Miracle-dz/UniFAR-FTUs huggingface dataset:
An UNC-40 pathway directs postsynaptic membrane extension in Caenorhabditis elegans

The postsynaptic membrane of the embryonic neuromuscular junction undergoes a dramatic expansion during later development to facilitate the depolarization of larger muscles. In C. elegans, the postsynaptic membrane resides at the termini of plasma membrane extensions called muscle arms. Membrane extension to the motor axons during larval development doubles the number of muscle arms, making them a tractable model to investigate both postsynaptic membrane expansion and guided membrane extension. To identify genes required for muscle arm extension, we performed a forward screen for mutants with fewer muscle arms. We isolated 23 mutations in 14 genes, including unc-40/Dcc, which encodes a transmembrane receptor that guides the migration of cells and extending axons in response to the secreted UNC-6/Netrin spatial cue. We discovered that UNC-40 is enriched at muscle arm termini and functions cell-autonomously to direct arm extension to the motor axons. Surprisingly, UNC-6 is dispensable for muscle arm extension, suggesting that UNC-40 relies on other spatial cues to direct arm extension. We provide the first evidence that the guanine-nucleotide exchange factor UNC-73/Trio, members of the WAVE actin-polymerization complex, and a homolog of the focal adhesion complex can function downstream of UNC-40 to direct membrane extension. Our work is the first to define a pathway for directed muscle membrane extension and illustrates that axon guidance components can play key roles in postsynaptic membrane expansion.
Controversies over the Epithelial-to-Mesenchymal Transition in Liver Fibrosis

Liver fibrosis is a universal consequence of chronic liver diseases. It is accompanied by activation of collagen-producing myofibroblasts, resulting in excessive deposition of extracellular matrix. The origin of myofibroblasts in the fibrotic liver has not been completely resolved and remains a matter of debate. Recently, the epithelial-to-mesenchymal transition (EMT) was proposed as one of the mechanisms that give rise to collagen-producing myofibroblasts in liver fibrosis. However, subsequent studies contradicted this hypothesis, and the EMT theory has become one of the most controversial and debatable issues in the field of liver fibrosis research. This review will summarize the existing literature on EMT in liver fibrosis and will analyze the causes for the contradictory results to draw a reasonable conclusion based on current knowledge in the field.
Erratum on: Neurogenesis in the embryonic and adult brain: same regulators, different roles

Reason for Erratum: Due to a typesetting error the spelling of a few terms was incorrect in “Notch Signaling” Section, paragraph 4. This error does not change the scientific conclusions of the article in any way. The publisher apologizes for this error and the correct text appears below: A tantalizing hypothesis for the mechanism underlying Notch function in stem cell quiescence comes from embryonic data showing that the levels of Hes proteins and proneural bHLHs oscillate in neural precursor cells (Imayoshi et al., 2013). Hes proteins are bHLH TFs that are induced by Notch activity and act as potent repressors of gene expression, and proneural bHLH genes are amongst their main targets (Imayoshi and Kageyama, 2014). Hes transcripts and proteins oscillate with a frequency of 2–3 h, because Hes proteins repress their own transcription and because this repression is only transient due to their short half-lives (Shimojo et al., 2008; Imayoshi et al., 2013). The oscillation of Hes proteins drives in opposite phase the oscillation of their targets, including the proneural proteins Neurog2 and Ascl1 (Shimojo et al., 2008; Imayoshi et al., 2013). Ascl1 has been shown to have two opposing roles in embryonic neurogenesis, promoting progenitor proliferation and driving their cell cycle exit and differentiation (Castro et al., 2011). Interestingly, the oscillating expression of Ascl1 promotes the proliferation of neural progenitors, while its stable expression instead drives differentiation (Imayoshi et al., 2013). The mechanisms that convert different Ascl1 dynamics into the activation of different gene expression programmes, promoting proliferation and differentiation, respectively, remain unknown. Whether Hes and Ascl1 proteins also oscillate in adult progenitors has not yet been established. Adult NSCs express high levels of Hes proteins, but an initial reduction in the amount of Notch signaling might initiate their oscillatory expression, which would thus trigger the oscillation of Ascl1 expression and the proliferation of NSCs. Subsequently, a complete loss of Notch activity in IPCs would stabilize Ascl1 expression and promote neuronal differentiation. Several observations support such a scenario. Ascl1 expression is indeed increased upon loss of RPBJk in NSCs, showing that also in the adult DG, Notch signaling suppresses its expression (Andersen et al., 2014). Differences in the intensity of Notch signaling have been singled out as possible causes of the heterogeneity in adult NSC behavior (Giachino and Taylor, 2014). Moreover, Ascl1 expression in adult NSCs is excluded from quiescent NSCs and confined to about a third of activated NSCs, suggesting that Ascl1 has indeed a dynamic expression in proliferating NSCs (Andersen et al., 2014). Further analysis will determine the importance of the interactions between the Notch-Hes pathways and Ascl1 in regulating the transitions between quiescent and activated NSCs and between NSCs and IPCs. The original article has been updated.
Characterization of denitrifying activity by the alphaproteobacterium, Sphingomonas wittichii RW1

