Miracle-dz/UniFAR-FTUs huggingface dataset:
Neural mechanisms of context-dependent processing of CO2 avoidance behavior in fruit flies

The fruit fly, Drosophila melanogaster, innately avoids even low levels of CO2. CO2 is part of the so-called Drosophila stress odor produced by stressed flies, but also a byproduct of fermenting fruit, a main food source, making the strong avoidance behavior somewhat surprising. Therefore, we addressed whether feeding states might influence the fly’s behavior and processing of CO2. In a recent report, we showed that this innate behavior is differentially processed and modified according to the feeding state of the fly. Interestingly, we found that hungry flies require the function of the mushroom body, a higher brain center required for olfactory learning and memory, but thought to be dispensable for innate olfactory behaviors. In addition, we anatomically and functionally characterized a novel bilateral projection neuron connecting the CO2 sensory input to the mushroom body. This neuron was essential for processing of CO2 in the starved fly but not in the fed fly. In this Extra View article, we provide evidence for the potential involvement of the neuromodulator dopamine in state-dependent CO2 avoidance behavior. Taken together, our work demonstrates that CO2 avoidance behavior is mediated by alternative neural pathways in a context-dependent manner. Furthermore, it shows that the mushroom body is not only involved in processing of learned olfactory behavior, as previously suggested, but also in context-dependent innate olfaction.
Characterization of spatial distribution of the bacterial community in the South Sea of Korea

In order to investigate the importance of spatial and environmental factors on the structure and diversity of bacterial communities, high-resolution 16S rRNA gene tag pyrosequencing was applied to bacterial communities in the littoral sea. Seawater samples were prepared from seven different stations in the South Sea of Korea, the marginal sea in the western Pacific Ocean, and were divided into three groups according to distances from the coastline. The majority of 19,860 sequences were affiliated with Alphaproteobacteria (58.2%), Gammaproteobacteria (7.9%), and Bacteroidetes (13.9%). The bacterioplankton community at each station was highly diverse and varied among the samples. Major bacterial lineages showed different niche preferences among three locational groups. Alphaproteobacteria was the most abundant bacterial class, and it harbored the most frequently recorded operational taxonomic units (OTUs) in all sampling stations. However, dominant groups at the order levels showed a clear difference among the samples. The SAR11 clade was more abundant in coastal waters while the Roseobacter clade prevailed at stations far away from the coastline. Furthermore, members of Actinobacteria and Cyanobacteria also exhibited spatial variability. The OM1 clade in Actinobacteria constituted a predominant fraction in coastal samples, but it was essentially absent at the distal stations closer to open ocean. In contrast, Synechococcus was the predominant taxon in the distal samples, accounting for 7.1–19.5%, but was hardly detected in coastal waters, representing less than 0.7%. In Bacteroidetes, NS5 and NS9 groups tended to inhabit coastal waters while the genera Polaribacter and Ulvibacter were more abundant in distal stations. Clustering analysis and principle coordinates analysis based on OTU data indicated that bacterial communities in the studied area were separated into three groups that coincided with locational grouping. Statistical analysis showed that phosphate and dissolved oxygen concentration had a significant influence on the bacterial community composition.
Predictive cruise control with autonomous overtaking

This paper studies the problem of optimally controlling an autonomous vehicle, to safely overtake a slow-moving leading vehicle. The problem is formulated to minimize deviation from a reference velocity and position trajectory, while keeping the vehicle on the road and avoiding collision with surrounding vehicles. We show that the optimization problem can be formulated as a convex program, by providing convex modeling steps that include change of reference frame, change of variables, sampling in relative longitudinal distance, convex relaxation and linearization. A case study is provided showing overtaking scenarios in proximity of an oncoming vehicle, and a vehicle driving on an adjacent lane and in the same direction as the leading vehicle.
Image Processing, Textural Feature Extraction and Transfer Learning based detection of Diabetic Retinopathy

