Miracle-dz/UniFAR-FTUs huggingface dataset:
Deletion of a kinesin I motor unmasks a mechanism of homeostatic branching control by neurotrophin-3

Development and function of highly polarized cells such as neurons depend on microtubule-associated intracellular transport, but little is known about contributions of specific molecular motors to the establishment of synaptic connections. In this study, we investigated the function of the Kinesin I heavy chain Kif5aa during retinotectal circuit formation in zebrafish. Targeted disruption of Kif5aa does not affect retinal ganglion cell differentiation, and retinal axons reach their topographically correct targets in the tectum, albeit with a delay. In vivo dynamic imaging showed that anterograde transport of mitochondria is impaired, as is synaptic transmission. Strikingly, disruption of presynaptic activity elicits upregulation of Neurotrophin-3 (Ntf3) in postsynaptic tectal cells. This in turn promotes exuberant branching of retinal axons by signaling through the TrkC receptor (Ntrk3). Thus, our study has uncovered an activity-dependent, retrograde signaling pathway that homeostatically controls axonal branching. DOI: http://dx.doi. org/10.7554/eLife.05061. 001
Runoff Water Quality from a Sierran Upland Forest, Transition Ecotone, and Riparian Wet Meadow

SSSAJ: Volume 75: Number 5 • September–October 2011 Soil Sci. Soc. Am. J. 75:1946–1957 Posted online 4 Aug. 2011 doi:10.2136/sssaj2011.0001 Received 6 Jan. 2011. *Corresponding author (wilymalr@cabnr.unr.edu). © Soil Science Society of America, 5585 Guilford Rd., Madison WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. Runoff Water Quality from a Sierran Upland Forest, Transition Ecotone, and Riparian Wet Meadow Forest, Range & Wildland Soils
A Comparison of Chemical and Isotopic Hydrograph Separation

As part of the construction of a simulation model to test an acid precipitation neutralization mechanism, the stream hydrograph was separated into its base flow and event water components using stable environmental isotopes of water, naturally occurring conservative tracer. Three snowmelt events and one storm event during the winter and spring of 1984 were studied at an instrumented watershed in the Hubbard Brook Experimental Forest, New Hampshire. Conditions for use of the isotopic tracer were not always met, however. During the latter part of the snowmelt and the storm the isotopic content of the groundwater and event water were not distinguishable. Furthermore, the isotopic content of the meltwater varied considerably over time, thereby reducing the precision of the hydrograph separation. Frequent sampling of the meltwater is mandatory to assess this variability. Because the concentration of major cations and anions was measured as well, chemical tracers could be compared to the isotopic tracer, when the isotopic hydrograph separation was reliable, to test whether the chemical tracer was conservative. Dissolved silica was found to act as a conservative tracer for this watershed.
Diagnostic Accuracy of the InBios Scrub Typhus Detect Enzyme-Linked Immunoassay for the Detection of IgM Antibodies in Northern Thailand

ABSTRACT In this study, we examined the diagnostic accuracy of the InBios Scrub Typhus Detect IgM enzyme-linked immunosorbent assay (ELISA) and determined the optimal diagnostic optical density (OD) cutoffs for screening and diagnostic applications based on prospectively collected, characterized samples from undifferentiated febrile illness patients in northern Thailand. Direct comparisons with the serological gold standard, indirect immunofluorescence assay (IFA), revealed strong statistical correlation of ELISA OD values and IFA IgM titers. Determination of the optimal ELISA cutoff for seroepidemiology or screening purposes compared to the corresponding IFA reciprocal titer of 400 as previously described for Thailand was 0.60 OD, which corresponded to a sensitivity (Sn) of 84% and a specificity (Sp) of 98%. The diagnostic performance against the improved and more-stringent scrub typhus infection criteria (STIC), correcting for low false-positive IFA titers, resulted in an Sn of 93% and an Sp of 91% at an ELISA cutoff of 0.5 OD. This diagnostic ELISA cutoff corresponds to IFA reciprocal titers of 1,600 to 3,200, which greatly reduces the false-positive rates associated with low-positive IFA titers. These data are in congruence with the recently improved serodiagnostic positivity criteria using the Bayesian latent class modeling approach. In summary, the InBios Scrub Typhus Detect IgM ELISA is affordable and easy-to-use, with adequate diagnostic accuracy for screening and diagnostic purposes, and should be considered an improved alternative to the gold standard IFA for acute diagnosis. For broader application, regional cutoff validation and antigenic composition for consistent diagnostic accuracy should be considered.
Long-Term Landscape Evolution: Early Miocene and Modern Rivers in Southern New South Wales, Australia