Sphingomonas wittichii RW1 has no reported denitrifying activity yet encodes nitrite and nitric oxide reductases. The aims of this study were to determine conditions under which S. wittichii RW1 consumes nitrite (NO−2) and produces nitrous oxide (N2O), examine expression of putative genes for N-oxide metabolism, and determine the functionality of chromosomal (ch) and plasmid (p) encoded quinol-dependent nitric oxide reductases (NorZ). Batch cultures of wildtype (WT) and a norZch mutant of S. wittichii RW1 consumed NO−2 and produced N2O during stationary phase. The norZch mutant produced N2O, although at significantly lower levels (c.a. 66–87%) relative to the WT. Rates of N2O production were 2–3 times higher in cultures initiated at low relative to atmospheric O2 per unit biomass, although rates of NO−2 consumption were elevated in cultures initiated with atmospheric O2 and 1 mM NaNO2. Levels of mRNA encoding nitrite reductase (nirK), plasmid-encoded nitric oxide dioxygenase (hmpp) and plasmid-encoded nitric oxide reductase (norZp) were significantly higher in the norZch mutant over a growth curve relative to WT. The presence of NO−2 further increased levels of nirK and hmpp mRNA in both the WT and norZch mutant; levels of norZp mRNA compensated for the loss of norZch expression in the norZch mutant. Together, the results suggest that S. wittichii RW1 denitrifies NO−2 to N2O and expresses gene products predicted to detoxify N-oxides. So far, only S. wittichii strains within four closely related taxa have been observed to encode both nirK and norZ genes, indicating a species-specific lateral gene transfer that may be relevant to the niche preference of S. wittichii.
Greenhouse energy consumption prediction using neural networks models

This work analyzes an energy consumption predictor for greenhouses using a multi-layer perceptron (MLP) artificial neural network (ANN) trained by means of the Levenbergh-Marquardt back propagation algorithm. The predictor uses cascade architecture, where the outputs of a temperature and relative humidity model are used as inputs for the predictor, in addition to time and energy consumption. The performance of the predictor was evaluated using real data obtained from a greenhouse located at the Queretaro State University, Mexico. This study shows the advantages of the ANN with a focus through analysis of variance (ANOVA). Energy consumption values estimated with an ANN were compared with regression-estimated and actual values using ANOVA and mean comparison procedures. Results show that the selected ANN model gave a better estimation of energy consumption with a 95% significant level. The study resents an algorithm based in ANOVA procedures and ANN models to predict energy consumption in greenhouses.
Native Morphology of Influenza Virions

