Miracle-dz/UniFAR-FTUs huggingface dataset:
Compiling and Mapping Global Permeability of the Unconsolidated and Consolidated Earth: GLobal HYdrogeology MaPS 2.0 (GLHYMPS 2.0)

The spatial distribution of subsurface parameters such as permeability are increasingly relevant for regional to global climate, land surface, and hydrologic models that are integrating groundwater dynamics and interactions. Despite the large fraction of unconsolidated sediments on Earth's surface with a wide range of permeability values, current global, high‐resolution permeability maps distinguish solely fine‐grained and coarse‐grained unconsolidated sediments. Representative permeability values are derived for a wide variety of unconsolidated sediments and applied to a new global map of unconsolidated sediments to produce the first geologically constrained, two‐layer global map of shallower and deeper permeability. The new mean logarithmic permeability of the Earth's surface is −12.7 ± 1.7 m2 being 1 order of magnitude higher than that derived from previous maps, which is consistent with the dominance of the coarser sediments. The new data set will benefit a variety of scientific applications including the next generation of climate, land surface, and hydrology models at regional to global scales.
Characterization of Problem Stores

This paper introduces the concept of problem stores: static stores whose dependent loads often miss in the cache. Accurately identifying problem stores allows the early determination of addresses likely to cause later misses, potentially allowing for the development of novel, proactive prefetching and memory hierarchy management schemes. We present a detailed empirical characterization of problem stores using the SPEC2000 CPU benchmarks. The data suggests several key observations about problem stores. First, we find that the number of important problem stores is typically quite small; the worst 100 problem stores write the values that will lead to about 90% of non-cold misses for a variety of cache configurations. We also find that problem stores only account for 1 in 8 dynamic stores, though they result in 9 of 10 misses. Additionally, the problem storesâ€™ dependent loads miss in the L2 cache a larger fraction of the time than loads not dependent on problem stores. We also observe the set of problem stores is stable across a variety of cache configurations. Finally, we found that the instruction distance from problem store to miss and problem store to evict is often greater than one million instructions, but the value is often needed within 100,000 instructions of the eviction.
Visualisation and categorisation of respiratory mechanism using self-organising maps

In post-operative patients it is sometimes necessary to push morphine-like analgesics to their limits for pain relief. Unfortunately, this can sometimes bring a significant risk of disrupting the control of breathing, and of precipitating life-threatening conditions. A possible way of monitoring patients is by studying the correlation between analgesia, airway obstruction and hypoxia. The first step towards achieving this objective is by visualising the relationship between different pairs of signals involved in respiratory mechanics. Based on previous work, where self-organising maps (SOMs) were used for representing these relationships on a breath by breath basis, it is demonstrated how it is now possible to automatically label nodes in the SOMs based on classification of the signals by a clinician. The use of a majority voting configuration of SOMs enables results to be presented with a confidence measure which enhances the medical applicability of the system. In addition, the ability to now visualise the transition between categories will enable further research into the significance of transition between the categories and the presence of possible new sub-categories.
CMEIAS-Aided Microscopy of the Spatial Ecology of Individual Bacterial Interactions Involving Cell-to-Cell Communication within Biofilms

This paper describes how the quantitative analytical tools of CMEIAS image analysis software can be used to investigate in situ microbial interactions involving cell-to-cell communication within biofilms. Various spatial pattern analyses applied to the data extracted from the 2-dimensional coordinate positioning of individual bacterial cells at single-cell resolution indicate that microbial colonization within natural biofilms is not a spatially random process, but rather involves strong positive interactions between communicating cells that influence their neighbors' aggregated colonization behavior. Geostatistical analysis of the data provide statistically defendable estimates of the micrometer scale and interpolation maps of the spatial heterogeneity and local intensity at which these microbial interactions autocorrelate with their spatial patterns of distribution. Including in situ image analysis in cell communication studies fills an important gap in understanding the spatially dependent microbial ecophysiology that governs the intensity of biofilm colonization and its unique architecture.
Robust moving least-squares fitting with sharp features

We introduce a robust moving least-squares technique for reconstructing a piecewise smooth surface from a potentially noisy point cloud. We use techniques from robust statistics to guide the creation of the neighborhoods used by the moving least squares (MLS) computation. This leads to a conceptually simple approach that provides a unified framework for not only dealing with noise, but also for enabling the modeling of surfaces with sharp features.Our technique is based on a new robust statistics method for outlier detection: the forward-search paradigm. Using this powerful technique, we locally classify regions of a point-set to multiple outlier-free smooth regions. This classification allows us to project points on a locally smooth region rather than a surface that is smooth everywhere, thus defining a piecewise smooth surface and increasing the numerical stability of the projection operator. Furthermore, by treating the points across the discontinuities as outliers, we are able to define sharp features. One of the nice features of our approach is that it automatically disregards outliers during the surface-fitting phase.
Stochastic Over-Subscription Planning Using Hierarchies of MDPs