Basaltic lavas that flowed into river valleys draining westward from the uplands of southern New South Wales have preserved the Early Miocene landscape to a remarkable degree. The reconstruction of this landscape shows that the major topographic features of the highest part of the Australian continent had taken on essentially their present form by the Mid-Tertiary, and that some of these features were formed during the Mesozoic. Plateau surfaces have been lowered by only about 2 to 5 m/Ma, and most major streams have incised by only about 5 to 18 m/Ma, with a maximum incision of 30 m/Ma, since the Early Miocene. Despite the passage of 20 Ma, stream gradients have not waned, nor have major breaks in profiles been eliminated. On the contrary the modern stream profiles are strikingly similar to their Early Miocene counterparts, suggesting that the evolution of the profiles has been determined mainly by variations in stream power, rather than by the headward retreat of nickpoints through the drainage system. These findings, together with those of earlier research in the uplands of New South Wales, imply a rate and pattern of Cenozoic denudation very much at odds with widely accepted models derived from areas, like the Appalachians, that have no chronological and stratigraphic datum comparable to the widespread lavas of southeastern Australia.
Suitable Wave-Height Parameter for Characterizing Breakwater Stability

The description of a sea state just by its variance spectral density and duration is not enough to analyze the stability of rubble- mound breakwaters, since it does not include an adequate characterization of the large waves in that sea state. Numerical simulation has been used to demonstrate that different time domain characteristics result from the simulation of a sea state solely defined by its spectrum and its duration. As a result, it is possible to obtain drastically different damage values on a given breakwater. A relationship between the groupiness factor and some extreme wave- height parameters such as H1/20 has also been illustrated by this numerical simulation. Because of these results, arguments for the use of a new wave parameter, which is based on the distribution of large wave heights, to characterize breakwater stability are made. This new parameter also accounts for the duration of the test. This paper may be helpful in explaining some of the variability found in the results of breakwater tests carried out by different laboratories.
Using Remotely Sensed Data To Identify AreasAt Risk: A Case Of Central Slovenia

People have lived with hazards since the dawn of the human race. Humanity has never (and nowhere) been fully safe against natural hazards. Hence the gathering of knowledge about these dangerous phenomena and the urgency to understand them is a necessity. Slovenia has a very diverse landscape and climate due to its position in between the Alps, Mediterranean Sea, Dinarides and Pannonian basin. Different natural or human factors have triggered numerous landslides and have caused considerable economic losses over the last 20 years in Slovenia. Traditional methods used for mapping and monitoring mass movements can benefit from the application of remote sensing techniques coupled with GIS analysis. The use of remote sensing technologies, whether air-borne, satellite or ground based allows a rapid acquisition of quantitative data over wide areas, reducing the field work and, as a consequence, the costs. Very useful among others is a satellite radar interferometry method of Persistent scatters (PSI) which enables very accurate component surface deformation velocity monitoring in the line-of-sight. This paper discusses the use of multiple image sets of SAR data acquired by past and current satellite platforms for monitoring landslides. Based on interferometric data the areas with slow ground motion will be identified and risk to the inhabitants on the tested area will be assessed based on the landslide
Total-Evidence Dating under the Fossilized Birth–Death Process

Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth–death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of data sets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants, and bees). Previous total-evidence dating analyses of this data set were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push toward more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.
Reduced muscle contraction and a relaxed posture during sleep-like Lethargus

Sleep is characterized by reduced muscle activity resulting in reduced movement and a typical posture compatible with relaxed muscles. Prior to each molt, C. elegans larvae go through a phase of behavioral quiescence called Lethargus. Lethargus has sleep-like properties, but a specific posture has not yet been described. Do C. elegans larvae relax their muscles during sleep and do they assume a typical posture? We measured worm posture and body wall muscle activity using calcium imaging across the sleep-wake-like cycle. We found that worms were less curved and had less muscle activity during the sleep-like state. We conclude that during Lethargus, muscle activity is reduced, resulting in a relaxed body posture typical for a sleep-like state.
Predicting the SARS-CoV-2 effective reproduction number using bulk contact data from mobile phones

