Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical categorization of human histological images

Histology is the science of understanding the structure of animals and plants, and studying the functional implications of biological structures. In this paper, we propose a statistical modeling approach to human histological image categorization. Texture features of the images are characterized by localized Gabor filters. The probabilistic distribution of the texture patterns from each category is approximated by a finite Gaussian mixture model. Expectation maximization (EM) procedure and minimum message length (MML) principle are used to perform density estimation and model selection, respectively. Component-wise EM and weak component annihilation are applied to avoid the drawbacks of the standard EM. Experimental validation is provided based on images from different organs and parts of the body.
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results

Cell division involves a complex series of events orchestrated by thousands of molecules. To study this process, researchers have employed mRNA expression profiling of synchronously growing cell cultures progressing through the cell cycle. These experiments, which have been carried out in several organisms, are not easy to access, combine and evaluate. Complicating factors include variation in interdivision time between experiments and differences in relative duration of each cell-cycle phase across organisms. To address these problems, we created Cyclebase, an online resource of cell-cycle-related experiments. This database provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from different experiments are normalized to a common timescale and are complimented with key cell-cycle information and derived analysis results. In Cyclebase version 2.0, we have updated the entire database to reflect changes to genome annotations, included information on cyclin-dependent kinase (CDK) substrates, predicted degradation signals and loss-of-function phenotypes from genome-wide screens. The web interface has been improved and provides a single, gene-centric graph summarizing the available cell-cycle experiments. Finally, key information and links to orthologous and paralogous genes are now included to further facilitate comparison of cell-cycle regulation across species. Cyclebase version 2.0 is available at http://www.cyclebase. org.
Development of endotoxin tolerance in humans in vivo

Objective: Endotoxin (lipopolysaccharide [LPS]) tolerance is characterized by a reduced responsiveness to a subsequent LPS challenge. In animal and human in vitro experiments, LPS tolerance is associated with an attenuated response of proinflammatory cytokines and an enhanced production of anti-inflammatory cytokines. It is unclear if this mechanism accounts for the development of LPS tolerance in humans in vivo. Design: Clinical experimental study. Setting: Intensive care research unit. Patients: Fourteen healthy male volunteers. Interventions: Intravenous injections of 2 ng/kg/day Escherichia coli LPS on 5 consecutive days. Measurements and Main Results: Symptom scores, vital signs, leukocyte (elastase) and endothelial cell activation (von Willebrand factor [vWF]), and circulating cytokine levels. On day 1, the symptom score increased to 6.1 ± 3.1, temperature to 37.8 ± 0.4°C, heart rate to 103 ± 6/min (p < 0.0001 for all parameters) compared with 0.3 ± 0.6, 36.2 ± 0.5°C, 79 ± 4/min on day 5, respectively (p < 0.0001 between days 1 and 5). On day 1, elastase, vWF, and all cytokine levels increased significantly (p < 0.001 for all, except transforming growth factor (TGF)-&bgr;, p = 0.02), whereas on day 5, this increase was significantly attenuated (p < 0.001) for elastase (61% ± 6%), vWF (68% ± 5%), tumor necrosis factor (97% ± 3%), interleukin (IL)-6 (88% ± 8%), IL-10 (87% ± 7%), and IL-1ra (93% ± 9% p = 0.018) but not for TGF-&bgr; (5% ± 22% p = 0.22). The tumor necrosis factor-&agr;/IL-10 ratio showed an initial proinflammatory phase, followed by an anti-inflammatory phase on the first day. The proinflammatory phase was attenuated with 95% ± 2%, whereas the reduction of the anti-inflammatory phase, without TGF-&bgr; levels, was 99% ± 1% on day 5 (p = 0.13 between phases). Conclusions: Endotoxin tolerance developed during five consecutive LPS administrations as demonstrated by the attenuated release of proinflammatory cytokines on the fifth day and was associated with less leukocyte and endothelial activation. In contrast to animal and human in vitro data, the attenuated response was not limited to the proinflammatory response, as a similar reduction in the anti-inflammatory cytokines was observed, with the exception of TGF-&bgr;.
Nephrology Referral and Outcomes in Critically Ill Acute Kidney Injury Patients