In over-subscription planning (OSP), the set of goals is not achievable jointly, and the task is to find a plan that attains the best feasible subset of goals given resource constraints. Recent classical OSP algorithms ignore the uncertainty inherent in many natural application domains where OSPs arise. And while modeling stochastic OSP problems as MDPs is easy, the resulting models are too large for standard solution approaches. Fortunately OSP problems have a natural two-tiered hierarchy, and in this paper we adapt and extend tools developed in the hierarchical reinforcement learning community in order to effectively exploit this hierarchy and obtain compact, factored policies. Typically, such policies are sub-optimal, but under certain assumptions that hold in our planetary exploration domain, our factored solution is, in fact, optimal. Our algorithms work by repeatedly solving a number of smaller MDPs, while propagating information between them. We evaluate a number of variants of this approach on a set of stochastic instances of a planetary rover domain, showing substantial performance gains.
A calculus for overloaded functions with subtyping

We present a simple extension of typed λ-claculus where functions can be overloaded by adding different “pieces of code”. In short, the code of an overloaded function is formed by several branches of code; the branch to execute is chosen, when the function is applied, according to a particular selection rule which depends on the type of the argument. The crucial feature of the present approach is that a subtyping relation is defied among types, such that the type of a term generally decreases during computation, and this fact induces a distinction between the “compile-time” type and the “run-time”type of a term. We study the case of overloaded functions where the branch selection depends on the run-time type of the argument, so that overloading cannot be eliminated by a static analysis of code, but is an essential feature to be dealt with during computation. We prove Confluence and Strong Normalization for this calculus as well as a generalized Subject-Reduction theorem (but proofs are ommitted in this abstract. The definition of this calculus is driven by the understanding of object-oriented features and the connections between our calculus and object-orientedness are extensively stressed. We show that this calculus provides a foundation for typed object-oriented languages which solves some of the problems of the standard record-based approach. It also provides a type-discipline for a relevant fragment of the “core framework” of CLOS.
Wheel running can accelerate or delay extinction of conditioned place preference for cocaine in male C57BL/6J mice, depending on timing of wheel access

Aerobic exercise may represent a useful intervention for drug abuse in predisposed individuals. Exercise increases plasticity in the brain that could be used to reverse learned drug associations. Previous studies have reported that exposing mice to a complex environment including running wheels after drug conditioning abolishes conditioned place preference (CPP) for cocaine, whereas running can enhance CPP when administered before conditioning. The purpose of the present study was to test the hypothesis that timing of exercise relative to conditioning has opposing effects on cocaine CPP. Male C57BL/6J mice experienced 30 days of running or sedentary treatments either before or after cocaine conditioning. Control animals always received saline and never cocaine, but otherwise underwent the same conditioning and exercise treatments. Animals were given bromodeoxyuridine injections at the onset of conditioning or exercise, and euthanized at the end of the study to quantify survival of new neurons in the hippocampus as a marker of plasticity. Wheel running accelerated extinction of CPP when running occurred entirely after drug conditioning, whereas running delayed extinction when administered before conditioning. A single conditioning day after running was sufficient to abolish the accelerated extinction observed when all conditioning preceded running. Running approximately doubled adult hippocampal neurogenesis, whereas cocaine had no effect. These results suggest that exercise‐induced plasticity can facilitate learning that context is no longer associated with drug. However, if drug exposure occurs after exercise, running‐induced plasticity may strengthen drug associations. The results provide insights into the interaction between exercise and drug conditioning that could have implications for drug abuse treatments.
An object‐oriented library for computational protein design

Recent advances in computational protein design have established it as a viable technique for the rational generation of stable protein sequences, novel protein folds, and even enzymatic activity. We present a new and object‐oriented library of code, written specifically for protein design applications in C++, called EGAD Library. The modular fashion in which this library is written allows developers to tailor various energy functions and minimizers for a specific purpose. It also allows for the generation of novel protein design applications with a minimal amount of code investment. It is our hope that this will permit labs that have not considered protein design to apply it to their own systems, thereby increasing its potential as a tool in biology. We also present various uses of EGAD Library: in the development of Interaction Viewer, a PyMOL plug‐in for viewing interactions between protein residues; in the repacking of protein cores; and in the prediction of protein–protein complex stabilities. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
To proliferate or not to proliferate.

