Miracle-dz/UniFAR-FTUs huggingface dataset:
Cattle production in the Amazon Rainforest: reasons for the success, challenges for ecological intensification

The current expansion of cattle ranching in the Amazon, especially in its Brazilian part, is responsible for a major change in the global livestock geography. Brazil is the leading bovine meat producer and exporter in the world, with a population of 202 million heads in 2008. The Amazon region accounts for nearly 80 million heads, and has the strongest growth rate, being associated with a strong meat and milk industry. This success of the cattle ranching activity has been hidden for a long time by the scientiﬁc community. It is now one of the major challenges of sustainable development on the continent. This communication is based on the results of several research projects from the Transamazoˆnia network, analyzing: production systems, commodity chains and territorial development strategies, with several methods, most of them based on systemic approaches. The paper discusses three mechanisms, explaining the impacts of livestock production on the Amazon Environment, and concludes on challenges for the research around the concept of ecological intensiﬁcation. The results show that the Amazonian farmers have been able, over 40 years of colonization, to build livestock systems relatively adapted to the agro-ecological conditions of the humid tropics, and to the speciﬁc contexts of the agrarian frontier. Differently than other agricultural activities in this region, the cattle ranching systems are based on ﬂexible and efﬁcient technical and economical systems, both at the farm or the commodity chain scale. Cattle ranching activities are now integrated in most of the production systems on the pioneer frontier, with many functions that stand beyond the sole production of income. Public policies and agricultural research has been decisive for starting this process, which is now controlled by a diversiﬁed private sector (including the large agro-business companies, and the settlers of agricultural reform). However, the Amazonian livestock system development remains very harmful in terms of environmental impact, including the associated
Rare variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations

Many G protein-coupled receptors (GPCRs) lack common variants that lead to reproducible genome-wide disease associations. Here we used rare variant approaches to assess the disease associations of 85 orphan or understudied GPCRs in an unselected cohort of 51,289 individuals. Rare loss-of-function variants, missense variants predicted to be pathogenic or likely pathogenic, and a subset of rare synonymous variants were used as independent data sets for sequence kernel association testing (SKAT). Strong, phenome-wide disease associations shared by two or more variant categories were found for 39% of the GPCRs. Validating the bioinformatics and SKAT analyses, functional characterization of rare missense and synonymous variants of GPR39, a Family A GPCR, showed altered expression and/or Zn2+-mediated signaling for members of both variant classes. Results support the utility of rare variant analyses for identifying disease associations for genes that lack common variants, while also highlighting the functional importance of rare synonymous variants. Author summary Rare variant approaches have emerged as a viable way to identify disease associations for genes without clinically important common variants. Rare synonymous variants are generally considered benign. We demonstrate that rare synonymous variants represent a potentially important dataset for deriving disease associations, here applied to analysis of a set of orphan or understudied GPCRs. Synonymous variants yielded disease associations in common with loss-of-function or missense variants in the same gene. We rationalize their associations with disease by confirming their impact on expression and agonist activation of a representative example, GPR39. This study highlights the importance of rare synonymous variants in human physiology, and argues for their routine inclusion in any comprehensive analysis of genomic variants as potential causes of disease.
Risk Preferences Are Not Time Preferences ∗

Risk and time are intertwined. The present is known while the future is inherently risky. Discounted expected utility provides a simple, coherent structure for analyzing decisions in intertemporal, uncertain environments. Critical to such analysis is the notion that certain and uncertain utility are functionally interchangeable. We document an important and robust violation of discounted expected utility, which is essentially a violation of this interchangeability. In parameter estimations, certain utility is found to be almost linear while uncertain utility is found to be substantially more concave. These results have implications for discounted expected utility theory and decision theory in general. Applications are made to dynamic inconsistency, the uncertainty effect, the estimation of risk preferences, and probability weighting. JEL classification: D81, D90
Contourlet-Based Image Watermarking Using Optimum Detector in a Noisy Environment

