Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling acoustic transmission loss due to sea ice cover

The propagation of underwater acoustic signals in polar regions is dominated by an upward refracting sound speed environment and the presence of a dynamic highly variable ice canopy. This paper provides an overview of the acoustic properties of sea ice and assesses the influence of ice canopy and water column properties on acoustic transmission loss for propagation within 20 km of a sound source at 20 m depth. The influence of the ice canopy is assessed first as a perfectly flat surface, and then as a statistically rough surface. A Monte Carlo method is used for the inclusion of ice deformation and roughness. This involves the creation of sets of synthetic ice profiles based on a given sea ice thickness distribution, followed by statistical methods for combining the output of individually evaluated ice realisations. The experimental situation being considered in the framing of this problem is that of an Autonomous Underwater Vehicle (AUV) operating within 50 m of the surface. This scenario is associated with a frequency band of interest of 9-12 kHz and a horizontal range of interest up to 20 km. The situation has been evaluated for a set of typical ice statistics using Ray and Beam acoustic propagation techniques. The sound speed profile (based on real data) results in a strong defocussing of direct path signals at ranges from 9-20 km and depths shallower than 50 m. This reduction in the signal strength of the direct path creates areas where the influence of surface reflected paths becomes significant. The inclusion of a perfectly flat ice layer reduces the transmission loss between 9-20 km by 15-50 dB. When the ice layer is included as a rough surface layer the results show a boost to signal strength of up to 8 dB in the small areas of maximum defocussing. Sea ice is a strongly time and space varying sea surface and exists in areas where defocussing of the direct path due to the sound speed profile reduces the range of direct path dominated transmission. This work presents methods for including a statistically relevant rough surface through a technique for generation of sets of surfaces based on ice deformation statistics. It outlines methods for including ice in acoustic modelling tools and demonstrates the influence of one set of ice statistics on transmission loss.
Named Entity Recognition in Wikipedia

Named entity recognition (NER) is used in many domains beyond the newswire text that comprises current gold-standard corpora. Recent work has used Wikipedia's link structure to automatically generate near gold-standard annotations. Until now, these resources have only been evaluated on newswire corpora or themselves. We present the first NER evaluation on a Wikipedia gold standard (WG) corpus. Our analysis of cross-corpus performance on WG shows that Wikipedia text may be a harder NER domain than newswire. We find that an automatic annotation of Wikipedia has high agreement with WG and, when used as training data, outperforms newswire models by up to 7.7%.
Mutations of the phage lambda nutL region that prevent the action of Nun, a site-specific transcription termination factor

Phage HK022 encodes a protein, Nun, that promotes transcription termination within the pL and pR operons of its relative, phage lambda. The lambda sequences required for termination had previously been shown to overlap the nut sites, which are essential for transcription antitermination during normal lambda growth. To further specify the Nun target and to determine its relation to the nut sites, we constructed deletion and base substitution mutations of the lambda nutL region and measured Nun-dependent reduction of the expression of a downstream reporter gene. The shortest construct that retained full Nun responsiveness was a 42-bp segment that included both boxA and boxB, sequences that have been implicated in lambda antitermination. Deletion of boxA reduced Nun termination, and deletion of both sequences eliminated Nun termination. Base substitutions in boxA and the proximal portion of boxB impaired Nun termination, while base substitutions between boxA and boxB, in the distal portion of boxB, and immediately downstream from boxB had no appreciable effect. The termination defect of all of the base substitution mutations was relieved by increasing the level of Nun protein; in contrast, the deletions and a multiple-base substitution did not regain full Nun responsiveness at elevated Nun concentrations. We also asked if these mutant nut regions retained their ability to interact with N, the lambda-encoded antitermination protein. A qualitative assay showed that mutations within boxA or boxB reduced interaction, while mutations outside boxA and boxB did not. These data show that (i) the recognition sites for N and Nun overlap to a very considerable extent but are probably not identical and (ii) a high concentration of Nun promotes its interaction with mutant nut sites, a behavior also reported to be characteristic of N.
Chronic Effects of Palmitate Overload on Nutrient-Induced Insulin Secretion and Autocrine Signalling in Pancreatic MIN6 Beta Cells

