Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear Compartmentalization Contributes to Stage-Specific Gene Expression Control in Trypanosoma cruzi

In the protozoan parasite Trypanosoma cruzi, as in other trypanosomatids, transcription of protein coding genes occurs in a constitutive fashion, producing large polycistronic transcription units. These units are composed of non-functionally related genes which are pervasively processed to yield each mRNA. Therefore, post-transcriptional processes are crucial to regulate gene expression. Considering that nuclear compartmentalization could contribute to gene expression regulation, we comparatively studied the nuclear, cytoplasmic and whole cell transcriptomes of the non-infective epimastigote stage of T. cruzi, using RNA-Seq. We found that the cytoplasmic transcriptome tightly correlates with the whole cell transcriptome and both equally correlate with the proteome. Nonetheless, 1,200 transcripts showed differential abundance between the nuclear and cytoplasmic fractions. For the genes with transcript content augmented in the nucleus, significant structural and compositional differences were found. The analysis of the reported epimastigote translatome and proteome, revealed scarce ribosome footprints and encoded proteins for them. Ontology analyses unveiled that many of these genes are distinctive of other parasite life-cycle stages. Finally, the relocalization of transcript abundance in the metacyclic trypomastigote infective stage was confirmed for specific genes. While gene expression is strongly dependent on transcript steady-state level, we here highlight the importance of the distribution of transcripts abundance between compartments in T. cruzi. Particularly, we show that nuclear compartmentation is playing an active role in the developmental stage determination preventing off-stage expression.
On resilience of structured peer-to-peer systems

We propose an approach to analyze the resilience to failures of structured P2P systems. The approach is Markov-chain based, and can be applied to systems with relatively stable size and uniformly distributed nodes. We apply our method to several well-known structured P2P systems. We find that finger neighbors and special neighbors have different influences on the resilience features of P2P systems. More particularly, finger neighbors have significant influence on the average path length while special neighbors influence the hit ratio. Following the above observation, we propose to add some finger neighbor(s) to nodes of the CAN (content-addressable network) system which originally have no such finger neighbor(s). We use the small-world phenomenon to form the CAN-small-world (CAN-SW) system. We then apply the proposed Markov-chain based approach to analyze its resilience. We find that the performance of the system under failures or not, has been improved significantly, particularly, in terms of the average path length.
A Content based CT Image Retrieval by Advance Multiple Comparison Technique

- In this paper, a content-based scheme to retrieve lung Computed Tomographic images (CT) is presented. It consists of a visual based user interface to allow the query be made by line-drawing the interested (abnormal) regions; and a training scheme to classify the relationship between the images stored in database. The system will output a set of candidate images that are textural-similar to the query image. Using this result system will calculate the average of affected area from these similar images that are once again compared with database images. Now the system will give a set of candidate images. It has only most similar images from the database. This approach is better than existing methods because here the system compared to the affected image with the database image in the first stage. At the second stage the system will calculate the average of affected area of similar images from the output of candidate images. Finally the system produced the images that are similar to the candidate images. The experimental result shows that in simple query, 98% of images can be correctly retrieved.
A distributed strategy for computing proximity operators

Various recent iterative optimization methods require to compute the proximity operator of a sum of functions. We address this problem by proposing a new distributed algorithm for a sum of non-necessarily smooth convex functions composed with arbitrary linear operators. In our approach, each function is associated with a node of a graph, which communicates with its neighbors. Our algorithm relies on a primal-dual splitting strategy that avoids to invert any linear operator, thus making it suitable for processing high-dimensional datasets. The proposed algorithm has a wide array of applications in signal/image processing and machine learning and its convergence is established.
Strategic Adaptation to Performance Objectives in a Dual-Task Setting

How do people interleave attention when multitasking? One dominant account is that the completion of a subtask serves as a cue to switch tasks. But what happens if switching solely at subtask boundaries led to poor performance? We report a study in which participants manually dialed a UK-style telephone number while driving a simulated vehicle. If the driver were to exclusively return his or her attention to driving after completing a subtask (i.e., using the single break in the xxxxx-xxxxxx representational structure of the number), then we would expect to see a relatively poor driving performance. In contrast, our results show that drivers choose to return attention to steering control before the natural subtask boundary. A computational modeling analysis shows that drivers had to adopt this strategy to meet the required performance objective of maintaining an acceptable lateral position in the road while dialing. Taken together these results support the idea that people can strategically control the allocation of attention in multitask settings to meet specific performance criteria.
Inflammation and Hyperglycemia Mediate Deaf1 Splicing in the Pancreatic Lymph Nodes via Distinct Pathways During Type 1 Diabetes

