Miracle-dz/UniFAR-FTUs huggingface dataset:
Short‐Term Dynamics of Root‐ and Shoot‐Derived Carbon from a Leguminous Green Manure

Although roots are an important source of soil organic matter (SOM) and are thought to be the major constituent of the particulate organic matter (POM) fraction, few studies have documented the fate of belowground C inputs in situ. The main purpose of this experiment was to determine the fate of root-derived C vs. shoot-derived C and to identify factors contributing to any differences in the retention of aboveground vs. belowground C inputs. We labeled hairy vetch (Vicia villosa Roth subsp. villosa) in situ with 13 CO 2 and followed both root- and shoot-derived C in total soil organic C (SOC) and labile C pools for the first growing season following hairy vetch incorporation. At the end of the growing season, nearly one-half of the root-derived C was still present in the soil, whereas only 13% of shoot-derived C remained. A greater proportion of root-derived C was found as occluded POM and associated with the clay and silt fraction. Greater root-derived C also was retained as chloroform-extractable microbial biomass. We suggest that three different mechanisms contributed to the increased retention of root-derived C: (i) the greater biochemical recalcitrance of root litter, (ii) increased physical protection of root-derived POM within aggregates, and (iii) the continuous nature of root C inputs from exudates and fine root turnover. We conclude that shoot residues are broken down rapidly and serve as the source of N for the following cash crop, whereas the root litter is probably largely responsible for the short-term soil structural improvements associated with the use of green manures. Furthermore, on the basis of these findings, we hypothesize that the greater retention of root-derived C in the first 6 mo of decomposition will increase the persistence of this C in SOM in the long term.
Journal Pre-proof Accommodating site variation in neuroimaging data using normative and hierarchical Bayesian models

results show the value of hierarchical Bayesian regression methods for accommodating 27 site variation in neuroimaging data, which provides an alternative to harmonization techniques. While the approach we propose may have broad utility, our approach is particularly well suited to normative modeling where the primary interest is in accurate modeling of inter-subject variation and statistical 30 quantiﬁcation of deviations from a reference model. and the brain structure. In addition, our model is fully Bayesian and entails a hierarchical structure, including priors and hyper-priors for each parameter. healthy control sample the imaging data ) 2014) data set to compare a non- linear, Gaussian process version of the normative model, to a linear hierarchical Bayesian version accounting for site effects that does not include the Gaussian Process term. We then show that the hierarchical Bayesian models including 160 a site parameter perform better than existing methods for dealing with additive and multiplicative (non-linear) site effects, including ComBat, ComBat Gam Pomponio and regressing out site. Subsequently, we validate the hierarchical Bayesian models in the autism sample of the ABIDE data set and test their ability to retain clinically useful variance while correcting for site effects. We ﬁnally discuss the normative hierarchical Bayesian methods with regard to their implications for neuroimaging data-sharing initiatives and their use as general technique to correct for site effects.
Bread, Beer and the Seeds of Change: Agriculture’s Imprint on World History

Part I. Background Chapter 1. Why Agriculture? Chapter 2. What Crops to Grow? Chapter 3. Beer and Bread Chapter 4. Human Nutrition and Health Chapter 5. Cropping Requirements Part II. Early Agricultural Societies Chapter 6. Sumerian (3500 to 2334 BCE) Chapter 7. Egyptian (3000 to 1070 BCE) Chapter 8. Chinese (206 BCE to 220 CE) Chapter 9. Bantu of Africa (500 BCE to 300 CE) Chapter 10. Maya (150 BCE to 910 CE) Part III. Technology Advances in Western Societies Chapter 11. Athenians (550 to 334 BCE) / Romans (509 BCE to 410 CE) Chapter 12. Feudal Europeans (800 to 1347) Chapter 13. British (1700 to 1850) Chapter 14. Development of Science and Technology (1850 to 1950) Chapter 15. Americans (1950 to present) Epilogue: Future of Grain Fermentation.
Identification of microRNAs in the West Nile virus vector Culex tarsalis

