Miracle-dz/UniFAR-FTUs huggingface dataset:
Anti-angiogenic therapy affects the relationship between tumor vascular structure and function : a correlation study between micro-CT angiography and DCE-MRI

Purpose: To compare the effects of two anti-angiogenic drugs, bevacizumab and a cytosolic phospholipase A2-α inhibitor (AVX235), on the relationship between vascular structure and dynamic contrast enhanced (DCE)-MRI measurements in a patient-derived breast cancer xenograft model. Methods: Mice bearing MAS98.12 tumors were randomized into three groups: bevacizumab-treated (n=9), AVX235-treated (n=9), and control (n=8). DCE-MRI was performed pre-and post-treatment. The median initial area under the concentration-time curve (IAUC60) and volume transfer constant (Ktrans) were computed for each tumor. The tumors were excised for ex vivo micro-CT angiography, from which the vascular surface area (VSA) and fractional blood volume (FBV) were computed. Spearman correlation coefficients (ρ) were computed to evaluate the associations between the DCE-MRI and micro-CT parameters. Results: With the groups pooled, IAUC60 and Ktrans correlated significantly with VSA (ρ=0.475 and 0.527, P=0.019 and 0.008). There were no significant correlations within the control group. There were various significant correlations within the treatment groups but the correlations in the bevacizumab group were of opposite sign, e.g., Ktrans vs. FBV: AVX235 ρ=0.800 (P=0.014), bevacizumab ρ=-0.786 (P=0.023). Conclusion: DCE-MRI measurements can highly depend on vascular structure. The relationship between vascular structure and function changed markedly after antiangiogenic treatment.
Lawrence Berkeley National Laboratory Recent Work Title Assessing the observed impact of anthropogenic climate change Permalink

Impacts of recent regional changes in climate on natural and human systems are documented across the globe, yet studies explicitly linking these observations to anthropogenic forcing of the climate are scarce. Here we provide a systematic assessment of the role of anthropogenic climate change for the range of impacts of regional climate trends reported in the IPCC’s Fifth Assessment Report. We find that almost two-thirds of the impacts related to atmospheric and ocean temperature can be confidently attributed to anthropogenic forcing. In contrast, evidence connecting changes in precipitation and their respective impacts to human influence is still weak. Moreover, anthropogenic climate change has been a major influence for approximately three quarters of the impacts observed on continental scales. Hence the effects of anthropogenic emissions can now be discerned not only globally, but also at more regional and local scales for a variety of natural and human systems.
Computing the Cassels-Tate pairing on 3-isogeny Selmer groups via cubic norm equations

We explain a method for computing the Cassels-Tate pairing on the 3-isogeny Selmer groups of an elliptic curve. This improves the upper bound on the rank of the elliptic curve coming from a descent by 3-isogeny, to that coming from a full 3-descent. One ingredient of our work is a new algorithm for solving cubic norm equations, that avoids the need for any S-unit computations. As an application, we show that the elliptic curves with torsion subgroup of order 3 and rank at least 13, found by Eroshkin, have rank exactly 13.
Some uses of structural equation modeling in validity studies: Extending IRT to external variables

A device for cutting and welding a plastic band for use in an automatic strapping machine, which comprises: a table provided with a cutting and welding mechanism thereunder; an upper band holding member which is supposed to hold the tip of the strapping band when said band is completely fed to cover the full length of the bottom of the table; a lower band holding member having a projection, which is disposed under the upper band holding member; and pectinate heat blades which are supposed to melt and penetrate the overlapped two portions of the band and thereafter weld them by the energy of a press member.
Thermodynamics of rotating thin shells in the BTZ spacetime

We investigate the thermodynamic equilibrium states of a rotating thin shell, i.e., a ring, in a ($2+1$)-dimensional spacetime with a negative cosmological constant. The inner and outer regions with respect to the shell are given by the vacuum anti-de Sitter and the rotating Ba\~nados-Teitelbom-Zanelli spacetimes, respectively. The first law of thermodynamics on the thin shell, together with three equations of state for the pressure, the local inverse temperature and the thermodynamic angular velocity of the shell, yields the entropy of the shell, which is shown to depend only on its gravitational radii. When the shell is pushed to its own gravitational radius and its temperature is taken to be the Hawking temperature of the corresponding black hole, the entropy of the shell coincides with the Bekenstein-Hawking entropy. In addition, we consider simple ans\"atze for the equations of state, as well as a power-law equation of state where the entropy and the thermodynamic stability conditions can be examined analytically.
2 0 O ct 2 01 7 Area deficits and the Bel-Robinson tensor

