Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of diet and time after bacterial infection on fecundity, resistance, and tolerance in Drosophila melanogaster

Abstract Mounting and maintaining an effective immune response in the face of infection can be costly. The outcome of infection depends on two host immune strategies: resistance and tolerance. Resistance limits pathogen load, while tolerance reduces the fitness impact of an infection. While resistance strategies are well studied, tolerance has received less attention, but is now considered to play a vital role in host–pathogen interactions in animals. A major challenge in ecoimmunology is to understand how some hosts maintain their fitness when infected while others succumb to infection, as well as how extrinsic, environmental factors, such as diet, affect defense. We tested whether dietary restriction through yeast (protein) limitation affects resistance, tolerance, and fecundity in Drosophila melanogaster. We predicted that protein restriction would reveal costs of infection. Because infectious diseases are not always lethal, we tested resistance and tolerance using two bacteria with low lethality: Escherichia coli and Lactococcus lactis. We then assayed fecundity and characterized bacterial infection pathology in individual flies at two acute phase time points after infection. As expected, our four fecundity measures all showed a negative effect of a low‐protein diet, but contrary to predictions, diet did not affect resistance to either bacteria species. We found evidence for diet‐induced and time‐dependent variation in host tolerance to E. coli, but not to L. lactis. Furthermore, the two bacteria species exhibited remarkably different infection profiles, and persisted within the flies for at least 7 days postinfection. Our results show that acute phase infections do not necessarily lead to fecundity costs despite high bacterial loads. The influence of intrinsic variables such as genotype are the prevailing factors that have been studied in relation to variation in host tolerance, but here we show that extrinsic factors should also be considered for their role in influencing tolerance strategies.
Hidden diversity of endophytic fungi in an invasive plant.

Fungal endophytes are important in plant ecology and common in plants. We attempted to test cointroduction and host-jumping hypotheses on a community basis by comparing endophytes isolated from invasive spotted knapweed (Centaurea stoebe, Asteraceae) in its native and invaded ranges. Of 92 combined, sequence-based haplotypes representing eight classes of Fungi, 78 occurred in only one of the two ranges. In the native range of C. stoebe, one haplotype of Alternaria alternata was clearly dominant, whereas in the invaded range, no haplotype was dominant. Many haplotypes were closely related to one another and novel. For example, six putative, new species of Botrytis were discovered as endophytes of C. stoebe, which has never been reported to have Botrytis spp. Apparent differences between the two communities of endophytes were significant according to an analysis of similarity, but phylogenetic community structure did not differ significantly between the ranges. Both host-jumping and cointroduction of fungal endophytes likely took place during the spotted knapweed invasion.
HISTONE PROTEASES IN CHRONIC GRANULOCYTIC LEUKAEMIA

Kass (1975) suggested that the histone patterns derived from different leukaemic cell lines were dependent on the cell of origin. We continued this work (Simpkins & Mahon, 1978) and showed that when nuclear chromatin was isolated in the presence of protease inhibitors that differences similar to those reported by Kass (1975) were found between myeloblastic and lymphoblastic leukaemias but not between monoblastic and lymphoblastic leukaemias. These differences were ascribed to a protease present in the myeloblasts. However, the questions still remain as to whether, in the intact cell, equimolar amounts of the nuclear core histones were present and whether the protease was liberated when the cells were disrupted and subsequently became bound to the isolated chromatin or actually coexisted with the nuclei in the intact cell. Chromatin was prepared from cells of chronic myelocytic leukaemias (Philadelphia chromosome positive); protein and DNA concentrations were determined according to Lowry et a1 ( 1 9 ~ 1 ) and Burton (1956), respectively. Histones were extracted from chromatin and from the whole buffy coat WBC and nuclei, and separated by polyacrylamide gels (Simpkins & Mahon, 1978). The chromatin preparations possessed DNA :protein ratios of 30: 70 and when histones were isolated from chromatin obtained from cells of CML in blast crisis (no identifiable granules), the previously reported degradation of histones H I , H2B and H3 was observed. However, when intact cells were extracted, approximately equimolar amounts of the core histones (H2A, H2B, H3 and H2) were observed. If nuclei were prepared from lysed cells, slight degradation ofhistones H2B and H3 was observed. When cells from CML patients not in blast crisis (mature myelocytes) were employed, less degradation was observed than with myeloblasts. The results suggest that histone hydrolysis is caused by a protease liberated during cell lysis which may be cytoplasmic and not nuclear in origin. This work was supported by grants CA-18890 from the National Institutes of Health. HENRY SIMPKINS Department of Pathology, University of Calgornia Irvine Medical Center, 101 City Drive South, Orange, California 92668, U.S.A.
OpenUAT: The open source ubiquitous authentication toolkit

