Miracle-dz/UniFAR-FTUs huggingface dataset:
Excessive activity of cathepsin K is associated with cartilage defects in a zebrafish model of mucolipidosis II

SUMMARY The severe pediatric disorder mucolipidosis II (ML-II; also known as I-cell disease) is caused by defects in mannose 6-phosphate (Man-6-P) biosynthesis. Patients with ML-II exhibit multiple developmental defects, including skeletal, craniofacial and joint abnormalities. To date, the molecular mechanisms that underlie these clinical manifestations are poorly understood. Taking advantage of a zebrafish model of ML-II, we previously showed that the cartilage morphogenesis defects in this model are associated with altered chondrocyte differentiation and excessive deposition of type II collagen, indicating that aspects of development that rely on proper extracellular matrix homeostasis are sensitive to decreases in Man-6-P biosynthesis. To further investigate the molecular bases for the cartilage phenotypes, we analyzed the transcript abundance of several genes in chondrocyte-enriched cell populations isolated from wild-type and ML-II zebrafish embryos. Increased levels of cathepsin and matrix metalloproteinase (MMP) transcripts were noted in ML-II cell populations. This increase in transcript abundance corresponded with elevated and sustained activity of several cathepsins (K, L and S) and MMP-13 during early development. Unlike MMP-13, for which higher levels of protein were detected, the sustained activity of cathepsin K at later stages seemed to result from its abnormal processing and activation. Inhibition of cathepsin K activity by pharmacological or genetic means not only reduced the activity of this enzyme but led to a broad reduction in additional protease activity, significant correction of the cartilage morphogenesis phenotype and reduced type II collagen staining in ML-II embryos. Our findings suggest a central role for excessive cathepsin K activity in the developmental aspects of ML-II cartilage pathogenesis and highlight the utility of the zebrafish system to address the biochemical underpinnings of metabolic disease.
Effects of Multiple Stressors on Eelgrass Restoration Projects

We have been monitoring several restored eelgrass meadows in Puget Sound and in the Northwest, and have found variable success in terms of the systems achieving identified goals. The monitoring has shown (1) early transplant survival is moderate, and no greater than 80% under optimal circumstances; (2) spread of eelgrass transplants is slow, and under optimal (mesocosm) conditions may take 2 years to occur; (3) spread may depend on below-ground organic matter and processes, as well as on grazers and predators; (4) as the meadow matures, plant size may increase as density decreases, indicating that measures in addition to shoot density should be used; (5) higher than normal summer temperatures, seaweed blooms, bioturbator activity, propeller scars, anchor chain drag, and boat wakes may act as cumulative multiple stressors of eelgrass transplants; (6) sites with marginal conditions for eelgrass may support eelgrass in''good'' years but may be unsuitable during other years; (7) site assessments and experimental plantings are useful in evaluating a site prior to full transplanting; (8) monitoring should be conducted for at least 5 years following planting to understand long-term sustainability of the system; and, (9) reference sites are critical to interpreting results.
Semdimentological Analysis of the Western Terminus Region of the Matanuska Glacier, Alaska,

Abstract : Sedimentation at the terminus of the Matanuska Glacier has been found to be primarily subaerial in a 100- to 300-m wide, ice-cored zone paralleling the edge of the active ice. Certain physical and chemical characteristics of the ice and debris of the superglacial, englacial and basal zones of the glacier indicate the debris of the basal zone, the primary source of sediment, is entrained during freeze-on of meltwater, probably surficially derived, to the glacier sole. Till formation results from the melting of buried ice of the basal zone. Melt-out till inherits the texture and particle orientations of basal ice debris; other properties are not as well preserved. Most deposits result from resedimentation of till and debris by sediment gravity flows, meltwater sheet and rill flow, slump, spall, and ice ablation. Depositional processes are interrelated in the process of backwasting of ice-cored slopes. Sediment flows are the primary process of resedimentation. Their physical characteristics, multiple mechanisms of flow and deposition, and characteristics of their deposits vary with the water content of the flow mass. Deposits of each process are distinguished from one another by detailed analysis of their internal organization, geometry and dimensions, and the presence of other internal and related external features. Genetic facies are defined by these characteristics. The interrelationship of processes develops a composite depositional sequence defined in terms of genetic facies associations; an upper, resedimented facies association, a middile, till facies association, and a lower, subglacial-resedimental facies association. The lateral and vertical distribution of genetic facies within the associations is mainly nonrepetitive.
Reductive dechlorination of dichlorophenols in anaerobic pond sediments (Chapter 13). Book chapter

