Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth and protein turnover in the skeletal muscles of broiler chicks.

Growth and protein turnover were examined in the breast (pectoralis thoracica) and the leg (gastrocnemius-peroneus) muscles of broiler chicks at 1, 2, 4, and 6 weeks posthatching. The fractional rate of protein synthesis (ks) was measured by an isotope emulsion method. The fractional degradation rate (kd) was calculated from the difference in ks and fractional deposition rate (kg), which was estimated from regression equations of muscle size and protein content on body weights. The growth rate (%/day) of skeletal muscle exceeded that of the whole body. Muscle growth involved an increase in the total deoxyribonucleic acid (DNA) and the DNA-unit size and a subsequent decrease in the concentrations of nucleic acids without alteration in the ribonucleic acid (RNA):DNA ratio and RNA and DNA activity. The ks in breast muscle protein fell markedly from 48 to 16%/day between 1 and 6 weeks posthatching, whereas in leg muscle, ks underwent a more gradual decrease; from 36 to 17%/day during the same period. These changes resulted mainly from the reduction of DNA and RNA concentrations with age. The kd decreased only slightly between 1 and 2 weeks in the both muscle groups. The kg also showed a developmental fall from 33 to 4%/day and from 21 to 4%/day in the breast and leg muscles, respectively, during the 5-week period. (ABSTRACT TRUNCATED AT 250 WORDS)
The Role and Mechanism of Erythrocyte Invasion by Francisella tularensis

Francisella tularensis is an extremely virulent bacterium that can be transmitted naturally by blood sucking arthropods. During mammalian infection, F. tularensis infects numerous types of host cells, including erythrocytes. As erythrocytes do not undergo phagocytosis or endocytosis, it remains unknown how F. tularensis invades these cells. Furthermore, the consequence of inhabiting the intracellular space of red blood cells (RBCs) has not been determined. Here, we provide evidence indicating that residing within an erythrocyte enhances the ability of F. tularensis to colonize ticks following a blood meal. Erythrocyte residence protected F. tularensis from a low pH environment similar to that of gut cells of a feeding tick. Mechanistic studies revealed that the F. tularensis type VI secretion system (T6SS) was required for erythrocyte invasion as mutation of mglA (a transcriptional regulator of T6SS genes), dotU, or iglC (two genes encoding T6SS machinery) severely diminished bacterial entry into RBCs. Invasion was also inhibited upon treatment of erythrocytes with venom from the Blue-bellied black snake (Pseudechis guttatus), which aggregates spectrin in the cytoskeleton, but not inhibitors of actin polymerization and depolymerization. These data suggest that erythrocyte invasion by F. tularensis is dependent on spectrin utilization which is likely mediated by effectors delivered through the T6SS. Our results begin to elucidate the mechanism of a unique biological process facilitated by F. tularensis to invade erythrocytes, allowing for enhanced colonization of ticks.
Prospects for comparison of matter and antimatter gravitation with ALPHA-g

The ALPHA experiment has recently entered an expansion phase of its experimental programme, driven in part by the expected benefits of conducting experiments in the framework of the new AD + ELENA antiproton facility at CERN. With antihydrogen trapping now a routine operation in the ALPHA experiment, the collaboration is leading progress towards precision atomic measurements on trapped antihydrogen atoms, with the first excitation of the 1S–2S transition and the first measurement of the antihydrogen hyperfine spectrum (Ahmadi et al. 2017 Nature 541, 506–510 (doi:10.1038/nature21040); Nature 548, 66–69 (doi:10.1038/nature23446)). We are building on these successes to extend our physics programme to include a measurement of antimatter gravitation. We plan to expand a proof-of-principle method (Amole et al. 2013 Nat. Commun. 4, 1785 (doi:10.1038/ncomms2787)), first demonstrated in the original ALPHA apparatus, and perform a precise measurement of antimatter gravitational acceleration with the aim of achieving a test of the weak equivalence principle at the 1% level. The design of this apparatus has drawn from a growing body of experience on the simulation and verification of antihydrogen orbits confined within magnetic-minimum atom traps. The new experiment, ALPHA-g, will be an additional atom-trapping apparatus located at the ALPHA experiment with the intention of measuring antihydrogen gravitation. This article is part of the Theo Murphy meeting issue ‘Antiproton physics in the ELENA era’.
Explaining Fixed Effects: Random Effects Modeling of Time-Series Cross-Sectional and Panel Data*