In this paper, an improved multiplicative image watermarking system is presented. Since human visual system is less sensitive to the image edges, watermarking is applied in the contourlet domain, which represents image edges sparsely. In the presented scheme, watermark data is embedded in directional subband with the highest energy. By modeling the contourlet coefficients with General Gaussian Distribution (GGD), the distribution of watermarked noisy coefficients is analytically calculated. The tradeoff between the transparency and robustness of the watermark data is solved in a novel fashion. At the receiver, based on the Maximum Likelihood (ML) decision rule, an optimal detector by the aid of channel side information is proposed. In the next step, a blind extension of the suggested algorithm is presented using the patchwork idea. Experimental results confirm the superiority of the proposed method against common attacks, such as Additive White Gaussian Noise (AWGN), JPEG compression, and rotation attacks, in comparison with the recently proposed techniques.
Clinical value of the measurable residual disease status within the ELN2017 risk groups in AML patients undergoing allogeneic stem cell transplantation

57%). the relapse rates for patients transplanted detectable MRD prior to were for the three ELN2017 groups increasing from ELN2017 favorable (5.1%) to ELN2017 intermediate (15%) to ELN2017 adverse (46%), leading to a significantly lower specificity of MRD detection in the ELN2017 adverse group (0.54) compared to the ELN2017 favorable (0.95, p < .01) or ELN2017 intermediate group (0.85; p < .01). These data show that while the chance to experience relapse is high for patients transplanted with a positive MRD status irrespective of the assigned ELN2017 risk group, an AML patient transplanted with a negative MRD status is relatively safe not to relapse, only if assigned to the ELN2017 favorable or ELN2017 intermediate group. In contrast, MRD-negative ELN2017 adverse patients have a much higher risk of experiencing relapse. These findings are supported by the data of a recent manuscript analyzing the utility of flow-based MRD prior to HSCT in patients with or without a monosomal karyotype (MKT) – an entity assigned to the ELN2017 adverse group. Here, MRD-negative patients harboring a MKT had a relapse risk as high as 46%. 2 In this the risk stratification by MRD status in patients without a MKT (3-years CIR 20% for MRD-negative patients vs. 64% for MRD-positive patients) was improved compared to the high risk population of patients with a MKT (3-years CIR 46% for MRD-negative patients vs. 72% for MRD-positive patients). 2
The robots are coming

On the Edge will place the spotlight on exciting, unusual and often controversial developments from the world of interaction design. It will discuss issues that challenge the current norm---whether in industry or academia---in a way that is not possible in either a shallow news article or a formal research paper. Topics can include a cool gadget that's just been launched in Tokyo's Akihabara district, or some far out research prototype presented at the latest SIGGRAPH or UbiComp conference. I will also introduce concepts and methods that put a new perspective on the profession. Prototypes are cool, but unless they come with a well-grounded theory and a connection to the world outside the lab, they will soon be forgotten and left in a pile together with last year's Tamagotchis and CHI papers. How can interaction designers---who already maintain a precarious balancing act on the borderline between art and science---create products and interfaces that have the potential to change peoples' lives, while simultaneously serving all their masters: commerce and culture, research and intuition, engineering and design, and so on? Welcome to life On The Edge.
Cognitive and Neural Correlates of Aerobic Fitness in Obese Older Adults

Background/Study Context: Aerobic fitness is associated with preserved cognition and brain volume in older adulthood. The current study investigated whether the benefits of aerobic fitness extend to obese older adults, a segment of the population that is rapidly growing and who exhibit compromised cognition and brain structure relative to their nonobese counterparts. Methods: Measures of obesity, aerobic fitness, cognition (processing speed, executive function, spatial ability, memory), and regional brain volumes (prefrontal gray, prefrontal white, hippocampus) were obtained from 19 obese older adults aged 65 to 75. Hierarchical linear regression analyses were conducted to examine the proportion of unique variance in cognitive and volumetric measures accounted for by aerobic fitness after controlling for covariates (age, gender, and waist circumference). Results: Aerobic fitness accounted for a significant amount of unique variance in processing speed (adjusted R 2 = .44), executive function (adjusted R 2 = .34), and hippocampal volume (adjusted R 2 = .27). Conclusion: This novel pattern of results suggests that obesity does not preclude the benefits of fitness for cognition and brain volume in older adults. Fitness appears to be a beneficial factor for maintenance of processing speed, executive function, and hippocampal volume, which are vulnerable to age- and/or obesity-related decline.
Noise improves collective decision-making by ants in dynamic environments

Recruitment via pheromone trails by ants is arguably one of the best-studied examples of self-organization in animal societies. Yet it is still unclear if and how trail recruitment allows a colony to adapt to changes in its foraging environment. We study foraging decisions by colonies of the ant Pheidole megacephala under dynamic conditions. Our experiments show that P. megacephala, unlike many other mass recruiting species, can make a collective decision for the better of two food sources even when the environment changes dynamically. We developed a stochastic differential equation model that explains our data qualitatively and quantitatively. Analysing this model reveals that both deterministic and stochastic effects (noise) work together to allow colonies to efficiently track changes in the environment. Our study thus suggests that a certain level of noise is not a disturbance in self-organized decision-making but rather serves an important functional role.
Tectonic control of bioalteration in modern and ancient oceanic crust as evidenced by carbon isotopes

Abstract We review the carbon‐isotope data for finely disseminated carbonates from bioaltered, glassy pillow rims of basaltic lava flows from in situ slow‐ and intermediate‐spreading oceanic crust of the central Atlantic Ocean (CAO) and the Costa Rica Rift (CRR). The δ13C values of the bioaltered glassy samples from the CAO show a large range, between −17 and +3‰ (Vienna Peedee belemnite standard), whereas those from the CRR define a much narrower range, between −17‰ and −7‰. This variation can be interpreted as the product of different microbial metabolisms during microbial alteration of the glass. In the present study, the generally low δ13C values (less than −7‰) are attributed to carbonate precipitated from microbially produced CO2 during oxidation of organic matter. Positive δ13C values >0‰ likely result from lithotrophic utilization of CO2 by methanogenic Archaea that produce CH4 from H2 and CO2. High production of H2 at the slow‐spreading CAO crust may be a consequence of fault‐bounded, high‐level serpentinized peridotites near or on the sea floor, in contrast to the CRR crust, which exhibits a layer‐cake pseudostratigraphy with much less faulting and supposedly less H2 production. A comparison of the δ13C data from glassy pillow margins in two ophiolites interpreted to have formed at different spreading rates supports this interpretation. The Jurassic Mirdita ophiolite complex in Albania shows a structural architecture similar to that of the slow‐spreading CAO crust, with a similar range in δ13C values of biogenic carbonates. The Late Ordvician Solund–Stavfjord ophiolite complex in western Norway exhibits structural and geochemical evidence for evolution at an intermediate‐spreading mid‐ocean ridge and displays δ13C signatures in biogenic carbonates similar to those of the CRR. Based on the results of this comparative study, it is tentatively concluded that the spreading rate‐dependent tectonic evolution of oceanic lithosphere has a significant control on the evolution of microbial life and hence on the δ13C biosignatures preserved in disseminated biogenic carbonates in glassy, bioaltered lavas.
Comparative analysis between a proxy‐based climate reconstruction and GCM‐based simulation of temperatures over the last millennium in China

The application of general circulation models (GCMs) could improve our understanding of climate forcing. Furthermore, longer climate records spanning a wider range of climate states could help in assessing the skill of the models for simulating climates different from the present. We first attempt to find a way to combine proxy records which are affected by different seasonal temperatures, and then present a large‐scale temperature reconstruction over the last millennium for China by combining the Beijing stalagmite layer series and the Qilian tree ring sequence to compare with the GCM‐based ECHO‐G simulated millennial temperature record for China. The correlation coefficient between the simulated and the reconstructed temperature records is 0.61 based on a 31‐year running mean (exceeding P < 0.01). An asymmetrical V‐like low‐frequency variation shown both by the combined proxy record and the simulated series is the major long‐term pattern in the last millennial temperature in China, suggesting that solar irradiance as well as greenhouse gases could explain much of the low‐frequency variations in the climate. However, there still exist high‐frequency discrepancies between the two time series, which may be due to (1) the overestimated climatic effect of volcanoes within the GCM and/or (2) proxies which are not sensitive enough to respond to the volcanic eruptions. Copyright © 2009 John Wiley & Sons, Ltd.
Redox modulation of STIM-ORAI signaling

STIM1 and ORAI1 constitute the core machinery of the ubiquitous store-operated calcium entry pathway and loss of function in these proteins is associated with severe immune and muscular disorders. Other isoforms - STIM1L, STIM2, ORAI2 and ORAI3 exhibit varied expression levels in different cell types along with several other interaction partners and thereby play different roles to facilitate, regulate and fine-tune the calcium entry. STIM proteins convey the Ca 2+ store-depletion message to the PM and thereby participate in refilling of the ER by physically interacting with the Ca 2+ -selective ORAI channels at the PM. STIM and ORAI are exposed to oxidative modifications in the ER, the cytosol, and at the cell surface, and redox-mediated alterations in STIM/ORAI coupling might contribute to autoimmune disorders and cancer progression. This review discusses the redox reactivity of cysteine residues in STIM and ORAI isoforms, focusing on the oxidative modifications of STIM and ORAI proteins by which STIM-ORAI signaling can be modulated.
An Exploration of Fixed and Random Effects Selection for Longitu- Dinal Binary Outcomes in the Presence of Non-ignorable Dropout 3.2 Variable Selection in Missing Data Mechanism 4 Simulation Studies

We explore a Bayesian approach to fixed and random effects selection for longitudinal binary outcomes that are subject to missing data caused by dropouts. We show via analytic results for a simple example that non-ignorable missing data lead to biased parameter estimates and thus result in selection of the wrong effects asymptotically and confirmed these results via simulation for more complex settings. By jointly modeling the longitudinal binary data with the dropout process, one is able to correct the bias in estimation and selection of fixed and random effects if the missing data are non-ignorable. We illustrate the approach using a clinical trial for acute ischemic stroke. It is often of interest to select important predictors for the longitudinal outcome from a large pool of candidates and the variable selection procedure often needs to involve selecting both fixed and random effects. One potential problem in applying the criterion-based strategies such as Akaike's information criterion or Bayesian information criterion is that the number of possible sub-models grows exponentially with the number of effects, which results in extensive computation when there are many candidate predictors. Model selection for fixed effects has been studied using both penalized likelihood However, missing data due to dropout or death during follow-up in longitudinal studies can compromise the validity of the above variable selection procedures when data are missing not at random (MNAR) or non-ignorable; we will use MNAR and non-ignorable interchangeably here though we recognize the scenario of non-ignorable MAR sometimes considered in mixture models. Non-ignorable missing data arise when the probability of missingness is related to the unobserved, missing components (Little and Rubin, 2002), and may lead to biased estimates in longitudinal analysis if the missing data mechanism is ignored. There has been a growing literature on joint analysis of longitudinal measurements and the missing data mechanism; by correctly modeling the association between the two, the bias caused by the missing data at the longitudinal endpoint can be removed. For joint analysis on normally-distributed longi-2 Ning Li et al.: Variable selection in the presence of non-ignorable dropout al. (2001), and Roy and Daniels (2008) extended joint models to the setting of generalized linear mixed models for the exponential family distributions. Although there is a need for research on variable selection in the presence of missing observations, literature in this area has been very limited. Mitra and Dunson (2010) developed a stochastic search variable selection approach …
Natural faulting and the mechanics of brittle shear failure