Background microRNAs (miRNAs) represent a group of small non-coding RNAs that are crucial gene regulators of important biological functions including development and pathogen defense in most living organisms. Presently, there is a lack of availability of information regarding the miRNAs in the mosquito Culex tarsalis, which is one of the most important vectors of West Nile virus (WNV) in the United States. We used small RNA sequencing data and in vitro and in vivo experiments to identify and validate the presence of a repertoire of miRNAs in Cx. tarsalis mosquitoes. Results Using bioinformatic approaches we analyzed small RNA sequencing data from the Cx. tarsalis CT embryonic cell line to discover 86 miRNAs. Consistent with other mosquitoes such as Aedes albopictus and Cx. quinquefasciatus, mi-184 was found to be the most abundant miRNA in Cx tarsalis. We also identified an additional 20 novel miRNAs from the recently sequenced Cx. tarsalis genome, for a total of 106 miRNAs identified in this study. The presence of selected miRNAs was biologically validated in both cell line and adult Cx. tarsalis mosquitoes using RT-qPCR and sequencing. Conclusions Cx. tarsalis is an important vector of many medically important pathogens including WNV and Western Equine encephalitis. Here we report a detailed insight into the miRNA population in Cx. tarsalis mosquitoes. These results will open new avenues of research deciphering the role of miRNAs in different Cx. tarsalis biological events such as development, metabolism, immunity and pathogen infection.
A new loss-of-function allele 28y reveals a role of ARGONAUTE1 in limiting asymmetric division of stomatal lineage ground cell Running title: AGO1 and stomatal spacing division

Research Article A new loss-of-function allele 28y reveals a role of ARGONAUTE1 in limiting asymmetric division of stomatal lineage ground cell Running title: AGO1 and stomatal spacing division Kezhen Yang, Min Jiang and Jie Le* Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Beijing 100093, China. These authors contributed equally to this work. * Correspondence: E-mail: lejie@ibcas.ac. cn
Nonreciprocal transmission in a nonlinear photonic‐crystal Fano structure with broken symmetry

Nanostructures that feature nonreciprocal light transmission are highly desirable building blocks for realizing photonic integrated circuits. Here, a simple and ultracompact photonic‐crystal structure, where a waveguide is coupled to a single nanocavity, is proposed and experimentally demonstrated, showing very efficient optical diode functionality. The key novelty of the structure is the use of cavity‐enhanced material nonlinearities in combination with spatial symmetry breaking and a Fano resonance to realize nonreciprocal propagation effects at ultralow power and with good wavelength tunability. The nonlinearity of the device relies on ultrafast carrier dynamics, rather than the thermal effects usually considered, allowing the demonstration of nonreciprocal operation at a bit‐rate of 10 Gbit s−1 with a low energy consumption of 4.5 fJ bit−1.
Metatranscriptomic response of the wheat holobiont to decreasing 1 soil water content 2

It is admitted that multicellular hosts and their microbiota form an indissociable unit, the 21 holobiont. Even though it is posited that this unit would react in a coordinated fashion to 22 environmental stress, the role of each of the partners is ill-defined. Here, we subjected wheat to a 23 gradient of water availability in the field using rainout shelters that let through 100%, 75%, 50% 24 and 25% of the precipitation. At the height of the growing season, we sampled plant roots and 25 rhizosphere, and extracted and sequenced their RNA. We more specifically compared the 100% 26 to the 25% treatments using differential abundance analysis. In the roots, the majority of the 27 differentially abundant (DA) transcripts belonged to the fungi, and most were overexpressed in 28 the 25% precipitation treatment. Approximately 10% of the DA transcripts belonged to the plant, 29 and most were underexpressed in the 25% precipitation treatment. In the rhizosphere, most of the 30 DA transcripts belonged to the bacteria and were mostly overexpressed in the 25% precipitation 31 treatment. Taken together, our results are showing that the response of the wheat holobiont to 32 decreasing precipitation levels is mostly carried out by fungi and bacteria, with very little 33 response from the plant itself.
Frontiers in Cellular Neuroscience Cellular Neuroscience

