Miracle-dz/UniFAR-FTUs huggingface dataset:
High-throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities

Background and Aims Phosphate (Pi) deﬁciency in soils is a major limiting factor for crop growth worldwide. Plant growth under low Pi conditions correlates with root architectural traits and it may therefore be possible to select these traits for crop improvement. The aim of this study was to characterize root architectural traits, and to test quantitative trait loci (QTL) associated with these traits, under low Pi (LP) and high Pi (HP) availability in Brassica napus. Methods Root architectural traits were characterized in seedlings of a double haploid (DH) mapping population (n = 190) of B. napus [‘Tapidor’ × ‘Ningyou 7’ (TNDH)] using high-throughput phenotyping methods. Primary root length (PRL), lateral root length (LRL), lateral root number (LRN), lateral root density (LRD) and biomass traits were measured 12 d post-germination in agar at LP and HP. Key Results In general, root and biomass traits were highly correlated under LP and HP conditions. ‘Ningyou 7’ had greater LRL, LRN and LRD than ‘Tapidor’, at both LP and HP availability, but smaller PRL. A cluster of highly significant QTL for LRN, LRD and biomass traits at LP availability were identified on chromosome A03; QTL for PRL were identified on chromosomes A07 and C06. Conclusions High-throughput phenotyping of Brassica can be used to identify root architectural traits which correlate with shoot biomass. It is feasible that these traits could be used in crop improvement strategies. The identification of QTL linked to root traits under LP and HP conditions provides further insights on the genetic basis of plant tolerance to P deﬁciency, and these QTL warrant further dissection.
A Case for Context-Aware TCP / IP Paper

This paper discusses the design and evaluation of CATNIP, a ContextAware Transport/Network Internet Protocol for the Web. This integrated protocol uses application-layer knowledge (i.e., Web document size) to provide explicit context information to the TCP and IP protocols. While this approach violates the traditional layered Internet protocol architecture, it enables informed decision-making, both at network endpoints and at network routers, regarding ¤ow control, congestion control, and packet discard decisions. We evaluate the performance of the context-aware TCP/IP approach £rst using ns-2 network simulation, and then using WAN emulation to test a prototype implementation of CATNIP in the Linux kernel of an Apache Web server. The advantages of the CATNIP approach are particularly evident in a congested Internet with 1-10% packet loss. Simulation results indicate a 10-20% reduction in TCP packet loss using simple endpoint control mechanisms, with no adverse impact on Web page retrieval times. More importantly, using CATNIP context information at IP routers can reduce mean Web page retrieval times by 20-80%, and the standard deviation by 60-90%. The CATNIP algorithm can also interoperate with Random Early Detection (RED) for active queue management.
On the Lifecycle Dynamics of Venture-Capital- and Non-Venture-Capital-Financed Firms

We use a new data set that tracks U.S. firms from their birth over two decades to understand the life cycle dynamics and outcomes (both successes and failures) of VC- and non-VC financed firms. We first ask to what market-wide and firm-level characteristics venture capitalists respond in choosing to make their investments and how this differs for firms financed solely by non-VC sources of entrepreneurial capital. We then ask what are the eventual differences in outcomes for firms that receive VC financing relative to non-VC-financed firms. Our findings suggest that VCs follow public market signals similar to other investors and typically invest largely in young firms, with potential for large scale being an important criterion. The main way that VC financed firms differ from matched non-VC financed firms, is they demonstrate remarkably larger scale both for successful and failed firms, at every point of the firms' life cycle. They grow more rapidly, but we see little difference in profitability measures at times of exit. We further examine a number of hypotheses relating to VC-financed firms' failure. We find that VC-financed firms' cumulative failure rates are lower than non-VC-financed firms but the story is nuanced. VC appears initially "patient" in that VC-financed firms are less likely to fail in the first five years but conditional on surviving past this point become more likely to fail relative to non-VC-financed firms. We perform a number of robustness checks and find that VC does not appear to have more stringent survival thresholds nor do VC-financed firm failures appear to be disguised as acquisitions nor do particular kinds of VC firms seem to be driving our results. Overall, our analysis supports the view that VC is "patient" capital relative to other non-VC sources of entrepreneurial capital in the early part of firms' lifecycles and that an important criterion for receiving VC investment is potential for large scale, rather than level of profitability, prior to exit.
The masses, radii and luminosities of the components of U Geminorum

