Miracle-dz/UniFAR-FTUs huggingface dataset:
A Study of the Effects of the Ice-Microphysics, Surface Friction, and Surface Heat Flux on Tropical Cyclone Formation§

This paper describes results from numerical experiments which have been performed to understand the effects of the ice microphysics, surface friction, and surface heat flux on tropical cyclone (TC) formation. This study uses the author's non-hydrostatic model that intends to resolve cumulus convection. However, the horizontal grid size is taken to be somewhat large; 2 km in an area of 600 km x 600 km. A non-uniform coarse grid is used in the surrounding area with 4,000-km square. Several buoyancy perturbations arranged in the west-east direction, and a weak vortex with the maximum wind speed of 5 m s -1 are given at the initial time of the numerical time integrations. It is confirmed from two numerical experiments with and without ice microphysics that the development of a vortex is slower, and TC formation is delayed, in the presence of ice microphysics. It is also confirmed that a vortex can develop even without surface friction. It is shown that a strong vortex with the maximum wind speed of 20~25 m s -1 can be obtained. As expected, however, no eye forms, and further development does not occur. That is, it is confirmed that surface friction is indispensable to eye formation and a very strong TC having an eye. As for the third concern of this study, it is shown that a vortex with the maximum wind speed of about 5 m s -1 does not develop in the absence of the surface heat flux. That is, the surface heat flux plays an important role even in a weak vortex. Important backgrounds and understandings that are concerned with these results are described, based on studies on TCs in the past 50 years.
Building text classifiers using positive and unlabeled examples

We study the problem of building text classifiers using positive and unlabeled examples. The key feature of this problem is that there is no negative example for learning. Recently, a few techniques for solving this problem were proposed in the literature. These techniques are based on the same idea, which builds a classifier in two steps. Each existing technique uses a different method for each step. We first introduce some new methods for the two steps, and perform a comprehensive evaluation of all possible combinations of methods of the two steps. We then propose a more principled approach to solving the problem based on a biased formulation of SVM, and show experimentally that it is more accurate than the existing techniques.
Evolution of contourite systems in the late Cretaceous Chalk Sea along the Tornquist Zone

Based on integration of seismic reflection and well data analysis this study examines two major contourite systems that developed during the late Cretaceous in the southern Baltic Sea. The evolution of these Chalk Sea contourite systems between the Kattegat and the southern Baltic Sea started when Turonian to Campanian inversion tectonics overprinted the rather flat sea floor of the epeiric Chalk Sea. The Tornquist Zone and adjacent smaller blocks were uplifted and formed elongated obstacles that influenced the bottom currents. As a consequence of the inversion, the sea floor west of the Tornquist Zone tilted towards the north‐east, creating an asymmetrical sub‐basin with a steep marginal slope in the north‐east and a gentle dipping slope in the south‐west. A south‐east directed contour current emerged in the Coniacian or Santonian along the south‐western basin margin, creating contourite channels and drifts. The previously studied contourite system offshore Stevns Klint is part of this system. A second, deeper and north‐west directed counter‐flow emerged along and parallel to the Tornquist Zone in the later Campanian, but was strongest in the Maastrichtian. This bottom current moderated the evolution of a drift‐moat system adjacent to the elevated Tornquist Zone. The near surface Alnarp Valley in Scania represents the Danian palaeo‐moat that linked the Pomeranian Bay with the Kattegat. The previously studied contourite system in the Kattegat represents the north‐western prolongation of this system. This study links previous observations from the Kattegat and offshore Stevns Klint to the here inferred two currents, a more shallow, south‐east directed and a deeper, north‐west directed flow.
Predicting Future Clinical Changes of MCI Patients Using Longitudinal and Multimodal Biomarkers