This editorial refers to ‘Cardiomyocyte cell cycle control and growth estimation in vivo —an analysis based on cardiomyocyte nuclei’ by S. Walsh et al . , pp. 365–373, this issue. Cardiomyocytes in mammalian hearts undergo significant reduction in their cell proliferation capacity soon after birth, which is not disputed. However, it remains uncertain whether the adult heart contains a limited capacity for cell proliferation. Through the use of immunohistochemical staining methods, it has been reported that adult mouse cardiomyocytes can re-enter the cell cycle and duplicate.1,2 However, the origin of the cell-cycle-positive cells was not determined. Others reported permanent inhibition of cell-cycle progression in adult cardiomyocytes in mice.3 With advances in lineage tracing technology, a recent genetic labelling study demonstrated that stem or precursor cells did not contribute significantly to the formation of cardiomyocytes during normal ageing up to 1 year in the mouse. In contrast, precursor cells may participate in the formation of new cardiomyocytes after cardiac injury.4 In humans, high myocyte proliferation rates that could result in the exchange of all cardiomyocytes within 5 years have been reported by employing immunostaining technology on sections of human patients who died of acute myocardial infarction.5 In contrast, using 14C dating analyses in humans, Bergmann et al . 6 reported that cardiomyocytes are renewed with a gradual decrease from …
Efficacy and safety of midodrine in the treatment of dialysis-associated hypotension

Dialysis-associated hypotension is a morbid problem in haemodialysis patients. Employment of midodrine at the start of dialysis has reduced the severity and frequency of hypotensive episodes in these patients. Through selective α1-adrenergic receptor-binding, desglymidodrine, the active metabolite of midodrine, raises blood pressure by enhancing venous and arterial tone. This medication has been demonstrated to be effective and safe in the acute and chronic treatment of haemodialysis-associated hypotension in end stage renal disease patients.
Heightened tissue factor associated with tissue factor pathway inhibitor and prognosis in patients with unstable angina.

BACKGROUND This study was designed to evaluate the plasma levels of tissue factor (TF) and tissue factor pathway inhibitor (TFPI) in patients with unstable angina and investigate whether there is a relationship between these levels and unfavorable outcome. METHODS AND RESULTS The plasma TF and free TFPI antigen levels were determined in plasma samples taken from 51 patients with unstable angina, 56 with stable exertional angina, and 55 with chest pain syndrome. The plasma TF and free TFPI antigen levels were higher in the unstable angina group than in the stable exertional angina and chest pain syndrome group. There was a good correlation between TF and TFPI. We established borderline as maximum level in the patients with chest pain syndrome. Seven patients (of the 22 in the high TF group) required revascularization to control their unstable angina during in-hospital stay. On the other hand, only 1 of the 29 patients in the low TF group required myocardial revascularization. Four patients of the 14 patients in the high free TFPI group required myocardial revascularization during in-hospital stay, and 4 of the 37 patients in the low free TFPI group required myocardial revascularization. We compared the TF and free TFPI levels between the cardiac event (+) group and cardiac event (-) group. TF levels were significantly higher in the cardiac event (+) group than in the cardiac event (-) group. CONCLUSIONS We have demonstrated that not only the plasma TF levels but also the plasma-free TFPI levels are elevated in patients with unstable angina. Patients with unstable angina and heightened TF and free TFPI are at increased risk for unfavorable outcomes. The heightened TF level was a more important predictor in patients with unstable angina.
Neurophysiologic study of central pain in patients with Parkinson disease

Background: Patients with Parkinson disease (PD) may present with various types of pain. In some instances, no cause can be identified and pain is considered a primary disorder (primary central pain [PCP]). We hypothesized that PCP in patients with PD (PD-PCP) may be due to a dysfunction of pain pathways or the processing of pain inputs in the CNS. Methods: We carried out a psychophysical and neurophysiologic study in 9 patients with PD-PCP, 9 patients with PD without pain (PD-NoP), and 9 healthy control subjects. We assessed the clinical characteristics of pain, performed quantitative sensory testing with thermal probes, and recorded laser-evoked potentials (LEPs) and laser-induced sudomotor skin responses (l-SSRs) in “off” and “on” conditions. Results: In “off” condition, patients with PD-PCP had lower heat pain and laser pinprick thresholds, higher LEP amplitudes, and less habituation of the l-SSR in comparison with PD-NoP patients and control subjects. Abnormalities were more marked in the most affected side. In “on” condition, psychophysical and neurophysiologic differences disappeared or were significantly attenuated. Conclusion: Conduction along peripheral and central pain pathways is normal in patients with Parkinson disease with or without primary central pain. However, apart from signs of hyperalgesia, our patients exhibited lack of habituation of sympathetic sudomotor responses to repetitive pain stimuli, suggesting an abnormal control of the effects of pain inputs on autonomic centers. Abnormalities were attenuated by l-dopa, suggesting that the dysfunction may occur in dopamine-dependent centers regulating both autonomic function and inhibitory modulation of pain inputs.
Estimating β from redshift‐space distortions in the 2dF galaxy survey