Authenticating spontaneous interactions between devices and users is challenging for several reasons: the wireless (and therefore invisible) nature of device communication, the heterogeneous nature of devices and lack of appropriate user interfaces in mobile devices, and the requirement for unobtrusive user interaction. The most promising approach that has been proposed in literature involves the exploitation of so-called auxiliary channels for authentication to bridge the gap between usability and security. This concept has spawned the independent development of various authentication methods and research prototypes, that, unfortunately, remain hard to compare and interchange and are rarely available to potential application developers. We built a system which implements and unifies these approaches. In this paper, we present OpenUAT, an open source toolkit that implements our novel, unified cryptographic authentication protocol (UACAP), and a comprehensive range of specific auxiliary channels. We evaluated OpenUAT based on a user study in which we compared four authentication methods implemented by the toolkit. The user study showed that users tend to prefer the visual channel in spite of its comparatively poor performance.
The AP-2 Complex Is Excluded from the Dynamic Population of Plasma Membrane-associated Clathrin*

Numerous biologically relevant substrates are selectively internalized via clathrin-mediated endocytosis. At the plasma membrane the AP-2 complex plays a major role in clathrin coat formation, interacting with both cargo and clathrin. Utilizing simultaneous dual-channel total internal reflection fluorescence microscopy we have analyzed components of the AP-2 complex (α- and β2-adaptin) during clathrin-mediated endocytosis. Although in static images enhanced green fluorescent protein-tagged AP-2 markers significantly co-localized with clathrin and other components of clathrin-coated pits, AP-2 did not seem to be present in clathrin spots that appeared to undergo internalization or motility parallel to the plane of the plasma membrane. Two populations of clathrin at the plasma membrane seem to exist, the dynamic and the static, and AP-2 appears to be only found within the latter. These results suggest that colocalized clathrin/AP-2 puncta may represent loci for coated pit production and that previous models that assumed AP-2 was retained within clathrin coats during endocytosis may need to be re-evaluated.
Speakers’ Intention Prediction Using Statistics of Multi-level Features in a Schedule Management Domain

Speaker's intention prediction modules can be widely used as a pre-processor for reducing the search space of an automatic speech recognizer. They also can be used as a preprocessor for generating a proper sentence in a dialogue system. We propose a statistical model to predict speakers' intentions by using multi-level features. Using the multi-level features (morpheme-level features, discourse-level features, and domain knowledge-level features), the proposed model predicts speakers' intentions that may be implicated in next utterances. In the experiments, the proposed model showed better performances (about 29% higher accuracies) than the previous model. Based on the experiments, we found that the proposed multi-level features are very effective in speaker's intention prediction.
Approximating Linear Threshold Predicates

We study constraint satisfaction problems on the domain {−1, 1}, where the given constraints are homogeneous linear threshold predicates, that is, predicates of the form sgn(<i>w</i><sub>1</sub><i>x</i><sub>1</sub> + ⋯ + <i>w</i><sub>n</sub><i>x</i><sub>n</sub>) for some positive integer weights <i>w</i><sub>1</sub>, . , <i>w</i><sub>n</sub>. Despite their simplicity, current techniques fall short of providing a classification of these predicates in terms of approximability. In fact, it is not easy to guess whether there exists a homogeneous linear threshold predicate that is approximation resistant or not. The focus of this article is to identify and study the approximation curve of a class of threshold predicates that allow for nontrivial approximation. Arguably the simplest such predicate is the majority predicate sgn(<i>x</i><sub>1</sub> + ⋯ + <i>x</i><sub>n</sub>), for which we obtain an almost complete understanding of the asymptotic approximation curve, assuming the Unique Games Conjecture. Our techniques extend to a more general class of “majority-like” predicates and we obtain parallel results for them. In order to classify these predicates, we introduce the notion of <i>Chow-robustness</i> that might be of independent interest.
Preoperative assessment enables the early diagnosis and successful treatment of lymphedema

The incidence of breast cancer (BC)‐related lymphedema (LE) ranges from 7% to 47%. Successful management of LE relies on early diagnosis using sensitive measurement techniques. In the current study, the authors demonstrated the effectiveness of a surveillance program that included preoperative limb volume measurement and interval postoperative follow‐up to detect and treat subclinical LE.
Multiscale model of tumor-derived capillary-like network formation