Accurate prediction of clinical changes of mild cognitive impairment (MCI) patients, including both qualitative change (i.e., conversion to Alzheimer's disease (AD)) and quantitative change (i.e., cognitive scores) at future time points, is important for early diagnosis of AD and for monitoring the disease progression. In this paper, we propose to predict future clinical changes of MCI patients by using both baseline and longitudinal multimodality data. To do this, we first develop a longitudinal feature selection method to jointly select brain regions across multiple time points for each modality. Specifically, for each time point, we train a sparse linear regression model by using the imaging data and the corresponding clinical scores, with an extra ‘group regularization’ to group the weights corresponding to the same brain region across multiple time points together and to allow for selection of brain regions based on the strength of multiple time points jointly. Then, to further reflect the longitudinal changes on the selected brain regions, we extract a set of longitudinal features from the original baseline and longitudinal data. Finally, we combine all features on the selected brain regions, from different modalities, for prediction by using our previously proposed multi-kernel SVM. We validate our method on 88 ADNI MCI subjects, with both MRI and FDG-PET data and the corresponding clinical scores (i.e., MMSE and ADAS-Cog) at 5 different time points. We first predict the clinical scores (MMSE and ADAS-Cog) at 24-month by using the multimodality data at previous time points, and then predict the conversion of MCI to AD by using the multimodality data at time points which are at least 6-month ahead of the conversion. The results on both sets of experiments show that our proposed method can achieve better performance in predicting future clinical changes of MCI patients than the conventional methods.
TNF-α tolerance blocks LPS-induced hypophagia but LPS tolerance fails to prevent TNF-α-induced hypophagia.

To investigate the role of tumor necrosis factor-α (TNF-α) in bacterial lipopolysaccharide (LPS)-induced hypophagia, we tested whether a cross tolerance between LPS and TNF-α exists with respect to their anorectic effects. Only the first of three subsequent intraperitoneal injections of LPS (100 μg/kg body wt) given every second day at dark onset (12:12-h light-dark cycle) led to a significant reduction of food intake in male rats. Likewise, intraperitoneal injections of human recombinant TNF-α (150 μg ≥ 3 × 106 U/kg body wt) also resulted in tolerance to its hypophagic effect. LPS tolerance did not alter the hypophagic response to subsequently injected TNF-α ( n = 14). However, TNF-α pretreatment completely blocked the hypophagic response to LPS ( n = 14). The results demonstrate that tolerance to the hypophagic effect of exogenous TNF-α is sufficient to eliminate LPS-induced hypophagia. This is consistent with the hypothesis that endogenous TNF-α plays a major role in LPS-induced hypophagia. The ineffectiveness of LPS tolerance to attenuate TNF-α-induced hypophagia is compatible with findings demonstrating that reduced TNF-α production is an important feature of LPS tolerance.
VpreB1/VpreB2/λ5 Triple-Deficient Mice Show Impaired B Cell Development but Functional Allelic Exclusion of the IgH Locus1

At the precursor B cell stage during bone marrow B cell development, Ig μH chain associates with surrogate L (SL) chain, which is encoded by the three genes VpreB1, VpreB2, and λ5, to form the pre-B cell receptor (pre-BCR). Surface expression of the pre-BCR is believed to signal both proliferation and allelic exclusion of the IgH locus. Mice which lack either VpreB1/VpreB2 or λ5 show a lack of precursor B cell expansion but normal IgH allelic exclusion. This would suggest that one of either λ5 or VpreB can make a pre-BCR-like complex which is still able to signal allelic exclusion but not proliferation. To investigate this, we established mice lacking all components of the SL chain. These mice showed severely impaired B cell development which was similar to that previously found in mice lacking either λ5 or VpreB1/VpreB2. Surprisingly, the IgH locus was still allelically excluded and thus the SL chain appears not to be involved in allelic exclusion.
Surgical versus conservative interventions for anterior cruciate ligament ruptures in adults.