The time required for the microbially mediated dechlorination of chloroaromatics in anaerobic freshwater sediments may be dependent upon sediment microbial communities and physical characteristics, as well as chlorine position on the aromatic ring. To better understand such possible relationships, the authors studied the reductive dechlorination of three dichlorophenol isomers in anaerobic sediments collected every other month for a year from five sites in one pond. Numbers of specific dechlorinating microorganisms were estimated by a most proable number technique, and sediment temperature, pH, Eh, and organic carbon content were determined. Levels of dissolved organic carbon, sulfate, and nitrate also were quantified in water samples collected with the anaerobic sediments. The relative susceptibility of the 2,4-, 2,5-, and 3,4- isomers to dechlorination was determined in sediment slurries. Dechlorination to monochlorophenols required from 2 to more than 32 weeks for completion, with the relative rates being 2,4->2,5->3,4-. The number of specific dechlorinating microbes appears to be important in determining the time required for the transformation.
On Strategy-proofness and the Salience of Single-peakedness in a Private Goods Economy

We consider strategy-proof rules operating on a rich domain of preference profiles in a set up where multiple private goods have to be assigned to a set of agents with entitlements where preferences display satiation. We show that if the rule is in addition "desirable", in that it is tops-only, continuous, same-sided and individually rational with respect to the entitlements, then the preferences in the domain have to satisfy a variant of single-peakedness (referred to as semilattice single-peakedness). We also provide a converse of this main finding. It turns out that this domain coincides with the one already identified in a general set up with a public good. Finally, we relate semilattice single-peaked domains to well-known restricted domains under which strategy-proof and desirable rules do exist.
Parametric and non-parametric approaches for runoff and rainfall regionalization

The information on river flows is important for a number of reasons including; the construction of hydraulic structures for water management, for equitable distribution of water and for a number of environmental issues. The flow measurement devices are generally installed across the workspace at various locations to get data on river flows but due to a number of technical and accessibility issues, it is not always possible to get continuous data. The amount rainfall in a basin area also contributes towards the river flows and intense rainfall can cause flooding. The extended rainfall maps for the study areas to analyze these extreme events can be of great practical and theoretical interest. This thesis can be generally regarded as a work on catchment hydrology and mapping rainfall extremes to estimate certain hydrological variables that are not only useful for future research but also for practical designing and management issues. We analyzed a number of existing techniques available in literature to extend the hydrological information from gauged basin to ungauged basin; and suggested improvements. The three main frontiers of our work are: Monthly runoff regime regionalization, Flow duration curves (FDCs) regionalization and preparing rainfall hazardous maps. The proposed methods of regionalization for runoff regime and FDCs are tested for the basins located in northern Italy; whereas for rainfall extremes, the procedure is applied to the data points located in northern part of Pakistan
Weak lensing shear and aperture mass from linear to non-linear scales

We describe the predictions for the smoothed weak lensing shear, γ s , and aperture mass, M ap , of two simple analytical models of the density field: the minimal tree model and the stellar model. Both models give identical results for the statistics of the three-dimensional density contrast smoothed over spherical cells and only differ by the detailed angular dependence of the many-body density correlations. We have shown in previous work that they also yield almost identical results for the probability distribution function (PDF) of the smoothed convergence, κ s . We find that the two models give rather close results for both the shear and the positive tail of the aperture mass. However, we note that at small angular scales (θ s ≤ 2 arcmin) the tail of the PDF, P(M ap ), for negative M ap shows a strong variation between the two models, and the stellar model actually breaks down for θ s ≤ 0.4 arcmin and M ap < 0. This shows that the statistics of the aperture mass provides a very precise probe of the detailed structure of the density field, as it is sensitive to both the amplitude and the detailed angular behaviour of the many-body correlations. On the other hand, the minimal tree model shows good agreement with numerical simulations over all the scales and redshifts of interest, while both models provide a good description of the PDF, P(γ is ), of the smoothed shear components. Therefore, the shear and the aperture mass provide robust and complementary tools to measure the cosmological parameters as well as the detailed statistical properties of the density field.
The atomic struture of inversion domains and grain boundaries in wurtzite semonconductors : an investigation by atomistic modelling and high resolution transmission electron microscopy

Au cours de ce travail, nous avons etudie deux types de defauts interfaciaux: domaines d’inversion (DI) et joints de grains (JG) dans des semiconducteurs de structure wurtzite (nitrures- d’elements III, ZnO et l’heterostructure ZnO/GaN) en utilisant le MET haute resolution et la modelisation ab initio. Dans le cas des DI, nos analyses theoriques montrent qu'une configuration tete-a-tete avec une sequence d'empilement a l’interface AaBbAa-AcCaA (H4) est la structure la plus stable dans les composes binaires (nitrures et ZnO wurtzites). De plus, un gaz d’electrons (2DEG) ou de trous (2DHG) a 2 dimensions est forme pour les configurations « tete-a-tete » ou queue-a-queue. A l’interface ZnO/GaN, l'observation de MET tres haute resolution a confirme la configuration H4 avec une interface -Zn-O-Ga-N. Notre modelisation theorique a mis en evidence la formation d’un gas de trous a 2 dimensions a cette heterointerface. Nous avons aussi realise l’etude topologique, theorique et par MET des joints de grains de rotation autour de l’axe [0001] dans ces materiaux. Dans le GaN, nous avons trouve que les plans du joint sont simplement formes par des dislocations de type a deja connues pour le materiau en couche mince. Par contre, dans ZnO, la theorie topologique est completement demontree, et la dislocation [101 0] est une brique de base dans la constitution des joints de grains avec des cycles d’atomes 6-8-4-.
The IntraCONtinental BasinS (ICONS) Atlas - Applications in Eastern Australia