We present a phase-resolved spectroscopic study of the secondary star in the cataclysmic variable (CV) U Gem. We use our data to measure the radial velocity semi-amplitude, systemic velocity and rotational velocity of the secondary star. Combining this with literature data allows us to determine masses and radii for both the secondary star and white dwarf, which are independent of any assumptions about their structure. We use these to compare their properties to those of field stars and find that both components follow field mass–radius relationships. The secondary star has the mass, radius, luminosity and photometric temperature of an M2 star, but a spectroscopic temperature of M4. The latter may well be due to a high metallicity. There is a troubling inconsistency between the radius of the white dwarf inferred from its gravitational redshift and inclination and that inferred from its temperature, flux and astrometric distance. We find that there are two fundamental limits to the accuracy of the parameters we can derive. First, the radial velocity curve of the secondary star deviates from a sinusoid, in part because of its asphericity (which can be modelled) and in part because the line flux is not evenly distributed over its surface. Secondly, we cannot be certain which spectral type is the best match for the lines of the secondary star, and the derived rotational velocity is a function of the spectral type of the template star used.
Elliptic inflation: generating the curvature perturbation without slow-roll

There are many inflationary models in which the inflaton field does not satisfy the slow-roll condition. However, in such models, it is always difficult to generate the curvature perturbation during inflation. Thus, to generate the curvature perturbation, one must introduce another component into the theory. To cite a case, curvatons may generate the dominant part of the curvature perturbation after inflation. However, we question whether it is realistic to consider the generation of the curvature perturbation during inflation without slow-roll. Assuming multifield inflation, we encounter the generation of curvature perturbation during inflation without slow-roll. The potential along the equipotential surface is flat by definition and thus we do not have to worry about symmetry. We also discuss KKLT (Kachru–Kallosh–Linde–Trivedi) models, in which corrections lifting the inflationary direction may not become a serious problem if there is a symmetry enhancement at the tip (not at the moving brane) of the inflationary throat.
Optimization of end-of-life good disassembly using an Ant Colony System

In a modern productive scenario the problem represented by the tons of scraps daily produced in the industrialized countries is often face by recycling. In this paper a contribution to the improvement of the recycling process performed by the disassembly of end-of-life widely diffused goods is proposed. An optimization methodology named “Ant Colony Optimization” (ACO) is proposed as an innovative tool for approaching the problem of detecting the best way in disassembling goods for recycling purposes. The implementation details have been presented, as well as the application in three meaningful case studies represented by typical widely diffused goods.
Chemical evolution and nature of damped Lyman α systems

We study the nature of damped Lyman α systems (DLAs) by means of a comparison between the observed abundances and models of chemical evolution of galaxies of different morphological type. In particular, we compare for the first time the abundance ratios as functions of metallicity and redshift with dust-corrected data. We have developed detailed models following the evolution of several chemical elements (H, D, He, C, N, O, Ne, Mg, Si, S, Fe, Ni and Zn) for elliptical, spiral and irregular galaxies. Each of the models is calibrated to reproduce the main features of a massive elliptical, the Milky Way and the Large Magellanic Cloud (LMC), respectively. In addition, we also run some models for dwarf irregular starburst galaxies. All the models share the same up to date nucleosynthesis prescriptions but differ in their star formation histories. The role of supernovae of different types (II, Ia) is studied in each galaxy model. Our main conclusions are as follows. (i) When dust depletion is taken into account, most of the claimed α/Fe overabundances disappear and DLAs show solar or subsolar abundance ratios. (ii) The majority of DLAs can be explained either by discs of spirals observed at large galactocentric distances or by irregular galaxies, such as the LMC, or by starburst dwarf irregulars observed at different times after the last burst of star formation. (iii) Elliptical galaxies cannot be DLA systems because they reach too high a metallicity at early times and their abundance ratios show overabundances of α-elements relative to Fe over a large range of [Fe/H]. (iv) The observed neutral gas cosmic evolution is compared with our predictions but no firm conclusions can be drawn in the light of the available data.
Proposed IMS Architectures for evaluation QoE of the IPTV service

In this paper, we propose three IMS Architectures for evaluation QoE of the IPTV service considering Subjective Measurement; in this case, we added QoE AS, which applies in a periodical time a survey to collect the QoE value, Objective Measurement; in this architecture, we propose collected information about the QoS from the IMS Policy and Charging Control entity, then, We could calculate the QoE value using a mathematical model. Finally, an Automatic Measurement; in this case, we propose an comparison of the videos (the original video and the received video) and according with the results of comparison we could calculate the QoE value. Also in this paper shown how they could be implemented for future works.
Partitioning Grammars and composing

GLR parsers have been criticized by various authors for their potentially large sizes. Other parsers also have individual weaknesses and strengths. Our heterogeneous parsing algorithm is based on GLR parsers that handle the size and other problems by partitioning the grammarduring compilingand assembling the partitioned sub-grammars during parsing. We discuss diierent parsers for diierent grammars and present some intuitive considerations for the partitioning.
Stable, detyrosinated microtubules function to localize vimentin intermediate filaments in fibroblasts