Solid tumors recruit and form blood vessels, used for maintenance and growth as well as for formation and spread of metastases. Vascularization is therefore a pivotal switch in cancer malignancy: an accurate analysis of its driving processes is a big issue for the development of treatments. In vitro experiments have demonstrated that cultured tumor-derived endothelial cells (TECs) are able to organize in a connected network, which mimics an in vivo capillary-plexus. The process, called tubulogenesis , is promoted by the activity of soluble peptides (such as VEGFs), as well as by the following intracellular calcium signals. We here propose a multilevel approach, reproducing selected features of the experimental system: it incorporates a continuous model of microscopic VEGF-induced events in a discrete mesoscopic Cellular Potts Model (CPM). The two components are interfaced, producing a multiscale framework characterized by a constant flux of information from finer to coarser levels. The simulation results, in agreement with experimental analysis, allow to identify the key mechanisms of network formation. In particular, we provide evidence that the nascent pattern is characterized by precise topological properties, regulated by the initial cell density in conjunction with the degree of the chemotactic response and the directional persistence of cell migration.
Real-time Head Pose Estimation Using a Webcam: Monocular Adaptive View-based Appearance Model

Abstract : Accurately estimating the person's head position and orientation is an important task for a wide range of applications such as driver awareness and human-robot interaction. Over the past two decades, many approaches have been suggested to solve this problem, each with its own advantages and disadvantages. In this paper, we present a probabilistic framework called Monocular Adaptive View-based Appearance Model (MAVAM) which integrates the advantages from two of these approaches: (1) the relative precision and user-independence of differential registration, and (2) the robustness and bounded drift of keyframe tracking. In our experiments, we show how the MAVAM model can be used to estimate head position and orientation in real-time using a simple monocular camera. Our experiments on two previously published datasets show that the MAVAM framework can accurately track for a long period of time (more than 2 minutes) with an average accuracy of 3.9 degrees and 1.2 inches with an inertial sensor and a 3D magnetic sensor.
Fast pattern recognition using gradient-descent search in an image pyramid

A new technique for fast pattern recognition using normalized grey-scale correlation (NGC) is described. While NGC has traditionally been slow due to computational intensity issues, the introduction of both a pyramid structure and a local estimate of the correlation surface gradient allows for recognition in 10-50 ms using modest microcomputer hardware. The algorithm is designed to analyze the target off-line prior to starting the search. Issues surrounding determining an appropriate depth for the pyramid representation and performing sub-pixel localization of the target instance are discussed. The speed and robustness of the method makes it attractive for industrial applications.
The myristoylated amino terminus of Galpha(i)(1) plays a critical role in the structure and function of Galpha(i)(1) subunits in solution.

To determine the role of the myristoylated amino terminus of Galpha in G protein activation, nine individual cysteine mutations along the myristoylated amino terminus of Galpha(i) were expressed in a functionally Cys-less background. Thiol reactive EPR and fluorescent probes were attached to each site as local reporters of mobility and conformational changes upon activation of Galpha(i)GDP by AlF(4)(-), as well as binding to Gbetagamma. EPR and steady state fluorescence anisotropy are consistent with a high degree of immobility for labeled residues in solution all along the amino terminus of myristoylated Galpha(i). This is in contrast to the high mobility of this region in nonmyristoylated Galpha(i) [Medkova, M. , et al. (2002) Biochemistry 41, 9962-9972]. Steady state fluorescence measurements revealed pronounced increases in fluorescence upon activation for residues 14-17 and 21 located midway through the 30-amino acid stretch comprising the amino-terminal region. Collectively, the data suggest that myristoylation is an important structural determinant of the amino terminus of Galpha(i) proteins.
An Official Journal of the American Heart Association BRIEF REVIEWS The Concept of Active State in Striated Muscle

FOR THE purposes of this review, it will be helpful to consider the simple block diagram of a striated muscle system shown in Figure 1. The system has been generalized, in order to be applicable to heart muscle, by including an inotropic state mechanism. The parallel elastic component is necessary to account for resting tension. However, neither of these elements will be discussed further. According to the classical model for muscle contraction proposed by Hill, a contracting muscle can be represented by a contractile component (CC) in series with a series elastic component (SEC). In the resting state, the CC is freely extensible, whereas in the active state it is supposed to resist strongly any attempt to suddenly change its length. The properties of the active CC are such that its force-velocity behavior can be described by the following equation:
Classification of Twitter Accounts into Automated Agents and Human Users