and Duffy, 1981). However, attributing these results to MD-induced plasticity of inhibitory networks is difficult, as blockade of GABA receptors in normal cats both broadens receptive field properties and unmasks previously subthreshold responses (Sillito, 1975). A similar unmasking was also observed for responses evoked through either the deprived or non-deprived eye in MD animals (Sillito et al., 1981). In recent years rodents have emerged as the preferred system for studies of visual cortical plasticity, and questions of the relative contribution of MD-induced changes in excitation and inhibition have been readdressed with new approaches. Several lines of evidence demonstrate that the mechanisms of long-term depression (LTD) of excitatory synapses play a central role in the weakening of visual responses (reviewed in Smith et al., 2009). Brief MD leads to reduced surface expression of AMPA-type glutamate receptors and occludes subsequent induction of LTD (Heynen et al., 2003; Crozier et al., 2007). Furthermore, molecular manipulations that block AMPA receptor endocytosis exclusively in excitatory neurons completely prevent the loss of deprived-eye responses following MD (Yoon et al., 2009; McCurry et al., 2010). In addition, it has recently been shown that the full OD shift in cortical layer 4 is expressed by modifications of excitatory thalamocortical synaptic currents (Khibnik et al., 2010). However, additional work has shown that cortical inhibitory networks can also be strongly affected by MD. Brief periods of deprivation induce potentiation of feedback inhibition involving fast-spiking (FS) basket cells in layer 4 of the monocular visual cortex in rats studied ex vivo (Maffei et al., 2006). Additionally, two recent studies used calcium imaging in mice in vivo and found MD-induced OD shifts in both excitatory and inhibitory neurons (Gandhi et al., 2008; Kameyama et al., 2010). Thus, both the inputs to and outputs from inhibitory neurons can be modified by deprivation. Ocular dominance (OD) plasticity is the preeminent model of experience-dependent plasticity in the mammalian nervous system. Retinotopically matched inputs from both eyes converge on individual cortical neurons to produce binocular vision. The strength and persistence of these connections is highly susceptible to manipulations that asymmetrically degrade the quality of visual experience, such as monocular deprivation (MD, Wiesel and Hubel, 1963). Awake recordings in juvenile mice have shown that a brief period of monocular lid suture produces an OD shift solely through the loss of responsiveness to the deprived eye (Frenkel and Bear, 2004). Broadly speaking, there are two categories of changes …
Heat Fluxes and River Energy Budget on the Example of Lowland Świder River

Abstract The paper present the energy budget of the downstream part of lowland Świder River, right tributary of the Vistula River in Mazovian Lowland, Poland. Heat fluxes were calculated on the example of four days, representing different meteorological and vegetative conditions. Results confirmed the dominant role of radiation, which accounted for an average of 90.7% and 79.7% gains and losses of thermal energy. Participation of non-radiative components proved to be far less crucial; the average contribution of condensation, sensible heat transfer, bed conduction and friction in energy gains accounted respectively to 0.0%, 0.6%, 2.9% and 5.9%, while the average contribution of evaporation, sensible heat transfer and bed conduction in energy losses reached respectively 4.5%, 1.1% and 14.6%. The results showed significant effect of riparian vegetation and cloud cover on river heat fluxes
Karst water resources in a changing world: Review of hydrological modeling approaches

Karst regions represent 7–12% of the Earth's continental area, and about one quarter of the global population is completely or partially dependent on drinking water from karst aquifers. Climate simulations project a strong increase in temperature and a decrease of precipitation in many karst regions in the world over the next decades. Despite this potentially bleak future, few studies specifically quantify the impact of climate change on karst water resources. This review provides an introduction to karst, its evolution, and its particular hydrological processes. We explore different conceptual models of karst systems and how they can be translated into numerical models of varying complexity and therefore varying data requirements and depths of process representation. We discuss limitations of current karst models and show that at the present state, we face a challenge in terms of data availability and information content of the available data. We conclude by providing new research directions to develop and evaluate better prediction models to address the most challenging problems of karst water resources management, including opportunities for data collection and for karst model applications at so far unprecedented scales.
Prevalence Of Osteoporosis And Osteopenia Among Pakistani Pre And Post Menopausal Women

