Miracle-dz/UniFAR-FTUs huggingface dataset:
Collaborative Behavior and Winning Challenges in Competitive Software Crowdsourcing

Software Crowdsourcing (SW CS) allows a requester to increase the speed of its software development efforts by submitting a task to be performed by the crowd. SW CS is usually structured around software platforms, which are used by crowd members to identify a task suited for them, gather information about this task, and finally, submit a solution for it. In competitive software crowdsourcing, members of the crowd independently create solutions while competing against each other by monetary rewards for task completion. While competition usually reduces collaboration, in this paper, we investigated how crowd members create a collaborative behavior during programming challenges using online forums to help each other, share useful information, and discuss important documents and artifacts. We also investigated different collaborative behaviours by crowd members and and how this collaboration is associated with crowd members' improved outcome in the challenges. These results are based on analysis of the online forums from Topcoder, one of the largest competitive SW CS platforms
Pili Expression in Geobacter sulfurreducens Lacking the Putative Gene for the PilB Pilus Assembly Motor

Multiple lines of evidence suggest that electrically conductive pili (e-pili) are an important conduit for long-range electron transport in Geobacter sulfurreducens, a common model microbe for the study of extracellular electron transport mechanisms. One strategy to study the function of e-pili has been to delete the gene for PilB, the pilus assembly motor protein, in order to prevent e-pili expression. However, we found that e-pili are still expressed after the gene for PilB is deleted. Conducting probe atomic force microscopy revealed filaments with the same diameter and similar current-voltage response as e-pili harvested from wild-type G. sulfurreducens or when e-pili are heterologously expressed from the G. sulfurreducens pilin gene in E. coli. Immunogold labeling demonstrated that a G. sulfurreducens strain expressing e-pili with a His-tag continued to express His-tag labelled e-pili when the PilB gene was deleted. Strains with the PilB gene deleted produced maximum current densities comparable to wild-type controls. These results demonstrate that deleting the gene for PilB is not an appropriate strategy for constructing strains of G. sulfurreducens without e-pili, necessitating a reinterpretation of the results of previous studies that have employed this approach. Importance Geobacter sulfurreducens is a model microbe for the study of biogeochemically and technologically significant processes such as the reduction of Fe(III) oxides in soils and sediments; bioelectrochemical applications that produce electric current from waste organic matter or drive useful processes with the consumption of renewable electricity; direct interspecies electron transfer in anaerobic digestors and methanogenic soils and sediments; and metal corrosion. The phenotypes associated with gene deletions are an important strategy for determining the mechanisms for extracellular electron transfer in G. sulfurreducens. The results reported here demonstrate that a gene deletion previously thought to prevent the expression of electrically conductive pili in G. sulfurreducens does not have the intended result. Conductive pili continue to be expressed. This finding is important for interpreting the results of several previous studies on conductive pili function.
Mutations in Drosophila tRNA processing factors cause phenotypes similar to Pontocerebellar Hypoplasia

Mature tRNAs are generated by multiple RNA processing events, which can include the excision of intervening sequences. The tRNA splicing endonuclease (TSEN) complex is responsible for cleaving these intron-containing pre-tRNA transcripts. In humans, TSEN copurifies with CLP1, an RNA kinase. Despite extensive work on CLP1, its in vivo connection to tRNA splicing remains unclear. Interestingly, mutations in CLP1 or TSEN genes cause neurological diseases in humans that are collectively termed Pontocerebellar Hypoplasia (PCH). In mice, loss of Clp1 kinase activity results in premature death, microcephaly and progressive loss of motor function. To determine if similar phenotypes are observed in Drosophila, we characterized mutations in crowded-by-cid (cbc), the CLP1 ortholog, as well as in the fly ortholog of human TSEN54. Analyses of organismal viability, larval locomotion and brain size revealed that mutations in both cbc and Tsen54 phenocopy those in mammals in several details. In addition to an overall reduction in brain lobe size, we also found increased cell death in mutant larval brains. Ubiquitous or tissue-specific knockdown of cbc in neurons and muscles reduced viability and locomotor function. These findings indicate that we can successfully model PCH in a genetically-tractable invertebrate.
Antisense oligonucleotides targeting UBE3A-ATS restore expression of UBE3A by relieving transcriptional interference