Online social networks (OSNs) have seen a remarkable rise in the presence of surreptitious automated accounts. Massive human user-base and business-supportive operating model of social networks (such as Twitter) facilitates the creation of automated agents. In this paper we outline a systematic methodology and train a classifier to categorise Twitter accounts into ‘automated’ and ‘human’ users. To improve classification accuracy we employ a set of novel steps. First, we divide the dataset into four popularity bands to compensate for differences in types of accounts. Second, we create a large ground truth dataset using human annotations and extract relevant features from raw tweets. To judge accuracy of the procedure we calculate agreement among human annotators as well as with a bot detection research tool. We then apply a Random Forests classifier that achieves an accuracy close to human agreement. Finally, as a concluding step we perform tests to measure the efficacy of our results.
Impacts of interactive dust and its direct radiative forcing on interannual variations of temperature and precipitation in winter over East Asia

We used two 150 year preindustrial simulations of the Community Earth System Model, one with interactive dust and the other with prescribed dust, to quantify the impacts of changes in wind during East Asian winter monsoon (EAWM) season on dust emissions, and the resulting consequences for interannual variations of temperature and precipitation over East Asia. The simulated December‐January‐February dust column burden and dust optical depth are lower over northern China in the strongest EAWM years than those of the weakest years by 38.3% and 37.2%, respectively. The decrease in dust over the dust source regions and the downwind region leads to an increase in direct radiative forcing (RF) at the surface by up to 1.5 W m−2. The effects of EAWM‐related variations in surface winds, precipitation, and their effects on dust emissions and wet removal contribute 67% to the total dust‐induced variations of direct RF at the surface and partly offset the cooling that occurs with the EAWM strengthening by heating the surface. The variations of surface air temperature induced by the changes in wind and dust emissions between the strongest and weakest EAWM years (strongest minus weakest) decrease by 0.4–0.6 K from eastern coastal China to Japan, which weakens the impact of EAWM on surface air temperature by 3–18% in these regions. The warming results from the combined effects of changes in direct RF, turbulent heat flux at the surface, and northwesterly wind anomalies that bring cold and dry air from Siberia to these regions. Over eastern coastal China, the variations of large‐scale precipitation induced by the feedback of EAWM‐related changes in wind on dust emissions decrease by 10–30% in winter because of the reduced changes in surface air temperature and the anomalous circulation.
Improving text categorization bootstrapping via unsupervised learning

We propose a text-categorization bootstrapping algorithm in which categories are described by relevant seed words. Our method introduces two unsupervised techniques to improve the initial categorization step of the bootstrapping scheme: (i) using latent semantic spaces to estimate the similarity among documents and words, and (ii) the Gaussian mixture algorithm, which differentiates relevant and nonrelevant category information using statistics from unlabeled examples. In particular, this second step maps the similarity scores to class posterior probabilities, and therefore reduces sensitivity to keyword-dependent variations in scores. The algorithm was evaluated on two text categorization tasks, and obtained good performance using only the category names as initial seeds. In particular, the performance of the proposed method proved to be equivalent to a pure supervised approach trained on 70--160 labeled documents per category.
Identifying Protein Complexes in High-Throughput Protein Interaction Screens Using an Infinite Latent Feature Model

We propose a Bayesian approach to identify protein complexes and their constituents from high-throughput protein-protein interaction screens. An infinite latent feature model that allows for multi-complex membership by individual proteins is coupled with a graph diffusion kernel that evaluates the likelihood of two proteins belonging to the same complex. Gibbs sampling is then used to infer a catalog of protein complexes from the interaction screen data. An advantage of this model is that it places no prior constraints on the number of complexes and automatically infers the number of significant complexes from the data. Validation results using affinity purification/mass spectrometry experimental data from yeast RNA-processing complexes indicate that our method is capable of partitioning the data in a biologically meaningful way. A supplementary web site containing larger versions of the figures is available at http://public.kgi. edu/wild/PSBO6/index.html.
MorePhone: a study of actuated shape deformations for flexible thin-film smartphone notifications

We present MorePhone, an actuated flexible smartphone with a thin-film E Ink display. MorePhone uses shape memory alloys to actuate the entire surface of the display as well as individual corners. We conducted a participatory study to determine how users associate urgency and notification type with full screen, 1 corner, 2 corner and 3 corner actuations of the smartphone. Results suggest that with the current prototype, actuated shape notifications are useful for visual feedback. Urgent notifications such as alarms and voice calls were best matched with actuation of the entire display surface, while less urgent notifications, such as software notifications were best matched to individual corner bends. While different corner actuations resulted in significantly different matches between notification types, medium urgency notification types were treated as similar, and best matched to a single corner bend. A follow-up study suggested that users prefer to dedicate each corner to a specific type of notification. Users would like to personalize the assignment of corners to notification type. Animation of shape actuation significantly increased the perceived urgency of any of the presented shapes.