The first law of causal diamonds relates the area deficit of a small ball relative to flat space to the matter energy density it contains. At second order in the Riemann normal coordinate expansion, this energy density should receive contributions from the gravitational field itself. In this work, we study the second-order area deficit of the ball in the absence of matter and analyze its relation to possible notions of gravitational energy. In the small ball limit, any proposed gravitational energy functional should evaluate to the Bel-Robinson energy density W in vacuum spacetimes. A direct calculation of the area deficit reveals a result that is not simply proportional to W . We discuss how the deviation from W is related to ambiguities in defining the shape of the ball in curved space, and provide several proposals for fixing these shape ambiguities.
Autonomous navigation performance during the Hartley 2 comet flyby

On November 4, 2010, the EPOXI spacecraft performed a 700-km flyby of the comet Hartley 2 as follow-on to the successful 2005 Deep Impact prime mission. EPOXI, an extended mission for the Deep Impact Flyby spacecraft, returned a wealth of visual and infrared data from Hartley 2, marking the fifth time that high-resolution images of a cometary nucleus have been captured by a spacecraft. The highest resolution science return, captured at closest approach to the comet nucleus, was enabled by use of an onboard autonomous navigation system called AutoNav. AutoNav estimates the comet-relative spacecraft trajectory using optical measurements from the Medium Resolution Imager (MRI) and provides this relative position information to the Attitude Determination and Control System (ADCS) for maintaining instrument pointing on the comet. For the EPOXI mission, AutoNav was tasked to enable continuous tracking of a smaller, more active Hartley 2, as compared to Tempel 1, through the full encounter while traveling at a higher velocity. To meet the mission goal of capturing the comet in all MRI science images, position knowledge accuracies of ± 3.5 km (3-σ) cross track and ± 0.3 seconds (3-σ) time of flight were required. A flight-code-in-the-loop Monte Carlo simulation assessed AutoNav’s statistical performance under the Hartley 2 flyby dynamics and determined optimal configuration. The AutoNav performance at Hartley 2 was successful, capturing the comet in all of the MRI images. The maximum residual between observed and predicted comet locations was 20 MRI pixels, primarily influenced by the center of brightness offset from the center of mass in the observations and attitude knowledge errors. This paper discusses the Monte Carlo-based analysis that led to the final AutoNav configuration and a comparison of the predicted performance with the flyby performance.
SHCal13 Southern Hemisphere Calibration, 0–50,000 Years cal BP

The Southern Hemisphere SHCal04 radiocarbon calibration curve has been updated with the addition of new data sets extending measurements to 2145 cal BP and including the ANSTO Younger Dryas Huon pine data set. Outside the range of measured data, the curve is based upon the ern Hemisphere data sets as presented in IntCal13, with an interhemispheric offset averaging 43 ± 23 yr modeled by an autoregressive process to represent the short-term correlations in the offset.
truncatus ) in the Eastern 1 Mediterranean Sea 2 3 4

