Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of magnetic resonance imaging for acute ischemic stroke.

BACKGROUND Although computed tomography (CT) is still considered to be the gold standard of brain imaging before thrombolysis, new reperfusion strategies in acute ischemic stroke lead to more extensive use of magnetic resonance imaging (MRI). METHODS AND RESULTS Diffusion- (DWI) and perfusion-weighted (PWI) MRI with MRI angiography are considered the most important examinations in diagnosis of acute ischemic stroke before reperfusion therapy. The effort to extend strict therapeutic time window resulted in the PWI/DWI mismatch concept, established to identify the presence of ischemic penumbra. Nevertheless, a lack of standards for methodology and analysis and existence of different alternative interpretations of such mismatch still present significant limitations of its use in routine clinical practice. CONCLUSION MRI allows accurate diagnosis of the infarct lesion, detection of cerebral arterial occlusion or significant stenosis with evaluation of actual collateral flow and may also display certain reversible ischemic changes. However, the main objective for MRI still remains: improvement of non-invasive rapid and accurate identification of brain tissue at risk for infarction, which may be salvaged by safe and effective reperfusion therapy.
400 Gb/s Programmable Packet Parsing on a Single FPGA

Packet parsing is necessary at all points in the modern networking infrastructure, to support packet classification and security functions, as well as for protocol implementation. Increasingly high line rates call for advanced hardware packet processing solutions, while increasing rates of change call for high-level programmability of these solutions. This paper presents an approach for harnessing modern Field Programmable Gate Array (FPGA) devices, which are a natural technology for implementing the necessary high-speed programmable packet processing. The paper introduces PP: a simple high-level language for describing packet parsing algorithms in an implementation-independent manner. It demonstrates that this language can be compiled to give high-speed FPGA-based packet parsers that can be integrated alongside other packet processing components to build network nodes. Compilation involves generating virtual processing architectures tailored to specific packet parsing requirements. Scalability of these architectures allows parsing at line rates from 1 to 400 Gb/s as required in different network contexts. Run-time programmability of these architectures allows dynamic updating of parsing algorithms during operation in the field. Implementation results show that programmable packet parsing of 600 million small packets per second can be supported on a single Xilinx Virtex-7 FPGA device handling a 400 Gb/s line rate.
Substructural logic and partial correctness

We formulate a noncommutative sequent calculus for partial correctness that subsumes propositional Hoare Logic. Partial correctness assertions are represented by intuitionistic linear implication. We prove soundness and completeness over relational and trace models. As a corollary, we obtain a complete sequent calculus for inclusion and equivalence of regular expressions.
The herpes simplex virus UL37 protein is phosphorylated in infected cells

The herpes simplex virus type 1 (HSV-1) UL37 open reading frame encodes a 120-kDa late (gamma 1), nonstructural protein in infected cells. Recent studies in our laboratory have demonstrated that the UL37 protein interacts in the cytoplasm of infected cells with ICP8, the major HSV-1 DNA-binding protein. As a result of this interaction, the UL37 protein is transported to the nucleus and can be coeluted with ICP8 from single-stranded DNA columns. Pulse-labeling and pulse-chase studies of HSV-1-infected cells with [35S]methionine and 32Pi demonstrated that UL37 was a phosphoprotein which did not have a detectable rate of turnover. The protein was phosphorylated soon after translation and remained phosphorylated throughout the viral replicative cycle. UL37 protein expressed from a vaccinia virus recombinant was also phosphorylated during infection, suggesting that the UL37 protein was phosphorylated by a cellular kinase and that interaction with the ICP8 protein was not a prerequisite for UL37 phosphorylation.
Analyzing social media marketing in the high-end fashion industry using Named Entity Recognition

We study the marketing strategies of high-end fashion brands in social media. In particular, we focus on the informational content of brands' posts in Instagram. Using Named Entity Recognition (NER) in Natural Language Processing (NLP), we develop a novel procedure to classify posts according to their information content. In addition, we apply NER to department store listings and expert runway reviews to obtain measures of brand leadership and brand similarity. Regression analyses show that, while follower brands respond to brand similarity and competitive pressure by relying on informational posts, the informational content of leaders presents a U-shaped relation with brand similarity. We interpret this finding using two theories from the marketing literature: the tradeoff between new and existing customers, and marketing life cycle of industries.
Tree-like counterexamples in model checking