Influenza A virus is an enveloped virus with a segmented, single-strand, negative-sense RNA genome. Its virions show spherical or filamentous shapes of about 100 nm in diameter and occasionally irregular morphology, which exemplifies the pleomorphic nature of these virions. Each viral RNA segment forms a ribonucleoprotein complex (RNP), along with an RNA-dependent RNA polymerase complex and multiple copies of nucleoproteins; the RNPs reside in the enveloped virions. Here, we focus on electron microscopic analyses of influenza virions and RNPs. Based on the morphological and structural observations obtained by using electron microscopic techniques, we present a model of the native morphology of the influenza virion.
Floorplan and power/ground network co-synthesis for fast design convergence

As technology advances, the metal width decreases while the global wire length increases. This trend makes the resistance of the power wire increase substantially. Further, the threshold voltage scales nonlinearly, raising the ratio of the threshold voltage to the supply voltage and making the voltage (IR) drop in the power/ground (P/G) network a serious problem in modern IC design. Traditional P/G network analysis methods are often very computationally expensive, and it is thus not feasible to co-synthesize P/G network with floorplan. To make the co-synthesis feasible, we need not only an efficient, effective, and flexible floorplanning algorithm, but also a very efficient, yet sufficiently accurate P/G network analysis method. In this paper, we present a method for floorplan and P/G network co-synthesis based on an efficient P/G network analysis scheme and the B*-tree floorplan representation. We integrate the co-synthesis into a commercial design flow to develop an effective power integrity (IR-drop) driven design methodology. Experimental results based on a real-world circuit design and the MCNC benchmarks show that our design methodology successfully fixes the IR-drop errors earlier at the floorplanning stage and thus enables the single-pass design convergence.
Basin‐scale assessment of the land surface energy budget in the National Centers for Environmental Prediction operational and research NLDAS‐2 systems

This paper compares the annual and monthly components of the simulated energy budget from the North American Land Data Assimilation System phase 2 (NLDAS‐2) with reference products over the domains of the 12 River Forecast Centers (RFCs) of the continental United States (CONUS). The simulations are calculated from both operational and research versions of NLDAS‐2. The reference radiation components are obtained from the National Aeronautics and Space Administration Surface Radiation Budget product. The reference sensible and latent heat fluxes are obtained from a multitree ensemble method applied to gridded FLUXNET data from the Max Planck Institute, Germany. As these references are obtained from different data sources, they cannot fully close the energy budget, although the range of closure error is less than 15% for mean annual results. The analysis here demonstrates the usefulness of basin‐scale surface energy budget analysis for evaluating model skill and deficiencies. The operational (i.e., Noah, Mosaic, and VIC) and research (i.e., Noah‐I and VIC4.0.5) NLDAS‐2 land surface models exhibit similarities and differences in depicting basin‐averaged energy components. For example, the energy components of the five models have similar seasonal cycles, but with different magnitudes. Generally, Noah and VIC overestimate (underestimate) sensible (latent) heat flux over several RFCs of the eastern CONUS. In contrast, Mosaic underestimates (overestimates) sensible (latent) heat flux over almost all 12 RFCs. The research Noah‐I and VIC4.0. 5 versions show moderate‐to‐large improvements (basin and model dependent) relative to their operational versions, which indicates likely pathways for future improvements in the operational NLDAS‐2 system.
Health Hazards Related to Computer Use: Experience of the National Institute for Medical Research in Tanzania

This paper is based on a study conducted in 2006 to assess the impact of computer usage on health of National Institute for Medical Research (NIMR) staff. NIMR being a research Institute, most of its staff spend substantial part of their working time on computers. There was notion among NIMR staff on possible prolonged computer usage health hazards. Hence, a study was conducted to establish facts and possible mitigation measures. A total of 144 NIMR staff were involved in the study of whom 63.2% were males and 36.8% females aged between 20 and 59 years. All staff cadres were included in the sample. The functions performed by Institute staff using computers includes; data management, proposal development and report writing, research activities, secretarial duties, accounting and administrative duties, on-line information retrieval and online communication through e-mail services. The interviewed staff had been using computers for 1-8 hours a day and for a period ranging from 1 to 20 years. The study has indicated ergonomic hazards for a significant proportion of interviewees (63%) of various kinds ranging from backache to eyesight related problems. The authors highlighted major issues which are substantially applicable in preventing occurrences of computer related problems and they urged NIMR Management and/or the government of Tanzania opts to adapt their practicability.
Inter-Colony Comparison of Diving Behavior of an Arctic Top Predator: Implications for Warming in the Greenland Sea

The goal of this study was to assess how diverse oceanographic conditions and prey communities affect the foraging behavior of little auks Alle alle. The Greenland Sea is characterized by 3 distinct water masses: (1) the East Greenland Current (EGC), which carries Arctic waters southward; (2) the Sorkapp Current (SC), which originates in the Arctic Ocean but flows north along the west coast of Spitsbergen; and (3) the West Spitsbergen Current (WSC), which carries warm Atlantic-derived water north. Each of these 3 water masses is characterized by a distinct mesozooplankton community. Little auks breeding adjacent to the EGC have access to large, lipid-rich Calanus copepods, whereas those adjacent to the SC have medium sized prey, while those near the WSC are limited to even smaller, less profitable prey. We used time−depth recorders to compare the time allocation and diving behavior of little auks adjacent to each of these 3 water masses. We predicted that birds in the EGC would not have to forage as intensively as those in the SC or WSC. We found that little auks foraging in the EGC spent less time at sea, spent less time flying, dived less often, made fewer long, deep dives, and made fewer V-shaped searching dives. This indicates that the EGC provides a more favorable foraging environment than do the warmer water masses to the east. Comparing the foraging behavior of little auk populations confined to Arctic versus Atlantic-influenced waters can provide insight into the potential impacts of future warming in the Greenland Sea.
Incremental cluster-based retrieval using compressed cluster-skipping inverted files

We propose a unique cluster-based retrieval (CBR) strategy using a new cluster-skipping inverted file for improving query processing efficiency. The new inverted file incorporates cluster membership and centroid information along with the usual document information into a single structure. In our incremental-CBR strategy, during query evaluation, both best(-matching) clusters and the best(-matching) documents of such clusters are computed together with a single posting-list access per query term. As we switch from term to term, the best clusters are recomputed and can dynamically change. During query-document matching, only relevant portions of the posting lists corresponding to the best clusters are considered and the rest are skipped. The proposed approach is essentially tailored for environments where inverted files are compressed, and provides substantial efficiency improvement while yielding comparable, or sometimes better, effectiveness figures. Our experiments with various collections show that the incremental-CBR strategy using a compressed cluster-skipping inverted file significantly improves CPU time efficiency, regardless of query length. The new compressed inverted file imposes an acceptable storage overhead in comparison to a typical inverted file. We also show that our approach scales well with the collection size.
Can anaerobic oxidation of methane prevent seafloor gas escape in a warming climate?

Abstract. Assessments of future climate-warming-induced seafloor methane (CH4) release rarely include anaerobic oxidation of methane (AOM) within the sediments. Considering that more than 90 % of the CH4 produced in ocean sediments today is consumed by AOM, this may result in substantial overestimations of future seafloor CH4 release. Here, we integrate a fully coupled AOM module with a numerical hydrate model to investigate under what conditions rapid release of CH4 can bypass AOM and result in significant fluxes to the ocean and atmosphere. We run a number of different model simulations for different permeabilities and maximum AOM rates. In all simulations, a future climate warming scenario is simulated by imposing a linear seafloor temperature increase of 3 ∘C over the first 100 years. The results presented in this study should be seen as a first step towards understanding AOM dynamics in relation to climate change and hydrate dissociation. Although the model is somewhat poorly constrained, our results indicate that vertical CH4 migration through hydraulic fractures can result in low AOM efficiencies. Fracture flow is the predicted mode of methane transport under warming-induced dissociation of hydrates on upper continental slopes. Therefore, in a future climate warming scenario, AOM might not significantly reduce methane release from marine sediments.
The development of novel adhesion promoters for waterborne coatings and polypropylene car bumpers

The ability of waterborne coatings to adhere to polypropylene-based substrates is a challenge in the automotive industry. This thesis seeks to explore novel methods to improve the adhesion and provide coated substrates of an industrial standard. Two methods are explored, whereby a physical entanglement method is found to be unsuccessful but a chemical bonding method is found to give patentable results. It is found that the UV curing of carbene precursors as candidate adhesion promoters, gives an adhesive force which is comparable to the industrial state of the art method, flaming. Initially, the UV energy initiates CH insertion reactions, which covalently graft the adhesion promoter to the polypropylene surface. Secondly, the hydrophilic functional groups of the adhesion promoter adhere to the waterborne basecoat, thus optimal adhesion is achieved. Statistical modelling of the results reveals that the adhesive strength depends on the UV intensity, the adhesion promoter concentration and functional group type. To explore the industrial applicability, the safety and stability during storage and the aesthetics of the adhesion promoters were investigated. This research is the first step to developing a formulation that is able to replace the current flaming method.
Goal priming and eating behavior: enhancing self-regulation by environmental cues.

OBJECTIVE Several lines of research have shown that the confrontation with attractive food can trigger overeating, especially in restrained eaters. This effect may be driven by a hedonic orientation toward food which temporarily overrules the goal of dieting in the regulation of behavior. The present study was designed to provide an experimental demonstration of this effect in a naturalistic setting, and to show that reactivating the goal of dieting by a subtle prime in the environment can help restrained eaters to regulate their eating behavior in tempting situations. DESIGN In a local store where the smell of grilled chicken was present, we observed the number of free meat snacks customers sampled from a tray after they had been primed with the dieting goal or not. MAIN OUTCOME MEASURES Number of snacks consumed. RESULTS Consistent with hypotheses, restrained eaters ate more than unrestrained eaters in the control condition. However, they reduced their eating behavior when primed with dieting, whereas this manipulation did not affect unrestrained eaters. CONCLUSION This study shows that unobtrusively priming the goal of dieting can enhance self-regulation in tempting eating situations. These results are discussed in the context of recent advances in our understanding of nonconscious behavior regulation and their applications to health behavior.
Kalman tracking based on TDOA for UMTS mobile location

A potentiality of the location problem in wireless networks that has not been explored enough is the mobility of the user equipment (UE). This paper deals with UMTS mobile location tracking using Kalman filtering based on TDOA (time difference of arrival) measurements. The performance of the proposed approach is compared with the CRB (Cramer Rao bound) for the static location estimator.
Replicating MSR: A study of the potential replicability of papers published in the Mining Software Repositories proceedings

This paper is the result of reviewing all papers published in the proceedings of the former International Workshop on Mining Software Repositories (MSR) (2004–2006) and now Working Conference on MSR (2007–2009). We have analyzed the papers that contained any experimental analysis of software projects for their potentiality of being replicated. In this regard, three main issues have been addressed: i) the public availability of the data used as case study, ii) the public availability of the processed dataset used by researchers and iii) the public availability of the tools and scripts. A total number of 171 papers have been analyzed from the six workshops/working conferences up to date. Results show that MSR authors use in general publicly available data sources, mainly from free software repositories, but that the amount of publicly available processed datasets is very low. Regarding tools and scripts, for a majority of papers we have not been able to find any tool, even for papers where the authors explicitly state that they have built one. Lessons learned from the experience of reviewing the whole MSR literature and some potential solutions to lower the barriers of replicability are finally presented and discussed.