21 The drivers of population differentiation in oceanic dispersal organisms have been crucial for research in 22 evolutionary biology. Adaptation to different environments is commonly invoked as an alternative to geographic 23 isolation, as a driver of differentiation in the oceans. In this study, we investigate the population structure and 24 phylogeography of the bottlenose dolphin (Tursiops truncatus) in the Mediterranean Sea, using microsatellite 25 loci and the entire mtDNA control region. By further comparing the Mediterranean populations with the well 26 described Atlantic populations, we addressed the following hypotheses: 1) bottlenose dolphins show population 27 structure within the environmentally complex Eastern Mediterranean Sea; 2) population structure was gained 28 locally or otherwise results from chance distribution of pre-existing genetic structure; 3) strong demographic 29 variations within the Mediterranean basin have affected genetic variation sufficiently to bias detected patterns of 30 population structure. Our results suggest that bottlenose dolphin exhibits population structures that correspond 31 well to the main Mediterranean basins. Furthermore, we found evidence for fine-scale population division 32 within the Adriatic and the Levantine seas. We further describe for the first time, a distinction between 33 populations inhabiting pelagic and coastal regions within the Mediterranean. Phylogeographic analysis, 34 suggests that current genetic structure results mostly from stochastic distribution of Atlantic genetic variation, 35 resulting from a recent post-glacial expansion. Comparison with Atlantic mtDNA haplotypes, further suggest 36 the existence of a metapopulation across North Atlantic/Mediterranean, with pelagic regions acting as source for 37 coastal environments. 38 39 40
Diurnal activity patterns suggest nocturnal foraging in Northern Fulmar (Fulmarus glacialis) / Dagligt virksemi hjá havhesti (Fulmarus glacialis) bendir á, at hann leitar sær føði um náttina

Urtak Eygleiðingar við myndatolum av i alt 12 havhestareiðrum i Foroyum arini 2006 (sjey reiður) og 2007 (fimm reiður) vistu, at greiður samanhangur var millum, naer havhesturin kom til og for av reiðrinum, og daglongd, solarris og solsetur. Við tveimum undantokum vorðu oll skiftini a reiðrinum gjord millum kl. 7 um morgunin og kl. 19 um kvoldið. Ungarnir vorðu sum oftast mataðir millum kl. 9 um morgunin og kl. 18 um kvoldið. Hesar eygleiðingar saman við urslitunum fra eini foðikanning, ið visti týdningin av prikkafiski sum foði, geva goða abending um, at havhesturin leitar saer foði um nattina. A bstract The continued camera observations of nest­site attendance at a total of 12 nests in 2006 (7 nests) and 2007 (5 nests) showed a strong correlation between nest­site attendance and sunrise, day patterns. Optical devices for night observations have been available for a long time but have rarely been used to study nest­site attendance by this species. I studied the daily nest­site attendance, chick feeding schedule and incubation rhythm of the Northern Fulmar at a small colony on the Faroe Islands throughout night and day for two years using surveillance cameras with infrared LEDs. The attendance patterns were analysed to see if they correlated to sunrise, sunset and day length and analysed in relation to time of day for incubation shifts, and feeding of the chicks. Since a previous study showed that the diurnally migrating Glacier lantern fish ( Benthosema glaciale ) was an important part of the diet of the Northern Fulmars on the Faroe Islands (Danielsen et al., 2010), I postulate that the birds would be away from the colony at night, in order to forage out at sea. Furthermore underlining the importance of doing observations during both day and night is the fact that although birds might show signs of breeding by staying faithfully at the nest and apparently incubate during day­time, this is not necessarily true when also adding observations during the night. This can easily lead to biased estimates regarding how many of the birds in the colony are actually producing eggs. This information is important for e.g. estimating breeding colony size (Mallory and Forbes, 2007).
Title Defining the functional surface of the Est 2 catalytic subunit of yeast telomerase

ix Introduction.1 Materials and Methods.5 Chapter 1: A novel strategy for identifying separation-of-function mutations in EST2.8 Chapter 2: Domain by domain analysis of EST2.10 Chapter 2.1: TEN Domain.10 Chapter 2.2: RNA Binding Domain.12 Chapter 2.3: Reverse Transcriptase Domain.13 Chapter 2.4: C-terminal Domain.13 Chapter 3: Genetic Analysis.15 Figures and Tables.16 Supplemental Figures.33 Discussion.36 References.38
Living with Bushfire Risk: Social and Environmental Influences on Preparedness

This paper discusses the process of developing a model capable of informing the development of community outreach strategies to facilitate the sustained adoption of bushfire preparedness measures. Following the identification of anomalies in defining the predictors of preparedness, a qualitative study of the reasoning processes that influence whether or not people decided to prepare for bushfire hazards is presented. The findings of the qualitative study are used to revise the preparedness model. Finally, using data from 482 residents in high bushfire risk areas in Hobart, the ability of the revised model to account for differences in levels of household preparedness is discussed.
Molecular characterization of three soil-borne sugar beet-infecting viruses based on the coat protein gene.