This article challenges Fixed Effects (FE) modeling as the ‘default’ for time-series-cross-sectional and panel data. Understanding different within and between effects is crucial when choosing modeling strategies. The downside of Random Effects (RE) modeling—correlated lower-level covariates and higher-level residuals—is omitted-variable bias, solvable with Mundlak's (1978a) formulation. Consequently, RE can provide everything that FE promises and more, as confirmed by Monte-Carlo simulations, which additionally show problems with Plümper and Troeger's FE Vector Decomposition method when data are unbalanced. As well as incorporating time-invariant variables, RE models are readily extendable, with random coefficients, cross-level interactions and complex variance functions. We argue not simply for technical solutions to endogeneity, but for the substantive importance of context/heterogeneity, modeled using RE. The implications extend beyond political science to all multilevel datasets. However, omitted variables could still bias estimated higher-level variable effects; as with any model, care is required in interpretation.
Key Survival Factor, Mcl-1, Correlates with Sensitivity to Combined Bcl-2/Bcl-xL Blockade

An estimated 40,000 deaths will be attributed to breast cancer in 2016, underscoring the need for improved therapies. Evading cell death is a major hallmark of cancer, driving tumor progression and therapeutic resistance. To evade apoptosis, cancers use antiapoptotic Bcl-2 proteins to bind to and neutralize apoptotic activators, such as Bim. Investigation of antiapoptotic Bcl-2 family members in clinical breast cancer datasets revealed greater expression and more frequent gene amplification of MCL1 as compared with BCL2 or BCL2L1 (Bcl-xL) across three major molecular breast cancer subtypes, Luminal (A and B), HER2-enriched, and Basal-like. While Mcl-1 protein expression was elevated in estrogen receptor α (ERα)-positive and ERα-negative tumors as compared with normal breast, Mcl-1 staining was higher in ERα+ tumors. Targeted Mcl-1 blockade using RNAi increased caspase-mediated cell death in ERα+ breast cancer cells, resulting in sustained growth inhibition. In contrast, combined blockade of Bcl-2 and Bcl-xL only transiently induced apoptosis, as cells rapidly acclimated through Mcl-1 upregulation and enhanced Mcl-1 activity, as measured in situ using Mcl-1/Bim proximity ligation assays. Importantly, MCL1 gene expression levels correlated inversely with sensitivity to pharmacologic Bcl-2/Bcl-xL inhibition in luminal breast cancer cells, whereas no relationship was seen between the gene expression of BCL2 or BCL2L1 and sensitivity to Bcl-2/Bcl-xL inhibition. These results demonstrate that breast cancers rapidly deploy Mcl-1 to promote cell survival, particularly when challenged with blockade of other Bcl-2 family members, warranting the continued development of Mcl-1–selective inhibitors for targeted tumor cell killing. Implications: Mcl-1 levels predict breast cancer response to inhibitors targeting other Bcl-2 family members, and demonstrate the key role played by Mcl-1 in resistance to this drug class. Mol Cancer Res; 15(3); 259–68. ©2016 AACR.
On isolating points using unit disks

Given a set of points in the plane and a set of disks (that we think of as wireless sensors) which separate the points, we consider the problem of selecting a minimum subset of the disks such that any path between any pair of points is intersected by at least one of the selected disks. We present a $(9 + \epsilon)$-approximation algorithm for this problem and show that it is NP-complete even if all disks have unit radius and no disk contains any points. Using a similar hardness reduction, we further show that the Multiterminal Cut problem remains NP-complete on unit disk graphs. Lastly, we prove that removing a minimum subset of a collection of unit disks, such that the plane minus the arrangement of the remaining disks consists of a single connected region is also NP-complete.
Biology of Vascular Endothelial Growth Factor C in the Morphogenesis of Lymphatic Vessels

Because virtually all tissues contain blood vessels, the importance of hemevascularization has been long recognized in regenerative medicine and tissue engineering. However, the lymphatic vasculature has only recently become a subject of interest. Central to the task of growing a lymphatic network are lymphatic endothelial cells (LECs), which constitute the innermost layer of all lymphatic vessels. The central molecule that directs proliferation and migration of LECs during embryogenesis is vascular endothelial growth factor C (VEGF-C). VEGF-C is therefore an important ingredient for LEC culture and attempts to (re)generate lymphatic vessels and networks. During its biosynthesis VEGF-C undergoes a stepwise proteolytic processing, during which its properties and affinities for its interaction partners change. Many of these fundamental aspects of VEGF-C biosynthesis have only recently been uncovered. So far, most—if not all—applications of VEGF-C do not discriminate between different forms of VEGF-C. However, for lymphatic regeneration and engineering purposes, it appears mandatory to understand these differences, since they relate, e.g., to important aspects such as biodistribution and receptor activation potential. In this review, we discuss the molecular biology of VEGF-C as it relates to the growth of LECs and lymphatic vessels. However, the properties of VEGF-C are similarly relevant for the cardiovascular system, since both old and recent data show that VEGF-C can have a profound effect on the blood vasculature.
Surface-Enhanced Resonance Raman Scattering of Rhodamine 6G in Dispersions and on Films of Confeito-Like Au Nanoparticles

Surface-enhanced resonance Raman scattering (SERRS) of rhodamine 6G was measured on confeito-like Au nanoparticles (CAuNPs). The large CAuNPs (100 nm in diameter) in aqueous dispersion systems showed stronger enhancing effect (analytical enhancement factor: over 105) of SERRS than the small CAuNPs (50 nm in diameter), while the spherical Au nanoparticles (20 nm in diameter) displayed rather weak intensities. Especially, minor bands in 1400–1600 cm−1 were uniquely enhanced by the resonance effect of CAuNPs. The enhancement factors revealed a concentration dependence of the enhancing effect at low concentration of rhodamine 6G. This dependency was due to a large capacity of hot-spots on CAuNPs, which were formed without agglomeration. The surface-enhancing behaviour in the film systems was similar to that in the dispersions, although the large CAuNPs had lower enhancing effect in the films, and the small CAuNPs and the spherical Au nanoparticles were more effective in their films. These results suggest that the CAuNPs have an advantage in ultrasensitive devices both in dispersions and films, compared to the agglomerate of spherical Au nanoparticles.
Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models

Emerging insights into factors responsible for soil organic matter stabilization and decomposition are being applied in a variety of contexts, but new tools are needed to facilitate the understanding, evaluation, and improvement of soil biogeochemical theory and models at regional to global scales. To isolate the effects of model structural uncertainty on the global distribution of soil carbon stocks and turnover times we developed a soil biogeochemical testbed that forces three different soil models with consistent climate and plant productivity inputs. The models tested here include a first‐order, microbial implicit approach (CASA‐CNP), and two recently developed microbially explicit models that can be run at global scales (MIMICS and CORPSE). When forced with common environmental drivers, the soil models generated similar estimates of initial soil carbon stocks (roughly 1,400 Pg C globally, 0–100 cm), but each model shows a different functional relationship between mean annual temperature and inferred turnover times. Subsequently, the models made divergent projections about the fate of these soil carbon stocks over the 20th century, with models either gaining or losing over 20 Pg C globally between 1901 and 2010. Single‐forcing experiments with changed inputs, temperature, and moisture suggest that uncertainty associated with freeze‐thaw processes as well as soil textural effects on soil carbon stabilization were larger than direct temperature uncertainties among models. Finally, the models generated distinct projections about the timing and magnitude of seasonal heterotrophic respiration rates, again reflecting structural uncertainties that were related to environmental sensitivities and assumptions about physicochemical stabilization of soil organic matter. By providing a computationally tractable and numerically consistent framework to evaluate models we aim to better understand uncertainties among models and generate insights about factors regulating the turnover of soil organic matter.
On the Effectiveness of Uniform Subsidies in Increasing Market Consumption

