable toxicity from such a biological triplet. Patients were treated in a multiarm phase 1 study using different combinations of chemotherapy, immunomodulators, and anti-CD20 monoclonal antibodies in combinationwithidelalisib(www.clinicaltrials.gov;#NCT01088048). Wereportonthecohortofpatientstreatedwithidelalisib,lenalidomide,andrituximab.Theinclusioncriteriawererelapsed indolent lymphoma, age . 18 years, measurable disease, and per-formance status # 2. Patients were excluded if they had anticancer therapy within 4 weeks, prior allogeneic stem cell transplant, or active central nervous system involvement, were pregnant or breast-feeding, or had active serious infection, serum creatinine $ 2.0 mg/dL, neutrophils , 1.0 3 10 9 /Lorplatelets , 75 3 10 9 /L,bilirubin . 2mg/dL, aspartate aminotransferase or alanine aminotransferase (ALT) $ 2 times the upper limit of normal, Child-Pugh class B or C hepatic impairment, infection with HIV or hepatitis B or C virus, or prior treatment with idelalisib.
Edinburgh Research Explorer Charles Bonnet Syndrome

Several theories propose that the cortex implements an internal model to explain, predict, and learn about sensory data, but the nature of this model is unclear. One condition that could be highly informative here is Charles Bonnet syndrome (CBS), where loss of vision leads to complex, vivid visual hallucinations of objects, people, and whole scenes. CBS could be taken as indication that there is a generative model in the brain, specifically one that can synthesise rich, consistent visual representations even in the absence of actual visual input. The processes that lead to CBS are poorly understood. Here, we argue that a model recently introduced in machine learning, the deep Boltzmann machine (DBM), could capture the relevant aspects of (hypothetical) generative processing in the cortex. The DBM carries both the semantics of a probabilistic generative model and of a neural network. The latter allows us to model a concrete neural mechanism that could underlie CBS, namely, homeostatic regulation of neuronal activity. We show that homeostatic plasticity could serve to make the learnt internal model robust against e.g. degradation of sensory input, but overcompensate in the case of CBS, leading to hallucinations. We demonstrate how a wide range of features of CBS can be explained in the model and suggest a potential role for the neuromodulator acetylcholine. This work constitutes the first concrete computational model of CBS and the first application of the DBM as a model in computational neuroscience. Our results lend further credence to the hypothesis of a generative model in the brain.
Infectionand CD8 T Cells in Murine Cytomegalovirus Comparing the Kinetics of NK Cells, CD4,

NK cells recognize virus-infected cells with germline-encoded activating and inhibitory receptors that do not undergo genetic recombination or mutation. Accordingly, NK cells are often considered part of the innate immune response. The innate response comprises rapid early defenders that do not form immune memory. However, there is increasing evidence that experienced NK cells provide increased protection to secondary infection, a hallmark of the adaptive response. In this study, we compare the dynamics of the innate and adaptive immune responsesby examining the kinetic proﬁles of the NK and T cellresponse to murine CMVinfection. We ﬁndthat, unexpectedly, the kineticsofNK cell proliferation is neitherearliernor faster than the CD4 or CD8 T cellresponse. Furthermore, early NK cell contraction after the peak of the response is slower than that of T cells. Finally, unlike T cells, experienced NK cells do not experience biphasic decay after the response peak, a trait associated with memory formation. Rather, NK cell contraction is continuous, constant, and returns to below endogenous preinfection levels. This indicates that the reason why Ag-experienced NK cells remain detectable for a prolonged period after adoptive transfer and infection is in part due to the high precursor frequency, slow decay rate, and low background levels of Ly49H + NK cells in recipient DAP12-deﬁcient mice. Thus, the quantitative contribution of Ag-experienced NK cells in an endogenous secondary response, with higher background levels of Ly49H + NK cells, may be not be as robust as the secondary response observed in T cells. The Journal of Immunology , 2011, 187: 1385–1392.
Sexual behaviour and contraceptive use among youth in the Balkans