Significance Numerous COVID-19 studies used mobile phone data but with limited power in accounting for infection numbers. We have evaluated deidentified Global Positioning System (GPS) data from over 1 million devices in Germany and inferred contacts from coproximity of devices. Through calculating the contact graphs, we derived a contact index (CX) that exhibits a high correlation with the incidence-based reproduction number R so that changes in CX precede those in R by more than 2 wk. CX thus is an early indicator for outbreaks and can be used to guide social-distancing policies. Further questions, including those for the efficacy of vaccination, can be addressed with our method. We discuss limitations, e.g., transmission on international travel, and the relation to superspreading. Over the last months, cases of SARS-CoV-2 surged repeatedly in many countries but could often be controlled with nonpharmaceutical interventions including social distancing. We analyzed deidentified Global Positioning System (GPS) tracking data from 1.15 to 1.4 million cell phones in Germany per day between March and November 2020 to identify encounters between individuals and statistically evaluate contact behavior. Using graph sampling theory, we estimated the contact index (CX), a metric for number and heterogeneity of contacts. We found that CX, and not the total number of contacts, is an accurate predictor for the effective reproduction number R derived from case numbers. A high correlation between CX and R recorded more than 2 wk later allows assessment of social behavior well before changes in case numbers become detectable. By construction, the CX quantifies the role of superspreading and permits assigning risks to specific contact behavior. We provide a critical CX value beyond which R is expected to rise above 1 and propose to use that value to leverage the social-distancing interventions for the coming months.
Volatile solubilities in magmas: Transport of volatiles from mantles to planet surfaces

Experimental measurements of the solubility of CO2, CO, CH4, H2, and H2O in silicate melt were made at pressures from 10 to 20 Kb and temperatures of 1200°C. The C-O-H fluid phase was buffered by graphite, iron, and wustite. Detailed measurements were made on melts of NaAlSi3O8 composition and the results confirmed for alkalic and tholeiitic basalt liquids. The melt volatiles have dramatically lower H2/H2O and higher CO/CO2 ratios than the fluid. The result is large differences between the C-O-H compositions of the melt and the fluid (fluids about 16 atm % C, 6% O, and 78% H; melts about 4% C, 32% O, and 64% H). The measured solubilities allow calculation of activity coefficients for volatile species in the melt. They are, roughly, CO = 0.1, H2O = 0.6, CO2 = 1, H2 = 3, and CH4 = 60. This two-order-of-magnitude variation in activity coefficients causes the significant volatile fractionation observed between fluid and melt. We argue that the same fractionation will occur in the more usual case of fluid-absent partial melting of planetary mantles. The fractionation is such that reducing mantles will form magmas that yield volcanic gases about 1.5 orders-of-magnitude more oxidizing than the mantle source, while oxidizing mantles will form magmas with more reduced volcanic gases. We conclude that a volcanic gas composition cannot be directly used to estimate either the oxygen fugacity or volatile composition of its magma source region. The results suggest that volcanic gases will normally lie in the “neutral” range of oxygen fugacity, near that of the quartz-fayalite-magnetite buffer. These gases are predominately H2O with minor CO2, CO, H2, and CH4.
Radar backscatter measurements from Platform Noordwijk in the North Sea

Results from radar backscatter experiments conducted over the North Sea in Project Noordwijk in the years 1977, 1978, and 1979 are reported. For these measurements a short-range X -band FM/CW scatterometer was used. Data obtained were the average normalized backscatter \gamma(\sigma\deg) of the sea as a function of grazing angle, windspeed, and look direction. The fading spectra and the autocorrelation function of \gamma(t) were also determined and compared with the output of the oceanographic sensors of the platform.
TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase

We present TFAM, an automated, statistical method to classify the identity of tRNAs. TFAM, currently optimized for bacteria, classifies initiator tRNAs and predicts the charging identity of both typical and atypical tRNAs such as suppressors with high confidence. We show statistical evidence for extensive variation in tRNA identity determinants among bacterial genomes due to variation in overall tDNA base content. With TFAM we have detected the first case of eukaryotic-like tRNA identity rules in bacteria. An α-proteobacterial clade encompassing Rhizobiales, Caulobacter crescentus and Silicibacter pomeroyi, unlike a sister clade containing the Rickettsiales, Zymomonas mobilis and Gluconobacter oxydans, uses the eukaryotic identity element A73 instead of the highly conserved prokaryotic element C73. We confirm divergence of bacterial histidylation rules by demonstrating perfect covariation of α-proteobacterial tRNAHis acceptor stems and residues in the motif IIb tRNA-binding pocket of their histidyl-tRNA synthetases (HisRS). Phylogenomic analysis supports lateral transfer of a eukaryotic-like HisRS into the α-proteobacteria followed by in situ adaptation of the bacterial tDNAHis and identity rule divergence. Our results demonstrate that TFAM is an effective tool for the bioinformatics, comparative genomics and evolutionary study of tRNA identity.
Persistence of neuronal representations through time and damage in the hippocampus

