Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance Limits Due to Inter-Cluster Data Forwarding in Wire-Limited ILP Microprocessors

The growing speed gap between transistors and wire interconnects is forcing the development of distributed, or clustered, architectures. These designs partition the chip into small regions with fast intra-cluster communication. Longer latency is required to communicate between clusters. The hardware and/or software is responsible for scheduling instructions to clusters such that critical path communication occurs within a cluster. This paper explores fundamental interactions between semiconductor technology and clustered architectures. The relationship between key technology parameters (inter-cluster wire delay and transistor switching delay) and key architecture parameters (superscalar vs multithreaded instruction dispatch, and value prediction support) is investigated. The GENESYS modeling tool is used to predict inter-cluster latencies as VLSI technology advances. The study shows that performance limits of the conventional superscalar approach are substantially higher with zero-delay wires. As wire delay increases, performance of these designs degrade quickly. Threaded designs are more tolerant to wire delay. It is seen that the optimal thread size changes with advancing VLSI technology, suggesting a highly adaptive architecture. Value prediction is shown to be useful in all cases, but provides more benefit to the multi-threaded design.
A compact model of AlGaN/GaN HEMTs power transistors based on a surface-potential approach

In this paper we present a compact model for AlxGa1-xN/GaN High Electron Mobility Transistors (HEMTs) developed for circuit simulation of power transistors. A physical approach is followed and drain current and intrinsic node charges are calculated using the surface-potential formalism. The HSP model (acronym for HEMT Surface-Potential model) presented here includes: dependence on the aluminum content of the energy band-gap and of the spontaneous and piezoelectric polarizations, incomplete donor activation, temperature dependence of different parameters and self-heating effect. Moreover, a physical self-heating model including heat diffusion from channel to substrates of different thermal conductivities is implemented. Other effects, like series resistances, velocity saturation and channel length modulation -which are important when the HEMT transistor works at high voltage and high current- are also incorporated in the model.
Combinational equivalence checking through function transformation

Circuits can be simplified for combinational equivalence checking by transforming internal functions, while preserving their ranges. In this paper, we investigate how to effectively apply the idea to improve equivalence checking. We propose new heuristics to identify groups of nets in a cut, and elaborate detailed aspects of the new equivalence checking method. With a given miter, we identify a group of nets in a cut and transform the function of each net into a more compact representation with less variables. These new compact parametric representations preserve the range of nets as well as of the cut. This transformation significantly reduces the size of intermediate BDDs and enables the verification to be conclusive for many designs which state-of-the-art equivalence checkers fail to verify. Iterative groupings and transformations are performed until no grouping is possible for a cut. Then we proceed to the next cut and continue until the compare point is reached. Our experimental results show the effectiveness of our strategy and new grouping heuristics on the new method.
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria.

Recent bioinformatics-aided searches have identified many new small RNAs (sRNAs) in the intergenic regions of the bacterium Escherichia coli. Here, a shot-gun cloning approach (RNomics) was used to generate cDNA libraries of small sized RNAs. Besides many of the known sRNAs, we found new species that were not predicted previously. The present work brings the number of sRNAs in E.coli to 62. Experimental transcription start site mapping showed that some sRNAs were encoded from independent genes, while others were processed from mRNA leaders or trailers, indicative of a parallel transcriptional output generating sRNAs co-expressed with mRNAs. Two of these RNAs (SroA and SroG) consist of known (THI and RFN) riboswitch elements. We also show that two recently identified sRNAs (RyeB and SraC/RyeA) interact, resulting in RNase III-dependent cleavage. To the best of our knowledge, this represents the first case of two non-coding RNAs interacting by a putative antisense mechanism. In addition, intracellular metabolic stabilities of sRNAs were determined, including ones from previous screens. The wide range of half-lives (<2 to >32 min) indicates that sRNAs cannot generally be assumed to be metabolically stable. The experimental characterization of sRNAs analyzed here suggests that the definition of an sRNA is more complex than previously assumed.
A Comparison of Remote Sensing Methods for Estimating Above-Ground Carbon Biomass at a Wetland Restoration Area in the Southeastern Coastal Plain

Developing accurate but inexpensive methods for estimating above-ground carbon biomass is an important technical challenge that must be overcome before a carbon offset market can be successfully implemented. Previous studies have shown that full-waveform LiDAR (light detection and ranging) is well suited for modeling above-ground biomass in mature forests; however, there has been little previous research on the ability of discrete-return LiDAR to model above-ground biomass in areas with relatively sparse vegetation. This study compared the abilities of discrete-return LiDAR and high-resolution optical imagery to model above-ground carbon biomass at a wetland restoration area in eastern North Carolina. The optical imagery model explained more of the overall variation in biomass at the study site than the LiDAR model did (R 2 values of 0.36 and 0.19 respectively). Moreover, the optical imagery model was better able to detect high and low biomass areas than the LiDAR model. These results suggest that the ability of discrete-return LiDAR to model above-ground biomass is rather limited in areas with relatively small trees and that high spatial resolution optical imagery may be the better tool in such areas.
From Greenland to green lakes: Cultural eutrophication and the loss of benthic pathways in lakes