Background Sustained exposure of pancreatic β cells to an increase in saturated fatty acids induces pleiotropic effects on β-cell function, including a reduction in stimulus-induced insulin secretion. The objective of this study was to investigate the effects of chronic over supply of palmitate upon glucose- and amino acid-stimulated insulin secretion (GSIS and AASIS, respectively) and autocrine-dependent insulin signalling with particular focus on the importance of ceramide, ERK and CaMKII signalling. Principal Findings GSIS and AASIS were both stimulated by >7-fold resulting in autocrine-dependent activation of protein kinase B (PKB, also known as Akt). Insulin release was dependent upon nutrient-induced activation of calcium/calmodulin-dependent protein kinase II (CaMKII) and extracellular signal-regulated kinase (ERK) as their pharmacological inhibition suppressed GSIS/AASIS significantly. Chronic (48 h, 0.4 mM) palmitate treatment blunted glucose/AA-induced activation of CaMKII and ERK and caused a concomitant reduction (∼75%) in GSIS/AASIS and autocrine-dependent activation of PKB. This inhibition could not be attributed to enhanced mitochondrial fatty acid uptake/oxidation or ceramide synthesis, which were unaffected by palmitate. In contrast, diacylglycerol synthesis was elevated suggesting increased palmitate esterification rather than oxidation may contribute to impaired stimulus-secretion coupling. Consistent with this, 2-bromopalmitate, a non-oxidisable palmitate analogue, inhibited GSIS as effectively as palmitate. Conclusions Our results exclude changes in ceramide content or mitochondrial fatty acid handling as factors initiating palmitate-induced defects in insulin release from MIN6 β cells, but suggest that reduced CaMKII and ERK activation associated with palmitate overload may contribute to impaired stimulus-induced insulin secretion.
Heterogeneity in storage pool deficiency: studies on granule-bound substances in 18 patients including variants deficient in alpha-granules, platelet factor 4, beta-thromboglobulin, and platelet-derived growth factor.

Patients with storage pool deficiency (SPD) have been found previously to have diminished amounts of substances that are stored in platelet-dense granules (storage pool ATP and ADP, calcium. and serotonin) and impaired platelet aggregation responses. In these studies on 1 8 patients with SPD. we measured. in addition to these dense granule substances, platelet factor 4 (PF4). /1-thromboglobulin (/ITG). heparin-neutralizing activity (HNA). fibrinogen. and platelet-derived growth factor (PDGF). In addition, we quantified the number of a-granules. dense granules. and mitochondria in their platelets. Our findings demonstrated several defects that identified subtypes of SPD. In two groups of patients (seven patients with albinism and four miscellaneous unrelated patients). we found only a deficiency of dense granules and dense granule substances (#{212}-SPD). In the seven other patients. we observed variable deficiencies of a-granules and of HNA. PF4. 9TG. fibrinogen. and PDGF in addition to dense granule defects. We have designated ab-SPD as the subtype in one patient who showed the greatest a-granule defects. whereas partial deficiencies of a-granules and granule-bound substances were observed in six members of two unrelated families (a 6-SPD). The levels of three secretable acid hydrolases (/3-glucuronidase, /9-N-acetylglucosaminidase, and /3-galactosidase) were normal in all groups of patients. including those with a-granule defects. In addition to identifying subtypes within the SPD syndrome. our findings support the view that PDGF, PF4, /9TG. and fibrinogen are stored in a-granules. whereas secretable acid hydrolases are stored in other organelles. The findings in this study further suggest that SPD could be the result of several abnormalities of granule morphogenesis in the megakaryocyte.
Memory-optimal neural network approximation

We summarize the main results of a recent theory—developed by the authors—establishing fundamental lower bounds on the connectivity and memory requirements of deep neural networks as a function of the complexity of the function class to be approximated by the network. These bounds are shown to be achievable. Specifically, all function classes that are optimally approximated by a general class of representation systems—so-called affine systems—can be approximated by deep neural networks with minimal connectivity and memory requirements. Affine systems encompass a wealth of representation systems from applied harmonic analysis such as wavelets, shearlets, ridgelets, α-shearlets, and more generally α-molecules. This result elucidates a remarkable universality property of deep neural networks and shows that they achieve the optimum approximation properties of all affine systems combined. Finally, we present numerical experiments demonstrating that the standard stochastic gradient descent algorithm generates deep neural networks which provide close-to-optimal approximation rates at minimal connectivity. Moreover, stochastic gradient descent is found to actually learn approximations that are sparse in the representation system optimally sparsifying the function class the network is trained on.
Network information flow

We introduce a new class of problems called network information flow which is inspired by computer network applications. Consider a point-to-point communication network on which a number of information sources are to be multicast to certain sets of destinations. We assume that the information sources are mutually independent. The problem is to characterize the admissible coding rate region. This model subsumes all previously studied models along the same line. We study the problem with one information source, and we have obtained a simple characterization of the admissible coding rate region. Our result can be regarded as the max-flow min-cut theorem for network information flow. Contrary to one's intuition, our work reveals that it is in general not optimal to regard the information to be multicast as a "fluid" which can simply be routed or replicated. Rather, by employing coding at the nodes, which we refer to as network coding, bandwidth can in general be saved. This finding may have significant impact on future design of switching systems.
The invariant chain is required for intracellular transport and function of major histocompatibility complex class II molecules