SUMMARY Sugar beet (Beta vulgaris L. ssp. vulgaris) hosts the soil-borne viruses Beet necrotic yellow vein virus (BNYVV), Beet soil-borne virus (BSBV), Beet soil-borne mosaic virus (BSBMV) and Beet virus Q (BVQ). Only a few isolates of these viruses have been characterized at the coat protein (CP) gene level. In this work, CP gene sequences were determined of three isolates each of BNYVV, BSBV and BVQ from different parts of Poland (Wielkopolska, Mazowsze and Dolny Slask). Phylogenetic analysis showed that Polish BNYVV isolates belong to the A and B type groups. The CP gene of the three BSBV isolates had 98-100% identity with comparable sequences available in GenBank. CP genes of the three BVQ isolates were almost identical to one another (9899%) and contained three additional nucleotides, resulting in a further amino acid residue (arginine) at position 86, as reported by Lennefors et al. (2005).
Sensitivity of the mussel Mytilus edulis to substrate‑borne vibration in relation to anthropogenically generated noise

© 2015 Inter-Research. Many anthropogenic activities in the oceans involve direct contact with the seabed (for example pile driving), creating radiating particle motion waves. However, the consequences of these waveforms to marine organisms are largely unknown and there is little information on the ability of invertebrates to detect vibration, or indeed the acoustic component of the signal. We quantified sensitivity of the marine bivalve Mytilus edulis to substrate-borne vibration by exposure to vibration under controlled conditions. Sinusoidal excitation by tonal signals at frequencies within the range 5 to 410 Hz was applied during the tests, using the 'staircase' method of threshold determination. Thresholds were related to mussel size and to seabed vibration data produced by anthropogenic activities. Clear behavioural changes were observed in response to the vibration stimulus. Thresholds ranged from 0.06 to 0.55 m s -2 (acceleration, root mean squared), with valve closure used as the behavioural indicator of reception and response. Thresholds were shown to be within the range of vibrations measured in the vicinity of anthropogenic operations such as pile driving and blasting. The responses show that vibration is likely to impact the overall fitness of both individuals and mussel beds of M. edulis due to disruption of natural valve periodicity, which may have ecosystem and commercial implications. The observed data provide a valuable first step to understanding the impacts of such vibration upon a key coastal and estuarine invertebrate which lives near industrial and construction activity, and illustrate that the role of seabed vibration should not be underestimated when assessing the impacts of noise pollution.
Lawrence Berkeley National Laboratory Recent Work Title Demosaicing : Image reconstruction from color CCD samples

A simplified color image formation model is used to construct an algorithm for image reconstruction from CCD sensors' samples. The proposed method involves two successive steps. The first is motivated by Cok's [1] template matching technique, while the second step uses steerable inverse diffusion in color. Classical linear signal processing techniques tend to over smooth the image and result in noticeable color art effects along edges and sharp features. The question is how should the different color channels support each other to form the best possible reconstruction. Our answer is to let the edges support the color information, and the color channels support the edges, and thereby achieve better perceptual results than those that are bounded by the sampling theoretical limit.
A co-locating fast file system for UNIX

The Co-locating Fast File System (C-FFS) was first developed by Greg Ganger and Frans Kaashoek[1]. Like their earlier design, the Co-locating Fast File System described in this thesis improves small file performance through the use of embedded indoes, co-location of related small files on disk, and aggressive prefetching. This thesis moves beyond the earlier work to present a design and working implementation of a UNIX C-FFS. Unlike the earlier design, this file system provides strict UNIX semantics. The thesis goes into detail about the changes necessary to integrate the co-location and pre-fetching algorithms into a modern UNIX operating system. Novel co-location algorithms, which allow for co-location based on arbitrary criteria, are presented. The thesis presents benchmarks which show that C-FFS achieve near 90% of the disk bandwidth of large file reads on small file reads. Embedding inodes in directories provides most of the gain in bandwidth by allowing the file system to place all data relevant to a file on the same track. Thesis Supervisor: M. Frans Kaashoek Title: Associate Professor
Comparison of the performance of statistical models that predict soil respiration from forests.