Peripheral tolerance is partially controlled by the expression of peripheral tissue antigens (PTAs) in lymph node stromal cells (LNSCs). We previously identified a transcriptional regulator, deformed epidermal autoregulatory factor 1 (Deaf1), that can regulate PTA expression in LNSCs of the pancreatic lymph nodes (PLNs). During the pathogenesis of type 1 diabetes (T1D), Deaf1 is spliced to form the dominant-negative isoform Deaf1-Var1. Here we show that Deaf1-Var1 expression correlates with the severity of disease in NOD mice and is reduced in the PLNs of mice that do not develop hyperglycemia. Inflammation and hyperglycemia independently drive Deaf1 splicing through activation of the splicing factors Srsf10 and Ptbp2, respectively. Inflammation induced by injection of activated splenocytes increased Deaf1-Var1 and Srsf10, but not Ptbp2, in the PLNs of NOD.SCID mice. Hyperglycemia induced by treatment with the insulin receptor agonist S961 increased Deaf1-Var1 and Ptbp2, but not Srsf10, in the PLNs of NOD.B10 and NOD mice. Overexpression of PTBP2 and/or SRSF10 also increased human DEAF1-VAR1 and reduced PTA expression in HEK293T cells. These data suggest that during the progression of T1D, inflammation and hyperglycemia mediate the splicing of DEAF1 and loss of PTA expression in LNSCs by regulating the expression of SRSF10 and PTBP2.
@Scale: Insights from a large, long-lived appliance energy WSN

We present insights obtained from conducting a year-long, 455 meter deployment of wireless plug-load electric meters in a large commercial building. We develop a stratified sampling methodology for surveying the energy use of Miscellaneous Electric Loads (MELs) in commercial buildings, and apply it to our study building. Over the deployment period, we collected over nine hundred million individual readings. Among our findings, we document the need for a dynamic, scalable IPv6 routing protocol which supports point-to-point routing and multiple points of egress. Although the meters are static physically, we find that the set of links they use is dynamic; not using such a dynamic set results in paths that are twice as long. Finally, we conduct a detailed survey of the accuracy possible with inexpensive AC metering hardware. Based on a 21-point automated calibration of a population of 500 devices, we find that it is possible to produce nearly utility-grade metering data.
Amon: An Advanced Mesh-like Optical NoC

Optical networks-on-chip constitute a promising approach to tackle the power wall problem present in large-scale circuit design. In this paper, we propose Amon, an all-optical, mesh-like design based on passive microrings and wave-length division multiplexing, including the switch architecture and a contention-free routing algorithm. Amon provides power efficiency by decreasing the number of microrings, wavelengths and path lengths, which, in turn, reduces ring heater and laser power, and the required area. An analytic comparison of Amon against the state-of-the-art, low power, ring-based designs QuT and Spidergon shows that Amon significantly reduces network diameter and number of microrings. Our experimental results using DSENT show that Amon provides better scalability up to 256 nodes, significant power and area savings of up to 68% and 21%, respectively, while imposing only low wiring overhead and design complexity. Finally, Amon provides a tile-based structure which should facilitate VLSI integration.
Robot-Centric Activity Prediction from First-Person Videos: What Will They Do to Me?

In this paper, we present a core technology to enable robot recognition of human activities during human-robot interactions. In particular, we propose a methodology for early recognition of activities from robot-centric videos (i.e., first-person videos) obtained from a robot's viewpoint during its interaction with humans. Early recognition, which is also known as activity prediction, is an ability to infer an ongoing activity at its early stage. We present an algorithm to recognize human activities targeting the camera from streaming videos, enabling the robot to predict intended activities of the interacting person as early as possible and take fast reactions to such activities (e.g., avoiding harmful events targeting itself before they actually occur). We introduce the novel concept of'onset' that efficiently summarizes pre-activity observations, and design a recognition approach to consider event history in addition to visual features from first-person videos. We propose to represent an onset using a cascade histogram of time series gradients, and we describe a novel algorithmic setup to take advantage of such onset for early recognition of activities. The experimental results clearly illustrate that the proposed concept of onset enables better/earlier recognition of human activities from first-person videos collected with a robot. Categories and Subject Descriptors I.2. 10 [Artificial Intelligence]: Vision and Scene Understanding–video analysis; I.4. 8 [Image Processing and Computer Vision]: Scene Analysis-motion; I.2. 9 [Artificial Intelligence]: Robotics–sensors
Ore Genesis and Formation Age of the Gaogangshan Mo Deposit, Heilongjiang Province, NE China

