Miracle-dz/UniFAR-FTUs huggingface dataset:
Warming and shrub encroachment decrease decomposition in arid alpine and subalpine ecosystems

ABSTRACT Climate change is shifting species distributions and altering plant community composition worldwide. For instance, with rising temperatures shrubs are encroaching into alpine ecosystems, resulting in important implications for ecosystem functioning. In particular, woody-plant encroachment could slow decomposition in systems traditionally dominated by herbaceous species. To evaluate how litter decomposition responded jointly to warming and shrub presence, we conducted a passive warming chamber experiment in subalpine and alpine plant communities in the White Mountains of California. Passive warming chambers were placed over plots with and without the range-expanding sagebrush Artemisia rothrockii at two elevations. Litter from A. rothrockii and the common perennial herb Trifolium andersonii decomposed for two years under the experimental treatments. Nitrate availability was measured with ion-exchange resins during the same time period. Warming decreased decomposition rates overall, associated with decreased soil moisture, but did not influence soil nitrate availability. Sagebrush presence decreased both decomposition rates and nitrate availability. Hence, future warming in this system will likely reduce decomposition rates, both directly and indirectly, via shrub encroachment. However, impacts on nutrient mineralization are less clear. These findings highlight how shifting species composition, through processes such as range expansions, can influence ecosystem responses to climate change.
Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors upon Addition of Phosphorus

ABSTRACT Phosphorus was added as a nutrient to bench-scale and pilot-scale biologically active carbon (BAC) reactors operated for perchlorate and nitrate removal from contaminated groundwater. The two bioreactors responded similarly to phosphorus addition in terms of microbial community function (i.e., reactor performance), while drastically different responses in microbial community structure were detected. Improvement in reactor performance with respect to perchlorate and nitrate removal started within a few days after phosphorus addition for both reactors. Microbial community structures were evaluated using molecular techniques targeting 16S rRNA genes. Clone library results showed that the relative abundance of perchlorate-reducing bacteria (PRB) Dechloromonas and Azospira in the bench-scale reactor increased from 15.2% and 0.6% to 54.2% and 11.7% after phosphorus addition, respectively. Real-time quantitative PCR (qPCR) experiments revealed that these increases started within a few days after phosphorus addition. In contrast, after phosphorus addition, the relative abundance of Dechloromonas in the pilot-scale reactor decreased from 7.1 to 0.6%, while Zoogloea increased from 17.9 to 52.0%. The results of this study demonstrated that similar operating conditions for bench-scale and pilot-scale reactors resulted in similar contaminant removal performances, despite dramatically different responses from microbial communities. These findings suggest that it is important to evaluate the microbial community compositions inside bioreactors used for drinking water treatment, as they determine the microbial composition in the effluent and impact downstream treatment requirements for drinking water production. This information could be particularly relevant to drinking water safety, if pathogens or disinfectant-resistant bacteria are detected in the bioreactors.
Climate and Water Conflicts Coevolution from Tropical Development and Hydro‐Climatic Perspectives: A Case Study of Costa Rica

Costa Rica is a nation with a vast wealth of water resources; however, recently the country has faced water conflicts (WC) due to social, economic, legal, and political impediments in response to limited water availability during El Niño events and inefficient use of its water resources. This study presents a spatial distribution and temporal analysis of WC in Costa Rica from 2005 to 2015. In total, 719 WC were analyzed of which 54% were among private individuals and government. The largest urban areas and the Grande de Tárcoles Basin were identified as the main “hot spot” for the conflicts. WC were mainly caused by spills of wastewater, water pollution, water shortage, infrastructure damage, and flooding, and can be predicted using a multiple linear model including the population size and the number of hydro‐meteorological events (HME) (R2 = 0.77). The identified HME also coevolved significantly with the changes in precipitation regimes (r = 0.67, p = 0.021). Our results suggest that there is a need to recognize that water infrastructure longevity across the country concatenates and amplifies WC, mainly in the most populated area located in the Central Valley. Implications of our findings include the need for truly integrated water resources management plans that include, for example, WC as indicators of hydro‐climatic changing conditions and water supply and sanitation infrastructure status.
Natural Genetic Transformation Generates a Population of Merodiploids in Streptococcus pneumoniae