Separate populations of microtubules (MTs) distinguishable by their level of posttranslationally modified tubulin subunits and by their stability in vivo have been described. In polarized 3T3 cells at the edge of an in vitro wound, we have found a striking preferential coalignment of vimentin intermediate filaments (IFs) with detyrosinated MTs (Glu MTs) rather than with the bulk of the MTs, which were tyrosinated MTs (Tyr MTs). Vimentin IFs were not stabilizing the Glu MTs since collapse of the IF network to a perinuclear location, induced by microinjection of monoclonal anti-IF antibody, had no noticeable effect on the array of Glu MTs. To test whether Glu MTs may affect the organization of IFs we regrew MTs in cells that had been treated with nocodazole to depolymerize all the MTs and to collapse IFs; the reextension of IFs into the lamella lagged behind the rapid regrowth of Tyr MTs, but was correlated with the slower reformation of Glu MTs. Similar realignment of IFs with newly formed Glu MTs was observed in serum-starved cells treated with either serum or taxol to induce the formation of Glu MTs. Next, we microinjected affinity purified antibodies specific for Glu tubulin (polyclonal SG and monoclonal 4B8) and specific for Tyr tubulin (polyclonal W2 and monoclonal YL1/2) into 3T3 cells. Both injected SG and 4B8 antibodies labeled the subset of endogenous Glu MTs; W2 and YL1/2 antibodies labeled virtually all of the cytoplasmic MTs. Injection of SG or 4B8 resulted in the collapse of IFs to a perinuclear region. This collapse was comparable to that observed after complete MT depolymerization by nocodazole. Injection of W2, YL1/2, or nonspecific control IgGs did not result in collapse of the IFs. Taken together, these results show that Glu MTs localize IFs in migrating 3T3 fibroblasts and suggest that detyrosination of tubulin acts as a signal for the recruitment of vimentin IFs to MTs.
Effect of abusive supervision on pro-social citizenship behaviors: The mediating role of interactional justice, organization-based self esteem and meaning of work

The aim of the present study is to check the effect of abusive supervision on pro-social silence and pro-social voice through three mediating variables―interactional justice, meaning of work and organization based self-esteem in the context of Pakistan. Data were collected from 917 subordinate-supervisor dyads from Pakistan. Results from structural equation modeling revealed that only interactional justice partially mediates the negative relation of abusive supervision with pro-social voice pro-social silence, whereas meaning of work and organization-based self-esteem did not show significant mediating effects. The present study will broaden the existing literature regarding the effect of abusive supervision on pro-social voice and pro-social silence― the two very distinct and essential forms of OCB considering the boundary conditions of a developing Asian country such as Pakistan. Conducting such study in Pakistan clarifies the difference in the attitude and the reaction of employees against abusive supervision in a developing Asian country, as these cultures are featured by high power distance and unemployment that affect these behaviors differently effect of abusive supervision on pro-social citizenship behaviors: the mediating role of interactional justice, organization based self-esteem and meaning of work.
CMCompare webserver: comparing RNA families via covariance models

A standard method for the identification of novel non-coding RNAs is homology search by covariance models. Covariance models are constructed for specific RNA families with common sequence and structure (e.g. transfer RNAs). Currently, there are models for 2208 families available from Rfam. Before being included into a database, a proposed family should be tested for specificity (finding only true homolog sequences), sensitivity (finding remote homologs) and uniqueness. The CMCompare webserver (CMCws) compares Infernal RNA family models to (i) identify models with poor specificity and (ii) explore the relationship between models. The CMCws provides options to compare new models against all existing models in the current Rfam database to avoid the construction of duplicate models for the same non-coding RNA family. In addition, the user can explore the relationship between two or more models, including whole sets of user-created family models. Visualization of family relationships provides help in evaluating candidates for clusters of biologically related families, called clans. The CMCws is freely available, without any login requirements, at http://rna.tbi. univie.ac. at/cmcws, and the underlying software is available under the GPL-3 license.
Extracellular Redox Regulation of Intracellular Reactive Oxygen Generation, Mitochondrial Function and Lipid Turnover in Cultured Human Adipocytes