We study the problem faced by a central planner trying to increase the consumption of a good, such as new malaria drugs in Africa. The central planner allocates subsidies to its producers, subject to a budget constraint and endogenous market response. The policy most commonly implemented in practical applications of this problem is uniform, in the sense that it allocates the same per-unit subsidy to every firm, primarily because of its simplicity and perceived fairness. Surprisingly, we identify sufficient conditions of the firms’ marginal costs such that uniform subsidies are optimal, even if the firms’ efficiency levels are arbitrarily different. Moreover, this insight is usually preserved even if the central planner is uncertain about the specific market conditions. Further in many cases, uniform subsidies simultaneously attain the best social welfare solution. Additionally, simulation results in relevant settings where uniform subsidies are not optimal suggest that they induce a nearly optimal market .
‘An Apotheosis of Well-Being’: Durkheim on austerity and double-dip recessions

This article is an attempt to contribute a view on the economic crisis from classical sociology, a voice often missing from the sociological response to the crisis. The work of Émile Durkheim provides a unique perspective here centred on morality and inequality produced in a historical context akin to our neoliberal times. It is argued there are four key points to take from Durkheim’s work. First, that the initial credit crunch can be more fully understood with reference to the economic anomie which Durkheim sees as ‘chronic’ in a time of marketisation. Second, that this creates an antagonistic relationship between a supposedly self-dependent rich and lazy poor. Third, this conception of self-dependency and individual initiative makes any attempt to regulate the economy akin to sacrilege. Finally, the state is unwilling to intervene due to the emergence of ‘pseudo-democracies’. Therefore, Durkheim’s theory accounts for the initial crisis, austerity and double-dip recessions in a sociological framework. The article concludes by returning to the centrality of morality to the crisis for Durkheim and highlighting the omission of this in contemporary debates.
Parallelizing Preferential Attachment Models for Generating Large-Scale Social Networks that Cannot Fit into Memory

Social network generation is an important problem in social network analysis. The goal is to produce artificial networks that preserve some real world properties of social networks. As one of most popular social network generation algorithms, the Barabási -- Albert (BA) model is a method that can generate random social networks with power-law degree distribution. This paper discusses the situation of generating large-sized social network that cannot fit into the memory. We design a parallel framework to tackle this problem. The challenge lies in the fact that the preferential attachment mechanism used in the BA model has direct conflict with the concept of parallelism. To achieve the preferential attachment, during the generation processes the degree information of nodes needs to be known, which prohibits the parallelism that allows nodes to generate edges independently. To handle this issue, this paper proposes a method to generate the expected accumulated degree of vertices for the parallel BA model. We further propose several novel techniques to reduce the complexity of generating N vertices with P processes to O(NlogN/P). We implement the model using MapReduce and the experiment results show that our model can produce billion-sized scale-free networks in minutes.
On Fully Dynamic Graph Sparsifiers

We initiate the study of fast dynamic algorithms for graph sparsification problems and obtain fully dynamic algorithms, allowing both edge insertions and edge deletions, that take polylogarithmic time after each update in the graph. Our three main results are as follows. First, we give a fully dynamic algorithm for maintaining a (1 ± ϵ)-spectral sparsifier with amortized update time poly(log n, ϵ<sup>-1</sup>). Second, we give a fully dynamic algorithm for maintaining a (1 ± ϵ)-cut sparsifier with worst-case update time poly(log n, ϵ<sup>-1</sup>). Both sparsifiers have size n · poly(log n, ϵ<sup>-1</sup>). Third, we apply our dynamic sparsifier algorithm to obtain a fully dynamic algorithm for maintaining a (1 - ϵ)-approximation to the value of the maximum flow in an unweighted, undirected, bipartite graph with amortized update time poly(log n, ϵ<sup>-1</sup>).
Dietary sodium bicarbonate, cool temperatures, and feed withdrawal: impact on arterial and venous blood-gas values in broilers.