Objectives To assess sexual and health seeking behaviour related to contraception among high school students in Bosnia (Sarajevo), the FYR of Macedonia (Skopje), and Serbia and Montenegro (Belgrade and Podgorica). Methods A standardized questionnaire was self-administered by 2150 urban high school students. Multiple logistic regression analyses accounting for within-class correlation were applied to identify determinants of sexual behaviour, and the use of contraception and sexual and reproductive health (SRH) care. Results In this group of youth with a mean age of 16.7 years, 41.3% of the boys and 20.8% of the girls had already experienced sexual intercourse. Mean age at sexual debut differed between sexually active boys (15.5) and girls (16.3). A condom was used at first sex by 73.7% of the boys and by 69.0% of the girls. Condoms were consistently used during sexual intercourse with the current or last partner by 64.3% of the boys and 48.5% of the girls. Oral contraception was resorted to by 0.0% (Macedonia) to 10.6% (Bosnia) of sexually active girls. One third of sexually active girls and 18.0% of sexually active boys had ever refrained from seeking medical advice on SRH despite feeling the need for it, mainly because of feelings of shame, fear and insecurity. TV or radio and friends were mostly mentioned as useful sources of information on contraceptives. Conclusions Age at sexual debut and the proportion of sexually active youth in these Balkan states do not differ from those in other parts of Europe. However, declining condom use after sexual initiation is not compensated by having recourse to other contraceptive methods, as seen in some West-European countries. The role of mass media in dissemination of information and tackling barriers to SRH care should be explored.
InsectsProtein Mediates Nodulation Response in Noduler, A Novel Immune Up-Regulated

Insect immune system comprises of both humoral and cellular defenses. Nodulation is one of the major, yet very poorly understood cellular responses against microbial infections in insects. Through screening for novel immune genes from an Indian saturniid silkmoth Antheraea mylitta , we identiﬁed a protein up-regulated in hemolymph within minutes upon bacterial challenge. We have shown here, for ﬁrst time, the involvement of this novel protein in mediating nodulation response against bacteria and hence designated it as Noduler. Noduler possessed a characteristic reeler domain found in several extracellular matrix vertebrate proteins. Noduler was shown in vitro to bind a wide range of bacteria, yeast, and also insect hemocytes. Fur-thermore, Noduler speciﬁcally bound LPS, lipotechoic acid, and (cid:1) -1, 3 glucan components of microbial cell walls. RNA-interference mediated knock-down of the Noduler resulted in signiﬁcant reduction in the number of nodules and consequent increase in bacterial load in larval hemolymph. The results suggest that the Noduler is widely conserved and is involved in very early clearance of bacteria by forming nodules of hemocytes and bacterial complexes in insects. The results would promote further studies for understanding of the crucial but hitherto overlooked nodulation mechanism in insects and also provide cues for the study of similar mammalian proteins whose function is not understood. The Journal of Immunology, 2007, 179: 6943–6951.
Regolith flow on top-shaped asteroids

We develop a continuum framework of regolith flow on asteroids. We focus on top-shaped asteroids that may be taken as consisting of regolith lying on a solid core. Depth-averaging is employed to model the regolith flow, and effects due to the asteroid’s rotation and its complex gravity field are retained. Angular momentum conservation is invoked to couple regolith flow to the asteroid’s changing shape and spin. This framework is first used to explore the equilibrium of regolith as a function of its friction, and the asteroid’s shape and spin rate. Next, we study regolith flow on top-shaped spinning asteroids and find conditions for the regolith’s shedding or deposition. We also discuss how the regolith’s flow and the asteroid’s spin influence each other. Finally, as an application, we propose and investigate the following evolution history of Bennu: a fast spinning Bennu was slowed down by multiple, impact-induced global landslides to its present spin state. Regolith was shed if the spin was higher than a critical rate. Once the spin rate fell below this critical value, regolith flow from higher latitudes began depositing regolith at its equator, giving Bennu its distinctive shape.
The thermal niche and phylogenetic assembly of evergreen tree metacommunities in a mid-to-upper tropical montane zone