We have used a combination of openly available regional and global crustal and lithosphere datasets to create a framework for intracontinental basin evaluation. In this paper, we focus on the intracontinental Murray and Eromanga basins in eastern Australia. We assess the total sediment thickness versus crustal thinning observed underneath a given basin to evaluate alternative total tectonic subsi dence estimates, and alternative basin formation mechanisms. This is of particular interest for large intracontinental basins, which frequently display a history of slow subsidence over long time inter vals, even though they are located far away from active plate boundaries. These basins do not show signs of extensive brittle deformation, and continue subsiding long after initial thermal disturbances have decayed. Conventional basin models fail to explain the unexpected excess accumulation of sediments in these basins. Hence, this phenomenon is commonly referred to as ‘anomalous tectonic subsidence’. Our workfl ow combines the computation of various parameters from the raw data, such as anomalous sediment thickness or anomalous tectonic subsidence, and ties plate tectonic data together with dynamic topography models. The atlas is primarily focussed on the total tectonic subsidence (TTS). It is calculated alternatively based on total sediment thickness, or on the observed basement crustal thickness (BCT). Digital grids of these parameters illustrate differences between extension and tectonic subsidence estimates derived from ei ther sediment thickness in a given basin, or the amount of observed crustal thinning below the basement. We demonstrate that large-scale crustal structure data from global and regional datasets allows the computation of robust regional anomalous total tectonic subsidence estimates. The computed subsidence anomalies can then be compared with predictions of different models of basin formation, and provide a basis for further investigation of the causes of intracontinental basin subsidence. A web-based version of the ICONS atlas is available at: http://www.earthbyte. org/Resources/ICONS/index.html. For eastern Australia, the importance of mantle-driven dynamic topography through time can be clearly demonstrated in the Murray and Eromanga basins. The Tertiary marine flooding and sedimentation history of both basins can be reconstructed accurately if eustatic sea level fluctuations are com bined with a dynamic topography model and plate kinematics. Our results indicate that the interplay of eustatic sea level change and dynamic topography is responsible for observed anomlous tectonic subsidence patterns recorded in the Murray and Eromanga basins.
CHI '11 Extended Abstracts on Human Factors in Computing Systems

Over the last year or so, we have been blessed with the challenge, the opportunity, and the distinct pleasure of organizing the CHI 2011 Conference on Human Factors in Computing Systems, the premier international conference for the field of human-computer interaction. CHI 2011 takes place in gorgeous, energetic, sophisticated Vancouver BC, a city renowned for its innovation in entertainment, sustainability, accessibility, and inclusivity. The New York Times calls it, "a liquid city, a tomorrow city, equal parts India, China, England, France and the Pacific Northwest. " Vancouver lays a beautiful backdrop for our conference, which boasts nearly 30 years of wonderful work. Behind the success of the conference is our diverse community of faculty and students, of researchers and practitioners, of young and, well, also of experienced. It is a community of designers, technologists, psychologists, social scientists, biologists, artists, engineers, anthropologists, musicians; the list goes on. Wherever we are, we are always a community of near and far. Most impressively, ours is a community that cares deeply about innovating, learning, sharing, and interacting; all with the common goal of using technology to shape the way people around the world live and play. Returning attendees will recognize the general conference format - 2 days of small intimate workshops, followed by 4 days of technical content, all surrounded by social and intellectual exchanges. In addition to the familiar venues that form the core of the conference, we have also arranged various special events, such an keynotes by Howard Rheingold and Ethan Zuckerman; invited talks by ACM SIGCHI award winners Terry Winograd, Larry Tesler, Alan Newell, and Clayton Lewis; an HCI museum exhibit hosted by Bill Buxton; and a panel celebrating Stu Card's achievements and contributions to the field of HCI. With the record number of submissions and accepted content this year, we hope that you will utilize the print and electronic programs, but also the daily CHI Madness presentations that provide a glimpse of the day ahead. In the interest of continuing to evolve the conference to best serve our needs, we will experiment with shorter talks this year (20 minute slots for long pieces of content and 10 for shorter ones) to infuse even more energy into the program. We will also have a pretty full slate of social media applications to help you connect with other attendees and to provide you with the fullest experience possible.
Atom‐Interferometry Measurement of the Fine Structure Constant