The Gaogangshan Mo deposit, located in the northern part of the Lesser Xing'an Range (the eastern part of the Xing'an–Mongolia Orogenic Belt), is one of the newly discovered Mo deposits in northeast China. Ore bodies occur in the granite and are generally in vein and stockwork forms. Major metallic minerals in the ore include pyrite and molybdenite. The styles of mineralization are disseminated, veinlet–disseminated, and veinlet. The major types of wall–rock alteration are silicification–potassic alteration, phyllic alteration and propylitization. Fluid inclusion analyses indicate that the ore‐forming fluid during the major mineralization stage is an H2O–NaCl–CO2 system, with wide homogenization temperature and salinity ranges. The abundant CO2–rich and coexisting halite–bearing fluid inclusion assemblages in the main stage of mineralization highlight the significance of intensive fluid boiling for porphyry Mo mineralization. Comprehensive study of the ore‐forming conditions, geological features of the deposit, micro‐thermometric analysis of fluid inclusions and comparison of the Gaogangshan deposit with other typical porphyry deposits leads to the conclusion that the deposit is a porphyry type. We obtained a weighted mean age of the molybdenite deposit at Gaogangshan of 250.7 ± 1.8 Ma. The isotopic dating results indicate that the Gaogangshan deposit was formed in the Permo–Triassic, which is the earliest Mo–only deposit in northeast China. The formation of the Gaogangshan Mo deposit may be related to the extension and break–up of the Songnen Block and Jiamusi Block in the Permo–Triassic.
Improving Antarctic tide models by assimilation of ICESat laser altimetry over ice shelves

Assimilation of laser altimeter data from the Ice, Cloud and land Elevation Satellite (ICESat) significantly improves the accuracy of ocean tide models for the Ross Ice Shelf (RIS). For the most energetic tidal harmonic, K1, assimilation reduces the root‐mean‐square error (RMSE) between the model and a set of 16 independent tide records on and near the RIS from 6.0 to 2.8 cm, and the combined RMSE for the six most energetic tidal harmonics from 7.7 to 5.4 cm. When only the six most recent and highest‐quality tide records are considered, the combined RMSE is 4.8 cm. This value is close to the uncertainty expected from tidal analyses of the short (∼1–2 month) validation records, indicating that assessing further improvements in tide model accuracy will require development of a higher quality validation data set.
Violence detection in hollywood movies by the fusion of visual and mid-level audio cues

Detecting violent scenes in movies is an important video content understanding functionality e.g., for providing automated youth protection services. One key issue in designing algorithms for violence detection is the choice of discriminative features. In this paper, we employ mid-level audio features and compare their discriminative power against low-level audio and visual features. We fuse these mid-level audio cues with low-level visual ones at the decision level in order to further improve the performance of violence detection. We use Mel-Frequency Cepstral Coefficients (MFCC) as audio and average motion as visual features. In order to learn a violence model, we choose two-class support vector machines (SVMs). Our experimental results on detecting violent video shots in Hollywood movies show that mid-level audio features are more discriminative and provide more precise results than low-level ones. The detection performance is further enhanced by fusing the mid-level audio cues with low-level visual ones using an SVM-based decision fusion.
Double-tracer autoradiographic study of protein synthesis and glucose consumption in rats with focal cerebral ischemia.

A double-tracer autoradiographic method for simultaneous measurement of regional glucose utilization (rCMRglc) and regional protein synthesis (PS) in consecutive brain sections is described and applied to study the metabolism of the ischemic penumbra 2 h after occlusion of the middle cerebral artery (MCAO) in rats. In halothane anesthesia, the left middle cerebral artery was permanently occluded. Two hours after MCAO an i.v. bolus injection of 14C-deoxyglucose and 3H-leucine was given and circulated for 45 min. Two sets of brain sections were processed for quantitative autoradiography. Neighboring brain sections exposed an X-ray film (3H-insensitive), and a 3H-sensitive for determination of rCMRglc and PS, respectively. Sections for PS determination were washed in trichloroacetic acid (TCA) prior to film exposure in order to remove 14C-deoxyglucose and unincorporated 3H-leucine. Regional rates of PS and glucose utilization were measured by densitometric image analysis. Normal rates of metabolism were defined as mean +/- 2 SD of values in the non-ischemic cortex. The volumes of ischemic cortex displaying normal rates of PS and glucose utilization, respectively, were measured. The cortical volume with normal PS was significantly less than that of normal rCMRglc: 142 (127-147) mm3 vs. 203 (184-206) mm3. Treatment with the glutamate antagonists MK-801 (1 mg kg-1) and NBQX (30 mg kg-1 x 2) did not significantly change this, although MK-801 tended to reduce the size of the metabolic penumbra calculated as the difference between ischemic cortex with reduced PS and ischemic cortex with reduced rCMRglc.
A Review of Surgical Repair Methods and Patient Outcomes for Gluteal Tendon Tears