Robust memories through neuron networks How does the brain store information over a long period of time? Gonzalez et al. chronically implanted custom-built high-sensitivity microendoscopes and performed long-term imaging of neuronal activity in freely moving mutant mice. The majority of neurons were active on most days, but their firing rate changed across sessions and tasks. Although the responses of individual neurons changed, the responses of groups of neurons with synchronous activity were very stable across days and weeks. In addition, the network activity in hippocampal area CA1 recovered after an extended period without performing the task or even after abnormal activity induced by local lesions. These findings indicate the presence of attractor-like ensemble dynamics as a mechanism by which the representations of an environment are encoded in the brain. Science, this issue p. 821 Neuronal representations in networks of neurons with synchronized activity are stable over weeks, even after damage or lack of training. How do neurons encode long-term memories? Bilateral imaging of neuronal activity in the mouse hippocampus reveals that, from one day to the next, ~40% of neurons change their responsiveness to cues, but thereafter only 1% of cells change per day. Despite these changes, neuronal responses are resilient to a lack of exposure to a previously completed task or to hippocampus lesions. Unlike individual neurons, the responses of which change after a few days, groups of neurons with inter- and intrahemispheric synchronous activity show stable responses for several weeks. The likelihood that a neuron maintains its responsiveness across days is proportional to the number of neurons with which its activity is synchronous. Information stored in individual neurons is relatively labile, but it can be reliably stored in networks of synchronously active neurons.
Impacts of air pollution exposure on the allergenic properties of Arizona cypress pollens

Epidemiological studies have demonstrated that urbanization and high levels of vehicle emissions correlated with the increasing trend of pollen-induced respiratory allergies. Numerous works have investigated the role of pollutants in the pathogenesis of respiratory diseases but impacts of anthropogenic pollution on pollen allergenic properties are still poorly understood. The objective of this survey was to evaluate impacts of the traffic-related pollution on the structure and allergenic protein content of Arizona cypress (Cupressus arizonica, CA) pollens, recognized as a rising cause of seasonal allergy in various regions worldwide. According to our results, traffic-related air pollution by its direct effects on the elemental composition of pollens considerably increased the fragility of the pollen exine, causing numerous cracks in its surface and facilitating pollen content liberation. Pollen grains were also covered by numerous submicronic orbicules which may act as effective vectors for pollen-released components into the lower regions of respiratory organs. On the other hand, this study provides us reliable explications about the low efficiency of standard commercial allergens in the diagnosis of the Arizona cypress pollen allergy in Tehran. Although traffic related pollution affects the allergenic components of CA pollens, the repercussions on the respiratory health of urban populations have yet to be clarified and need further investigations.
Overexpression of transposable elements underlies immune overdrive and poor clinical outcome in cancer patients

The immune system plays a key role in protection against cancer. Increased immune infiltration in tumor tissue is usually associated with improved clinical outcome, but in colorectal cancer, excessive immune infiltration has also been shown to lead to worst prognosis. The factors underlying this immune overdrive phenotype remains unknown. In this study, using colorectal cancer as a model, we develop a transposable element (TE) expression score that stratifies patients into four clusters with distinctive prognosis. Those with the highest TE expression are associated with immune overdrive and have the poorest outcomes. Importantly, this association is independent of microsatellite instability status and tumor mutation burden. To demonstrate that TE reactivation is responsible for the immune overdrive phenotype, we show that cell lines treated with DNA methyltransferase inhibitors also have a high TE expression score and activation of cellular innate immune response pathways. Finally, a pan-cancer survey of TE expression identify a subset of kidney renal clear cell carcinoma with a similar adverse immune overdrive phenotype with poor prognosis. Together, our findings reveal that TE expression underlies the immune overdrive phenotype in cancer and is predicative of immune infiltration and patient prognosis in cancer patients.
Metabolic crossfeeding structures the assembly of polysaccharide degrading communities

Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders structure the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical crossfeeding structure that allows biopolymer degraders to shape the dynamics of community assembly. One sentence summary Specialized biopolymer degraders structure microbial community assembly through interconnected modes of metabolic crossfeeding