Background Delayed nephrology consultation (NC) seems to be associated with worse prognosis in critically ill acute kidney injury (AKI) patients. Design, Setting, Participants, & Measurements The aims of this study were to analyze factors related with timing of NC and its relation with AKI patients' outcome in intensive care units of a tertiary hospital. AKI was defined as an increase ≥50% in baseline serum creatinine (SCr). Early NC and delayed NC were defined as NC performed before and two days after AKI diagnosis day. Multivariable logistic regression and propensity scores (PS) were used to adjust for confounding and selection biases. Hospital mortality and dialysis dependence on hospital discharge were the primary outcomes. Results A total of 366 AKI patients were analyzed and NCs were carried out in 53.6% of the patients. Hospital mortality was 67.8% and dialysis required in 31.4% patients (115/366). Delayed NCs (34%) occurred two days after AKI diagnosis day. This group presented higher mortality (OR: 4.04/CI: 1.60–10.17) and increased dialysis dependence (OR: 3.00/CI: 1.43–6.29) on hospital discharge. Four variables were retained in the PS model for delayed NC: diuresis (1000 ml/24 h - OR: 1.92/CI: 1.27–2.90), SCr (OR: 0.49/CI: 0.32–0.75), surgical AKI (OR: 3.67/CI: 1.65–8.15), and mechanical ventilation (OR: 2.82/CI: 1.06–7.44). After correction by PS, delayed NC was still associated with higher mortality (OR: 3.39/CI: 1.24–9.29) and increased dialysis dependence (OR: 3.25/CI: 1.41–7.51). Delayed NC was associated with increased mortality either in dialyzed patients (OR: 1.54/CI: 1.35–1.78) or non-dialyzed patients (OR: 2.89/CI: 1.00–8.35). Conclusion Delayed NC was associated with higher mortality and increased dialysis dependence rates in critically ill AKI patients at hospital discharge. Further studies are necessary to ascertain whether this effect is due to delayed nephrology intervention or residual confounding factors.
Fitting Dynamical Models to Observations of Globular Clusters

The basic ingredients of models for the internal dynamics of globular clusters are reviewed, with an emphasis on the description of equilibrium configurations. The development of progressive complexity in the models is traced, concentrating on the inclusion of velocity anisotropy, rotation, and integrals of motion other than energy. Applications to observations of extragalactic globulars and to combined radial-velocity and proper-motion datasets are discussed.
The Central Paratethys palaeoceanography: A water circulation model based on microfossil proxies, climate, and changes of depositional environment

A comprehensive “model” of the semi-closed Central Paratethys Sea history was proposed for the entire time span of 25 Ma. Publications and datasets of the last decades were compiled and reviewed in the light of the Western Carpathian basins record, reflecting its changing palaeogeography, palaeoenvironment, and water circulation regimes. Moreover, a set of modified palinspastic palaeogeographic maps were reconstructed taking into account the enormous changes in depositional systems and sedimentary facies, reflecting the tectonic events from the Oligocene to Miocene. The study discusses possible gateways/straits assuming two way circulations, where the surface and deep water can be exchanged between the Mediterranean, Central Paratethys, and the Eastern Paratethys. It is suggested, that a good correlation between the regional Central Paratethys and the standard Mediterranean zonations based on planktic organisms can be achieved only in sequences deposited during anti-estuarine circulation regimes. Correlation of sequences deposited during the estuarine circulation of water masses becomes problematic, making hard to define above all the Early/Middle Miocene boundary. To solve problems of the regional biostratigraphy, and the definition of correlation levels between the Mediterranean, Central Paratethys, and Eastern Paratethys, the existing and new Sr-isotope dating was used as well. Dating of specific sediments of low oxic conditions or evaporitic events was also used as time horizons for the Central Paratethys.
Comparative analysis of energy-based criteria for dynamics-based robot motion optimization