Advanced hip imaging and surgical findings have demonstrated that a common cause of greater trochanteric pain syndrome (GTPS) is gluteal tendon tears. Conservative measures are initially employed to treat GTPS and manage gluteal tears, though patients frequently undergo multiple courses of non-operative treatment with only temporary pain relief. Therefore, a number of surgical treatment options for recalcitrant GTPS associated with gluteal tears have been reported. These have included open trans-osseous or bone anchored suture techniques, endoscopic methods and the use of tendon augmentation for repair reinforcement. This review describes the anatomy, pathophysiology and clinical presentation of gluteal tendon tears. Surgical techniques and patient reported outcomes are presented. This review demonstrates that surgical repair can result in improved patient outcomes, irrespective of tear aetiology, and suggests that the patient with “trochanteric bursitis” should be carefully assessed as newer surgical techniques show promise for a condition that historically has been managed conservatively.
A Domain-Specific Approach to the Development of Ontology-Based Document Assessment Assistants

The second author of this paper incrementally developed, over the years, a manual process to systematically evaluate English essays by maintaining an ontology of comments crafted with the goal of pinpointing the occurrence of mined negative writing patterns (i.e., those whose use is discouraged), as well as positive ones (i.e., those whose use is praised). In this paper we report on how the automation of this process, using domain-specific approaches, led to the development of an ontology-based assessment assistant for a specific word processing system. We also report on our approach, currently underway, to extending this solution to a product line of ontology-based assessment assistants over a family of word processing systems and course management systems.
Self-Monitoring with Reversible Grammars

We describe a method and its implementation for self-monitoring during natural language generation. In situations of communication where the generation of ambiguous utterances should be avoided our method is able to compute an unambiguous utterance for a given semantic input. The proposed method is based on a very strict integration of parsing and generation. During the monitored generation step, a previously generated (possibly) ambiguous utterance is parsed and the obtained alternative derivation trees are used as a 'guide' for re-generating the utterance. To achieve such an integrated approach the underlying grammar must be reversible.
SAR polarimetry for sea oil slick observation

In this article, a review of polarimetric synthetic aperture radar (SAR) methods for sea oil slick observation is presented. Marine oil pollution monitoring is a topic of great applicative and scientific relevance. In this framework, the use of remotely sensed measurements is of special interest and, in particular, the SAR because of its almost all-weather and all-day imaging capability at fine spatial resolution is the most effective tool. Conventional single-polarization SAR oil spill monitoring techniques are limited in their capability to detect oil slicks since they strongly rely on suitable thresholds, training samples, and ancillary information. Hence, an expert image analyst is due. The launch of a number of polarimetric SAR missions, along with the understanding of the peculiar physical mechanisms governing the scattering by an oil slick, led to a new paradigm (known as physical processing) that fostered a set of polarimetric algorithms particularly robust and efficient. Hence, suitable polarimetric models that exploit the departure from the slick-free sea Bragg scattering have been developed to effectively address oil slick monitoring. A set of polarimetric features extracted following such electromagnetic models have been proved to be reliable for oil slick monitoring. Polarimetric SAR observations led to a significant improvement in sea oil slick observation since they allow distinguishing oil slicks from a broad class of lookalikes in an unsupervised way. In addition, deeper information on the damping properties of the pollutant can be also inferred, which is of paramount importance for remediation purposes. Such physical processing has been demonstrated to be robust at variance of microwave carrier frequency, e.g. L-, C-, and X-band, and suitable to be exploited to extract information by dual-polarized, full-polarized, and compact modes. All these make such a physical approach of operational interest since it is able to exploit a larger set of SAR measurements building up a virtual constellation. In this review all these are detailed.
Electron Transfer Interactome of Cytochrome c

Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET) is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes – necessary for a comprehensive understanding of the cellular signaling and metabolism – is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc). Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1) reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2) indicates that the ET can take place from more than one protein-protein orientation, and 3) suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility.