Miracle-dz/UniFAR-FTUs huggingface dataset:
Incorporating Cold-Air Pooling into Downscaled Climate Models Increases Potential Refugia for Snow-Dependent Species within the Sierra Nevada Ecoregion, CA

We present a unique water-balance approach for modeling snowpack under historic, current and future climates throughout the Sierra Nevada Ecoregion. Our methodology uses a finer scale (270 m) than previous regional studies and incorporates cold-air pooling, an atmospheric process that sustains cooler temperatures in topographic depressions thereby mitigating snowmelt. Our results are intended to support management and conservation of snow-dependent species, which requires characterization of suitable habitat under current and future climates. We use the wolverine (Gulo gulo) as an example species and investigate potential habitat based on the depth and extent of spring snowpack within four National Park units with proposed wolverine reintroduction programs. Our estimates of change in spring snowpack conditions under current and future climates are consistent with recent studies that generally predict declining snowpack. However, model development at a finer scale and incorporation of cold-air pooling increased the persistence of April 1st snowpack. More specifically, incorporation of cold-air pooling into future climate projections increased April 1st snowpack by 6.5% when spatially averaged over the study region and the trajectory of declining April 1st snowpack reverses at mid-elevations where snow pack losses are mitigated by topographic shading and cold-air pooling. Under future climates with sustained or increased precipitation, our results indicate a high likelihood for the persistence of late spring snowpack at elevations above approximately 2,800 m and identify potential climate refugia sites for snow-dependent species at mid-elevations, where significant topographic shading and cold-air pooling potential exist.
Asymmetric Programming: A Highly Reliable Metadata Allocation Strategy for MLC NAND Flash Memory-Based Sensor Systems

While the NAND flash memory is widely used as the storage medium in modern sensor systems, the aggressive shrinking of process geometry and an increase in the number of bits stored in each memory cell will inevitably degrade the reliability of NAND flash memory. In particular, it's critical to enhance metadata reliability, which occupies only a small portion of the storage space, but maintains the critical information of the file system and the address translations of the storage system. Metadata damage will cause the system to crash or a large amount of data to be lost. This paper presents Asymmetric Programming, a highly reliable metadata allocation strategy for MLC NAND flash memory storage systems. Our technique exploits for the first time the property of the multi-page architecture of MLC NAND flash memory to improve the reliability of metadata. The basic idea is to keep metadata in most significant bit (MSB) pages which are more reliable than least significant bit (LSB) pages. Thus, we can achieve relatively low bit error rates for metadata. Based on this idea, we propose two strategies to optimize address mapping and garbage collection. We have implemented Asymmetric Programming on a real hardware platform. The experimental results show that Asymmetric Programming can achieve a reduction in the number of page errors of up to 99.05% with the baseline error correction scheme.
Rapid and efficient detection of Mycobacterium tuberculosis in respiratory and non-respiratory samples [Technical note].

The detection of Mycobacterium tuberculosis using a new commercial real-time polymerase chain reaction (PCR) assay (Xpert™ MTB/RIF) was evaluated on 91 respiratory and 89 non-respiratory samples recovered from 132 patients suspected of tuberculosis (TB). Overall, 31 (17.2%) of the 180 samples, including 17 respiratory and 14 non-respiratory (respectively 17 and 12 PCR-positive), yielded M. tuberculosis on culture. The sensitivity and specificity of PCR were respectively 100% and 100%, and 85.7% and 97.3% for respiratory and non-respiratory samples. Although the test is validated only for respiratory samples, our findings suggest that it could be useful for the diagnosis of extra-pulmonary TB.
Search and replication in unstructured peer-to-peer networks

Decentralized and unstructured peer-to-peer networks such as Gnutella are attractive for certain applications because they require no centralized directories and no precise control over network topology or data placement. However, the flooding-based query algorithm used in Gnutella does not scale; each query generates a large amount of traffic and large systems quickly become overwhelmed by the query-induced load. This paper explores, through simulation, various alternatives to Gnutella's query algorithm, data replication strategy, and network topology. We propose a query algorithm based on multiple random walks that resolves queries almost as quickly as Gnutella's flooding method while reducing the network traffic by two orders of magnitude in many cases. We also present simulation results on a distributed replication strategy proposed in [8]. Finally, we find that among the various network topologies we consider, uniform random graphs yield the best performance.
Comparison of Endoscopic Submucosal Dissection and Surgery for Differentiated Type Early Gastric Cancer within the Expanded Criteria

Background/Aims Endoscopic submucosal dissection (ESD) is a novel alternative treatment for differentiated early gastric cancer (EGC) without lymph node metastasis. We conducted this study to verify the therapeutic usefulness of ESD for treating differentiated EGC compared to that of surgery. Methods This is a retrospective cohort study of 382 patients treated with differentiated EGC from March 2006 to May 2010. The propensity score yielded 275 matched patients. They were divided into an ESD group of 175 people and a gastrectomy group of 100 people. The patient demographics, pathologic characteristics, length of hospital stay, complication rate and survival rate were compared. Results The complication rate was higher for the gastrectomy group than for the ESD group (15.0% vs. 5.1%, p=0.007). The average length of patient hospitalization was longer after gastrectomy than after ESD (8.6 days vs. 2.4 days, p<0.001). There were two cases of mortality in the surgery group within 30 days of procedure. The 5-year survival rates of the two groups did not show a statistically significant difference (92.0% vs. 93.3%, p=0.496). Conclusions The long-term survival rates of ESD and gastrectomy were not significantly different. The complication rate was lower for ESD than for gastrectomy, and the length of hospital stay was shorter after ESD than after gastrectomy.
Neural Entrainment to Rhythmically Presented Auditory, Visual, and Audio-Visual Speech in Children

Auditory cortical oscillations have been proposed to play an important role in speech perception. It is suggested that the brain may take temporal “samples” of information from the speech stream at different rates, phase resetting ongoing oscillations so that they are aligned with similar frequency bands in the input (“phase locking”). Information from these frequency bands is then bound together for speech perception. To date, there are no explorations of neural phase locking and entrainment to speech input in children. However, it is clear from studies of language acquisition that infants use both visual speech information and auditory speech information in learning. In order to study neural entrainment to speech in typically developing children, we use a rhythmic entrainment paradigm (underlying 2 Hz or delta rate) based on repetition of the syllable “ba,” presented in either the auditory modality alone, the visual modality alone, or as auditory-visual speech (via a “talking head”). To ensure attention to the task, children aged 13 years were asked to press a button as fast as possible when the “ba” stimulus violated the rhythm for each stream type. Rhythmic violation depended on delaying the occurrence of a “ba” in the isochronous stream. Neural entrainment was demonstrated for all stream types, and individual differences in standardized measures of language processing were related to auditory entrainment at the theta rate. Further, there was significant modulation of the preferred phase of auditory entrainment in the theta band when visual speech cues were present, indicating cross-modal phase resetting. The rhythmic entrainment paradigm developed here offers a method for exploring individual differences in oscillatory phase locking during development. In particular, a method for assessing neural entrainment and cross-modal phase resetting would be useful for exploring developmental learning difficulties thought to involve temporal sampling, such as dyslexia.
Image denoising using scale mixtures of Gaussians in the wavelet domain

We describe a method for removing noise from digital images, based on a statistical model of the coefficients of an overcomplete multiscale oriented basis. Neighborhoods of coefficients at adjacent positions and scales are modeled as the product of two independent random variables: a Gaussian vector and a hidden positive scalar multiplier. The latter modulates the local variance of the coefficients in the neighborhood, and is thus able to account for the empirically observed correlation between the coefficient amplitudes. Under this model, the Bayesian least squares estimate of each coefficient reduces to a weighted average of the local linear estimates over all possible values of the hidden multiplier variable. We demonstrate through simulations with images contaminated by additive white Gaussian noise that the performance of this method substantially surpasses that of previously published methods, both visually and in terms of mean squared error.
Neural Dynamics and Interactions in the Human Ventral Visual Pathway

The ventral visual pathway in the brain plays central role in visual object recognition. The classical model of the ventral visual pathway, which poses it as a hierarchical, distributed and feed-forward network, does not match the actual structure of the pathway, which is highly interconnected with reciprocal and non-hierarchical projections. Here we address three major consequences of this non-classical structure with regard to neural dynamics and interactions: (i) the model does not consider any extended information processing dynamics; (ii) the model does not allow for adaptive and recurrent interactions between areas; (iii) the model only characterizes evoked-response with no state-dependence from the neural context. To begin to address these gaps in the classical model, we focus on the categorical-selective regions in the ventral pathway and study the neural dynamics and interactions using intracranial electroencephalography (iEEG), which overcomes the limitations of spatiotemporal resolution in current non-invasive human neuroimaging techniques. With respect to the first consequence, we applied multivariate pattern analysis (MVPA) methods to the iEEG signal to analyze the dynamic roles of the word and face sensitive areas. We found that both areas demonstrated a similar multi-stage information processing dynamic wherein the representation in category-selective fusiform gyrus evolves from a gist category-level and similarity-based representation to an invariant and highly detailed individual representation over the course of 500 ms. In addition, our results also suggest a dissociation between structural and motion in the face processing streams. Regarding to the second consequence, we introduced a novel method termed Multi-Connection Pattern Analysis (MCPA) to extract the discriminant information about cognitive states solely from the shared activity between neural populations from the interacting brain areas. Our results on iEEG and fMRI data with MCPA support the hypothesis that individual-level exemplar information is not only encoded by the population activity within certain brain populations, but also represented through recurrent interactions between multiple distributed populations at the network level. Finally, to address the third consequence, we designed a two-stage generalized linear model to study the relationship between category tuning and the ongoing neural activity in category selective cortical areas. We used this model to demonstrate that endogenous activity modulates the category selective tuning in the post-stimulus evoked response, and the same aspects of endogenous activity that modulate tuning also predict perceptual behavior. Taken together, in this thesis we develop and apply statistical methods to assess the properties of the non-classical structure in the ventral visual stream, and highlight contributions of regions to multiple stages of processing through interactive and distributed computation that is influenced by ongoing neural context.
Using science to create a better place

Elvidge, D. & Kelman C. (2008) Using Science to Create a Better Place. Environment Agency. Title Using Science to Create a Better Place Science report Authors Danny Elvidge, Clive Kelman Contributors Great Britain, Environment Agency Staff, Great Britain. Environment Agency Edition illustrated Publisher Environment Agency, 2008 ISBN 1844328732, 9781844328734 Length 66 pages
Direct comparison of two different mesalamine formulations for the induction of remission in patients with ulcerative colitis: A double-blind, randomized study

Background: Mesalamine is the first‐line drug for the treatment of ulcerative colitis (UC). We directly compared the efficacy and safety of two mesalamine formulations for the induction of remission in patients with UC. Methods: In a multicenter, double‐blind, randomized study, 229 patients with mild‐to‐moderate active UC were assigned to 4 groups: 66 and 65 received a pH‐dependent release formulation of 2.4 g/day (pH‐2.4 g) or 3.6 g/day (pH‐3.6 g), respectively; 65 received a time‐dependent release formulation of 2.25 g/day (Time‐2.25 g), and 33 received placebo (Placebo). The drugs were administered three times daily for eight weeks. The primary endpoint was a decrease in the UC disease activity index (UC‐DAI). Results: In the full analysis set (n = 225) the decrease in UC‐DAI in each group was 1.5 in pH‐2.4 g, 2.9 in pH‐3.6 g, 1.3 in Time‐2.25 g and 0.3 in Placebo, respectively. These results demonstrate the superiority of pH‐3.6 g over Time‐2.25 g (P = 0.003) and the noninferiority of pH‐2.4 g to Time‐2.25 g. Among the patients with proctitis‐type UC, a significant decrease in UC‐DAI was observed in pH‐2.4 g and pH‐3.6 g as compared to Placebo, but not in Time‐2.25 g. No differences were observed in the safety profiles. Conclusions: Higher dose of the pH‐dependent release formulation was more effective for induction of remission in patients with mild‐to‐moderate active UC. Additionally, the pH‐dependent release formulation was preferable to the time‐dependent release formulation for patients with proctitis‐type UC (UMIN Clinical Trials Registry, no. C000000288). (Inflamm Bowel Dis 2010)
Late activation of the 9-oxylipin pathway during arbuscular mycorrhiza formation in tomato and its regulation by jasmonate signalling

The establishment of an arbuscular mycorrhizal (AM) symbiotic interaction is a successful strategy for the promotion of substantial plant growth, development, and fitness. Numerous studies have supported the hypothesis that plant hormones play an important role in the establishment of functional AM symbiosis. Particular attention has been devoted to jasmonic acid (JA) and its derivates, which are believed to play a major role in AM symbiosis. Jasmonates belong to a diverse class of lipid metabolites known as oxylipins that include other biologically active molecules. Recent transcriptional analyses revealed up-regulation of the oxylipin pathway during AM symbiosis in mycorrhizal tomato roots and indicate a key regulatory role for oxylipins during AM symbiosis in tomato, particularly those derived from the action of 9-lipoxygenases (9-LOXs). Continuing with the tomato as a model, the spatial and temporal expression pattern of genes involved in the 9-LOX pathway during the different stages of AM formation in tomato was analysed. The effects of JA signalling pathway changes on AM fungal colonization were assessed and correlated with the modifications in the transcriptional profiles of 9-LOX genes. The up-regulation of the 9-LOX oxylipin pathway in mycorrhizal wild-type roots seems to depend on a particular degree of AM fungal colonization and is restricted to the colonized part of the roots, suggesting that these genes could play a role in controlling fungal spread in roots. In addition, the results suggest that this strategy of the plant to control AM fungi development within the roots is at least partly dependent on JA pathway activation.
Transforming K-12 computing education

This critical perspective focuses on the new Advanced Placement® Computer Science Principles course and its place in the larger CS10K Initiative. CS Principles as defined by the College Board is a framework; several different, aligned curricula have been created, each with its own model of teacher professional development. Together, these courses have been piloted with hundreds of teachers and thousands of students. This perspective provides context for those efforts and discusses their status entering the critical year leading to the first official AP CS Principles courses (beginning in Fall 2016) and the first official AP CS Principles exam (Spring 2017).
Dynamic Performance of a Radial Weak Power System with Multiple Static VAR Compensators

This paper deals with the dynamic performance of a radial weak, heavily shunt compensated power system, with three Static Var Compensators (SVCs) of relatively large rating, installed at short distances from each other. Dynamic interactions between the SVCs control systems and between them and the network are analysed by using eigenvalues and frequency response techniques. Some noteworthy effects concerning the SVCs' regulators' stability, that may arise in such systems, are here described. These effects, revealed in the eigenvalue analysis, were confirmed in TNA simulations. A brief description of the mathematical formulation and the complete system data are also included.
Dont Breathe and Drive? Pollutants Lurk inside Vehicles

The ability of human immunodeficiency virus type 1 (HIV-1) to develop high levels of genetic diversity, and thereby acquire mutations to escape immune pressures, contributes to the difficulties in producing a vaccine. Possibly no single HIV-1 sequence can induce sufficiently broad immunity to protect against a wide variety of infectious strains, or block mutational escape pathways available to the virus after infection. The authors describe the generation of HIV-1 immunogens that minimizes the phylogenetic distance of viral strains throughout the known viral population (the center of tree [COT]) and then extend the COT immunogen by addition of a composite sequence that includes high-frequency variable sites preserved in their native contexts. The resulting COT+ antigens compress the variation found in many independent HIV-1 isolates into lengths suitable for vaccine immunogens. It is possible to capture 62% of the variation found in the Nef protein and 82% of the variation in the Gag protein into immunogens of three gene lengths. The authors put forward immunogen designs that maximize representation of the diverse antigenic features present in a spectrum of HIV-1 strains. These immunogens should elicit immune responses against high-frequency viral strains as well as against most mutant forms of the virus.
Natriuretic Peptides, Heart, and Adipose Tissue: New Findings and Future Developments for Diabetes Research