Background Many tissues play an important role in metabolic homeostasis and the development of diabetes and obesity. We hypothesized that the circulating redox metabolome is a master metabolic regulatory system that impacts all organs and modulates reactive oxygen species (ROS) production, lipid peroxidation, energy production and changes in lipid turnover in many cells including adipocytes. Methods Differentiated human preadipocytes were exposed to the redox couples, lactate (L) and pyruvate (P), β–hydroxybutyrate (βOHB) and acetoacetate (Acoc), and the thiol-disulfides cysteine/ cystine (Cys/CySS) and GSH/GSSG for 1.5–4 hours. ROS measurements were done with CM-H2DCFDA. Lipid peroxidation (LPO) was assessed by a modification of the thiobarbituric acid method. Lipolysis was measured as glycerol release. Lipid synthesis was measured as 14C-glucose incorporated into lipid. Respiration was assessed using the SeaHorse XF24 analyzer and the proton leak was determined from the difference in respiration with oligomycin and antimycin A. Results Metabolites with increasing oxidation potentials (GSSG, CySS, Acoc) increased adipocyte ROS. In contrast, P caused a decrease in ROS compared with L. Acoc also induced a significant increase in both LPO and lipid synthesis. L and Acoc increased lipolysis. βOHB increased respiration, mainly due to an increased proton leak. GSSG, when present throughout 14 days of differentiation significantly increased fat accumulation, but not when added later. Conclusions We demonstrated that in human adipocytes changes in the external redox state impacted ROS production, LPO, energy efficiency, lipid handling, and differentiation. A more oxidized state generally led to increased ROS, LPO and lipid turnover and more reduction led to increased respiration and a proton leak. However, not all of the redox couples were the same suggesting compartmentalization. These data are consistent with the concept of the circulating redox metabolome as a master metabolic regulatory system.
Mitigation Measures for Pandemic Influenza in Italy: An Individual Based Model Considering Different Scenarios

Background Individual-based models can provide the most reliable estimates of the spread of infectious diseases. In the present study, we evaluated the diffusion of pandemic influenza in Italy and the impact of various control measures, coupling a global SEIR model for importation of cases with an individual based model (IBM) describing the Italian epidemic. Methodology/Principal Findings We co-located the Italian population (57 million inhabitants) to households, schools and workplaces and we assigned travel destinations to match the 2001 census data. We considered different R0 values (1.4; 1.7; 2), evaluating the impact of control measures (vaccination, antiviral prophylaxis -AVP-, international air travel restrictions and increased social distancing). The administration of two vaccine doses was considered, assuming that first dose would be administered 1-6 months after the first world case, and different values for vaccine effectiveness (VE). With no interventions, importation would occur 37–77 days after the first world case. Air travel restrictions would delay the importation of the pandemic by 7–37 days. With an R0 of 1.4 or 1.7, the use of combined measures would reduce clinical attack rates (AR) from 21–31% to 0.3–4%. Assuming an R0 of 2, the AR would decrease from 38% to 8%, yet only if vaccination were started within 2 months of the first world case, in combination with a 90% reduction in international air traffic, closure of schools/workplaces for 4 weeks and AVP of household and school/work close contacts of clinical cases. Varying VE would not substantially affect the results. Conclusions This IBM, which is based on country-specific demographic data, could be suitable for the real-time evaluation of measures to be undertaken in the event of the emergence of a new pandemic influenza virus. All preventive measures considered should be implemented to mitigate the pandemic.
Modelling Health State Valuation Data

An important task in deriving a summary measure of health is to incorporate stated preferences into health state classifications. This paper examines a range of alternative econometric models for dealing with a skewed, truncated, non-continuous and hierarchical (at the individual level) data set of standard gamble valuations of health states defined by the health state classification the SF-6D. Alternative specifications incorporating random effects for the individual level clustering, Tobit models to deal with skewness and truncation and ordered probit for the non-continuity did not produce models better than the simple mean model and were often worse in terms of inconsistency, fit and heterogeneity.
Challenges for social sensing using WiFi signals

Smartphones are an attractive option for social sensing due to their widespread market penetration rate and advanced sensing capabilities. Enabling social sensing on smartphones would require techniques that can accurately detect and characterize physical proximity, an important prerequisite for the capture of more complex social phenomena. One of the most promising modalities for this purpose is WiFi, as it works both indoors and outdoors, and as WiFi signal environment tends to contain significant spatial variation. A challenge in using WiFi, however, is that the signals are affected by many noise sources, such as fast fading, body attenuation, hardware differences and varying access points densities. In this paper we review existing work on using WiFi for social sensing and outline challenges that have to be addressed to utilize WiFi at large for social sensing.
Making revision reversible: an approach based on polynomials

This paper deals with iterated belief change and proposes a drastic revision rule that modifies a plausibility ordering of interpretations in such a way that any world where the input observation holds is more plausible that any world where it does not. This change rule makes sense in a dynamic context where observations are received, and the newer observations are considered more plausible than older ones. It is shown how to encode an epistemic state using polynomials equipped with the lexicographic ordering. This encoding makes it very easy to implement and iterate the revision rule using simple operations on these polynomials. Moreover, polynomials allow to keep track of the sequence of observations. Lastly, it is shown how to efficiently compute the revision rule at the syntactical level, when the epistemic state is concisely represented by a prioritized belief base. Our revision rule is the most drastic one can think of, in accordance with Darwiche and Pearl's principles, and thus contrasts with the minimal change rule called natural belief revision. The paper also shows how to obtain the reversibility of Boutilier's natural belief revision and possibilistic revision using polynomials.