Angelman syndrome (AS) is a rare neurodevelopmental disorder caused by loss of function of the maternally inherited UBE3A allele. In neurons, the paternal allele of UBE3A is silenced in cis by the long noncoding RNA, UBE3A-ATS. Unsilencing paternal UBE3A by reducing UBE3A-ATS is a promising therapeutic approach for the treatment of AS. Here we show that targeted cleavage of UBE3A-ATS using antisense oligonucleotides (ASOs) restores UBE3A and rescues electrophysiological phenotypes in human AS neurons. We demonstrate that cleavage of UBE3A-ATS results in termination of its transcription by displacement of RNA Polymerase II. Reduced transcription of UBE3A-ATS allows transcription of UBE3A to proceed to completion, providing definitive evidence for the transcriptional interference model of paternal UBE3A silencing. These insights into the mechanism by which ASOs restore UBE3A inform the future development of nucleotide-based approaches for the treatment of AS, including alternative strategies for cleaving UBE3A-ATS that can be developed for long-term restoration of UBE3A function.
De novo synthesized polyunsaturated fatty acids operate as both host immunomodulators and nutrients for Mycobacterium tuberculosis

Successful control of Mycobacterium tuberculosis (Mtb) infection by macrophages relies on immunometabolic reprogramming, where the role of fatty acids (FAs) remains poorly understood. Recent studies unraveled Mtb’s capacity to acquire saturated and monounsaturated FAs via the Mce1 importer. However, upon activation macrophages produce polyunsaturated FAs (PUFAs), mammal-specific FAs mediating the generation of key immunomodulatory eicosanoids. Here, we asked whether de novo synthesis of PUFAs is modulated in Mtb-infected macrophages and benefits host or pathogen. Quantitative lipidomics revealed that Mtb infection activates the early PUFA biosynthetic pathway for production of eicosanoids. While PUFA synthesis blockade significantly impaired the inflammatory and antimicrobial responses of infected macrophages, it had no effect on Mtb growth in vivo. Using a click-chemistry approach, we found that Mtb efficiently imports PUFAs of the ω6 subset via Mce1 in axenic culture, including the eicosanoid precursor arachidonic acid (AA). Notably, Mtb preferentially internalized AA over all other FAs within infected macrophages, but here Mtb’s import of AA was largely Mce1-independent and correlated with elevated AA uptake by host cells. Together, these findings reveal AA as a major FA substrate for intracellular Mtb. They suggest that Mtb’s hijacking of host-derived AA may counteract its stimulatory effect on anti-mycobacterial immune responses.
Tracking Neural Markers of Template Formation and Implementation in Attentional Inhibition under Different Distractor Consistency

Performing visual search tasks requires optimal attention deployment to promote targets and inhibit distractors. Rejection templates based on the feature of the distractor can be built to constrain the search process. We measured electroencephalography (EEG) of human participants of both sexes when they performed a visual search task in conditions where the distractor cues were constant within a block (fixed cueing) or changed on a trial-by-trial basis (varied cueing). In the fixed-cueing condition, sustained decoding of the cued colors could be achieved during the retention interval, and participants with higher decoding accuracy showed larger suppression benefits of the distractor cueing in the search period. In the varied-cueing condition, the cued color could only be transiently decoded after its onset, and higher decoding accuracy was observed from the participants who demonstrated lower suppression benefit. The differential neural representations of the to-be-ignored color in the two cueing conditions as well as their reverse associations with behavioral performance implied that rejection templates were formed in the fixed-cueing condition but not in the varied-cueing condition. Additionally, we observed stronger posterior alpha lateralization and midfrontal theta/beta power during the retention interval of the varied-cueing condition, indicating the cognitive costs in template formation caused by the trialwise change of distractor colors. Together, our findings revealed the neural markers associated with the critical roles of distractor consistency in linking template formation to successful inhibition. SIGNIFICANCE STATEMENT How do we strategically build a rejection template based on distractor features to filter out matched items when performing visual search tasks? Previous studies have suggested that the consistency of the to-be-ignored feature may play a significant role in this process. We recorded scalp EEGs when human participants searched for a target among distractors. Capitalized on multivariate decoding technique and time-frequency analysis, we revealed the neural markers of the rejection template under different distractor consistencies. Being able to track these processes in visual search could help us to understand the connection between template formation and successful distractor inhibition. Our findings may also benefit future EEG-based interventions on individuals with deficits in attentional control.
Successful microbial colonization of space using an anti-aggregation strategy

Many organisms live in habitats with limited nutrients or space, competition for these resources is ubiquitous. Although spatial factors related to population’s manner of colonizing space influences its success in spatial competition, what these factors are and to what extent they influence the outcome remains under-explored. Here, we applied a simulated competitive model to explore the spatial factors affecting outcomes of competition for space. By quantifying spatial factors using ‘Space Accessibility’, we show that colonizing space in an anti-aggregation manner contributes to microbial competitive success. We also find that the competitive edge derived from being anti-aggregation in colonizing space, which results in a higher ‘Space Accessibility’, neutralizes the disadvantage arising from either lower growth rate or lower initial abundance. These findings shed light on the role of space colonization manners on maintaining biodiversity within ecosystems and provide novel insights critical for understanding how competition for space drives evolutionary innovation.
Distributed and multifaceted effects of threat and safety

