Miracle-dz/UniFAR-FTUs huggingface dataset:
Differences in photosynthetic behaviour of Kappaphycus alvarezii and Kappaphycus striatus during dehydration and rehydration

Abstract The kappa-carrageenan-producing seaweed Kappaphycus striatus is different from K. alvarezii in that it grows well in the intertidal zone, where the thalli are exposed periodically to dehydration and rehydration. To investigate the specific tolerance mechanism of K. striatus, the photosynthetic behaviour of K. alvarezii and K. striatus exposed to osmotic variation was compared. K. striatus had a lower dehydration rate in the dark treatments and a higher rehydration rate in both the dark and light treatments as compared with K. alvarezii. The FV/FM of K. striatus was significantly higher than that of K. alvarezii during the process of dehydration and rehydration in both the light and dark treatments. The increase in amplitude of JIP-test fluorescence parameters VK, VJ and VI of K. striatus was smaller than that of K. alvarezii during the dehydration process in both the light and dark treatments. The increased amplitude of VK, VJ and VI in K. striatus was significantly lower than that in K. alvarezii when they were rehydrated in the dark treatments. Therefore, during the process of dehydration and rehydration, the tolerance of the oxygen evolving complex, the ability to balance photosynthetic light absorption and energy utilization, as well as the tolerance of PSII reaction centres were relatively higher in K. striatus compared with K. alvarezii. Such an increased tolerance of PSII may help to improve the tolerance of the whole plant to dehydration.
SCHEME-BURD: Stata module to provide a ColorBrewer-inspired graphics scheme with qualitative and blue-to-red diverging colors

The burd scheme is an alternative rendering of the s2color scheme based on Svend Juul's lean scheme and Cynthia Brewer's "RdBu" ColorBrewer scheme. The burd3 to burd11 sub-schemes provide blue-to-red diverging color scales for up to 11 data classes, which might be useful to plot ordered response scales in survey data.
PSO-SVM hybrid system for melanoma detection from histo-pathological images

This paper introduces an automated system for skin cancer (melanoma) detection from Histo-pathological images sampled from microscopic slides of skin biopsy. The proposed system is a hybrid system based on Particle Swarm Optimization and Support Vector Machine (PSO-SVM). The features used are extracted from the grayscale image histogram, the co-occurrence matrix and the energy of the wavelet coefficients resulting from the wavelet packet decomposition. The PSO-SVM system selects the best feature set and the best values for the SVM parameters (C and γ) that optimize the performance of the SVM classifier. The system performance is tested on a real dataset obtained from the Southern Pathology Laboratory in Wollongong NSW, Australia. Evaluation results show a classification accuracy of 87.13%, a sensitivity of 94.1% and a specificity of 80.22%. The sensitivity and specificity results are comparable to those obtained by dermatologists.
and Maximum Likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: A response to

Our recent study evaluated the performance of parsimony and probabilistic models of phylogenetic inference based on categorical data [1]. We found that a Bayesian implementation of a probabilistic Markov model produced more accurate results than either of the competing parsimony approaches (the main method currently employed), and the Maximum Likelihood implementation of the same model. This occurs principally because the results of Bayesian analyses are less resolved (less precise) as a measure topological uncertainty is intrinsically recovered in this MCMC-based approach and can be used to construct a majority-rule consensus tree that reflects this. Of the three main methods, Maximum Likelihood performed the worst of all as a single exclusively bifurcating tree is estimated in this framework which does not integrate an intrinsic measure of support. In their comment on our article, Brown and colleagues [2] argue that our experiments are invalid because we did not employ uncertainty measures after obtaining a Maximum Likelihood estimate of the topology. When bootstrapping is employed, a 50% consensus tree constructed from the bootstrap distribution is often indistinguishable from the majority-rule consensus tree constructed from the posterior sample obtained in a Bayesian analysis. This result is not entirely unexpected, as the Maximum Likelihood and Bayesian statistical frameworks share many statistical similarities, including a dependence on a likelihood function that incorporates the Mk model in this context. On this basis, Brown and colleagues conclude that they
Information geometric measurements of generalisation

Neural networks can be regarded as statistical models, and can be analysed in a Bayesian framework. Generalisation is measured by the performance on independent test data drawn from the same distribution as the training data. Such performance can be quantified by the posterior average of the information divergence between the true and the model distributions. Averaging over the Bayesian posterior guarantees internal coherence; Using information divergence guarantees invariance with respect to representation. The theory generalises the least mean squares theory for linear Gaussian models to general problems of statistical estimation. The main results are: (1)~the ideal optimal estimate is always given by average over the posterior; (2)~the optimal estimate within a computational model is given by the projection of the ideal estimate to the model. This incidentally shows some currently popular methods dealing with hyperpriors are in general unnecessary and misleading. The extension of information divergence to positive normalisable measures reveals a remarkable relation between the dlt dual affine geometry of statistical manifolds and the geometry of the dual pair of Banach spaces Ld and Ldd . It therefore offers conceptual simplification to information geometry. The general conclusion on the issue of evaluating neural network learning rules and other statistical inference methods is that such evaluations are only meaningful under three assumptions: The prior P(p) , describing the environment of all the problems; the divergence Dd , specifying the requirement of the task; and the model Q , specifying available computing resources.
Short-term exposure to nitrogen dioxide provides basal pathogen 36 resistance 37

summary: Fumigation of Arabidopsis with the gaseous signaling ABSTRACT 72 Nitrogen dioxide (NO 2 ) forms in plants under stress conditions, but little is known about its physiological functions. Here, we explored the physiological functions of NO 2 in plant cells 74 using short-term fumigation of Arabidopsis ( Arabidopsis thaliana ) for 1 h with 10 parts per 75 million (ppm) NO 2. Although leaf symptoms were absent, the expression of genes related to 76 pathogen resistance was induced. Fumigated plants developed basal disease resistance, or 77 pattern-triggered immunity (PTI), against the necrotrophic fungus Botrytis cinerea and the 78 hemibiotrophic bacterium Pseudomonas syringae . Functional salicylic acid (SA) and 79 jasmonic acid (JA) signaling pathways were both required for full expression of NO 2 -induced 80 resistance against B. cinerea . An early peak of SA accumulation immediately after NO 2 81 exposure was followed by transient accumulation of oxophytodienoic acid. Simultaneous 82 NO 2 -induced expression of genes involved in jasmonate biosynthesis and jasmonate 83 catabolism resulted in the complete suppression of JA and JA-isoleucine (JA-Ile) 84 accumulation, which was accompanied by a rise in the levels of their catabolic intermediates 85 12-OH-JA, 12-OH-JA-Ile, and 12-COOH-JA-Ile. NO 2 -treated plants emitted the volatile 86 monoterpene α-pinene and the sesquiterpene longifolene (syn. junipene), which could 87 function in signaling or direct defense against pathogens. NO 2 -triggered B. cinerea 88 resistance was dependent on enhanced early callose deposition and , PHYTOALEXIN DEFICIENT 3 ( PAD3 ) functions but independent of camalexin, CYP81F2 , 4-OH-indol-3-ylmethylglucosinolate In sum, exogenous NO 2 triggers basal pathogen resistance, pointing to a possible role for 92 endogenous NO 2 in defense signaling. Additionally, the study revealed the involvement of catabolism and volatiles in pathogen immunity. affect the chemical of multitrophic interactions with aphids their parasitoids.
University of Birmingham Ebola virus persistence in breast milk after no reported illness

A 9-month-old infant died from Ebola virus (EBOV) disease with unknown epidemiological link. While her parents did not report previous illness, laboratory investigations revealed persisting EBOV RNA in the mother’s breast milk and the father’s seminal fluid. Genomic analysis strongly suggests EBOV transmission to the child through breastfeeding.
Measurements of CP asymmetries in charmless four-body b0 and b0 decays

Asearchfor CP violationincharmlessfour-body decays of Λ 0 b and Ξ 0 b baryons with a proton and three charged mesons in the ﬁnal state is performed. To cancel out production and detection charge-asymmetry effects, the search is carried out by measuring the difference between the CP asymmetries in a charmless decay and in a decay with an intermediate charmed baryon with the same particles in the ﬁnal state. The data sample used was recorded in 2011 and 2012 with the LHCb detector and corresponds to an integrated luminosity of 3 fb − 1 . A total of 18 CP asymmetries are considered, either accounting for the full phase space of the decays or exploring speciﬁc regions of the decay kinematics. No signiﬁcant CP -violation effect is observed in any of the measurements.
CALC-PVM: A Parallel SIMPLEC Multiblock Solver for Turbulent Flow in Complex Domains

A ﬁnite volume code CALC-BFC (Boundary Fitted Coordinates) is extended with PVM (Parallel Virtual Machine) for parallel computations of turbulent ﬂow in complex multiblock domains. The main features are the use of general curvilinear coordinates, pressure correction scheme (SIMPLEC), Cartesian velocity components as principal unknowns, and colocated grid arrangement together with Rhie and Chow interpolation. Taking advantage of the communication facilities of PVM, the problem can be run in parallel on several processors on everything from NOW (Network Of Workstations) to distributed and shared memory supercomputers. Subdividing a 130x82x82 node turbulent backward facing step ﬂow calculation into 2x1x2 blocks and distributing it on four processors gives a speedup of 4.3 and subdividing it into 4x1x2 blocks and distributing it on eight processors gives a speedup of 8.3 on a 64 processor SUN Enterprise 10000 shared memory machine.
Importance of predicting the dose temporal profile for large solar energetic particle events

It has been proposed that proton intensities on the stream‐limited plateau present a minimal radiation hazard to astronauts, and hazardous intensities occur upon coronal‐mass‐ejection‐driven shock arrival at the spacecraft. Forecasts then need only predict the arrival time and severity of the shock prior to its arrival at the spacecraft. We evaluated dose to the bone marrow, eye, and skin for the largest events since 1996, in terms of the >10 MeV proton flux, prior to and after shock arrival. Doses at shock arrival were compared to the space‐permissible exposure limits (SPELs), and for five of the seven events, limits were exceeded for aluminum shielding thicknesses up to 3 g cm−2 prior to the arrival of the shocks. The 30‐d SPELs have been exceeded as early as 9 h after event initiation, but more generally, sometime between 20 and 50 h after event initiation. These results suggest that one cannot simply predict the arrival time and intensity of a shock if exceeding the 30‐d SPELs is to be avoided. Similarly, waiting for the shock to arrive at a sentinel spacecraft such as the Advanced Composition Explorer to provide a 1‐h warning of shock intensity may not prevent one from exceeding the 30‐d SPELs. In order to predict when 30‐d SPELs will be exceeded for a given event, one must forecast the dose temporal profile associated with that event.
Telomerase Expression in Cervical Dysplasia and Carcinoma

Telomerase activity has been detected in a broad range of human malignant neoplasms, and its expression may represent an essen tial step in the malignant transformation of tissues; however, the expression of telomerase in premalignant lesions remains rela tively unexplored. We tested tissue sections of cervical squamous cell carcinomas and squamous intraepithelial lesions, samples of benign reactive atypia, and normal cervical mucosa from hysterec tomy and cone biopsy specimens for the expression of telomerase. Mirror-image sections from each sample were paraffin embedded and processed for histologic analysis. The test samples of cervical tissue were crushed under liquid nitrogen, and telomerase activity was determined by the telomeric repeat amplification protocol. invasive squamous cell carcinoma. Twenty-five of 26 samples (96%) of high-grade squamous intraepithelial lesion also tested positively for telomerase activity, including 10 of 10 samples of moderate dysplasia, 12 of 13 samples of severe dysplasia, and 3 of 3 samples of carcinoma in situ. Telomerase activity was detected in 14 of 25 samples (56%) of low-grade squamous intraepithelial lesion and in 10 of 18 samples (56%) of reactive atypia but was detected in only 9 of 50 samples (18%) of histologically normal cervical mucosa. These results suggest that telomerase expression may be a marker of premalignant and malignant squamous cell lesions of the uterine cervix, although it is also expressed in a high proportion of cases of reactive atypia. Am J Clin Pathol 1998;109:153-162.
Pigment-dispersing factor is present in circadian clock neurons of pea aphids and may mediate photoperiodic signalling to insulin-producing cells

The neuropeptide Pigment-Dispersing Factor (PDF) plays a pivotal role in the circadian clock of most Ecdysozoa and is additionally involved in the timing of seasonal responses of several photoperiodic species. The pea aphid, Acyrthosiphon pisum, is a paradigmatic photoperiodic species with an annual life cycle tightly coupled to the seasonal changes in day length. Nevertheless, PDF could not be identified in A. pisum so far. In the present study, we identified a PDF-coding gene that has undergone significant changes in the otherwise highly conserved insect C-terminal amino acid sequence. A newly generated aphid-specific PDF antibody stained four neurons in each hemisphere of the aphid brain that co-express the clock protein Period and have projections to the pars lateralis that are highly plastic and change their appearance in a daily and seasonal manner, resembling those of the fruit fly PDF neurons. Most intriguingly, the PDF terminals overlap with dendrites of the insulin-like peptide (ILP) positive neurosecretory cells in the pars intercerebralis and with putative terminals of Cryptochrome (CRY) positive clock neurons. Since ILP has been previously shown to be crucial for seasonal adaptations and CRY might serve as a circadian photoreceptor vital for measuring day length, our results suggest that PDF plays a critical role in aphid seasonal timing.
Package ‘RcppCensSpatial’

It provides to in linear spatial with censored/missing responses via the Expectation-Maximization (EM), the Stochastic Approximation EM (SAEM), the EM (MCEM) algorithm. These algorithms are widely used to compute the maximum likelihood (ML) estimates in problems with incomplete data. The EM algorithm computes the ML estimates when a closed expression for the expectation of the complete-data log-likelihood function is available. In the MCEM algorithm, the conditional expectation is substituted by a Monte Carlo approximation based on many independent simulations of the missing data. In contrast, the SAEM algorithm splits the E-step into simulation and integration steps. This package also the standard error of the estimates using the Louis method. Moreover, it has a function that performs spatial prediction in new
Stress MAPK Regulation A Role for cFLIP in B Cell Proliferation and

Fas/Apo-1 signals through the FADD (Fas-associated death domain) adaptor protein, which recruits and activates the apical caspase 8 and leads to apoptosis. Cellular FLIP (cFLIP) is a homolog of caspase 8 and is also capable of binding to FADD. Previous studies suggest that cFLIP could either enhance or inhibit apoptosis and lead to NF- (cid:1) B and Erk1/2 activation. Like FADD or caspase 8 deﬁciency, a lack of cFLIP disrupts embryogenesis and T cell proliferation. It has been demonstrated that B cells lacking either FADD or caspase 8 were defective in both Fas-induced apoptosis and TLR-induced proliferation, which indicates that these death-inducing proteins have an additional role in regulating innate immunity. To analyze the function of cFLIP in B cells, conditional deletion of cFLIP was induced by using CD19 Cre . The resulting B cell-speciﬁc cFLIP-deﬁcient mice were found to have reduced numbers of peripheral B cells that were hypersensitive to Fas-induced apoptosis and impaired in proliferation induced by TLRs and the BCR. Furthermore, there was aberrant expression of costimulatory proteins and activation markers in cFLIP-deﬁcient B cells. Whereas LPS-induced activation of NF- (cid:1) B and Erk1/2 appears to be unaffected, p38 and Jnk were spontaneously activated and hyperinduced in cFLIP-deﬁcient B cells. Therefore, these data revealed novel functions of cFLIP in B cells. The Journal of Immunology, 2009, 182: 207–215.
The benefits of completing homework for students with different aptitudes in an introductory physics course

We examine the relationship between homework completion and exam performance for students having different physics aptitudes for five different semesters of an introductory electricity and magnetism course. In our analysis, we plot exam scores versus homework completion scores and calculate the slopes of the line fits and the Pearson correlations. On average, completing many homework problems correlated to better exam scores only for students with high physics aptitude. Low aptitude physics students had a negative correlation between exam performance and completing homework; the more homework problems they did, the worse their performance was on exams. One explanation for this effect is that the assigned homework problems placed an excessive cognitive load on low aptitude students. As a result, no learning or even negative learning might have taken place when low aptitude students attempted to do assigned homework. Another explanation is based on the fact that the negative benefit effects first appeared when magnetism concepts were introduced. According to this explanation, low aptitude students had difficulty consolidating knowledge of magnetic fields with previously-learned knowledge of electric fields. A third possibility, that a high homework copying rate by low aptitude students impeded learning, is rejected because two different analyses revealed no evidence of homework copying.
Peripheral Require TCR Signaling for Homeostasis in T Cells d g high CD45RB+ Innate-like CD27