Partial duplication of genetic material is prevalent in eukaryotes and provides potential for evolution of new traits. Prokaryotes, which are generally haploid in nature, can evolve new genes by partial chromosome duplication, known as merodiploidy. Little is known about merodiploid formation during genetic exchange processes, although merodiploids have been serendipitously observed in early studies of bacterial transformation. Natural bacterial transformation involves internalization of exogenous donor DNA and its subsequent integration into the recipient genome by homology. It contributes to the remarkable plasticity of the human pathogen Streptococcus pneumoniae through intra and interspecies genetic exchange. We report that lethal cassette transformation produced merodiploids possessing both intact and cassette-inactivated copies of the essential target gene, bordered by repeats (R) corresponding to incomplete copies of IS861. We show that merodiploidy is transiently stimulated by transformation, and only requires uptake of a ∼3-kb DNA fragment partly repeated in the chromosome. We propose and validate a model for merodiploid formation, providing evidence that tandem-duplication (TD) formation involves unequal crossing-over resulting from alternative pairing and interchromatid integration of R. This unequal crossing-over produces a chromosome dimer, resolution of which generates a chromosome with the TD and an abortive chromosome lacking the duplicated region. We document occurrence of TDs ranging from ∼100 to ∼900 kb in size at various chromosomal locations, including by self-transformation (transformation with recipient chromosomal DNA). We show that self-transformation produces a population containing many different merodiploid cells. Merodiploidy provides opportunities for evolution of new genetic traits via alteration of duplicated genes, unrestricted by functional selective pressure. Transient stimulation of a varied population of merodiploids by transformation, which can be triggered by stresses such as antibiotic treatment in S. pneumoniae, reinforces the plasticity potential of this bacterium and transformable species generally.
Nutrition and Immunity

Summary Nutrition has been known to impact animal immunity for some time, but recent data have demonstrated important impacts of the immune system on metabolism. This cross-talk, mediated by absorbed nutrients, intermediary metabolites, and inflammatory compounds, is especially prevalent during the transition to lactation. A clearer picture is emerging at the mechanistic level to explain why cows with metabolic disorders are more prone to infections and vice-versa. Nutritional strategies that control body condition in dry cows, provide adequate dietary antioxidants, and use bioactive nutrients to influence inflammatory signals can help to limit disease incidence during the transition period.
Ground‐Based Field Measurements of PM2.5 Emission Factors From Flaming and Smoldering Combustion in Eucalypt Forests

In fire‐prone areas such as southern Australia and parts of the United States, prescribed burning is a common fire management tool to reduce fuel load for wildfire suppression purposes. The burns are typically undertaken during calm and stable conditions when the burn extent and duration can be carefully controlled. This often coincides with poor atmospheric ventilation, leading to a buildup of smoke, which can impact air quality and human health. The low intensity of these burns also means that the plume is less buoyant and the main impact on local populations is due to emissions during the slow and prolonged smoldering combustion of heavy fuels. This study presents emission measurements of PM2.5 at prescribed burns in eucalypt forests of southern Australia using a smoke collection method suitable for both flaming combustion of fine fuels and residual smoldering combustion of heavy fuels and logs. The median PM2.5 emission factors (EFs) measured were 16.9‐g/kg fuel during flaming combustion and 38.8‐g/kg fuel during smoldering combustion. The correlation between PM2.5 EFs and modified combustion efficiency highlights two distinct trends at low modified combustion efficiency, attributed to the distinct combustion processes of glowing char combustion and pyrolysis. Hence, two distinct relationships were developed that best fitted the measurements and that can be used to extrapolate measured EFs to a wider range of fuel and burning conditions. The results from this study addressed a gap in our knowledge of particle emissions during burns in eucalypt forests under different burning conditions and help to better forecast and manage air quality impacts from prescribed burns on nearby communities.
Deep and Wide Multiscale Recursive Networks for Robust Image Labeling

Feedforward multilayer networks trained by supervised learning have recently demonstrated state of the art performance on image labeling problems such as boundary prediction and scene parsing. As even very low error rates can limit practical usage of such systems, methods that perform closer to human accuracy remain desirable. In this work, we propose a new type of network with the following properties that address what we hypothesize to be limiting aspects of existing methods: (1) a `wide' structure with thousands of features, (2) a large field of view, (3) recursive iterations that exploit statistical dependencies in label space, and (4) a parallelizable architecture that can be trained in a fraction of the time compared to benchmark multilayer convolutional networks. For the specific image labeling problem of boundary prediction, we also introduce a novel example weighting algorithm that improves segmentation accuracy. Experiments in the challenging domain of connectomic reconstruction of neural circuity from 3d electron microscopy data show that these "Deep And Wide Multiscale Recursive" (DAWMR) networks lead to new levels of image labeling performance. The highest performing architecture has twelve layers, interwoven supervised and unsupervised stages, and uses an input field of view of 157,464 voxels ($54^3$) to make a prediction at each image location. We present an associated open source software package that enables the simple and flexible creation of DAWMR networks.
Activation of a Dimeric Metabotropic Glutamate Receptor by Intersubunit Rearrangement*

Although many G protein-coupled receptors (GPCRs) can form dimers, a possible role of this phenomenon in their activation remains elusive. A recent and exciting proposal is that a dynamic intersubunit interplay may contribute to GPCR activation. Here, we examined this possibility using dimeric metabotropic glutamate receptors (mGluRs). We first developed a system to perfectly control their subunit composition and show that mGluR dimers do not form larger oligomers. We then examined an mGluR dimer containing one subunit in which the extracellular agonist-binding domain was uncoupled from the G protein-activating transmembrane domain. Despite this uncoupling in one protomer, agonist stimulation resulted in symmetric activation of either transmembrane domain in the dimer with the same efficiency. This, plus other data, can only be explained by an intersubunit rearrangement as the activation mechanism. Although well established for other types of receptors such as tyrosine kinase and guanylate cyclase receptors, this is the first clear demonstration that such a mechanism may also apply to GPCRs.
Sinorhizobial chemotaxis: a departure from the enterobacterial paradigm.

Motile bacteria display a surprisingly sophisticated sensory behaviour. By monitoring changes in the chemical composition of their environment, they migrate towards food sources (attractants) and flee from noxious chemicals (repellents). This behaviour, named chemotaxis, involves information processing of signals from receptors that sense the environment, and signal transduction to the flagellar motor to modulate its rotation accordingly. Since the pioneering work of Julius Adler almost 40 years ago (Adler, 1965), genetic, biochemical and biophysical studies of chemotaxis have been focussed mostly on enterobacteria, essentially on Escherichia coli and Salmonella, thus contributing greatly to the goal of ‘understanding a simple behaviour at the molecular level ’ (Parkinson, 1987). Today, the enterobacterial sensory pathway and all central components of the signal transduction chain as well as interactions between these proteins have been identified (for recent reviews see Bren & Eisenbach, 2000; Falke et al., 1997; Grebe & Stock, 1998; Macnab, 1996). However, many molecular details of receptor function, signal amplification and signal processing, of flagellar motor mechanics and regulation are still not understood. The more recent interest in non-enteric and even archaeal chemosensory systems has expanded our view and revealed fascinating variations on a general theme (for reviews see Armitage & Schmitt, 1997; Manson et al., 1998; Marwan & Oesterhelt, 2000). Concurrences observed between bacteria and archaea suggest an early origin of the prokaryotic chemosensory system – as long as 3 billion years ago. Differences between present-day systems point to a diverging evolution and the need for adaptation to different habitats. For the investigator, this departure from the established scheme poses an interesting challenge, as it may conceal new answers to hitherto unsolved questions.
The Caenorhabditis elegans P21-activated kinases are differentially required for UNC-6/netrin-mediated commissural motor axon guidance

P21 activated kinases (PAKs) are major downstream effectors of rac-related small GTPases that regulate various cellular processes. We have identified the new PAK gene max-2 in a screen for mutants disrupted in UNC-6/netrin-mediated commissural axon guidance. There are three Caenorhabditis elegans PAKs. We find that each C. elegans PAK represents a distinct group previously identified in other species. Here we examine their roles in the postembryonic migration of the P cell neuroblasts and the axon guidance of the ventral cord commissural motoneurons (VCCMNs). We find that the two PAKs, max-2 and pak-1, are redundantly required for P cell migration and function with UNC-73/Trio and the rac GTPases (CED-10 and MIG-2). During axon guidance of the VCCMNs, PAK-1 also acts with the rac GTPases, CED-10 and MIG-2, and is completely redundant with MAX-2. Interestingly, we find that unlike MAX-2 activity during P cell migration, for motoneuron axon guidance max-2 is also required in parallel to this PAK-1 pathway, independent of rac GTPase signaling. Finally, we provide evidence that MAX-2 functions downstream of the UNC-6/netrin receptor UNC-5 during axon repulsion and is an integral part of its signaling.
Lack To Transfer The Performance's Improvements Obtained In Virtual Reality Environment To Balance Control In Patients With Chronic Sequels Of Stroke

Objectives: Despite the recent enlargement in the usage of Virtual Reality environments for rehabilitation in Stroke, the potential for transference/generalization of gains to similar task performed in real environments remains uncertain. Thus, the purpose of this study was to verify the transference/generalization of gains obtained by training in Virtual Reality environments (VR) to similar balance tasks in real environment in patients with chronic sequels of Stroke. Participants: Twenty-nine chronic stroke patients. Interventions: Three sessions of balance training in VR using five games from Nintendo Wii Fit™ for experimental group (EG). Verbal orientation about falls preventions for control group (CG). Main outcome measures: The transference/generalization of gains obtained in VR training was assessed through performance in four balance tests with similar demand than games using a force plate in two assessment time points: at baseline (BA) and at end of study (EA). Results: The ANOVA for repeated measure showed that there were statistically significant improvements for all trained games after the training. However, there were no statistical significant differences in the balance tests performance between BA and EA, for both groups. Conclusions: Patients with chronic sequels with stroke were unable to transfer/generalize the gains obtained in VR to similar balance tasks performed in real environment.
A Method for Deriving the Boundary Layer Mixing Height from MODIS Atmospheric Profile Data

The planetary boundary layer is the medium of energy, moisture, momentum and pollutant exchange between the surface and the atmosphere. In this paper, a method to derive the boundary layer mixing height (MH) was introduced and applied over the Heihe river basin. Atmospheric profiles from the MODerate Resolution Imaging Sepctroradiometer (MODIS) instrument onboard the NASA-Aqua satellite were used for the high spatial resolution of this method. A gap-filling method was used to replace missing MODIS data. In situ MH data were also calculated from HIWATER (Heihe Watershed Allied Telemetry Experimental Research) and WATER (Watershed Allied Telemetry Experimental Research) observational radiosonde sounding data from 2008 and 2012 using the Richardson number method combined with a subjective method. The MH occurs where there is an abrupt decrease in the MR (water vapor mixing ratio). The minimum vertical gradient of the MR is used to determine the MH. The method has an average RMSE of 370 m under clear skies and convective conditions. The seasonal variation in the MH at the Gaoya radiosonde station is also presented. The study demonstrates that remote sensing methodologies can successfully estimate the MH without the help of field measurements.
Foot-mounted inertial navigation made easy