Frost and freezing temperatures have posed an obstacle to tropical woody evergreen plants over evolutionary time scales. Thus, along tropical elevation gradients, frost may influence woody plant community structure by filtering out lowland tropical clades and allowing extra-tropical lineages to establish at higher elevations. Here we assess the extent to which frost and freezing temperatures influence the taxonomic and phylogenetic structure of naturally patchy evergreen forests (locally known as shola) along a mid-upper montane elevation gradient in the Western Ghats, India. Specifically, we examine the role of large-scale macroclimate and factors affecting local microclimates, including shola patch size and distance from shola edge, in driving shola metacommunity structure. We find that the shola metacommunity shows phylogenetic overdispersion with elevation, with greater representation of extra-tropical lineages above 2000 m, and marked turnover in taxonomic composition of shola woody communities near the frost-affected forest edge above 2000 m, from those below 2000 m. Both minimum winter temperature and patch size were equally important in determining metacommunity structure, with plots inside very large sholas dominated by older tropical lineages, with many endemics. Phylogenetic overdispersion in the upper montane shola metacommunity thus resulted from tropical lineages persisting in the interiors of large closed frost-free sholas, where their regeneration niche has been preserved over time.
Induced aseismic slip and the onset of seismicity in displaced faults

Abstract We address aseismic fault slip and the onset of seismicity resulting from depletion-induced or injection-induced stresses in reservoirs with pre-existing vertical or inclined faults. Building on classic results, we discuss semi-analytical modelling techniques for fault slip including dislocation theory, Cauchy-type singular integral equations and the use of Chebyshev polynomials for their solution and an eigenvalue-based stability analysis. We consider slip patch development during depletion for faults with zero, constant static and slip-weakening friction, and our results confirm earlier findings based on numerical simulation, in particular the aseismic growth of two slip patches that may subsequently merge and/or become unstable resulting in nucleation of seismic slip. New findings include improved approximate expressions for the induced seismic moment per unit strike length and a description of the effect of coupling between the slip patches which affects both forward simulation and eigenvalue computation for high values of the ratio of fault throw to reservoir height. Our implementation based on analytical inversion and semi-analytical integration with Chebyshev polynomials is more efficient and more robust than our numerical integration approach. It is not yet well suited for Monte Carlo simulation, which typically requires sub-second simulation times, but with some further development that option seems to be within reach. Moreover, our results offer a possibility for embedded fault modelling in large-scale numerical simulation tools.
Caloric restriction stress causes epigenetic effects evidenced by longevity in Caenorhabditis elegans

Abstract. Caenorhabditis elegans are members of the nematode family and have been used as model organisms of epigenetic studies for many years. C. elegans have a relatively short life cycle; the worms grow from an egg to an adult within the span of about 3-4 days and an overall lifespan of about 2-3 weeks. The worms are very easy to maintain, requiring for survival only nematode growth medium (NGM) agar plates that are kept at a temperature of about 20-25 °C and contain E. coli for food. For this study, which replicates aspects of a study reported by Kishimoto et al. (2017), C. elegans was used to explore the epigenetic effects of stress on longevity. The animals in this study that were subjected to the environmental stressor starvation showed an increase in overall lifespan based on the statistical analysis of a Kaplan-Meier Survivorship test. This increased survival rate was also found to be passed to at least three subsequent generations who were grown under unstressed conditions. These results showcase the hormetic epigenetic effects of starvation in C. elegans.
Chara contraria var. hispidula Braun (Charales) in Newfoundland, Canada a new variety described from North America

ABSTRACT A Chara exhibiting extreme morphological features including stipulodes, spine cells, and bracteoles is described and subjected to barcoding procedures to determine whether it belongs to the Chara contraria group or the C. hispida group. MatK barcoding clearly placed it in the C. contraria clade which was consistent with gametangial morphology, but not stipulode, spine cell and bracteole morphology. The specimen was determined to be included in the Chara contraria var. hispidula taxon, not previously reported or described for Newfoundland, Canada, or the USA.
Effects of Elevation Gradient on Soil Carbon and Nitrogen in a Typical Karst Region of Chongqing, Southwest China