Sustained anticipation of unpredictable aversive events generates anticipatory processing that is central to anxiety. In the present functional Magnetic Resonance Study (fMRI) study, we examined how sustained threat is processed in the human brain. We used a relatively large sample (N = 109) and employed a Bayesian multilevel analysis approach to contrast threat and safe periods. Our analyses demonstrated that the effect of sustained threat is heterogeneous and distributed across the brain. Thus, the impact of threat is widespread, and not restricted to a small set of putatively emotion-related regions, such as the amygdala and the bed nucleus of the stria terminalis. Both transient and sustained, and increased and decreased responses during threat were observed. Our study reveals that transitioning between threat and safe states, and vice versa, leads to a widespread switch in brain responding that involves most of the brain.
TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells

The signalling pathways that maintain primed human pluripotent stem cells (hPSCs) have been well characterised, revealing a critical role for TGFβ/Activin/Nodal signalling. In contrast, the signalling requirements of naïve human pluripotency have not been fully established. Here, we demonstrate that TGFβ signalling is required to maintain naïve hPSCs. The downstream effector proteins – SMAD2/3 – bind common sites in naïve and primed hPSCs, including shared pluripotency genes. In naïve hPSCs, SMAD2/3 additionally bind to active regulatory regions near to naïve pluripotency genes. Inhibiting TGFβ signalling in naïve hPSCs causes the downregulation of SMAD2/3-target genes and pluripotency exit. Single-cell analyses reveal that naïve and primed hPSCs follow different transcriptional trajectories after inhibition of TGFβ signalling. Primed hPSCs differentiate into neuroectoderm cells, whereas naïve hPSCs transition into trophectoderm. These results establish that there is a continuum for TGFβ pathway function in human pluripotency spanning a developmental window from naïve to primed states.
Sphingolipids are involved in Pieris brassicae egg-induced cell death in Arabidopsis thaliana

In Brassicaceae, hypersensitive-like (HR-like) cell death is a central component of direct defenses triggered against eggs of the large white butterfly Pieris brassicae. The signaling pathway leading to HR-like in Arabidopsis is mainly dependent on salicylic acid (SA) accumulation, but downstream components are unclear. Here, we found that treatment with P. brassicae egg extract (EE) trigger changes in expression of sphingolipid metabolism genes in Arabidopsis and Brassica nigra. Disruption of ceramide synthase activity led to a significant decrease of EE-induced HR-like whereas SA signaling and reactive oxygen species levels were unchanged, suggesting that ceramides are downstream activators of HR-like. Sphingolipid quantifications showed that ceramides with C16:0 side-chains accumulated in both species, and this response was independent on SA accumulation. Finally, we provide genetic evidence that the modification of fatty acyl chains of sphingolipids modulates HR-like. Altogether, these results show that sphingolipids play a key and specific role during insect egg-triggered HR-like.
Gastric neurons in the nucleus tractus solitarius are selective to the orientation of gastric electrical stimulation

Objective. Gastric electrical stimulation (GES) is a bioelectric intervention for gastroparesis, obesity, and other functional gastrointestinal disorders. In a potential mechanism of action, GES activates the nerve endings of vagal afferent neurons and induces the vago-vagal reflex through the nucleus tractus solitarius (NTS) in the brainstem. However, it is unclear where and how to stimulate in order to optimize the vagal afferent responses. Approach. To address this question with electrophysiology in rats, we applied mild electrical currents to two serosal targets on the distal forestomach with dense distributions of vagal intramuscular arrays (IMAs) that innervated the circular and longitudinal smooth muscle layers. During stimulation, we recorded single and multi-unit responses from gastric neurons in NTS and evaluated how the recorded responses depended on the stimulus orientation and amplitude. Main results. We found that NTS responses were highly selective to the stimulus orientation for a range of stimulus amplitudes. The strongest responses were observed when the applied current flowed in the same direction as the IMAs in parallel with the underlying smooth muscle fibers. Our results suggest that gastric neurons in NTS may encode the orientation-specific activity of gastric smooth muscles relayed by vagal afferent neurons. Significance. This finding suggests that the orientation of GES is critical to effective engagement of vagal afferents and should be considered in light of the structural phenotypes of vagal terminals in the stomach.
Hnf1b-CreER, a model used for fate mapping pancreatic lineages, achieves efficient Cre-mediated recombination in duct and islet δ cells