Despite being around for almost two decades, foot-mounted inertial navigation only has gotten a limited spread. Contributing factors to this are lack of suitable hardware platforms and difficult system integration. As a solution to this, we present an open-source wireless foot-mounted inertial navigation module with an intuitive and significantly simplified dead reckoning interface. The interface is motivated from statistical properties of the underlying aided inertial navigation and argued to give negligible information loss. The module consists of both a hardware platform and embedded software. Details of the platform and the software are described, and a summarizing description of how to reproduce the module are given. System integration of the module is outlined and finally, we provide a basic performance assessment of the module. In summary, the module provides a modularization of the foot-mounted inertial navigation and makes the technology significantly easier to use.
Mean platelet volume and platelet counts in type 2 Diabetes: Mellitus on treatment and non-diabetic mellitus controls in Lagos, Nigeria

Introduction The Mean platelet volume and platelet counts are indicators of thrombotic potentials, and risk factors for microvascular complications in diabetics. This study aimed to establish variations in platelet counts and mean platelet volume in type 2 diabetic patients on treatment and non-diabetic controls. Methods This was an unmatched case-control study involving 200 participants consisting of 100 diabetics and 100 non-diabetic controls. Four and half milliliters of blood was collected from diabetics and non diabetic controls into EDTA anticoagulant tubes. Full blood count was performed using the Sysmex KN-21N, (manufactured by Sysmex corporation Kobe, Japan) a three- part auto analyzer able to run 19 parameters per sample including platelet counts and mean platelet volume. Results The mean fasting blood sugar for the diabetics was 147.85±72.54 mg/dl and the controls 95.20±30.10 mg/dl. The mean platelet count for the diabetics was 235.29±76.81*109/L and controls, 211.32±66.44*109/L. The mean platelet volume, for the diabetics was 8.69±0.67 fl and the controls, 8.91±0.80 fl. There was a statistically significant difference in platelet counts of diabetics and healthy controls p =0.038 while none existed between the mean platelet volume in diabetics and healthy controls p = 0.593. Conclusion This study revealed a higher mean platelet count for diabetics on treatment than for non diabetic controls while mean platelet volume was lower in cases than controls. However, both parameters in diabetics on treatment were within the normal reference range for healthy individuals.
Eye Tracking for Everyone

From scientific research to commercial applications, eye tracking is an important tool across many domains. Despite its range of applications, eye tracking has yet to become a pervasive technology. We believe that we can put the power of eye tracking in everyone's palm by building eye tracking software that works on commodity hardware such as mobile phones and tablets, without the need for additional sensors or devices. We tackle this problem by introducing GazeCapture, the first large-scale dataset for eye tracking, containing data from over 1450 people consisting of almost 2:5M frames. Using GazeCapture, we train iTracker, a convolutional neural network for eye tracking, which achieves a significant reduction in error over previous approaches while running in real time (10-15fps) on a modern mobile device. Our model achieves a prediction error of 1.71cm and 2.53cm without calibration on mobile phones and tablets respectively. With calibration, this is reduced to 1.34cm and 2.12cm. Further, we demonstrate that the features learned by iTracker generalize well to other datasets, achieving state-of-the-art results. The code, data, and models are available at http://gazecapture.csail. mit.edu.
Robust tracking performance and disturbance rejection for a class of nonlinear systems using disturbance observers

This paper is concerned with disturbance rejection performance in single-input single-output (SISO) nonlinear systems described by uncertain linear dynamics and bounded nonlinearities. After transforming the nonlinear terms into an equivalent bounded disturbance at the output of a linear system, a disturbance observer (DOB) is added to achieve robust disturbance rejection. The DOB design is formulated as Luenberger observer state estimation for an augmented system which contains at least one eigenvalue at the origin. The synthesis of a (sub)optimal DOB is carried out by solving multi-objective H∞ sensitivity optimization. The design approach is applied to an inverted pendulum with actuator backlash.