A cross-sectional study was conducted on 1416 women (age: 25 years or more), belonging to Pre and post-menopausal women (1351 & 65 respectively). All subjects were interviewed by using a structured Performa for prevalence of risk factors. Bone mineral density (BMD) was measured to determine the degree of Osteoporosis and Osteopenia by speed of sound (SOS) and broad band ultrasound attenuation (BUA) in the calcaneus bone. It was observed that 272 (19.2%) amongst all subjects were osteoporotic, 890 (62.9%) osteopenic whereas only 254 (17.9%) were normal. When assessment was done in groups, it was found that out of the total postmenopausal women (n=65), 32 (49.5%) were osteoporotic while 28 (43.1%) were found to be osteopenic. On the other hand, in premenopausal women group (n=1351), 240 (17.83%) were found to be Osteoporotic while 862 (63.8%) were found to be Osteopenic. There was however no significant relation in the BMI of all the three groups. The prevalence of osteoporosis was found to be high in postmenopausal but Osteopenia in premenopausal women was reported to be alarmingly high in premenopausal women probably due to lifestyle and dietary risk factors. There is a need to explore the precise causative factors associated with the high prevalence of Osteopenia recorded in the present study.
Prediction of Protein Subcellular Locations with Feature Selection and Analysis

In this paper, we propose a strategy to predict the subcellular locations of proteins by combining various feature selection methods. Firstly, proteins are coded by amino-acid composition and physicochemical properties, then these features are arranged by Minimum Redundancy Maximum Relevance method and further filtered by feature selection procedure. Nearest Neighbor Algorithm is used as a prediction model to predict the protein subcellular locations, and gains a correct prediction rate of 70.63%, evaluated by Jackknife cross-validation. Results of feature selection also enable us to identify the most important protein properties. The prediction software is available for public access on the website http://chemdata.shu. edu.cn/sub22/, which may play a important complementary role to a series of web-server predictors summarized recently in a review by Chou and Shen (Chou, K.C., Shen, H.B. Natural Science, 2009, 2, 63-92, http://www.scirp.org/journal/NS/).
Spatio-temporal Segmentation of Video Data

Image segmentation provides a powerful semantic description of video imagery essential in image understanding and efficient manipulation of image data. In particular, segmentation based on image motion defines regions undergoing similar motion allowing image coding system to more efficiently represent video sequences. This paper describes a general iterative framework for segmentation of video data. The objective of our spatiotemporal segmentation is to produce a layered image representation of the video for image coding applications whereby video data is simply described as a set of moving layers.
EFFECT OF COMBINATION THERAPY WITH BEVACIZUMAB AND DEXAMETHASONE INTRAVITREAL IMPLANT IN PATIENTS WITH RETINAL VEIN OCCLUSION