Elevation changes create gradients in abiotic factors, which in turn affect soil erosion and carbon cycling. However, how elevation changes control soil ecological processes through temperature and the mechanism that affects the carbon cycle remain unclear. Therefore, we have studied the distribution of temperature, bulk density (BD), soil pH, mean weight diameter (MWD), clay, and diversity of soil fungal community diversity, and discussed the critical factors affecting soil organic carbon (SOC) and nitrogen (N) in a typical karst mountainous area. The results showed that the dominant phyla were Ascomycota (42.28%), Mortierellomycota (20.6%), Basidiomycota (17.83%), and Rozellomycota (11.82%). The elevation distributions of MWD, fungal diversity, the rate of SOC and N stocks change per temperature index, and SOC and N stocks all exhibited unimodal patterns. Additionally, temperature, fungal diversity, MWD, BD, and clay were the dominant factors explaining the variability of SOC and N, and SOC and N had a positive relationship with pH, BD, MWD, clay‐silt content, warmth index, and Sobs and Shannon diversity. Analyses showed that the warmth index regulated soil aggregates through fungal diversity and combined with BD to affect carbon sequestration, which was controlled by clay, the C:N ratio, and pH during the process. These conclusions have important implications for improving the SOC sequestration capacity in karst mountainous areas.
Integrating a deep forest algorithm with vector‐based cellular automata for urban land change simulation

With the capacity to represent irregular geographical entities precisely, vector‐based cellular automata (VCA) have been extensively employed in urban land change simulation at the land parcel level. However, while more driving factors are considered, modeling the complicated nonlinear relationship between land parcel attributes and multiple land‐use changes is increasingly difficult. Moreover, in VCA, the driving factors are unstructured and cannot be directly modeled by traditional deep learning methods, which can only be applied to structured data processing. In order to address these problems, a new VCA model DF‐VCA that adopts the deep forest (DF) algorithm for mining CA transition rules was proposed to simulate urban land‐use change at the parcel level. The DF algorithm is a new deep learning method that can directly mine high‐level features from unstructured data and obtain accurate land‐use transition rules. The proposed DF‐VCA model was applied to simulate the urban land change in Shenzhen, China. Compared with several traditional VCA models, the DF‐VCA model achieved the best simulation performance at parcel‐level (Figure of Merit = 39.88%), pattern‐level (similarity = 96.47%), and community‐level (correlation coefficient = 0.9269). The results show that the DF‐VCA model with strong representative learning ability could simulate urban land change at fine scales precisely. Furthermore, the proposed DF‐VCA model was applied in Shenzhen's future land change simulations to guide sustainable urban development.
Do image resolution and classifier choice impact island biogeographical parameters of terrestrial islands?

Island biogeography provides concepts for conservation management as fragmented habitats are comparable to ocean islands. Remote sensing can help to extract terrestrial habitat islands on the landscape scale. However, little is known about the effects of image resolution and classification algorithms on resulting island size and related parameters. We study the combined effect of three image resolutions (2, 10, and 30 m) and three classification algorithms (Artificial Neural Network, Random Forest, Support Vector Machine) by extracting quartz islands from WorldView‐2 imagery using image segmentation. We compared four island parameters (i.e., area, distance, shape index, and perimeter–area ratio between resolutions and classifiers). We found that in all cases, image resolution and classification algorithms had a strong effect. However, image resolution was more important for area and shape. Artificial Neural Network always provided the best performance as a classifier (OA: 0.880, kappa: 0.801, F1: 0.912). Hence, conservation strategies could lead to different results when different pattern extraction strategies are applied. Future studies which aim at extracting terrestrial habitat islands from image datasets should aim for the highest possible resolution and compare the outcomes of different classifiers to ensure the best possible results.