Counter examples for specification violations provide engineers with important debugging information. Although counterexamples are considered one of the main advantages of model checking, state-of the art model checkers are restricted to relatively simple counterexamples, and surprisingly little research effort has been put into counterexamples. In this paper, we introduce a new general framework for counterexamples. The paper has three main contributions: (i) We determine the general form of ACTL counterexamples. To this end, we investigate the notion of counterexample and show that a large class of temporal logics beyond ACTL admits counterexamples with a simple tree-like transition relation. We show that the existence of tree-like counterexamples is related to a universal fragment of extended branching time logic based on w-regular temporal operators. (ii) We present new symbolic algorithms to generate tree-like counterexamples for ACTL specifications. (iii) Based on tree-like counterexamples we extend the abstraction refinement methodology developed recently by Clarke et al. (CAV'2000) to full ACTL. This demonstrates the conceptual simplicity and elegance of tree-like counterexamples.
Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis

Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810–11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.
Tags and Dependencies: an Integrated View of Document Annotation

Metadata provided by annotations are an essential prerequisite for the realization of the semantic web. The manifold of metadata uses on the other hand also implies an abundance of different annotation types and formats, each requiring a different semantic treatment of the data. For semantically rich documents this results in a hybrid mixture of metadata about one and the same document. Further metadata diversity arises, if more than one author contributes to the annotation as it is typical for the now popular social tagging systems. Documents however, despite this heterogeneity show common structural properties that can be classified as logical, conceptual, and referential. There are intrinsic dependencies within and across those structures that have to be made explicit. We argue that the dependency structure as an explicit annotation is essential for any semantically rich document in order to be better understandable not only for man but also for machine.
Decision-making framework for refactoring

Refactoring has been defined as improving code quality without affecting its functionality. When refactoring is overlooked in daily development, the likelihood of larger refactorings increases with time. Disadvantages of larger refactorings include that they disrupt the daily work, require additional planning effort, and often they need to be justified to stakeholders. In this paper, we investigate with interviews how professionals make refactoring decisions. As a result, we present a framework for decision making for larger refactoring operations describing the key stages in a refactoring workflow. Furthermore, one actual industry case of refactoring decision making is presented in detail.
Experimental Analysis of Power Estimation Models of CMOS VLSI Circuits

In this paper, we discuss on accuracy of power dissipation models for CMOS VLSI circuits. Some researchers have proposed several e cient power estimation methods for CMOS circuits [1][2][3][4]. However, we do not know how accurate they are because we have not established a method to compare the estimated results of power consumption with power consumption of actual VLSI chips. To evaluate the accuracy of several kinds of power dissipation models in chip-level, block-level and gate-level etc., we have been (i) Measuring power consumption of actual microprocessors, (ii) Estimating power consumption with several kinds of power dissipation models, and (iii) Comparing (i) with (ii). The experimental results show as follows: (1) Power estimation at gate level is accurate enough. (2) Estimating power of a clock tree independently makes estimation more accurate. (3) Area of each functional block is a good approximation of load capacitance of the block. key words: CMOS VLSI circuits, low power design, power estimation
Robust vision-based driver state classification in the dazzling avoidance system

This paper presents a robust approach to classify the driver state in a novel advanced driver assistance system named ShadeVision, which aims to improve the driving safety and comfort by avoiding the dazzling effect. Different from the existing algorithms for driver state classification, our proposed method is capable of identifying the "dazzled state" of the driver, which can function as a supplement for the regular dazzling detection algorithm, particularly at dawn and dusk. To this end, the driver's head is captured by a high-speed camera mounted in the vehicle. After segmenting the eye region, we design a new feature vector of the eye to classify the eye state in a single frame. Afterwards, the driver states are classified based on the eye states in successive frames. Finally, on-road tests are carried out to verify the effectiveness of the proposed algorithm.
Dewar valence isomers, the third type of environmentally relevant DNA photoproducts induced by solar radiation

UV-induced DNA damage is the main initiating event in solar carcinogenesis. UV radiation is known to induce pyrimidine dimers in DNA, including cyclobutane dimers and (6-4) photoproducts which have been extensively studied. In contrast, much less attention has been paid to Dewar valence isomers, the photoisomerisation product of (6-4) photoproducts. Yet, the available data show that Dewar isomers can be produced by exposure to sunlight and may lead to mutations. Dewars are thus environmentally and biologically relevant. The present review summarizes currently available information on the formation, mutagenic properties and repair of this class of UV-induced DNA damage.
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly

Significance The expression level of a gene is a leading determinant of its rate of protein sequence evolution, but the underlying mechanisms are unclear. We show that as the mRNA concentration increases, natural selection for mRNA folding intensifies, resulting in larger fractions of mutations deleterious to mRNA folding and lower rates of protein evolution. Counterintuitively, selection for mRNA folding also impacts the nonsynonymous-to-synonymous nucleotide substitution rate ratio, requiring a revision of the current interpretation of this ratio as a measure of protein-level selection. These findings demonstrate a prominent role of selection at the mRNA level in molecular evolution. The cause of the tremendous among-protein variation in the rate of sequence evolution is a central subject of molecular evolution. Expression level has been identified as a leading determinant of this variation among genes encoded in the same genome, but the underlying mechanisms are not fully understood. We here propose and demonstrate that a requirement for stronger folding of more abundant mRNAs results in slower evolution of more highly expressed genes and proteins. Specifically, we show that: (i) the higher the expression level of a gene, the greater the selective pressure for its mRNA to fold; (ii) random mutations are more likely to decrease mRNA folding when occurring in highly expressed genes than in lowly expressed genes; and (iii) amino acid substitution rate is negatively correlated with mRNA folding strength, with or without the control of expression level. Furthermore, synonymous (dS) and nonsynonymous (dN) nucleotide substitution rates are both negatively correlated with mRNA folding strength. However, counterintuitively, dS and dN are differentially constrained by selection for mRNA folding, resulting in a significant correlation between mRNA folding strength and dN/dS, even when gene expression level is controlled. The direction and magnitude of this correlation is determined primarily by the G+C frequency at third codon positions. Together, these findings explain why highly expressed genes evolve slowly, demonstrate a major role of natural selection at the mRNA level in constraining protein evolution, and reveal a previously unrecognized and unexpected form of nonprotein-level selection that impacts dN/dS.
Revision of Failed Midfoot Arthrodesis in Charcot Arthropathy

particularly in patients for whom instability and the potential for nonunion are increased (e.g., in those with neuropathy. There are current fixation options such as custom anatomically designed midfoot plates which provide stability as well as locking and compression capacity (Maxlock, Orthohelix, Akron OH, and DePuy, Warsaw IN). A novel alternative for fixation is using an intramedullary system (Tars-X, Extremity Medical, Parsipanny, NJ)
An integrated design of optimization and physical dynamics for energy efficient buildings: A passivity approach

In this paper, we address energy management for heating, ventilation, and air-conditioning (HVAC) systems in buildings, and present a novel combined optimization and control approach. We first formulate a thermal dynamics and an associated optimization problem. An optimization dynamics is then designed based on a standard primal-dual algorithm, and its strict passivity is proved. We then design a local controller and prove that the physical dynamics with the controller is ensured to be passivity-short. Based on these passivity results, we interconnect the optimization and physical dynamics, and prove convergence of the room temperatures to the optimal ones defined for unmeasurable disturbances. Finally, we demonstrate the present algorithms through simulation.
Non-AIDS-defining deaths and immunodeficiency in the era of combination antiretroviral therapy

Objective:To assess whether immunodeficiency is associated with the most frequent non-AIDS-defining causes of death in the era of combination antiretroviral therapy (cART). Design:Observational multicentre cohorts. Methods:Twenty-three cohorts of adults with estimated dates of human immunodeficiency virus (HIV) seroconversion were considered. Patients were seroconverters followed within the cART era. Measurements were latest CD4, nadir CD4 and time spent with CD4 cell count less than 350 cells/μl. Outcomes were specific causes of death using a standardized classification. Results:Among 9858 patients (71 230 person-years follow-up), 597 died, 333 (55.7%) from non-AIDS-defining causes. Non-AIDS-defining infection, liver disease, non-AIDS-defining malignancy and cardiovascular disease accounted for 53% of non-AIDS deaths. For each 100 cells/μl increment in the latest CD4 cell count, we found a 64% (95% confidence interval 58–69%) reduction in risk of death from AIDS-defining causes and significant reductions in death from non-AIDS infections (32, 18–44%), end-stage liver disease (33, 18–46%) and non-AIDS malignancies (34, 21–45%). Non-AIDS-defining causes of death were also associated with nadir CD4 while being cART-naive or duration of exposure to immunosuppression. No relationship between risk of death from cardiovascular disease and CD4 cell count was found though there was a raised risk associated with elevated HIV RNA. Conclusion:In the cART era, the most frequent non-AIDS-defining causes of death are associated with immunodeficiency, only cardiovascular disease was associated with high viral replication. Avoiding profound and mild immunodeficiency, through earlier initiation of cART, may impact on morbidity and mortality of HIV-infected patients.
Markov-based failure prediction for human motion analysis