BACKGROUND Anterior cruciate ligament rupture is a common knee injury. Surgical treatment, usually involving reconstruction of the ligament, is widely used especially in active individuals. OBJECTIVES Evaluation of the effect of surgical treatment compared with conservative treatment of anterior cruciate ligament (ACL) rupture. SEARCH STRATEGY We searched the Cochrane Musculoskeletal Injuries Group Specialised Register (January 2005), the Cochrane Central Register of Controlled Trials (The Cochrane Library Issue 1, 2005), MEDLINE (1966 to January Week 3 2005), EMBASE (1988 to 2005 Week 05), MEDIC (1978 to January 1999), Current Contents (9.2.1998 to 1.2.1999), BIOSIS (1970 to December 1998), reference lists of articles and consulted trialists and experts. SELECTION CRITERIA All randomised and quasi-randomised trials that compared surgical with conservative treatment of ACL rupture in adults. DATA COLLECTION AND ANALYSIS Two authors independently performed study selection, data extraction and quality assessment. MAIN RESULTS Two poor quality randomised trials conducted in the early 1980s were included in the review. The two trials differed considerably and no data pooling was done for the few shared outcome measures. One quasi-randomised trial of 167 people with a complete ACL rupture treated with repair or augmented repair versus conservative treatment found no difference in the return to sports activities between people treated surgically and those treated conservatively. Measures of knee stability and functional (Lysholm) knee scores were higher in surgically-treated participants. By the end of the follow-up period (average 55 months), three people treated with repair only and 16 treated conservatively had had ACL reconstruction. The other trial included 157 people with ACL injury. This found that conservatively-treated participants recovered from their injury more rapidly but, at the last follow up (minimum 13 months), the functional outcome was similar in both treatment groups. A large proportion of participants experienced some temporary discomfort after surgery and there were some more serious postoperative complications. There was less knee instability in surgically-treated participants and a tendency to fewer subsequent operations in the longer term. AUTHORS' CONCLUSIONS There is insufficient evidence from randomised trials to determine whether surgery or conservative management was best for ACL injury in the 1980s, and no evidence to inform current practice. Good quality randomised trials are required to remedy this situation.
Multiscale modelling of insulin secretion during an intravenous glucose tolerance test

Dysfunctional insulin secretion from pancreatic β-cells plays a major role in the development of diabetes. The intravenous glucose tolerance test (IVGTT) is a widely used clinical test to assess β-cell function. The analysis of IVGTT data is conveniently performed using mathematical models, which need to be fairly simple to enable parameter identifiability (minimal models), but should at the same time have sound biological foundation at the cellular level. Using mathematical analysis and model reduction, we show here that our recent mathematical model of insulin secretory granule dynamics in β-cells provides mechanistic underpinning for our minimal model of pancreatic insulin secretion during an IVGTT.
Neuroprotective Function of the PGE2 EP2 Receptor in Cerebral Ischemia

The cyclooxygenases COX-1 and COX-2 catalyze the first committed step of prostaglandin synthesis from arachidonic acid. Previous studies in rodent stroke models have shown that the inducible COX-2 isoform promotes neuronal injury, and the administration of COX-2 inhibitors reduces infarct volume. We investigated the function of PGE2, a principal prostaglandin product of COX-2 enzymatic activity, in neuronal survival in cerebral ischemia. PGE2 exerts its downstream effects by signaling through a class of four distinct G-protein-coupled EP receptors (for E-prostanoid: EP1, EP2, EP3, and EP4) that have divergent effects on cAMP and phosphoinositol turnover and different anatomical distributions in brain. The EP2 receptor subtype is abundantly expressed in cerebral cortex, striatum, and hippocampus, and is positively coupled to cAMP production. In vitro studies of dispersed neurons and organotypic hippocampal cultures demonstrated that activation of the EP2 receptor was neuroprotective in paradigms of NMDA toxicity and oxygen glucose deprivation. Pharmacologic blockade of EP2 signaling by inhibition of protein kinase A activation reversed this protective effect, suggesting that EP2-mediated neuroprotection is dependent on cAMP signaling. In the middle cerebral artery occlusion-reperfusion model of transient forebrain ischemia, genetic deletion of the EP2 receptor significantly increased cerebral infarction in cerebral cortex and subcortical structures. These studies indicate that activation of the PGE2 EP2 receptor can protect against excitotoxic and anoxic injury in a cAMP-dependent manner. Taken together, these data suggest a novel mechanism of neuroprotection mediated by a dominant PGE2 receptor subtype in brain that may provide a target for therapeutic intervention.
Point-of-care focused cardiac ultrasound for the assessment of thoracic aortic dimensions, dilation, and aneurysmal disease.