Benthic community responses to lake eutrophication are poorly understood relative to pelagic responses. We compared phytoplankton and periphyton productivity along a eutrophication gradient in Greenland, U.S., and Danish lakes. Phytoplankton productivity increased along the phosphorus gradient (total phosphorus [TP] = 2–430 mg m−3), but whole‐lake benthic algal productivity decreased, substantially depressing increases in primary productivity at the whole‐lake scale. In shallow, oligotrophic Greenland lakes, periphyton was responsible for 80–98% of primary production, whereas in Danish lakes with TP > 100 mg m−3, phytoplankton were responsible for nearly 100% of primary production. Benthic contributions ranged from 5 to 80% depending on morphometry and littoral habitat composition in lakes with intermediate phosphorus concentrations. Thus, eutrophication was characterized by a switch from benthic to pelagic dominance of primary productivity. Carbon stable isotope analysis showed that the redistribution of primary production entailed a similar shift from periphyton to phytoplankton in the diets of zoobenthos. Benthic and pelagic habitats were energetically linked through food web interactions, but eutrophication eroded the benthic primary production pathway.
A proximity/contact-force sensor for Human Safety in industrial robot environment

In this paper, a new approach based on a proximity/contact-force sensor to improve the Human Safety in the Human-Robot cooperative tasks is presented. The sensor is able to detect both the presence of a nearby object and the contact pressure exercised by an external object when a collision occurs. The sensor is interfaced with an ABB industrial robot using only the standard control unit; the standard RAPID primitives are used to define the robot task. The task speed is reduced as soon as an obstacle is detected by the proximity sensing element, while, the robot is stopped when a contact occurs, that is detected by a contact-force sensing element.
In-depth structural characterization of Kadcyla® (ado-trastuzumab emtansine) and its biosimilar candidate

ASBTRACT The biopharmaceutical industry has become increasingly focused on developing biosimilars as less expensive therapeutic products. As a consequence, the regulatory approval of 2 antibody-drug conjugates (ADCs), Kadcyla® and Adcetris® has led to the development of biosimilar versions by companies located worldwide. Because of the increased complexity of ADC samples that results from the heterogeneity of conjugation, it is imperative that close attention be paid to the critical quality attributes (CQAs) that stem from the conjugation process during ADC biosimilar development process. A combination of physicochemical, immunological, and biological methods are warranted in order to demonstrate the identity, purity, concentration, and activity (potency or strength) of ADC samples. As described here, we performed extensive characterization of a lysine conjugated ADC, ado-trastuzumab emtansine, and compared its CQAs between the reference product (Kadcyla®) and a candidate biosimilar. Primary amino acid sequences, drug-to-antibody ratios (DARs), conjugation sites and site occupancy data were acquired and compared by LC/MS methods. Furthermore, thermal stability, free drug content, and impurities were analyzed to further determine the comparability of the 2 ADCs. Finally, biological activities were compared between Kadcyla® and biosimilar ADCs using a cytotoxic activity assay and a HER2 binding assay. The in-depth characterization helps to establish product CQAs, and is vital for ADC biosimilars development to ensure their comparability with the reference product, as well as product safety.
A Concept Based Indexing Approach for Document Clustering

The research presented in this paper focuses on the pre-processing stage of the clustering process, proposing a novel indexing technique which goes beyond the syntax of terms; trying to capture their unambiguous meaning from their context and to derive a set of concepts to be used to represent the documents. This approach overcomes some of the major drawbacks deriving from the use of bag of words and term frequency based indexing techniques. The proposed approach is evaluated by using unsupervised performance measures and by comparing the clustering results achieved against the ones obtained when using a traditional indexing method. The experimental results show that better clustering results are achieved through the use of the proposed indexing approach, which also led to a substantial reduction of the index term dimension.
Survey of Inter-Satellite Communication for Small Satellite Systems: Physical Layer to Network Layer View

Small satellite systems enable a whole new class of missions for navigation, communications, remote sensing, and scientific research for both civilian and military purposes. As individual spacecraft are limited by the size, mass, and power constraints, mass-produced small satellites in large constellations or clusters could be useful in many science missions such as gravity mapping, tracking of forest fires, finding water resources, etc. The proliferation of small satellites will enable a better understanding of the near-Earth environment and provide an efficient and economical means to access the space through the use of multi-satellite solution. Constellation of satellites provide improved spatial and temporal resolution of the target. Small satellite constellations contribute innovative applications by replacing a single asset with several very capable spacecraft, which opens the door to new applications. Future space missions are envisioned to become more complex and operate farther from Earth, and will need to support autonomous operations with minimal human intervention. With increasing levels of autonomy, there will be a need for remote communication networks to enable communication between spacecraft. These space-based networks will need to configure and maintain dynamic routes, manage intermediate nodes, and reconfigure themselves to achieve mission objectives. Hence, inter-satellite communication is a key aspect when satellites fly in formation. In this survey, we present the various research being conducted in the small satellite community for implementing inter-satellite communications based on the open system interconnection (OSI) model. This survey also reviews the various design parameters applicable to the first three layers of the OSI model, i.e., physical, data link, and network layer. Based on the survey, we also present a comprehensive list of design parameters useful for achieving inter-satellite communications for multiple small satellite missions. Specific topics include proposed solutions for some of the challenges faced by small satellite systems, enabling operations using a network of small satellites, and some examples of small satellite missions involving formation flying aspects.
Mixtures of Chemical Pollutants at European Legislation Safety Concentrations: How Safe Are They?

The risk posed by complex chemical mixtures in the environment to wildlife and humans is increasingly debated, but has been rarely tested under environmentally relevant scenarios. To address this issue, two mixtures of 14 or 19 substances of concern (pesticides, pharmaceuticals, heavy metals, polyaromatic hydrocarbons, a surfactant, and a plasticizer), each present at its safety limit concentration imposed by the European legislation, were prepared and tested for their toxic effects. The effects of the mixtures were assessed in 35 bioassays, based on 11 organisms representing different trophic levels. A consortium of 16 laboratories was involved in performing the bioassays. The mixtures elicited quantifiable toxic effects on some of the test systems employed, including i) changes in marine microbial composition, ii) microalgae toxicity, iii) immobilization in the crustacean Daphnia magna, iv) fish embryo toxicity, v) impaired frog embryo development, and vi) increased expression on oxidative stress-linked reporter genes. Estrogenic activity close to regulatory safety limit concentrations was uncovered by receptor-binding assays. The results highlight the need of precautionary actions on the assessment of chemical mixtures even in cases where individual toxicants are present at seemingly harmless concentrations.
A framework for using multimedia for discussion-based education

This paper proposes a preliminary framework by which the power of multimedia systems can be harnessed for use in discursive educational interactions, such as educational debate. The framework uses concepts from dialogue game theory, and in particular the dialectical system "DC". The paper outlines the DC system in some detail and proposes means by which it can be integrated within a multimedia environment.
A System of User-Guided Biological Literature Search Engine

Efficiently finding most relevant publications in large corpora is an important research topic in information retrieval. The number of biological literatures grows exponentially in various publication databases. The objective of the study in this paper is to fast locate useful publications from large biomedical document collections based on users’ preferences. In this paper, a new iterative search paradigm is introduced which integrates biological background knowledge in organizing the results returned by search engines, and utilizes user feedbacks to filter irrelevant documents. A term weighting scheme based on Gene Ontology is introduced to improve similarity measurement of documents in biomedical domain. A prototype text retrieval system has been built based on this iterative search approach. Experimental results show that the system can filter a large number of irrelevant documents while keep most of the relevant documents with limited user interactions.
Evidence for Allosteric Interactions of Antagonist Binding to the Smoothened Receptor

The Smoothened receptor (Smo) mediates hedgehog (Hh) signaling critical for development, cell growth, and migration, as well as stem cell maintenance. Aberrant Hh signaling pathway activation has been implicated in a variety of cancers, and small-molecule antagonists of Smo have entered human clinical trials for the treatment of cancer. Here, we report the biochemical characterization of allosteric interactions of agonists and antagonists for Smo. Binding of two radioligands, [3H]3-chloro-N-[trans-4-(methylamino)cyclohexyl]-N-{[3-(4-pyridinyl)-phenyl]methyl}-1-benzothiophene-2-carboxamide (SAG-1.3) (agonist) and [3H]cyclopamine (antagonist), was characterized using human Smo expressed in human embryonic kidney 293F membranes. We observed full displacement of [3H]cyclopamine by all Smo agonist and antagonist ligands examined. N-[(1E)-(3,5-Dimethyl-1-phenyl-1H-pyrazol-4-yl)methylidene]-4-(phenylmethyl)-1-piperazinamine (SANT-1), an antagonist, did not fully inhibit the binding of [3H]SAG-1.3. In a functional cell-based β-lactamase reporter gene assay, SANT-1 and N-[3-(1H-benzimidazol-2-yl)-4-chlorophenyl]-3,4,5-tris(ethyloxy)-benzamide (SANT-2) fully inhibited 3-chloro-4,7-difluoro-N-[trans-4-(methylamino)cyclohexyl]-N-{[3-(4-pyridinyl)phenyl]methyl}-1-benzothiophene-2-carboxamide (SAG-1.5)-induced Hh pathway activation. Detailed “Schild-type” radioligand binding analysis with [3H]SAG-1.3 revealed that two structurally distinct Smoothened receptor antagonists, SANT-1 and SANT-2, bound in a manner consistent with that of allosteric modulation. Our mechanism of action characterization of radioligand binding to Smo combined with functional data provides a better understanding of small-molecule interactions with Smo and their influence on the Hh pathway.
EEG – EMG Information Flow in Movement-Activated Myoclonus in Patients with Progressive Myoclonic Epilepsies

We aimed this study at verifying the appropriateness of generalized partial directed coherence (GPDC) in detecting EEG–EMG information flow and identifying the characteristics of myoclonus-related EEG changes in patients with progressive myoclonus epilepsy (PME). Our results indicate that GPDC analysis is able to detect the presence of a different pattern of connectivity between the EMG and sensorimotor EEG derivations in all patients, namely a larger and more extensive flow of information in beta band coming out from the cortex and driving the muscular activity in patients with respect to controls.
Multi-structural databases

We introduce the Multi-Structural Database, a new data framework to support efficient analysis of large, complex data sets. An instance of the model consists of a set of data objects, together with a schema that specifies segmentations of the set of data objects according to multiple distinct criteria (e.g., into a taxonomy based on a hierarchical attribute). Within this model, we develop a rich set of analytical operations and design highly efficient algorithms for these operations. Our operations are formulated as optimization problems, and allow the user to analyze the underlying data in terms of the allowed segmentations. Our algorithms and results extend those of Fagin et al. [8] who studied composition of mappings given by several kinds of constraints. In particular, they proved that full source-to-target tuple-generating dependencies (tgds) are closed under composition, but embedded source-to-target tgds are not. They introduced a class of second-order constraints, SO tgds, that is closed under composition and has desirable properties for data exchange. We study constraints that need not be source-to-target and we concentrate on obtaining (first-order) embedded dependencies. As part of this study, we also consider full dependencies and second-order constraints that arise from Skolemizing embedded dependencies. For each of the three classes of mappings that we study, we provide (a) an algorithm that attempts to compute the composition and (b) sufficient conditions on the input mappings that guarantee that the algorithm will succeed. In addition, we give several negative results. In particular, we show that full dependencies are not closed under composition, and that second-order dependencies that are not limited to be source-to-target are not closed under restricted composition. Furthermore, we show that determining whether the composition can be given by these kinds of dependencies is undecidable.
Interactive exploration of volume line integral convolution based on 3D-texture mapping

Line integral convolution (LIC) is an effective technique for visualizing vector fields. The application of LIC to 3D flow fields has yet been limited by difficulties to efficiently display and animate the resulting 3D-images. Texture-based volume rendering allows interactive visualization and manipulation of 3D-LIC textures. In order to ensure the comprehensive and convenient exploration of flow fields, we suggest interactive functionality including transfer functions and different clipping mechanisms. Thereby, we efficiently substitute the calculation of LIC based on sparse noise textures and show the convenient visual access of interior structures. Further on, we introduce two approaches for animating static 3D-flow fields without the computational expense and the immense memory requirements for pre-computed 3D-textures and without loss of interactivity. This is achieved by using a single 3D-LIC texture and a set of time surfaces as clipping geometries. In our first approach we use the clipping geometry to pre-compute a special 3D-LIC texture that can be animated by time-dependent color tables. Our second approach uses time volumes to actually clip the 3D-LIC volume interactively during rasterization. Additionally, several examples demonstrate the value of our strategy in practice.
Obesity and lung function: a systematic review

ABSTRACT Obesity is a chronic disease characterized by the excessive accumulation of body fat that is harmful to the individuals. Respiratory disorders are among the comorbidities associated with obesity. This study had the objective of investigating the alterations in respiratory function that affect obese individuals. A systematic review was performed, by selecting publications in the science databases MEDLINE and LILACS, using PubMed and SciELO. The articles that assessed pulmonary function by plethysmography and/or spirometry in obese individuals aged under 18 years were included. The results demonstrated that the obese individuals presented with a reduction in lung volume and capacity as compared to healthy individuals. Reduction of total lung capacity and reduction of forced vital capacity, accompanied by reduction of the forced expiratory volume after one second were the most representative findings in the samples. The articles analyzed proved the presence of a restrictive respiratory pattern associated with obesity.