Given the failure of existing models for redshift-space distortions to provide a highly accurate measure of the �-parameter, and the ability of forthcoming surveys to obtain data with very low random errors, it becomes necessary to develop better models for these distortions. Here we review the failures of the commonly-used velocity dispersion models and present an empirical method for extractingfrom the quadrupole statistic that has little systematic offset over a wide range ofand cosmologies. This empirical model is then applied to an ensemble of mock 2dF southern strip surveys, to illustrate the technique and see how accurately we can recover the true value of �. We compare this treatment with the error we expect to find due only to the finite volume of the survey. We find that non-linear effects reduce the range of scales over which � can be fitted, and introduce covariances between nearby modes in addition to those introduced by the convolution with the survey window function. The result is that we are only able to constrainto a 1-� accuracy of 25% (� = 0.55 ± 0.14 for the cosmological model considered). We explore one possible means of reducing this error, that of cluster collapse, and show that accurate application of this method can greatly reduce the effect of non-linearities, improving the determination of �. We conclude by demonstrating that, when the contaminating effects of clusters are dealt with, this simple analysis of the full 2dF survey yields � = 0.55 ± 0.04. For this model this represents a determination ofto an accuracy of 8% and hence an important constraint on the cosmological density parameter 0.
Azithromycin in DuraSite® for the treatment of blepharitis

Blepharitis is a common inflammatory disease of the eyelid. Posterior blepharitis affects the posterior lamella of the eyelid and involves inflammation of the meibomian glands, whereas anterior blepharitis affects the anterior lamella of the eyelid and the eyelashes; either version can be inflammatory or infectious in nature. Each of these conditions can incite or propagate the other; anterior blepharitis, if not treated, can lead to meibomian gland disease, and vice versa. Blepharitis is typically chronic, and can be associated with a variety of systemic diseases such as dermatitis, as well as ocular diseases such as dry eye, conjunctivitis, or keratitis. The standard treatment regimen historically consists of lid hygiene with warm compresses and eyelid scrubs, although these treatment modalities may have limited efficacy for many patients, especially those with more severe disease. Adjunctive treatment includes systemic and topical antibiotics, topical corticosteroids, and tear replacement therapy. Topical antibiotics are recommended to decrease the bacterial load, and topical corticosteroids may help in cases of severe inflammation. Azithromycin ophthalmic solution 1% in DuraSite® (AzaSite®; Inspire Pharmaceuticals, Durham, North Carolina, USA) has been proposed as a novel treatment for posterior blepharitis, based on its well-known anti-infective profile, its anti-inflammatory properties, its excellent tissue penetration, and its regulatory approval for the treatment of bacterial conjunctivitis. This review focuses on an off-label indication for topical azithromycin 1% in DuraSite for the treatment of blepharitis.
JNK is a novel regulator of intercellular adhesion

c-Jun N-terminal Kinase (JNK) is a family of protein kinases, which are activated by stress stimuli such as inflammation, heat stress and osmotic stress, and regulate diverse cellular processes including proliferation, survival and apoptosis. In this review, we focus on a recently discovered function of JNK as a regulator of intercellular adhesion. We summarize the existing knowledge regarding the role of JNK during the formation of cell-cell junctions. The potential mechanisms and implications for processes requiring dynamic formation and dissolution of cell-cell junctions including wound healing, migration, cancer metastasis and stem cell differentiation are also discussed.
The sh-Lie algebra perturbation lemma

Abstract Let R be a commutative ring which contains the rationals as a subring and let g be a chain complex. Suppose given an sh-Lie algebra structure on g, that is, a coalgebra perturbation of the coalgebra differential on the cofree coaugmented differential graded cocommutative coalgebra T′ on the suspension of g and write the perturbed coalgebra as T″. Suppose, furthermore, given a contraction of g onto a chain complex M. We show that the data determine an sh-Lie algebra structure on M, that is, a coalgebra perturbation of the coalgebra differential on the cofree coaugmented differential graded cocommutative coalgebra S′ on the suspension of M, a Lie algebra twisting cochain from the perturbed coalgebra S″ to the loop Lie algebra L on the perturbed coalgebra T″, and an extension of this Lie algebra twisting cochain to a contraction of chain complexes from the Cartan–Chevalley–Eilenberg coalgebra on L onto S″ which is natural in the data. For the special case where M and g are connected we also construct an explicit extension of the perturbed retraction to an sh-Lie map. This approach includes a very general solution of the master equation.