Soil respiration (Rs) is an important source of CO 2 to the atmosphere, yet understanding the processes controlling the combined autotrophic and heterotrophic components has proven challenging. Numerous statistical models have been developed to explain Rs as a function of physical and chemical conditions, but there has been little effort to systematically evaluate and compare the performance of these different models. Soils in a sugar maple (Acer saccharum Marsh.) forest were monitored for Rs and its physical and chemical drivers, and the monitored data were used to fit the most common of these statistical models. Each model was fit using a repeated trials approach and the performance of the model was evaluated with a range of goodness-of-fit measures (RMSE, mean absolute error, r 2 , index of agreement, bias, and Akaike information criterion). An exponential model in which the exponent is a polynomial expression that is linear with respect to temperature (°C) and quadratic with respect to soil moisture (% by volume) explained 57% of the variance in Rs and performed well among the goodness-of-fit measures. Inclusion of C quantity and substrate quality (as measured by the C/N ratio) in the soils, however, increased the explanation of variance in Rs to 71%. This study shows that combining soil temperature and moisture drivers with soil C quantity and substrate quality significantly improves statistical models predicting soil respiration. Our findings support the comparison of the performance of different statistical models using a repeated trials approach coupled with a range of goodness-of-fit measures to identify controls on Rs within an ecosystem and to assess the generality of these controls on Rs across ecosystems.
Evaluating atmospheric methane inversion model results for Pallas, northern Finland

A state-of-the-art inverse model, CarbonTracker Data Assimilation Shell (CTDAS), was used to optimize estimates of methane (CH4) surface fluxes using atmospheric observations of CH4 as a constraint. The model consists of the latest version of the TM5 atmospheric chemistry-transport model and an ensemble Kalman filter based data assimilation system. The model was constrained by atmospheric methane surface concentrations, obtained from the World Data Centre for Greenhouse Gases (WDCGG). Prior methane emissions were specified for five sources: biosphere, anthropogenic, fire, termites and ocean, of which bio-sphere and anthropogenic emissions were optimized. Atmospheric CH 4 mole fractions for 2007 from northern Finland calculated from prior and optimized emissions were compared with observations. It was found that the root mean squared errors of the posterior esti - mates were more than halved. Furthermore, inclusion of NOAA observations of CH 4 from weekly discrete air samples collected at Pallas improved agreement between posterior CH 4 mole fraction estimates and continuous observations, and resulted in reducing optimized biosphere emissions and their uncertainties in northern Finland.
Living psychology: The ‘emotional warmth’ dimension of professional childcare

Children and young people in public care are arguably the most vulnerable group in our society and, despite considerable support and financial expenditure, the outcomes for these children have remained stubbornly poor. While the worthy intentions of government initiatives over recent years are not in question, it is clear that there is a need for a new theory-led, evidence-based model of professional care and support. This paper presents a psychological perspective which links early childhood experiences with restricted life outcomes. It argues that it is parental rejection (sometimes accompanied by abuse and neglect) which is a major mediating factor in the often-restricted life outcomes for many of these children.The ‘emotional warmth’ approach to professional childcare enables a visiting applied psychologist to empower residential and foster carers to provide high quality parenting, sensitive support for post-trauma stress and a deeper understanding of the (often hidden) signature strengths of these children and young people. The inclusion of these three components in a support plan is likely to promote positive emotional, social and academic development of children in public care. The major role of the applied psychologist consultant in the emotional warmth model is discussed and appropriate outcome measures for this approach to childcare are considered. ‘Foster and residential care is a complex activity. ’(National Institute for Health and Clinical Excellence/Social Care Institute for Excellence, 2010, p.9)‘We believe that the greatest gains in reforming our care system are to be made in identifying and removing whatever barriers are obstructing the development of good personal relationships, and putting in place all possible means of supporting such relationships where they occur. ’(House of Commons, 2009, p.27, para. 29)