Diabetic Retinopathy (DR) is one of the most common causes of blindness in adults. The need for automating the detection of DR arises from the deficiency of ophthalmologists in certain regions where screening is done, and this paper is aimed at mitigating this bottleneck. Images from publicly available datasets STARE, HRF, and MESSIDOR along with a novel dataset of images obtained from the Retina Institute of Karnataka are used for training the models. This paper proposes two methods to automate the detection. The first approach involves extracting features using retinal image processing and textural feature extraction, and uses a Decision Tree classifier to predict the presence of DR. The second approach applies transfer learning to detect DR in fundus images. The accuracies obtained by the two approaches are 94.4% and 88.8% respectively, which are competent to current automation methods. A comparison between these models is made. On consultation with Retina Institute of Karnataka, a web application which predicts the presence of DR that can be integrated into screening centres is made.
The Race Towards Digital Wellbeing: Issues and Opportunities

As smartphone use increases dramatically, so do studies about technology overuse. Many different mobile apps for breaking "smartphone addiction" and achieving "digital wellbeing" are available. However, it is still not clear whether and how such solutions work. Which functionality do they have? Are they effective and appreciated? Do they have a relevant impact on users' behavior? To answer these questions, (i) we reviewed the features of 42 digital wellbeing apps, (ii) we performed a thematic analysis on 1,128 user reviews of such apps, and (iii) we conducted a 3-week-long in-the-wild study of Socialize, an app that includes the most common digital wellbeing features, with 38 participants. We discovered that digital wellbeing apps are appreciated and useful for some specific situations. However, they do not promote the formation of new habits and they are perceived as not restrictive enough, thus not effectively helping users to change their behavior with smartphones.
Intramolecular and Intermolecular Interactions of Protein Kinase B Define Its Activation In Vivo

Protein kinase B (PKB/Akt) is a pivotal regulator of diverse metabolic, phenotypic, and antiapoptotic cellular controls and has been shown to be a key player in cancer progression. Here, using fluorescent reporters, we shown in cells that, contrary to in vitro analyses, 3-phosphoinositide–dependent protein kinase 1 (PDK1) is complexed to its substrate, PKB. The use of Förster resonance energy transfer detected by both frequency domain and two-photon time domain fluorescence lifetime imaging microscopy has lead to novel in vivo findings. The preactivation complex of PKB and PDK1 is maintained in an inactive state through a PKB intramolecular interaction between its pleckstrin homology (PH) and kinase domains, in a “PH-in” conformer. This domain–domain interaction prevents the PKB activation loop from being phosphorylated by PDK1. The interactive regions for this intramolecular PKB interaction were predicted through molecular modeling and tested through mutagenesis, supporting the derived model. Physiologically, agonist-induced phosphorylation of PKB by PDK1 occurs coincident to plasma membrane recruitment, and we further shown here that this process is associated with a conformational change in PKB at the membrane, producing a “PH-out” conformer and enabling PDK1 access the activation loop. The active, phosphorylated, “PH-out” conformer can dissociate from the membrane and retain this conformation to phosphorylate substrates distal to the membrane. These in vivo studies provide a new model for the mechanism of activation of PKB. This study takes a crucial widely studied regulator (physiology and pathology) and addresses the fundamental question of the dynamic in vivo behaviour of PKB with a detailed molecular mechanism. This has important implications not only in extending our understanding of this oncogenic protein kinase but also in opening up distinct opportunities for therapeutic intervention.
Identification of Granulocyte Colony-Stimulating Factor and Interleukin-6 as Candidate Biomarkers of CBLB502 Efficacy as a Medical Radiation Countermeasure