The major histocompatibility complex (MHC) class II-associated invariant chain (Ii) is thought to act as a chaperone that assists class II during folding, assembly, and transport. To define more precisely the role of Ii chain in regulating class II function, we have investigated in detail the biosynthesis, transport, and intracellular distribution of class II molecules in splenocytes from mice bearing a deletion of the Ii gene. As observed previously, the absence of Ii chain caused significant reduction in both class II-restricted antigen presentation and expression of class II molecules at the cell surface because of the intracellular accumulation of alpha and beta chains. Whereas much of the newly synthesized MHC molecules enter a high molecular weight aggregate characteristic of misfolded proteins, most of the alpha and beta chains form dimers and acquire epitopes characteristic of properly folded complexes. Although the complexes do not bind endogenously processed peptides, class II molecules that reach the surface are competent to bind peptides added to the medium, further demonstrating that at least some of the complexes fold properly. Similar to misfolded proteins, however, the alpha and beta chains are poorly terminally glycosylated, suggesting that they fail to reach the Golgi complex. As demonstrated by double label confocal and electron microscope immunocytochemistry, class II molecules were found in a subcompartment of the endoplasmic reticulum and in a population of small nonlysosomal vesicles possibly corresponding to the intermediate compartment or cis-Golgi network. Thus, although alpha and beta chains can fold and form dimers on their own, the absence of Ii chain causes them to be recognized as "misfolded" and retained in the same compartments as bona fide misfolded proteins.
Studies on Mechanical Properties of SCC with Construction and Demolition Waste as Coarse and Fine Aggregates

India being a fast growing economy has caused a boost in the construction industry. Increase in construction activities has resulted in accumulation of construction and demolition waste. These waste materials like mortar, concrete, tiles, glass, wood etc being non-biodegradable lead to pollution and also waste of land resource when used as dumping yards. As a solution to this problem these waste generated must be reduced, reused and recycled. For this purpose the coarse and fine aggregate content in SCC is attempted to be replaced by crushed construction and demolition waste. The objective of the research project is to study the mechanical properties of SCC when the fine aggregates are replaced by C&D waste in different percentages and hence to find the optimum replacement. Two cases will be investigated with five different types of C&D waste ie concrete waste, mortar waste, crushed tiles and manufactured sand as fine aggregate and recycled concrete aggregate as coarse aggregate where in one only the fine aggregate will be replaced where as in the second both coarse and fine aggregate will be replaced simultaneously .
Spatial properties of koniocellular cells in the lateral geniculate nucleus of the marmoset Callithrix jacchus

The receptive field dimensions, contrast sensitivity and linearity of spatial summation of koniocellular (KC), parvocellular (PC) and magnocellular (MC) cells in the lateral geniculate nucleus (LGN) of 11 adult marmosets were measured using achromatic sinusoidal gratings. The receptive field centre diameter of cells in each (PC, KC and MC) class increases with distance from the fovea. There is substantial overlap in centre size between the three cell classes at any eccentricity, but the PC cells have, on average, the smallest centres and the KC cells have the largest. Some PC and KC cells did not respond at all to the grating stimulus. The contrast sensitivity of the receptive field centre mechanism in KC cells decreases in proportion to the centre area. A similar trend was seen for the surround mechanism. These characteristics are common to PC and MC cells, suggesting that they originate at an early stage of visual processing in the retina. The KC cells showed, in general, lower peak evoked discharge rates than PC or MC cells. The spontaneous discharge rate of KC cells was lower than that of PC cells and similar to that of MC cells. The majority of cells in all divisions of the LGN show linear spatial summation. A few cells did show non‐linear spatial summation; these cells were predominantly located in the MC and ventral KC layers. The ventral KC layers below and between the MC layers contain cells with larger and more transiently responding receptive fields than cells in the more dorsal KC layers. We conclude that many of the contrast‐dependent spatial properties of cells in the marmoset LGN are common to PC, MC and KC cells. The main difference between KC cells and the other two classes is that there is more variability in their response properties, and they are less responsive to high spatial frequencies.
Mining the web for points of interest