We perform a comparative analysis of energy-based performance criteria for the dynamics-based optimization of robot trajectories. The performance criteria considered include minimum torque, electrical power loss, approximation to mechanical work, and energy loss due to friction. Our dynamics model takes into account rotor inertias and gearing, and also considers robots subject to a range of motion types and payloads. High fidelity numerical simulation experiments are performed and compared for the various performance criteria. Our analysis and findings refute some commonly held assumptions about dynamics-based robot motion optimization, and offer practical insights on how to effectively leverage robot dynamic models and optimization into industrial robot trajectory generation.
A novel signal processing method for MIMO radar based on channel estimation

Multiple Input Multiple Output (MIMO) radar is a new radar technique. It has many advantages over conventional phased radar in many ways such as anti-intercept of radar signal, low velocity target detection, and resolution. The signal transmit matrix of MIMO radar has much information such as target angle. In this paper, we analyze the signal model for MIMO radar. And then we present a new method to estimate the target angle from the matrix. At last, we show the efficiency by some simulations.
Weighted Sum Rate Maximization for Downlink OFDMA With Subcarrier-Pair Based Opportunistic DF Relaying

This paper addresses a weighted sum rate (WSR) maximization problem for downlink OFDMA aided by a decode-and-forward (DF) relay under a total power constraint. A novel subcarrier-pair based opportunistic DF relaying protocol is proposed. Specifically, user message bits are transmitted in two time slots. A subcarrier in the first slot can be paired with a subcarrier in the second slot for the DF relay-aided transmission to a user. In particular, the source and the relay can transmit simultaneously to implement beamforming at the subcarrier in the second slot. Each unpaired subcarrier in either the first or second slot is used for the source's direct transmission to a user. A benchmark protocol, same as the proposed one except that the transmit beamforming is not used for the relay-aided transmission, is also considered. For each protocol, a polynomial-complexity algorithm is developed to find at least an approximately optimum resource allocation (RA), by using continuous relaxation, the dual method, and Hungarian algorithm. Instrumental to the algorithm design is an elegant definition of optimization variables, motivated by the idea of regarding the unpaired subcarriers as virtual subcarrier pairs in the direct transmission mode. The effectiveness of the RA algorithm and the impact of relay position and total power on the protocols' performance are illustrated by numerical experiments. It is shown that for each protocol, it is more likely to pair subcarriers for relay-aided transmission when the total power is low and the relay lies in the middle between the source and user region. The proposed protocol always leads to a maximum WSR equal to or greater than that for the benchmark one, and the performance gain of using the proposed one is significant especially when the relay is in close proximity to the source and the total power is low. Theoretical analysis is presented to interpret these observations.
Class and Compassion: Socioeconomic Factors Predict Responses to Suffering Social Class and Responses to Threat

Previous research indicates that lower-class individuals experience elevated negative emotions as compared with their upper-class counterparts. We examine how the environments of lower-class individuals can also promote greater compassionate responding—that is, concern for the suffering or well-being of others. In the present research, we investigate class-based differences in dispositional compassion and its activation in situations wherein others are suffering. Across studies, relative to their upper-class counterparts, lower-class individuals reported elevated dispositional compassion (Study 1), as well as greater self-reported compassion during a compassion-inducing video (Study 2) and for another person during a social interaction (Study 3). Lower-class individuals also exhibited heart rate deceleration—a physiological response associated with orienting to the social environment and engaging with others— during the compassion-inducing video (Study 2). We discuss a potential mechanism of class-based influences on compassion, whereby lower-class individuals' are more attuned to others' distress, relative to their upper-class counterparts. Lower social class is defined by reduced material resources (e.g., lower income, educational attainment) and subordinate social rank visa `-vis others. Lacking resources and rank, lower-class individuals face harsher environments than their upper-class counterparts (Adler et al., 1994; Lareau, 2003) and these environments are theorized to shape emotional experiences. Researchers studying class-based patterns in emotion have almost exclusively concentrated on how lower-class individuals experience more negative emotions, such as anxiety, sadness, and anger, than upper-class individuals (see Gallo & Matthews, 2003 for a review). For example, lower-class individuals prove to be more emotionally reactive to ambiguous and negative social situations likely to report negative life experiences than their upper-class counterparts (Matthews et al., 2000). Given these findings, one might conclude that lower-class environments only promote the experience of negative emotional states, creating emotional vulnerabilities. However, drawing from, we hypothesize that relative to upper-class individuals, the harsher environments that lower-class individuals encounter will also tend to promote greater experiences of compassion, a prosocial emotion associated with approach-related and positively valenced feelings (e. Social class is a form of social hierarchy that arises from the amount of material resources an individual possesses (Oakes & Rossi, 2003), and one's perceived social rank in society relative to others (Kraus, Piff, & Keltner, 2009, 2011). As such, people typically measure the construct with indexes of material resource measures, such as financial wealth, educational attainment, or occupational prestige (Oakes & Rossi, 2003), as well as comparative rank perception measures wherein individuals rank themselves in society relative to others in terms …
Have You Lost the Thread? Discovering Ongoing Conversations in Scattered Dialog Blocks

Finding threads in textual dialogs is emerging as a need to better organize stored knowledge. We capture this need by introducing the novel task of discovering ongoing conversations in scattered dialog blocks. Our aim in this article is twofold. First, we propose a publicly available testbed for the task by solving the insurmountable problem of privacy of Big Personal Data. In fact, we showed that personal dialogs can be surrogated with theatrical plays. Second, we propose a suite of computationally light learning models that can use syntactic and semantic features. With this suite, we showed that models for this challenging task should include features capturing shifts in language use and, possibly, modeling underlying scripts.
A la carte proteomics with an emphasis on gel‐free techniques

Since the introduction of the proteome term somewhat more than a decade ago the field of proteomics witnessed a rapid growth mainly fueled by instrumental analytical improvements. Of particular notice is the advent of a diverse set of gel‐free proteomics techniques. In this review, we discuss several of these gel‐free techniques both for monitoring protein concentration changes and protein modifications, in particular protein phosphorylation, glycosylation, and protein processing. Furthermore, different approaches for (multiplexed) gel‐free proteome analysis are discussed.
Learning Shortest Paths for Word Graphs

The vast amount of information on the Web drives the need for aggregation and summarisation techniques. We study event extraction as a text summarisation task using redundant sentences which is also known as sentence compression. Given a set of sentences describing the same event, we aim at generating a summarisation that is (i) a single sentence, (ii) simply structured and easily understandable, and (iii) minimal in terms of the number of words/tokens. Existing approaches for sentence compression are often based on finding the shortest path in word graphs that is spanned by related input sentences. These approaches, however, deploy manually crafted heuristics for edge weights and lack theoretical justification. In this paper, we cast sentence compression as a structured prediction problem. Edges of the compression graph are represented by features drawn from adjacent nodes so that corresponding weights are learned by a generalised linear model. Decoding is performed in polynomial time by a generalised shortest path algorithm using loss augmented inference. We report on preliminary results on artificial and real world data.
Sleep transistor distribution in row-based MTCMOS designs

The Multi-Threshold CMOS (MTCMOS) technology has become a popular technique for standby power reduction. This technology utilizes high-Vth sleep transistors to reduce sub threshold leakage currents during the standby mode of CMOS VLSI Circuits. The performance of MTCMOS circuits strongly depends on the size of the sleep transistors and the parasitics on the virtual ground network. Given a placed net list of a row-based MTCMOS design and the number of sleep transistor cells on each standard cell row, this paper introduces an optimal algorithm for linearly placing the allocated sleep transistors on each standard cell row so as to minimize the performance degradation of the MTCMOS circuit, which is in part due to unwanted voltage drops on its virtual ground network. Experimental results show that, compared to existing methods of placing the sleep transistors on cell rows, the proposed technique results in up to 11% reduction in the critical path delay of the circuit.
Designing steep, sharp patterns on uniformly ion-bombarded surfaces

Significance Large-amplitude, steep structures are of interest for a variety of applications from micromechanics to data storage. Many such structures must be manufactured via effort-intensive direct engraving. Here, we present and experimentally test a method for designing simple structures that will evolve into a desired steep structure under uniform ion irradiation. This process is based on the mathematics of shock waves, a theory originally developed to understand fluids and gases. We show that the dynamics of uniformly bombarded surfaces are controlled by special, so-called undercompressive shocks, which manifest as steep parts of the surface that arise spontaneously and move predictably. Their evolution equation requires only one parameter that is easily measured. The proposed process is scalable with promise for high-throughput manufacturing. We propose and experimentally test a method to fabricate patterns of steep, sharp features on surfaces, by exploiting the nonlinear dynamics of uniformly ion-bombarded surfaces. We show via theory, simulation, and experiment that the steepest parts of the surface evolve as one-dimensional curves that move in the normal direction at constant velocity. The curves are a special solution to the nonlinear equations that arises spontaneously whenever the initial patterning on the surface contains slopes larger than a critical value; mathematically they are traveling waves (shocks) that have the special property of being undercompressive. We derive the evolution equation for the curves by considering long-wavelength perturbations to the one-dimensional traveling wave, using the unusual boundary conditions required for an undercompressive shock, and we show this equation accurately describes the evolution of shapes on surfaces, both in simulations and in experiments. Because evolving a collection of one-dimensional curves is fast, this equation gives a computationally efficient and intuitive method for solving the inverse problem of finding the initial surface so the evolution leads to a desired target pattern. We illustrate this method by solving for the initial surface that will produce a lattice of diamonds connected by steep, sharp ridges, and we experimentally demonstrate the evolution of the initial surface into the target pattern.
CS 229 Final Project : Clustering News Feeds with Flock

The rise of blogging and RSS (Really Simple Syndication) have created a more personalized way of reading the news, with a much richer diversity of information and perspectives. Unfortunately, though, the rapid growth of these technologies has created a new problem how to handle the vast amount of information now available. Unfortunately, while RSS aggregators have helped to bring all of the information to one place, they do not solve the problem of filtering through this huge amount of information. This problem tends to get worse as the reader begins to follow more and more blogs, and it is now common for blog readers to spend several hours every day going through all these stories. Many bloggers have discussed this problem; Google’s blog search tool shows 24,808 results for “information overload” .
‘Down-triage’ for children with abnormal vital signs: evaluation of a new triage practice at a paediatric emergency department in Japan

Objective Assessment of abnormal vital signs in triage is a challenge in the paediatric emergency department (PED), since vital signs may reflect anxiety, fever or pain rather than the clinical deterioration of the child. We aimed to evaluate the efficacy of subjective ‘down-triage’ (change of the initially determined acuity levels) of Japanese Triage and Acuity Scale (JTAS). Methods This is a retrospective cohort study of patients in PED up to 15 years of age at a tertiary paediatric medical centre in Japan during a 1-year period. At the end of every JTAS triage process, PED nurses were allowed to ‘down-triage’ acuity levels of well-appearing patients with abnormal HR or RR, which were presumably attributable to fever, crying or being upset. We compared predictive performance of the triage system before and after ‘down-triage’ using admission rate as the primary outcome. Results Among 37 961 PED visits during the study period, we analysed 37 219 records. A total of 17 089 patients (45.9%) were ‘down-triaged’ after their initial triage allocation upon arrival. Admission rates after ‘down-triage’ (83%, 33%, 7%, 1% and 3% for levels 1–5, respectively), compared with those of unmodified initial level (16%, 11%, 6%, 2% and 6% for levels 1–5, respectively), had a better apparent relevance with the anticipated admission rates of Canadian Triage and Acuity Scale. Conclusions Modification of JTAS through ‘down-triage’ by experienced staff improves prediction of disposition in a PED. Further research is needed to determine an objective protocol for ‘down-triage’ to ensure safe practice in a PED.