Sodium bicarbonate (NaHCO3) has been used successfully in mammals and birds to alleviate pulmonary hypertension. Experiment 1 was designed to provide measurements of arterial and venous blood-gas values from unanesthetized male broilers subjected to a cool temperature (16 degrees C) challenge and fed either a control diet or the same diet alkalinized by dilution with 1% NaHCO3. The incidences of pulmonary hypertension syndrome (PHS, ascites) for broilers fed the control or bicarbonate diets were 15.5 and 10.5%, respectively (P = 0.36, NS). Non-ascitic broilers fed the control diet were heavier than those fed the bicarbonate diet on d 49 (2,671 vs. 2,484 g, respectively); however, other comparisons failed to reveal diet-related differences in heart weight, pulse oximetry values, electrocardiogram amplitudes, or blood-gas values (P > 0.05). When the data were resorted into categories based on right:total ventricular weight ratios (RV:TV) indicative of normal (RV:TV < 0.28) or elevated (RV:TV > or = 0.28) pulmonary arterial pressures, broilers with elevated RV:TV ratios had poorly oxygenated arterial blood that was more acidic, had high partial pressure of CO2 (PCO2), and had higher HCO3 concentrations when compared with broilers with normal RV:TV ratios. Experiment 2 was conducted to determine if metabolic variations associated with differences in feed intake or environmental temperature potentially could mask an impact of diet composition on blood-gas values. Male broilers maintained at thermoneutral temperature (24 degrees C) either received feed ad libitum or had the feed withdrawn > or = 12 h prior to blood sampling. Broilers fed ad libitum had lower venous saturation of hemoglobin with O2, higher venous PCO2, and higher arterial HCO3 concentrations than broilers subjected to feed withdrawal. Broilers in experiment 2 fed ad libitum and exposed to cool temperatures (16 degrees C) had lower arterial partial pressure of O2 and higher venous PCO2 than broilers fed ad libitum and maintained at 24 degrees C. Overall, these results demonstrate that changes in diet composition (control vs. 1% NaHCO3 diets) had minimal impact on arterial and venous blood-gas variables when compared with the more dramatic differences associated with feed intake (ad libitum vs. > or = 12 h withdrawal), environmental temperature (24 vs. 16 degrees C), and the pathogenesis associated with PHS (RV:TV < 0.28 vs. > or = 0.28).
Bioremediation in Fractured Rock: 1. Modeling to Inform Design, Monitoring, and Expectations

Field characterization of a trichloroethene (TCE) source area in fractured mudstones produced a detailed understanding of the geology, contaminant distribution in fractures and the rock matrix, and hydraulic and transport properties. Groundwater flow and chemical transport modeling that synthesized the field characterization information proved critical for designing bioremediation of the source area. The planned bioremediation involved injecting emulsified vegetable oil and bacteria to enhance the naturally occurring biodegradation of TCE. The flow and transport modeling showed that injection will spread amendments widely over a zone of lower‐permeability fractures, with long residence times expected because of small velocities after injection and sorption of emulsified vegetable oil onto solids. Amendments transported out of this zone will be diluted by groundwater flux from other areas, limiting bioremediation effectiveness downgradient. At nearby pumping wells, further dilution is expected to make bioremediation effects undetectable in the pumped water. The results emphasize that in fracture‐dominated flow regimes, the extent of injected amendments cannot be conceptualized using simple homogeneous models of groundwater flow commonly adopted to design injections in unconsolidated porous media (e.g., radial diverging or dipole flow regimes). Instead, it is important to synthesize site characterization information using a groundwater flow model that includes discrete features representing high‐ and low‐permeability fractures. This type of model accounts for the highly heterogeneous hydraulic conductivity and groundwater fluxes in fractured‐rock aquifers, and facilitates designing injection strategies that target specific volumes of the aquifer and maximize the distribution of amendments over these volumes.