Miracle-dz/UniFAR-FTUs huggingface dataset:
Attentional Network for Visual Object Detection

We propose augmenting deep neural networks with an attention mechanism for the visual object detection task. As perceiving a scene, humans have the capability of multiple fixation points, each attended to scene content at different locations and scales. However, such a mechanism is missing in the current state-of-the-art visual object detection methods. Inspired by the human vision system, we propose a novel deep network architecture that imitates this attention mechanism. As detecting objects in an image, the network adaptively places a sequence of glimpses of different shapes at different locations in the image. Evidences of the presence of an object and its location are extracted from these glimpses, which are then fused for estimating the object class and bounding box coordinates. Due to lacks of ground truth annotations of the visual attention mechanism, we train our network using a reinforcement learning algorithm with policy gradients. Experiment results on standard object detection benchmarks show that the proposed network consistently outperforms the baseline networks that does not model the attention mechanism.
UCSD MOLECULE PAGES Complement C 5

Complement C3 is the central component of the human complement system. It is ~186 kDa in size, consisting of an α-chain (~110 kDa) and a β-chain (~75 kDa) that are connected by cysteine bridges. C3 in its native form is inactive. Cleavage of C3 into C3b (~177 kDa) and C3a (~9 kDa) is a crucial step in the complement activation cascade, which can be initiated by one or more of the three distinct pathways, called alternative, classical and lectin complement pathways. In the alternative pathway, hydrated C3 (C3(H20)) recruits complement factor B (fB), which is then cleaved by complement factor D (fD) to result in formation of the minor form of C3-convertase (C3(H20)Bb) that cleaves C3 into C3a and C3b. A small percent of the resulting C3b is rapidly deposited (opsonization through covalent bond) in the immediate vicinity of the site of activation (e.g. pathogen surface) and now forms the major form of C3-convertase (C3bBb), thereby creating an efficient cycle of C3 cleavage. Properdin, a positive regulator of the alternative pathway convertases, provides a hub for the assembly of C3bBb in addition to stabilization of the convertase. Classical and lectin pathways, when activated with recognition of pathogens or immune complexes use another C3-convertase (C4b2a) to cleave C3 into C3a and C3b. Although the three pathways are activated independently, they converge at C3 and use C3 as a substrate for their pathway specific C3-convertase: C3(H20)Bb, C3bBb or C4b2a. Further, C3b undergoes successive proteolytic cleavages by the regulatory complement factor I (fI) in presence of cofactors and lead to generation of iC3b (~174 kDa), C3d/C3dg (~33 kDa), C3c (~142 kDa) and C3f (~2 kDa). C3a is an anaphylatoxin while C3b is involved in opsonization of pathogens or apoptotic cells. Covalently bound C3b on pathogen/apoptotic cell surface is recognized by host immune cells through phagocytic (or complement component) receptors and induce subsequent immune response or directly target pathogen for clearance. The C3a fragment functions as a chemokine, and thereby recruits phagocytic and granulocytic cells to the sites of inflammation and cause strong proinflammatory signaling through their G-protein coupled receptors (GPCRs). As pathogen or apoptotic cell surface bound C3convertases (C3bBb or C4b2a) can induce the amplification of the alternative pathway, this pathway might contribute to the major part of the complement activation process, even when initially triggered by the classical pathway and/or lectin pathway. Continuous activation of complement pathways shifts the substrate preference from C3 to C5 by formation of C5-convertase (formed by addition of C3b fragment to C3-convertases, C3(H20)Bb3b, C3bBb3b and C4b2a3b). C5-convertase activates C5, which by series of additional steps, promotes killing of target cell (pathogen) by pore formation.
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS

MOTIVATION The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map. RESULTS Here we present a method for 'split' read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or single-end as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant. AVAILABILITY SplazerS is available from http://www.seqan. de/projects/ splazers. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Calcium Channel Blocker Nifedipine Slows Down Progression of Coronary Calcification in Hypertensive Patients Compared With Diuretics

Calcium controls numerous events within the vessel wall. Permeability of the endothelium is calcium dependent, as are platelet activation and adhesion, vascular smooth muscle proliferation and migration, and synthesis of fibrous connective tissue. Double-helix computerized tomography is a noninvasive technique that can detect, measure, and compare coronary calcification in the coronary arteries. Using this method, our objective was to determine whether administration of nifedipine once daily in lieu of diuretics in high-risk hypertensive patients will arrest or slow down the progression of coronary artery calcification. The study was designed as a side arm of INSIGHT (International Nifedipine Study: Intervention as Goal for Hypertension Therapy), aimed to show the efficacy of nifedipine once daily versus co-amilozide (hydrochlorothiazide 25 mg, amiloride 2.5 mg) in high-risk hypertensive patients. A total of 201 patients with a total calcium score of ≥10 at the onset of study who underwent an annual double-helix computerized tomography for 3 years were analyzed for efficacy. Inhibition of coronary calcium progression was significant in the nifedipine versus the co-amilozide group during the first year (3.18% versus 27%, respectively, P =0.02), not significant during the second year (28.5% versus 47%, respectively, P =0.14), and significant during the third year (40% versus 78%, respectively, P =0.02). The results point to a slower progression of coronary calcification in hypertensive patients on nifedipine once daily versus co-amilozide.
Modeling and Characterization of a Linear Piezomotor

This article presents the modeling and characterization of a new class of piezoelectric linear motor. The motor relies in its operation on a set of piezoelectric bimorphs which are sequentially activated to linearly move a drive rod along spring loaded rollers. Emphasis in this article is placed on studying the dynamic behavior of this class of piezoelectric motors, both theoretically and experimentally, in an effort to predict the piezomotor response to various loads and excitation schemes. To this end, a numerical model has been developed to simulate the dynamics of the piezoelectric bimorphs comprising the piezomotor. Friction between the bimorph elements and the drive rod are handled using an appropriate friction model. Experimental testing of the motor is carried out to validate the predictions of the theoretical model.
Bilevel Current Driving Technique for LEDs

The significant improvements recently achieved in LED technology in terms of lifetime, luminous efficacy, power rating, and color property render LED one of the most promising candidates to replace conventional light sources in various residential and industrial applications. The rapid advancement in the device characteristics has simultaneously stimulated interests in developing efficient LED drivers with optimized control circuitries. The two conventional techniques currently employed in most LED drivers, namely the amplitude-mode and pulsewidth modulation (PWM) mode driving techniques, suffer from the disadvantage that high luminous efficacy in the amplitude mode has to be traded for control flexibility in the PWM mode and vice versa . In this paper, a method is proposed to improve the luminous efficacy of conventional PWM-mode driving technique while retaining their control flexibility by introducing a dc-offset component into the PWM current. Two LEDs were used in the experimental verifications. Improvements of 17.6% and 18.1% on average were measured by maintaining a dc offset of 100 and 200 mA, respectively, in the LED current. Further improvement can be achieved by increasing the dc-offset current. The main tradeoff is the reduction of the dynamic range over which the average LED current can be controlled. For a given set of performance criteria, the proposed method offers designers of LED drivers the flexibility of balancing between luminous efficacy and dynamic range for control.
Extracting and Querying a Comprehensive Web Database

Recent research in domain-independent information extraction holds the promise of an automatically-constructed structured database derived from the Web. A query system based on this database would offer the same breadth as a Web search engine, but with much more sophisticated query tools than are common today. Unfortunately, these domain-independent Web extractors are usually not modelindependent; e.g., an extractor that only finds binary relations from text will be blind to relational data found in tables. Because a topic area often has a data model that is a natural fit (e.g., population statistics are usually in tables, while biographical facts about Einstein are embedded in text), even a high-quality domain-independent extractor will miss a substantial amount of data. Our omnivore system attempts to build a comprehensive Web database by running multiple domain-independent extractors in parallel over a Web crawl, then combining their outputs into a single large entity-relationship database. Each item in the database describes a single real-world entity, and can contain information drawn from a number of popular Web data models. The user can correct flaws in the database, and can query it using either a structured query language or a search-like interface. Due to the Web’s sheer size, users cannot be expected to know the result set’s metadata a priori, so omnivore automatically chooses an output model and schema when it renders results. In this paper we outline the omnivore architecture and provide specific details about our current prototype.
How does the context and design of participatory decision making processes affect their outcomes? Evidence from sustainable land management in global drylands

Although the design of participatory processes to manage social-ecological systems needs to be adapted to local contexts, it is unclear which elements of process design might be universal. We use empirical evidence to analyze the extent to which context and process design can enable or impede stakeholder participation and facilitate beneficial environmental and social outcomes. To explore the role of design and minor variations in local context on the outcomes of participatory processes, we interviewed participants and facilitators from 11 case studies in which different process designs were used to select sustainable land management options in Spain and Portugal. We analyzed interview data using quantitative and qualitative approaches. Results showed that although some aspects of local context affected process outcomes, factors associated with process design were more significant. Processes leading to more beneficial environmental and social outcomes included the following: the legitimate representation of stakeholders; professional facilitation including structured methods for aggregating information and balancing power dynamics among participants; and provision of information and decision-making power to all participants. Although processes initiated or facilitated by government bodies led to significantly less trust, information gain, and learning, decisions in these processes were more likely to be accepted and implemented. To further test the role of context in determining the outcomes of participation, we interviewed facilitators from a process that was replicated across 13 dryland study sites around the world, reflecting much greater national variations in context. The similarity of outcomes across these sites suggested that the socio-cultural context in which the process was replicated had little impact on its outcomes, as long as certain design principles were fulfilled. Overall, our findings provide a solid empirical basis for good practice in the design of participatory processes in the management of social-ecological systems.
Oxidative protein folding in eukaryotes: mechanisms and consequences

The endoplasmic reticulum (ER) provides an environment that is highly optimized for oxidative protein folding. Rather than relying on small molecule oxidants like glutathione, it is now clear that disulfide formation is driven by a protein relay involving Ero1, a novel conserved FADdependent enzyme, and protein disulfide isomerase (PDI); Ero1 is oxidized by molecular oxygen and in turn acts as a specific oxidant of PDI, which then directly oxidizes disulfide bonds in folding proteins. While providing a robust driving force for disulfide formation, the use of molecular oxygen as the terminal electron acceptor can lead to oxidative stress through the production of reactive oxygen species and oxidized glutathione. How Ero1p distinguishes between the many different PDI-related proteins and how the cell minimizes the effects of oxidative damage from Ero1 remain important open questions.
Performance evaluation of x-ray differential phase contrast computed tomography (PCT) with respect to medical imaging.

PURPOSE To evaluate the maximum performance gain that can theoretically be achieved with differential phase contrast computed tomography (PCT) compared with absorption-based CT, applied to in vivo medical imaging. METHODS We develop a mathematical framework for analyzing the performance of PCT relative to CT under ideal conditions. We validate our model by interpreting the results of published PCT experiments. Finally, we utilize our framework to evaluate the relative performance of PCT versus CT for in vivo medical imaging of the human body, investigating several clinically relevant material contrasts. RESULTS We show that the performance of PCT relative to CT depends on the ratio of phase contrast and absorption contrast of the examined materials and increases with increasing effective coherence length and increasing spatial resolution. The introduced effective coherence length characterizes an experimental PCT setup; it comprises coherence of the beam as well as properties of the x-ray interferometer. Whole body medical CT will not benefit from phase-contrast imaging, because the higher phase contrast is overcompensated by the low coherence lengths of PCT setups with low-brilliance sources, and by limited spatial resolution. The relative performance of PCT, which is inferior to CT for all examined material contrasts at the resolution level of today's medical CT, can be improved by increasing spatial resolution at the expense of increased patient dose. At the break-even point of equal performance for PCT and CT, a radiation dose at least 1 order of magnitude higher than today is required. Mammographic CT already operates at higher spatial resolution and may benefit from PCT for some applications in terms of reduced patient dose at equal image quality. CONCLUSIONS Phase-contrast imaging utilizing low-brilliance x-ray sources has limited potential for an application in routine whole body CT. Breast CT, however, may benefit from phase-contrast imaging. These conclusions are due to fundamental arguments and independent of whether technical issues (quality of gratings, etc.) can be solved. PCT will only be suitable for in vivo medical imaging if x-ray sources with much better spatial coherence are routinely available.
Codon catalog usage is a genome strategy modulated for gene expressivity

The nucleic acid sequence bank now contains 161 mRNAs, 43 new genes are added. One sequence, that of B. mori fibroin, is dropped due to uncertainty on the starting point for translation. Frequencies of all codons are given for each gene added and for each genome type in the total bank. A new series of correspondence analyses on codon use is presented, substantiating the genome hypothesis. Internal regulation of mRNA expression by different third base choices between quartet and duet codons is proposed for bacterial genes.
The Evolution of Modern Eukaryotic Phytoplankton

The community structure and ecological function of contemporary marine ecosystems are critically dependent on eukaryotic phytoplankton. Although numerically inferior to cyanobacteria, these organisms are responsible for the majority of the flux of organic matter to higher trophic levels and the ocean interior. Photosynthetic eukaryotes evolved more than 1.5 billion years ago in the Proterozoic oceans. However, it was not until the Mesozoic Era (251 to 65 million years ago) that the three principal phytoplankton clades that would come to dominate the modern seas rose to ecological prominence. In contrast to their pioneering predecessors, the dinoflagellates, coccolithophores, and diatoms all contain plastids derived from an ancestral red alga by secondary symbiosis. Here we examine the geological, geochemical, and biological processes that contributed to the rise of these three, distantly related, phytoplankton groups.
Tumor-Associated Macrophages as Major Players in the Tumor Microenvironment