Natriuretic peptides (NPs) play a key role in cardiovascular homeostasis, counteracting the deleterious effects of volume and pressure overload and activating antibrotic and antihypertrophic pathways in the heart. N-terminal B-type NP (NT-proBNP) also is a promising biomarker of global cardiovascular risk in the general population, and there is increasing interest on its potential use in diabetic patients for screening of silent cardiovascular abnormalities, cardiovascular risk stratification, and guided intervention. Recently, both atrial NP (ANP) and B-type NP (BNP) have emerged as key mediators in the control of metabolic processes including the heart in the network of organs that regulate energy usage and metabolism. Epidemiological studies have shown that ANP and BNP are reduced in people with obesity, insulin resistance, and diabetes, and this deficiency may contribute to enhance their global cardiovascular risk. Moreover, ANP and BNP have receptors in the adipose tissue, enhance lipolysis and energy expenditure, and modulate adipokine release and food intake. Therefore, low ANP and BNP levels may be not only a consequence but also a cause of obesity, and recent prospective studies have shown that low levels of NT-proBNP and midregional proANP (MR-proANP) are a strong predictor of type 2 diabetes onset. Whether ANP and BNP supplementation may result in either cardiovascular or metabolic benefits in humans remains, however, to be established.
Human cutaneous C fibres activated by cooling, heating and menthol

Differential A‐fibre block of human peripheral nerves changes the sensation evoked by innocuous cooling (∼24°C) of the skin from ‘cold’ to ‘hot’ or ‘burning’, and this has been attributed to activity in unidentified unmyelinated fibres that is normally masked or inhibited by activity in Aδ cold fibres. Application of the TRPM8 agonist menthol to the skin evokes ‘burning/stinging’ as well as ‘cold’, and the unpleasant sensations are also enhanced by A‐fibre block. In this study we used microneurography to search for C fibres in human skin activated by cooling and menthol, which could be responsible for these phenomena. Afferent C fibres were classified by activity‐dependent slowing as Type 1A (polymodal nociceptor), Type 1B (mechanically insensitive nociceptor) or Type 2 (cold sensitive), and their responses to heating and cooling ramps were measured before and after topical application of menthol preparations (2–50%). The only C fibres activated by menthol were the Type 2 fibres, which discharged vigorously with innocuous cooling and were strongly activated and sensitized to cooling by menthol. Unlike an Aδ cold fibre, they continued to discharge at skin temperatures down to 0°C, and most (13/15) were also activated by heating. We propose that the Type 2 C fibres, although resembling Aδ cold fibres in their responses to innocuous cooling and menthol, have a more complex sensory function, colouring with a ‘hot‐burning’ quality the perceptions of low and high temperatures. Their bimodal thermoreceptive properties may help account for several puzzling psychophysical phenomena, such as ‘innocuous cold nociception’, ‘paradoxical heat’ and the thermal grill illusion, and also for some neuropathic pains.
Efficient combination of multiple hyperspectral data processing chains using binary decision trees

According to the technical literature, there is no classification algorithm which is able to extract different classes with the same quality. In this paper we introduce a novel methodology to build a multi-stage, hierarchical data processing approach that is able to combine the advantages of different processing chains, which may be best suited for specific classes. The combination process is carried out using a binary decision tree (BDT) structure where at each node the most useful input information source, in the form of different processing chains, is used, according to the outcome of a simple learning mechanism on small training/validation subsets. Final results are instead achieved by applying the designed BDT to the whole data set. The usefulness of the procedure is proved by extensive analysis of a standard test data set, the Indian Pine AVIRIS set.