OBJECTIVES Thoracic aortic aneurysm and thoracic aortic dissection are related and potentially deadly diseases that present with nonspecific symptoms. Transthoracic echocardiography (TTE) may detect thoracic aortic pathology and is being increasingly performed by the emergency physician at the bedside; however, the accuracy of point-of-care (POC) focused cardiac ultrasound (FOCUS) for thoracic aortic aneurysm and thoracic aortic dissection has not been studied. The objective of this pilot study was to explore the agreement, sensitivity, and specificity of FOCUS for thoracic aortic dimensions, dilation, and aneurysm compared with CT angiography (CTA) as the reference standard. METHODS This study was a retrospective pilot analysis of image and chart data on consecutive patients presenting to an urban, academic emergency department (ED) between January 2008 and June 2010, who had both a FOCUS and a CTA for suspicion of thoracic aorta pathology. Thoracic aorta dimensions were measured from recordings by three ultrasound-trained emergency physicians blinded to any initial FOCUS and CTA results. CTA measurements were obtained by a radiologist blinded to the FOCUS results. Using cutoffs of 40 and 45 mm, we calculated the sensitivity and specificity of FOCUS for aortic dilation and aneurysm with the largest measurement on CT as the reference standard. Bland-Altman plots with 95% limits of agreement were used to demonstrate agreement for aortic measurements, kappa statistics to assess the degree of agreement between tests for aortic dilation, and intraclass correlation for interobserver and intraobserver variability. RESULTS Ninety-two patients underwent both FOCUS and CTA during the study period. Ten FOCUS studies had inadequate visualization for all measurements areas. Eighty-two patients were included in the final analysis. Mean (±SD) age was 58.1 (±16.6) years and 58.5% were male. Sensitivity, specificity, and the observed kappa value (95% confidence interval [CI]) between FOCUS and CTA for the presence of aortic dilation at the 40-mm cutoff were 0.77 (95% CI = 0.58 to 0.98), 0.95 (95% CI = 0.84 to 0.99), and 0.74 (95% CI = 0.58 to 0.90), respectively. The mean difference (95% limits of agreement) for the Bland-Altman plots was 0.6 mm (-5.3 to 6.5) for the sinuses of Valsalva, 4 mm (-2.7 to 10.7) for the sinotubular junction, 1.5 mm (-5.8 to 8.8) for the ascending aorta, and 2.2 mm (-5.9 to 10.3) for the descending aorta. CONCLUSIONS In this retrospective pilot study, FOCUS demonstrated good agreement with CTA measurements of maximal thoracic aortic diameter. FOCUS appears to be specific for aortic dilation and aneurysm when compared to CTA, but requires further prospective study.
Distributed Sequence Memory of Multidimensional Inputs in Recurrent Networks

Recurrent neural networks (RNNs) have drawn interest from machine learning researchers because of their effectiveness at preserving past inputs for time-varying data processing tasks. To understand the success and limitations of RNNs, it is critical that we advance our analysis of their fundamental memory properties. We focus on echo state networks (ESNs), which are RNNs with simple memoryless nodes and random connectivity. In most existing analyses, the short-term memory (STM) capacity results conclude that the ESN network size must scale linearly with the input size for unstructured inputs. The main contribution of this paper is to provide general results characterizing the STM capacity for linear ESNs with multidimensional input streams when the inputs have common low-dimensional structure: sparsity in a basis or significant statistical dependence between inputs. In both cases, we show that the number of nodes in the network must scale linearly with the information rate and poly-logarithmically with the ambient input dimension. The analysis relies on advanced applications of random matrix theory and results in explicit non-asymptotic bounds on the recovery error. Taken together, this analysis provides a significant step forward in our understanding of the STM properties in RNNs.
Coexistence of Equatorial Coupled Modes of ENSO

Abstract To study the regimes of leading ocean–atmosphere coupled modes of relevance to the El Nino–Southern Oscillation (ENSO) phenomenon, a comprehensive eigenmode analysis of an intermediate coupled model linearized with respect to an array of basic states is performed. Different kinds of leading modes are found to coexist and become unstable under wide ranges of basic states and parameter conditions. In particular, the two most important modes have periods of around 4 and 2 yr. They are referred to as the quasi-quadrennial (QQ) and the quasi-biennial (QB) modes, respectively. The positive coupled feedback destabilizes and quantizes the near-continuous spectrum for the low-frequency modes of the upper-ocean dynamics, giving rise to these leading modes with distinct periodicities. The primary mechanism for the phase transition of the QQ mode is due to the slow oceanic dynamic adjustment of equatorial heat content, which is consistent with the simple conceptual recharge oscillator, whereas anomalous adve.
Online Segment to Segment Neural Transduction

We introduce an online neural sequence to sequence model that learns to alternate between encoding and decoding segments of the input as it is read. By independently tracking the encoding and decoding representations our algorithm permits exact polynomial marginalization of the latent segmentation during training, and during decoding beam search is employed to find the best alignment path together with the predicted output sequence. Our model tackles the bottleneck of vanilla encoder-decoders that have to read and memorize the entire input sequence in their fixed-length hidden states before producing any output. It is different from previous attentive models in that, instead of treating the attention weights as output of a deterministic function, our model assigns attention weights to a sequential latent variable which can be marginalized out and permits online generation. Experiments on abstractive sentence summarization and morphological inflection show significant performance gains over the baseline encoder-decoders.
Immunoprotection of Recombinant Leptospiral Immunoglobulin-Like Protein A against Leptospira interrogans Serovar Pomona Infection

ABSTRACT We previously reported the cloning and characterization of leptospiral immunoglobulin-like proteins LigA and LigB of Leptospira interrogans. LigA and LigB are conserved at the amino-terminal region but are variable at the carboxyl-terminal region. Here, we evaluate the potential of recombinant LigA (rLigA) as a vaccine candidate against infection by L. interrogans serovar Pomona in a hamster model. rLigA was truncated into conserved (rLigAcon) and variable (rLigAvar) regions and expressed in Escherichia coli as a fusion protein with glutathione-S-transferase (rLigA). Golden Syrian hamsters were immunized at 3 and 6 weeks of age with rLigA (rLigAcon and rLigAvar) with aluminum hydroxide as an adjuvant. Hamsters given recombinant glutathione-S-transferase (rGST)-adjuvant and phosphate-buffered saline-adjuvant served as nonvaccinated controls. Three weeks after the last vaccination, all animals were challenged intraperitoneally with 108L. interrogans serovar Pomona bacteria (NVSL 1427-35-093002). All hamsters immunized with recombinant LigA survived after challenge and had no significant histopathological changes. In contrast, nonimmunized and rGST-immunized hamsters were subjected to lethal doses, and the hamsters that survived showed severe tubulointerstitial nephritis. All vaccinated animals showed a rise in antibody titers against rLigA. Results from this study indicate that rLigA is a potential vaccine candidate against L. interrogans serovar Pomona infection.
Clustering of galaxies at 3.6 μm in the Spitzer Wide-area Infrared Extragalactic legacy survey

We investigate the clustering of galaxies selected in the 3.6 μm band of the Spitzer Wide-area Infrared Extragalactic (SWIRE) legacy survey. The angular two-point correlation function is calculated for 11 samples with flux limits of S_(3.6)≥ 4–400 μJy, over an 8 deg^2 field. The angular clustering strength is measured at >5σ significance at all flux limits, with amplitudes of A = (0.49–29) × 10^(−3) at 1°, for a power-law model, Aθ^(−0.8). We estimate the redshift distributions of the samples using phenomological models, simulations and photometric redshifts, and so derive the spatial correlation lengths. We compare our results with the Galaxies In Cosmological Simulations (GalICS) models of galaxy evolution and with parametrized models of clustering evolution. The GalICS simulations are consistent with our angular correlation functions, but fail to match the spatial clustering inferred from the phenomological models or the photometric redshifts. We find that the uncertainties in the redshift distributions of our samples dominate the statistical errors in our estimates of the spatial clustering. At low redshifts (median z ≤ 0.5), the comoving correlation length is approximately constant, r_0= 6.1 ± 0.5 h^(−1) Mpc, and then decreases with increasing redshift to a value of 2.9 ± 0.3 h^(−1) Mpc for the faintest sample, for which the median redshift is z ~ 1. We suggest that this trend can be attributed to a decrease in the average galaxy and halo mass in the fainter flux-limited samples, corresponding to changes in the relative numbers of early- and late-type galaxies. However, we cannot rule out strong evolution of the correlation length over 0.5 < z < 1 .