During tumor progression, circulating monocytes and macrophages are actively recruited into tumors where they alter the tumor microenvironment to accelerate tumor progression. Macrophages shift their functional phenotypes in response to various microenvironmental signals generated from tumor and stromal cells. Based on their function, macrophages are divided broadly into two categories: classical M1 and alternative M2 macrophages. The M1 macrophage is involved in the inflammatory response, pathogen clearance, and antitumor immunity. In contrast, the M2 macrophage influences an anti-inflammatory response, wound healing, and pro-tumorigenic properties. Tumor-associated macrophages (TAMs) closely resemble the M2-polarized macrophages and are critical modulators of the tumor microenvironment. Clinicopathological studies have suggested that TAM accumulation in tumors correlates with a poor clinical outcome. Consistent with that evidence, experimental and animal studies have supported the notion that TAMs can provide a favorable microenvironment to promote tumor development and progression. In this review article, we present an overview of mechanisms responsible for TAM recruitment and highlight the roles of TAMs in the regulation of tumor angiogenesis, invasion, metastasis, immunosuppression, and chemotherapeutic resistance. Finally, we discuss TAM-targeting therapy as a promising novel strategy for an indirect cancer therapy.
The Greater Cincinnati/Northern Kentucky Stroke Study: preliminary first-ever and total incidence rates of stroke among blacks.

BACKGROUND AND PURPOSE The Greater Cincinnati/Northern Kentucky Stroke Study was designed to be the first large, population-based metropolitan study of temporal trends in stroke incidence rates and outcome within a biracial population. METHODS We are identifying all hospitalized and autopsied cases of stroke and transient ischemic attack (TIA) among the 1.3 million inhabitants of a five-county region of Greater Cincinnati/Northern Kentucky for the period 7/1/93-6/30/94. We have already prospectively monitored for out-of-hospital stroke and TIAs for this same time period at 128 screening sites, including a random sample of all primary care physicians and nursing homes in the region. We have already identified all hospitalized and autopsied cases of stroke and TIA among blacks for 1/1/93-6/30/93 and report preliminary incidence rates for this 6-month period. RESULTS The overall incidence rate for all first-ever hospitalized or autopsied stroke (excluding TIAs) among blacks in the Greater Cincinnati region was 288 per 100000 (95% CI, 250 to 325, age- and sex-adjusted to 1990 US population). The overall incidence rate for first-ever and recurrent stroke (excluding TIAs) was 411 per 100000 (95% CI, 366 to 456). By comparison, the overall incidence rate of first-ever stroke among whites in Rochester, Minn, during the period 1985-1989 was 179 per 100000 (95% CI, 164 to 194, age- and-sex adjusted to 1990 US population). The incidence rates among blacks in Greater Cincinnati were substantially greater than the rates among whites in Rochester, Minn, for all age categories except ages 75 and older, for which the rates were similar. CONCLUSIONS We conservatively estimate that 731100 first-ever or recurrent strokes occurred in the United States during 1996. Studies of first-ever as well as total stroke among biracial and representative populations are critical for understanding temporal trends in the incidence rate and the burden of stroke in the US population.
IMPROVING THE BEHAVIOUR OF SUPERVISOR UNDER BLOCKING

Abstract Sometimes, under control of a supervisor a discrete event system could constitute a conservative solution in this case relaxing the blocking becomes an inevitable fact to improve the performance. Meanwhile the balance between blocking and achievement has to be preserved. So the strings that drive the system to blocking and also the strings causing achievement have to be investigated in a numerical manner. For this purpose in this study a new performance measure is introduced. The elements of the performance measure depend on numeric values obtained from strings that correspond to blocking and success so the proposed formulation captures the fundamental trade-off motivated by the classical optimization approach. Then a new algorithm that explores the best result according to this performance measure is introduced.
Flow-insensitive type qualifiers

We describe flow-insensitive type qualifiers, a lightweight, practical mechanism for specifying and checking properties not captured by traditional type systems. We present a framework for adding new, user-specified type qualifiers to programming languages with static type systems, such as C and Java. In our system, programmers add a few type qualifier annotations to their program, and automatic type qualifier inference determines the remaining qualifiers and checks the annotations for consistency. We describe a tool CQual for adding type qualifiers to the C programming language. Our tool CQual includes a visualization component for displaying browsable inference results to the programmer. Finally, we present several experiments using our tool, including inferring const qualifiers, finding security vulnerabilities in several popular C programs, and checking initialization data usage in the Linux kernel. Our results suggest that inference and visualization make type qualifiers lightweight, that type qualifier inference scales to large programs, and that type qualifiers are applicable to a wide variety of problems.