This paper presents a new method of detecting and predicting motion tracking failures with applications in human motion and gait analysis. We define a tracking failure as an event and describe its temporal characteristics using a hidden Markov model (HMM). This stochastic model is trained using previous examples of tracking failures. We derive vector observations for the HMM using the noise covariance matrices characterizing a tracked, 3D structural model of the human body. We show a causal relationship between the conditional output probability of the HMM, as transformed using a logarithmic mapping function, and impending tracking failures. Results are illustrated on several multi-view sequences of complex human motion.
Inability to get up after falling, subsequent time on floor, and summoning help: prospective cohort study in people over 90

Objectives To describe the incidence and extent of lying on the floor for a long time after being unable to get up from a fall among people aged over 90; to explore their use of call alarm systems in these circumstances. Design 1 year follow-up of participants in a prospective cohort study of ageing, using fall calendars, phone calls, and visits. Setting Participants’ usual place of residence (own homes or care homes), mostly in Cambridge. Participants 90 women and 20 men aged over 90 (n=110), surviving participants of the Cambridge City over-75s Cohort, a population based sample. Main outcome measures Inability to get up without help, lying on floor for a long time after falling, associated factors; availability and use of call alarm systems; participants’ views on using call alarms to summon help if needed after falling. Results In one year’s intensive follow-up, 54% (144/265) of fall reports described the participant as being found on the floor and 82% (217/265) of falls occurred when the person was alone. Of the 60% who fell, 80% (53/66) were unable to get up after at least one fall and 30% (20/66) had lain on the floor for an hour or more. Difficulty in getting up was consistently associated with age, reported mobility, and severe cognitive impairment. Cognition was the only characteristic that predicted lying on the floor for a long time. Lying on the floor for a long time was strongly associated with serious injuries, admission to hospital, and subsequent moves into long term care. Call alarms were widely available but were not used in most cases of falls that led to lying on the floor for a long time. Comments from older people and carers showed the complexity of issues around the use of call alarms, including perceptions of irrelevance, concerns about independence, and practical difficulties. Conclusions Lying on the floor for a long time after falling is more common among the “oldest old” than previously thought and is associated with serious consequences. Factors indicating higher risk and comments from participants suggest practical implications. People need training in strategies to get up from the floor. Work is needed on access and activation issues for design of call alarms and information for their effective use. Care providers need better understanding of the perceptions of older people to provide acceptable support services.
The quest for pluripotency: a comparative analysis across mammalian species.

Pluripotency is the developmental potential of a cell to give rise to all the cells in the three embryonic germ layers, including germline cells. Pluripotent Stem cells (PSCs) can be embryonic, germ cell or somatic cell in origin and can adopt alternative states of pluripotency: naïve or primed. Although several reports have described the differentiation of PSCs to extra-embryonic lineages, such as primitive endoderm and trophectoderm, this is still debated among scientists in the field. In this review, we integrate the recent findings on pluripotency among mammals, alternative states of pluripotency, signaling pathways associated with maintaining pluripotency and the nature of PSCs derived from various mammals. PSCs from humans and mouse have been the most extensively studied. In other mammalian species, more research is required for understanding the optimum in vitro conditions required for either achieving pluripotency or preservation of distinct pluripotent states. A comparative high-throughput analysis of PSCs of genes expressed in naïve or primed states of humans, non-human primates (NHP) and rodents, based on publicly available data-sets revealed the probable prominence of seven signaling pathways common among these species, irrespective of the states of pluripotency. We conclude by highlighting some of the unresolved questions and future directions of research on pluripotency in mammals.