Objective: The objective of this study was to determine if dexamethasone intravitreal implant 0.7 mg (Ozurdex; Allergan, Inc) with bevacizumab (Avastin; Genentech, Inc) therapy can be synergistic, providing further improvements in visual acuity, sustainability, and macular thickness when compared with dexamethasone intravitreal implant 0.7 mg alone. Methods: This is a prospective, interventional case series intended to monitor changes in visual acuity and macular thickness in patients diagnosed with retinal vein occlusion (RVO), after injection of bevacizumab followed by a scheduled dexamethasone intravitreal implant. This study was designed to emulate patient care as received in the typical ophthalmology practice. Patients diagnosed with RVO, who were seen between September 2009 and July 2010, were included in this study if they had received previous anti–vascular endothelial growth factor therapy. Patients were included in analysis if the previous anti–vascular endothelial growth factor therapy was at least 6 weeks before and optical coherence tomography (OCT) was . 300 mm on spectral-domain OCT. Exclusion criteria included history of vitrectomy, and/or rubeotic or advanced glaucoma. All patients were evaluated with Snellen visual acuity and measured for macular thickness (calculated by spectraldomain OCT) and intraocular pressure. At baseline, all patients were injected with bevacizumab, followed by dexamethasone intravitreal implant injection 2 weeks later. These patients were reexamined on a monthly basis and retreated when edema occurred. Results: The primary outcome measure was the time to reinjection based on OCT and vision criteria. The secondary outcomes were increases in visual acuity and the reduction of OCT thickness during that period. Thirty-four eyes of 33 patients, with a mean age of 72.8 years, were identified. Thirty-five percent were diagnosed with central RVO, while the other 65% were with branch RVO. Of these patients, 97% gained vision during the study. Mean visual acuity improved from initially 11 letters to a maximum of 25 letters during the study period. In addition, vision improved by at least 15 letters in 29% of patients initially up to 64% during the study period. Macular thickness decreased with the combination treatment by OCT, and the effect continued an average of 126 days from the initial bevacizumab treatment. Retreatment was unnecessary in 18% of the population during the 6-month study period. Conclusion: This study demonstrates efficacy and the duration of effect using a combination of bevacizumab and dexamethasone versus dexamethasone alone. The combination is synergistic, increasing visual acuity and prolonging the time between injections, compared with either of these medications alone. Therefore, the combination of a vascular endothelial growth factor inhibitor and a dexamethasone implant may be a valuable option for RVO treatment. RETINA 32:1289–1294, 2012
Cell-specific Bioorthogonal Tagging of Glycoproteins

Altered glycosylation is an undisputed corollary of cancer development. Understanding these alterations is paramount but hampered by limitations underlying cellular model systems. For instance, the intricate interactions between tumour and host cannot be adequately recapitulated in monoculture of tumour-derived cell lines. More complex co-culture models usually rely on sorting procedures for proteome analyses and rarely capture the details of protein glycosylation. Here, we report a strategy termed Bio-Orthogonal Cell line-specific Tagging of Glycoproteins (BOCTAG). Cells are equipped by transfection with an artificial biosynthetic pathway that transforms bioorthogonally tagged sugars into the corresponding nucleotide-sugars. Only transfected cells incorporate bioorthogonal tags into glycoproteins in the presence of non-transfected cells. We employ BOCTAG as an imaging technique and to annotate cell-specific glycosylation sites in mass spectrometry-glycoproteomics. We demonstrate application in co-culture and mouse models, allowing for profiling of the glycoproteome as an important modulator of cellular function.
BodySpace: inferring body pose for natural control of a music player

We describe the BodySpace system, which uses inertial sensing and pattern recognition to allow the gestural control of a music player by placing the device at different parts of the body. We demonstrate a new approach to the segmentation and recognition of gestures for this kind of application and show how simulated physical model-based techniques can shape gestural interaction.
Mechanics of discontinuous faults

Fault traces consist of numerous discrete segments, commonly arranged as echelon arrays. In some cases, discontinuities influence the distribution of slip and seismicity along faults. To analyze fault segments, we derive a two-dimensional solution for any number of nonintersecting cracks arbitrarily located in a homogeneous elastic material. The solution includes the elastic interaction between cracks. Crack surfaces are assumed to stick or slip according to a linear friction law. For an array of echelon cracks the ratio of maximum slip to array length significantly underestimates the difference between the driving stress and frictional resistance. The ratio of maximum slip to crack length slightly overestimates this difference. Stress distributions near right- and left-stepping echelon discontinuities differ in two important ways. For right lateral shear and left-stepping cracks, normal tractions on the overlapped crack ends increase and inhibit frictional sliding, whereas for right-stepping cracks, normal tractions decrease and facilitate sliding. The mean compressive stress between right-stepping cracks also decreases and promotes the formation of secondary fractures, which tend to link the cracks and allow slip to be transferred through the discontinuity. For left-stepping cracks the mean stress increases; secondary fracturing is more restricted and tends not to link the cracks. Earthquake swarms and aftershocks cluster near right steps along right lateral faults. Our results suggest that left steps store elastic strain energy and may be sites of large earthquakes. Opposite behavior results if the sense of shear is left lateral.