A point of interest (POI) is a focused geographic entity such as a landmark, a school, an historical building, or a business. Points of interest are the basis for most of the data supporting location-based applications. In this paper we propose to curate POIs from online sources by bootstrapping training data from Web snippets, seeded by POIs gathered from social media. This large corpus is used to train a sequential tagger to recognize mentions of POIs in text. Using Wikipedia data as the training data, we can identify POIs in free text with an accuracy that is 116% better than the state of the art POI identifier in terms of precision, and 50% better in terms of recall. We show that using Foursquare and Gowalla checkins as seeds to bootstrap training data from Web snippets, we can improve precision between 16% and 52%, and recall between 48% and 187% over the state-of-the-art. The name of a POI is not sufficient, as the POI must also be associated with a set of geographic coordinates. Our method increases the number of POIs that can be localized nearly three-fold, from 134 to 395 in a sample of 400, with a median localization accuracy of less than one kilometer.
Effect of Acute Coronary Artery Occlusion on Local Myocardial Extracellular K+ Activity in Swine

We studied the time course, magnitude and homogeneity of the change in extracellular myocardial potassium activity after acute ligation of the left anterior descending coronary artery in pigs using potassium-sensitive electrodes made from a valinomycin-polyvinyl chloride matrix membrane. We also studied the relationship betweein the changes in potassium activity and the simultaneous changes in ventricular activation using the reference barrel of the K+ electrode to record ventricular electrograms. We found that the K+ rose sooner, more rapidly and to higher levels than previously reported. The K+ changes occurred in three phases: a phase of rapidly rising K+ that began within seconds of the ligation and lasted 5–15 minutes, a plateau phase that lasted approximately 15 minutes and a phase of slowly rising K+ that extended throughout the longest occlusion (60 minutes) used in this study. The K+ changes were reversed by release of the occlusion during the rapidly rising and plateau phases, but were not reversed by release of the occlusion during the phase of slowly rising K+. Inhomogeneities in the K+ rise appeared between the center and lateral margins of the midmyocardial ischemic zone, between the subendocardium and the subepicardium in the center of the ischemic zone, and between closely spaced electrodes located in the midmyocardial center of the ischemic zone. Thus, the change in K+ activity, as recorded by our electrodes, can be considered an excellent marker of ischemia. Changes in ventricular activation paralleled the K+ rise, the inhomogeneities of K+ rise and the reversal of the K+ rise after release but could not be entirely explained by the change in K+.
The power of the AC-DC circuit: Operating principles of a simple multi-functional transcriptional network motif

Genetically encoded regulatory circuits control biological function. A major focus of systems biology is to understand these circuits by establishing the relationship between specific structures and functions. Of special interest are multifunctional circuits that are capable of performing distinct behaviors without changing their topology. A particularly simple example of such a system is the AC-DC circuit. Found in multiple regulatory processes, this circuit consists of three genes connected in a combination of a toggle switch and a repressilator. Using dynamical system theory we analyze the available dynamical regimes to show that the AC-DC can exhibit both oscillations and bistability. We found that both dynamical regimes can coexist robustly in the same region of parameter space, generating novel emergent behaviors not available to the individual subnetwork components. We demonstrate that the AC-DC circuit provides a mechanism to rapidly switch between oscillations and steady expression and, in the presence of noise, the multi-functionality of the circuit offers the possibility to control the coherence of oscillations. Additionally, we provide evidence that the availability of a bistable oscillatory regime allows the AC-DC circuit to behave as an excitable system capable of stochastic pulses and spatial signal propagation. Taken together these results reveal how a system as simple as the AC-DC circuit can produce multiple complex dynamical behaviors in the same parameter region and is well suited for the construction of multifunctional synthetic genetic circuits. Likewise, the analysis reveals the potential of this circuit to facilitate the evolution of distinct patterning mechanisms.
Effects of Global Warming on Ancient Mammalian Communities and Their Environments

Background Current global warming affects the composition and dynamics of mammalian communities and can increase extinction risk; however, long-term effects of warming on mammals are less understood. Dietary reconstructions inferred from stable isotopes of fossil herbivorous mammalian tooth enamel document environmental and climatic changes in ancient ecosystems, including C3/C4 transitions and relative seasonality. Methodology/Principal Findings Here, we use stable carbon and oxygen isotopes preserved in fossil teeth to document the magnitude of mammalian dietary shifts and ancient floral change during geologically documented glacial and interglacial periods during the Pliocene (∼1.9 million years ago) and Pleistocene (∼1.3 million years ago) in Florida. Stable isotope data demonstrate increased aridity, increased C4 grass consumption, inter-faunal dietary partitioning, increased isotopic niche breadth of mixed feeders, niche partitioning of phylogenetically similar taxa, and differences in relative seasonality with warming. Conclusion/Significance Our data show that global warming resulted in dramatic vegetation and dietary changes even at lower latitudes (∼28°N). Our results also question the use of models that predict the long term decline and extinction of species based on the assumption that niches are conserved over time. These findings have immediate relevance to clarifying possible biotic responses to current global warming in modern ecosystems.