Given an ever-increasing risk of nuclear and radiological emergencies, there is a critical need for development of medical radiation countermeasures (MRCs) that are safe, easily administered, and effective in preventing and/or mitigating the potentially lethal tissue damage caused by acute high-dose radiation exposure. Because the efficacy of MRCs for this indication cannot be ethically tested in humans, development of such drugs is guided by the Food and Drug Administration's Animal Efficacy Rule. According to this rule, human efficacious doses can be projected from experimentally established animal efficacious doses based on the equivalence of the drug's effects on efficacy biomarkers in the respective species. Therefore, identification of efficacy biomarkers is critically important for drug development under the Animal Efficacy Rule. CBLB502 is a truncated derivative of the Salmonella flagellin protein that acts by triggering Toll-like receptor 5 (TLR5) signaling and is currently under development as a MRC. Here, we report identification of two cytokines, granulocyte colony-stimulating factor (G-CSF) and interleukin-6 (IL-6), as candidate biomarkers of CBLB502's radioprotective/mitigative efficacy. Induction of both G-CSF and IL-6 by CBLB502 1) is strictly TLR5-dependent, 2) occurs in a CBLB502 dose-dependent manner within its efficacious dose range in both nonirradiated and irradiated mammals, including nonhuman primates, and 3) is critically important for the ability of CBLB502 to rescue irradiated animals from death. After evaluation of CBLB502 effects on G-CSF and IL-6 levels in humans, these biomarkers will be useful for accurate prediction of human efficacious CBLB502 doses, a key step in the development of this prospective radiation countermeasure.
OLAP on Structurally Significant Data in Graphs

Summarized data analysis of graphs using OLAP (Online Analytical Processing) is very popular these days. However due to high dimensionality and large size, it is not easy to decide which data should be aggregated for OLAP analysis. Though iceberg cubing is useful, but it is unaware of the significance of dimensional values with respect to the structure of the graph. In this paper, we propose a Structural Significance, SS, measure to identify the structurally significant dimensional values in each dimension. This leads to structure aware pruning. We then propose an algorithm, iGraphCubing, to compute the graph cube to analyze the structurally significant data using the proposed measure. We evaluated the proposed ideas on real and synthetic data sets and observed very encouraging results.
Mannosidase Production by Viridans Group Streptococci

ABSTRACT The production of mannosidase activity by all currently recognized species of human viridans group streptococci was determined using an assay in which bacterial growth was dependent on the degradation of the high-mannose-type glycans of RNase B and subsequent utilization of released mannose. RNase B is an excellent substrate for the demonstration of mannosidase activity since it is a glycoprotein with a single glycosylation site which is occupied by high-mannose-type glycoforms containing five to nine mannose residues. Mannosidase activity was produced only by some members of the mitis group (Streptococcus mitis, Streptococcus oralis, Streptococcus gordonii, Streptococcus cristatus, Streptococcus infantis, Streptococcus parasanguinis, and Streptococcus pneumoniae) and Streptococcus intermedius of the anginosus group. None of the other species within the salivarius and mutans groups or Streptococcus peroris andStreptococcus sanguinis produced mannosidase activity. Using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, it was demonstrated that the Man5 glycan alone was degraded while Man6 to Man9, which contain terminal α(1→2) mannose residues in addition to the α(1→3), α(1→6), and β(1→4) residues present in Man5, remained intact. Investigations on mannosidase production using synthetic (4-methylumbelliferone- orp-nitrophenol-linked) α- or β-mannosides as substrates indicated that there was no correlation between degradation of these substrates and degradation of the Man5 glycan of RNase B. No species degraded these α-linked mannosides, while degradation of the β-linked synthetic substrates was restricted to strains within the Streptococcus anginosus, S. gordonii, and S. intermedius species. The data generated using a native glycoprotein as the substrate demonstrate that mannosidase production within the viridans group streptococci is more widely distributed than had previously been considered.
An efficient hardware design for HDTV H.264/AVC encoder

This paper presents a hardware efficient high definition television (HDTV) encoder for H.264/AVC. We use a two-level mode decision (MD) mechanism to reduce the complexity and maintain the performance, and design a sharable architecture for normal mode fractional motion estimation (NFME), special mode fractional motion estimation (SFME), and luma motion compensation (LMC), to decrease the hardware cost. Based on these technologies, we adopt a four-stage macro-block pipeline scheme using an efficient memory management strategy for the system, which greatly reduces on-chip memory and bandwidth requirements. The proposed encoder uses about 1126k gates with an average Bjontegaard-Delta peak signal-to-noise ratio (BD-PSNR) decrease of 0.5 dB, compared with JM15.0. It can fully satisfy the real-time video encoding for 1080p@30 frames/s of H.264/AVC high profile.
From Microbial Differentiation to Ribosome Engineering