Using an atom interferometer to measure the quotient of the reduced Planck's constant and the mass of a cesium‐133 atom ℏ/m Cs , the most accurate measurement of the fine structure constant α=1/137.035999046(27) is recorded, at an accuracy of 0.20 parts per billion (ppb). Using multiphoton interactions (Bragg diffraction and Bloch oscillations), the largest phase (12 million radians) of any Ramsey–Bordé interferometer and controlled systematic effects at a level of 0.12 ppb are demonstrated. Comparing the Penning trap measurements with the Standard Model prediction of the electron gyromagnetic anomaly ae based on the α measurement, a 2.5 σ tension is observed, rejecting dark photons as the reason for the unexplained part of the muon's gyromagnetic moment discrepancy at a 99% confidence level according to frequentist statistics. Implications for dark‐sector candidates (e.g., scalar and pseudoscalar bosons, vector bosons, and axial‐vector bosons) may be a sign of physics beyond the Standard Model. A future upgrade of the cesium fountain atom interferometer is also proposed to increase the accuracy of ℏ/m Cs by 1 to 2 orders of magnitude, which would help resolve the tension.
Public-Private Earnings Differentials during Economic Transition in Hungary

The paper explores the effect of economic transition on public-private sector pay differential across the pay distribution in Hungary from 1992 until 2003. Over the time period covered by the analysis the public sector had witnessed large-scale privatisations and restructuring through a number of wage reforms. The paper finds that both men and women in the public sector fared significantly worse than their private sector counterparts during 1990s, but this penalty declined to almost zero until 2003. The results from quantile regressions verified that the public sector pay distribution was more compressed than in the private sector and hence workers at and above the median fared significantly worse off having a public sector status even by the end of the period considered. These results are futher reinforced by the method of decomposition of differences in distributions. Moreover, the paper examines public sector pay penalties/premia for different skilled groups of workers. These results show that the public sector within-group earnings equalising effect for male graduates in Hungary was three times greater than the similar estimate reported by studies in developed market economies.
Un exemple de prévision des risques volcaniques au Pérou méridional (région d'Arequipa), fondé sur l'étude de l'activité éruptive récente du strato-volcan El Misti

L'analyse des produits eruptifs recents du volcan El Misti (Perou meridional) indique une alternance de dynamismes pliniens et peleens, avec des episodes de croissance et de destruction de domes produisant des coulees pyroclastiques. La derniere eruption majeure du Misti est survenue il y a 1920 ± 200 ans BP et environ 10 crises fumerolliennes ont eu lieu du XV e au XIX e siecle. Compte tenu de la courte distance separant la ville d'Arequipa (900 000 habitants) du cratere (15 km), le volcan fait peser au moins 5 types de menaces, parmi lesquelles les retombees pliniennes, les coulees pyroclastiques et les lahars ont tous une recurrence elevee dans un passe recent
Comparison of Species Distribution Models According to Location Data

We need to use the strength of each Species Distribution Model(SDM) because presence location data were only collected due to time and economic limitations in Korea. This study investigated and compared GAM(Generalized Additive Model) which is one of presence-absence models with Maxent(Maximum Entropy Model) which is one of presence only models according to location data(presence/absence data). The target species was Fisher(Martes pennanti) which is an endangered species in California, USA. We implemented environmental data such as topography, climate and vegetation, and applied models to sub-regions and study area. The results of this study were as follows. Firstly, GAM which used real presence and absence data was better than GAM which used pseudo-absence data and Maxent which used presence-only data. Secondly, Maxent was better than GAM when presence-only data were used. Lastly, each model which applied to different regions didn't predict other area well due to the difference of habitat environment and over-predicted outside of study area. We need to select an optimal model to predict a suitable habitat according to the type and distribution of location data.
ESTIMATING ACTIVE SUBSPACES WITH RANDOMIZED GRADIENT SAMPLING

In modern computer simulations, scientists and engineers seek to study the relationships between high-dimensional spaces of input parameters and quantities of interest. Due to the large number of input parameters and high cost of simulations, many methods have been proposed to reduce the dimension of the input parameter space. These methods often find small subsets or linear combinations of the input parameters that approximately preserve inputoutput relationships. This low-dimensional characterization of complex problems with hundreds or thousands of input parameters is a crucial tool for modern computer simulations. Active subspaces are powerful tools for identifying important directions in the high-dimensional space of input parameters [1, 2]. Let x 2 Rm be a vector of simulation inputs and assume that f(x) : Rm 7! R is the mapping between x and a quantity of interest. The active subspace is defined by the top n < m eigenvectors of the following m⇥m symmetric positive semidefinite matrix