The Hnf1b-CreERT2 BAC transgenic (Tg(Hnf1b-cre/ERT2)1Jfer) has been used extensively to trace the progeny of pancreatic ducts in development, regeneration, or cancer. This model originally showed that duct-like plexus cells of the embryonic pancreas are bipotent duct-endocrine progenitors, whereas adult mouse duct cells are not a common source of β cells in various regenerative settings. We have now examined Hnf1b-CreERT2 mice with a Rosa26-RFP reporter transgene. This showed inducible recombination of up to 96% adult duct cells, a much higher efficiency than the previously used β-galactosidase reporter. Despite this high duct-cell excision, recombination in α and β cells remained very low, similar to the previously used reporter transgene (Rosa26-βgalactosidase). However, nearly half of somatostatin-expressing δ cells showed reporter activation, which was due to Cre expression in δ cells rather than an indication of duct to δ cell conversions. The high recombination efficiency in duct cells indicates that the Hnf1b-CreERT2 model can be useful for both ductal fate mapping and genetic inactivation studies. The recombination in δ cells does not modify the interpretation of studies that failed to show duct conversions to other cell types, but needs to be considered in studies that use this model to modify the plasticity of pancreatic duct cells.
Countermeasures against Static Power Attacks - Comparing Exhaustive Logic Balancing and Other Protection Schemes in 28 nm CMOS -

In recent years it has been demonstrated convincingly that the standby power of a CMOS chip reveals information about the internally stored and processed data. Thus, for adversaries who seek to extract secrets from cryptographic devices via side-channel analysis, the static power has become an attractive quantity to obtain. Most works have focused on the destructive side of this subject by demonstrating attacks. In this work, we examine potential solutions to protect circuits from silently leaking sensitive information during idle times. We focus on countermeasures that can be implemented using any common digital standard cell library and do not consider solutions that require full-custom or analog design flow. In particular, we evaluate and compare a set of five distinct standard-cell-based hiding countermeasures, including both, randomization and equalization techniques. We then combine the hiding countermeasures with state-of-the-art hardware masking in order to amplify the noise level and achieve a high resistance against attacks. An important part of our contribution is the proposal and evaluation of the first ever standard-cell-based balancing scheme which achieves perfect data-independence on paper, i.e., in absence of intra-die process variations and aging effects. We call our new countermeasure Exhaustive Logic Balancing (ELB). While this scheme, applied to a threshold implementation, provides the highest level of resistance in our experiments, it may not be the most cost effective option due to the significant resource overhead associated. All evaluated countermeasures and combinations thereof are applied to a serialized hardware implementation of the PRESENT block cipher and realized as cryptographic co-processors on a 28nm CMOS ASIC prototype. Our experimental results are obtained through real-silicon measurements of a fabricated die of the ASIC in a temperature-controlled environment using a source measure unit (SMU). We believe that our elaborate comparison serves as a useful guideline for hardware designers to find a proper tradeoff between security and cost for almost any application.
Spatial Patterns in Actual Evapotranspiration Climatologies for Europe

Spatial patterns in long-term average evapotranspiration (ET) represent a unique source of information for evaluating the spatial pattern performance of distributed hydrological models on a river basin to continental scale. This kind of model evaluation is getting increased attention, acknowledging the shortcomings of traditional aggregated or timeseries-based evaluations. A variety of satellite remote sensing (RS)-based ET estimates exist, covering a range of methods and resolutions. There is, therefore, a need to evaluate these estimates, not only in terms of temporal performance and similarity, but also in terms of long-term spatial patterns. The current study evaluates four RS-ET estimates at moderate resolution with respect to spatial patterns in comparison to two alternative continental-scale gridded ET estimates (water-balance ET and Budyko). To increase comparability, an empirical correction factor between clear sky and all-weather ET, based on eddy covariance data, is derived, which could be suitable for simple corrections of clear sky estimates. Three RS-ET estimates (MODIS16, TSEB and PT-JPL) and the Budyko method generally display similar spatial patterns both across the European domain (mean SPAEF = 0.41, range 0.25–0.61) and within river basins (mean SPAEF range 0.19–0.38), although the pattern similarity within river basins varies significantly across basins. In contrast, the WB-ET and PML_V2 produced very different spatial patterns. The similarity between different methods ranging over different combinations of water, energy, vegetation and land surface temperature constraints suggests that robust spatial patterns of ET can be achieved by combining several methods.