Bacillus subtilis and Streptomyces spp. provide tractable experimental systems for studying cellular responses to adverse environmental conditions. During conditions of extreme nutrient limitation, these prokaryotes exhibit a wide range of adaptations, including the production and secretion of antibiotics and enzymes and the formation of aerial mycelium and spores. In response to these conditions, all bacteria, but not eukaryotic microorganisms, exhibit a “stringent response,” during which the unusual guanosine tetraphosphate, ppGpp, accumulates intracellularly. This is accompanied by a marked reduction in the GTP pool, due to ppGpp inhibition of IMP-dehydrogenase, and immediate repression of rRNA synthesis, due to the binding of ppGpp to RNA polymerase. This review summarizes our studies on the bacterial stringent response and its use in applied microbiology. We found that morphological differentiation results from a decrease in the pool of GTP, whereas physiological differentiation (antibiotic production) results from a more direct function of ppGpp. That is, we found that the Streptomyces GTP-binding protein Obg functions by sensing intracellular GTP levels and that certain mutations in the RNA polymerase β-subunit circumvent dependence on ppGpp in antibiotic production. X-ray crystallographic analysis provided a structural basis for the ppGpp regulation of transcription. On the basis of these findings, we have developed the novel concept of “ribosome engineering,” focusing on activation of dormant genes to elicit cellular function fully. Ribosome engineering can be applied to strain improvement, screening of novel metabolites, plant breeding, cell-free translation systems, and the treatment of tuberculosis.
A comparison of four methods of nu-meric entry on pen-based computers

Four numeric entry methods for pen-based computers were compared with respect to accuracy and speed. Sixteen subjects entered numbers on a digitizing display using four conditions: handwriting (with recognition software), keypad taping, pie pad, and moving pie menu. Keypad tapping was the most accurate (98.8%) and fastest (30.4 wpm) entry method. It was also most preferred by subjects. Handwriting was nearly as preferred as keypad tapping, even though it was substantially less accurate (89.6%) and slower (18.5 wpm). The pie menu conditions were least preferred, least accurate, and slowest. However, some subjects did achieve superior performance on the pie menu conditions; thus, with sufficient practice, pie menu entry may be a valid alternative to handwriting for numbers. These results call into question the presumed superiority of handwriting as the preferred entry method on penbased computers. La vitesse et la precision de quatre methodes d'entree de donnees sur un ordinateur a stylo ont ete comparees. Seize sujets ont ecrit des chiffres sur un ecran digital de quatres manieres differentes conditions: ecriture manuscrite (avec l'aide d'un programme d'interpretation), usage des touches numeriques, usage d'un pave circulaire et usage d'un menu circulaire d'eplac;:able. L'usage des touches numeriques est la methode la plus precise (98.8%) et la plus rapide (30.4 mpm). C'est aussi la methode que les sujets de l'experience ont preferee. La preference de l'ecriture a la main est presqu'egale a celle des touches numeriques mais la precision et la vitesse diminuent sensiblement (89.6% et 18.5 mpm). Les methodes utilisant le pave et le menu circulaires ont ete moins preferees, moins precises et les plus lentes. Cependant, certains sujets ont obtenu des resultats superieurs en utilisant le menu circulaire. Ainsi, avec suffisamment de pratique, le menu tDept. of Computing & Information Science University of Guelph Guelph, Ontario, NIG 2Wl mac@snowhite.cis. uoguelph.ca, nonnecke@snowhite.cis. uoguelph.ca, stan@snowhite.cis. uoguelph.ca circulaire pourrait etre une alternative a l'ecriture manuscrite. Ces resultats mettent en question la superiorite de l'ecriture manuscrite comme methode d'entree preferee pour l'ordinateurs a stylo.
Safe Type-level Abstraction in Scala Adriaan Moors