The theory of faulting developed since E. M. Anderson’s (1951) work, which is based on the concept of dislocations in an elastic continuum, is systematically discussed. Recent work enables the problem to be properly formulated in three dimensions and leads to the confirmation of Mohr’s hypothesis, on which Anderson’s theory was based, that faulting is independent of the intermediate principal stress. Estimates of the stress-differences existing in the crust and mantle (ranging up to several hundred MPa––several kb) emphasize the significance of conditions which enable the high friction existing on deep faults to be circumvented so that faulting can take place under small stress-differences. The Hubbert-Rubey (1959) hypothesis of lithostatic pore fluid pressures remains the most attractive mechanism for overcoming the problem of high friction.
Completing the fertility transition in the developing world: The role of educational differences and fertility preferences

This study summarizes patterns of educational differentials in wanted and unwanted fertility at different stages of the fertility transition. The data are from Demographic and Health Surveys in 57 less developed countries. As the transition proceeds, educational differentials in wanted fertility tend to decline and differentials in unwanted fertility tend to rise. An assessment of fertility patterns in developed and less developed countries with low fertility concludes that these differentials are likely to remain substantial when less developed countries reach the end of their transitions. This conclusion implies that the educational composition of the population remains a key predictor of overall fertility in late transitional countries and that low levels of schooling can be a cause of stalling fertility.
Bahama Platform Slopes: Carbonate Diagenesis Within and Below Thermocline: ABSTRACT

Sediments on Bahamian slopes, reef rubble, gully sands, and periplatform carbonate ooze, consist of calcite, magnesian calcite, and aragonite. When not continuously buried by new material, these sediments harden to limestone crusts, 10 cm to several meters thick, on the sea floor. The pathways of sea floor diagenesis vary with depth. (1) Reef wall and talus slope (50 to 400 m) are pervasively cemented by micritic magnesian calcite; botryoidal aragonite fills the large voids. There is no evidence of selective dissolution; primary and diagenetic minerals coexist. (2) On the gullied slopes between 500 and 1,300 m most sediment lithifies to calcite limestone or chalk, with 3 to 7 mol % MgCO3; however, about 20% of the samples are micritic magnesian calcite limeston s of 8 to 14% MgCO3. (3) On the gullied slopes from 1,300 to at least 2,500 m, calcite limestones with 2 to 4 mol % MgCO3 prevail. The downslope trend from aragonite and magnesian calcite to calcite is explained by the decrease in water temperature and carbonate saturation. The magnesian-calcite limestones between 500 and 1,300 m do not follow this trend even though their oxygen isotopes indicate formation in cold bottom water. Micritic ooids of magnesian calcite with globigerinids as nuclei and coccoliths in the cortex are associated with the limestone crusts and obviously form in this current-swept deep-water environment. This suggests that magnesian calcite precipitates from a pore fluid close to, and derived from, sea water. The microenvironment may be controlled by micro-organisms or by inorganic precipitation of calcium carbonate that increases the Mg:Ca ratio in the pore fluid, thus raising the magnesian c ntent of the precipitating calcite. End_of_Article - Last_Page 986------------
p27kip1 Controls Cell Morphology and Motility by Regulating Microtubule-Dependent Lipid Raft Recycling

ABSTRACT p27kip1 (p27) is an inhibitor of cyclin/cyclin-dependent kinase complexes, whose nuclear loss indicates a poor prognosis in various solid tumors. When located in the cytoplasm, p27 binds Op18/stathmin (stathmin), a microtubule (MT)-destabilizing protein, and restrains its activity. This leads to MT stabilization, which negatively affects cell migration. Here, we demonstrate that this p27 function also influences morphology and motility of cells immersed in three-dimensional (3D)matrices. Cells lacking p27 display a decrease in MT stability, a rounded shape when immersed in 3D environments, and a mesenchymal-amoeboid conversion in their motility mode. Upon cell contact to extracellular matrix, the decreased MT stability observed in p27 null cells results in accelerated lipid raft trafficking and increased RhoA activity. Importantly, cell morphology, motility, MT network composition, and distribution of p27 null cells were rescued by the concomitant genetic ablation of Stathmin, implicating that the balanced expression of p27 and stathmin represents a crucial determinant for cytoskeletal organization and cellular behavior in 3D contexts.