TCR signaling is required for homeostasis of naive ab T cells. However, whether such a signal is necessary for gd T cell homeostasis in the periphery remains unknown. In this study, we present evidence that a portion of V g 2 + gd T cells, one of the major gd T cell subsets in the secondary lymphoid organs, requires TCR signaling for homeostasis. To attenuate gd TCR signals, we generated mice lacking E g 4 (E g 4 2 / 2 ), an enhancer located at the 3 9 -most end of the TCR g locus. Overall, we found that in thymus, E g 4 loss altered V-J rearrangement, chromatin accessibility, and transcription of the TCR g locus in a distance-dependent manner. V g 2 + gd T cells in E g 4 2 / 2 mice developed normally both fetal and adult mouse thymi but were relatively reduced in number in spleen and lymph nodes. Although V g 2 TCR transcription decreased in all subpopulations of E g 4 2 / 2 mice, the number of V g 2 + gd T cells decreased and TCR signaling was attenuated only in the innate-like CD27 + CD45RB high subpopulation in peripheral lymphoid organs. Consistently, CD27 + CD45RB high V g 2 + gd T cells from E g 4 2 / 2 mice transferred into Rag2-deﬁcient mice were not efﬁciently recovered, suggesting that continuous TCR signaling is required for their homeostasis. Finally, CD27 + CD45RB high V g 2 + gd T cells from E g 4 2 / 2 mice showed impaired TCR-induced activation and antitumor responses. These results suggest that normal homeostasis of innate-like CD27 + CD45RB high V g 2
Actinide ions for testing the spatial α -variation hypothesis

Testing the spatial variation of fine-structure constant $\alpha$ indicated in [Webb et al., Phys. Rev. Lett. 107, 191101 (2011)] with terrestrial laboratory atomic measurements requires at least $\dot{\alpha}/\alpha \sim 10^{-19}~\textrm{y}^{-1}$ sensitivity. We conduct a systematic search of atomic systems for such a test that have all features of the best optical clock transitions leading to possibility of the frequency measurements with fractional accuracy on the level of $10^{-18}$ or better and have a factor of 100 extra enhancement of $\alpha$-variation in comparisons to experimental frequency ratio measurement accuracy. We identify the pair of actinide Cf$^{15+}$ and Es$^{16+}$ ions as the best system for a test of spatial $\alpha-$variation hypothesis as it satisfies both of these requirements and have sufficiently simple electronic structure to allow for high-precision predictions of all atomic properties required for rapid experimental progress.
Responses2 Suggest Opposite Effects on Allergic a and sIL-13R a Function of Soluble (s)IL-4R Differences in Expression, Affinity, and

IL-4 and IL-13 are each bound by soluble receptors (sRs) that block their activity. Both of these sRs (sIL-4R (cid:1) and sIL-13R (cid:1) 2) are present in low nanogram per milliliter concentrations in the serum from unstimulated mice, but differences in afﬁnity and half-life suggest differences in function. Serum IL-4/sIL-4R (cid:1) complexes rapidly dissociate, releasing active IL-4, whereas sIL-13R (cid:1) 2 and IL-13 form a stable complex that has a considerably longer half-life than uncomplexed IL-13, sIL-13R (cid:1) 2, IL-4, or sIL-4R (cid:1) . Approximately 25% of sIL-13R (cid:1) 2 in serum is complexed to IL-13; this percentage and the absolute quantity of sIL-13R (cid:1) 2 in serum increase considerably during a Th2 response. sIL-13R (cid:1) 2 gene expression is up-regulated by both IL-4 and IL-13; the effect of IL-4 is totally IL-4R (cid:1) -dependent while the effect of IL-13 is partially IL-4R (cid:1) -independent. Inhalation of an IL-13/ sIL-13R (cid:1) 2 complex does not affect the expression of IL-13-inducible genes but increases the expression of two genes, Vnn1 and Pira-1 , whose products activate APCs and promote neutrophilic inﬂammation. These observations suggest that sIL-4R