Most formal accounts of object-oriented languages have focussed on type soundness: the safety that type checking provides with respect to term-level computation and abstractions. However, with type-level abstraction mechanisms becoming increasingly more sophisticated, bringing this guarantee to the level of types has become quite pressing. We call this property kind soundness: kind checking ensures that type constructors are never applied to unexpected type arguments. We present Scalina, a purely object-oriented calculus that employs the same abstraction mechanisms at the type level as well as at the kind level. Soundness for both levels can thus be proven by essentially the same arguments. Kind soundness finally allows designers of type-level abstractions to join their term-level colleagues in relying on the compiler to catch deficiencies before they are discovered by their clients.
Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics

Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of orthologous sets of three fungi and their co-evolutionary relations, we demonstrate that co-evolutionary assumption may violate the Markov assumption. Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution.
Energy consumption and greenhouse gas emissions related to the use, maintenance, and disposal of a residential structure.

Virtual residential houses in Atlanta, Georgia, and Minneapolis, Minnesota, were analyzed to determine energy consumption and greenhouse gas emission during the building use, maintenance, and demolition phases of their life cycle. An analysis of Census data on housing stocks provided estimates for the useful life of a house. Home Energy Saver, an internet tool for energy analysis sponsored by the Department of Energy and available from the Lawrence Berkeley National Laboratory, was the primary tool used in assessing energy consumption for heating and cooling during the use phase of the buildings. A survey on the life span of house components by the National Association of Home Builders (NAHB) was used to estimate a maintenance/replacement schedule. Emissions during demolition and transport to the landfill were estimated based on the initial bill of materials in the house and distance to the landfill. The energy consumption over a 75-year life was estimated to be 4,575 GJ for the Atlanta wood frame, 4,725 GJ for the Atlanta concrete block structure, and 7,800 GJ for the Minneapolis wood frame. A steel-framed Home Energy Saver model was not available, but since the steel-framed house was designed to code for equal thermal properties with the wood frame house, we assume no difference. Energy consumption related to structural/exterior maintenance was estimated at 110.5 GJ for the Atlanta location and 73.3 GJ for Minneapolis, only 1-2% as large as used for heating and cooling. The energy needed for demolition and waste removal was even smaller. Carbon dioxide (CO 2 ) emissions from the consumed energy were estimated using the regional energy grids in SimaPro at 227,000 kg (501,000 lbs) for the Atlanta wood frame, 235,000 kg (519,000 lbs) for the concrete frame, and 338,000 kg (856,000 lbs) for the Minneapolis wood frame. CO 2 emissions related to structural (primarily exterior) maintenance were 4143 kg and 3468 kg, respectively, for Atlanta and Minneapolis. The emissions from deconstruction and waste removal were roughly 1/10 th that of maintenance. Reducing energy consumption during building use provides a major opportunity to reduce environmental burdens. When time-valued discounting over the building life is considered, reducing the burdens associated with product use and construction is equally important.
Wind of change: new insights on the ecology and evolution of pollination and mating in wind-pollinated plants.

BACKGROUND The rich literature that characterizes the field of pollination biology has focused largely on animal-pollinated plants. At least 10 % of angiosperms are wind pollinated, and this mode of pollination has evolved on multiple occasions among unrelated lineages, and hence this discrepancy in research interest is surprising. Here, the evolution and functional ecology of pollination and mating in wind-pollinated plants are discussed, a theoretical framework for modelling the selection of wind pollination is outlined, and pollen capture and the occurrence of pollen limitation in diverse wind-pollinated herbs are investigated experimentally. SCOPE AND CONCLUSIONS Wind pollination may commonly evolve to provide reproductive assurance when pollinators are scarce. Evidence is presented that pollen limitation in wind-pollinated plants may not be as common as it is in animal-pollinated species. The studies of pollen capture in wind-pollinated herbs demonstrate that pollen transfer efficiency is not substantially lower than in animal-pollinated plants as is often assumed. These findings challenge the explanation that the evolution of few ovules in wind-pollinated flowers is associated with low pollen loads. Floral and inflorescence architecture is crucial to pollination and mating because of the aerodynamics of wind pollination. Evidence is provided for the importance of plant height, floral position, and stamen and stigma characteristics in promoting effective pollen dispersal and capture. Finally, it is proposed that geitonogamous selfing may alleviate pollen limitation in many wind-pollinated plants with unisexual flowers.