Miracle-dz/UniFAR-FTUs huggingface dataset:
' s response to reviews Title : Efficacy and Safety of Active Negative Pressure Peritoneal Therapy for Reducing the Systemic Inflammatory Response After Damage Control Laparotomy ( The Intraperitoneal Vacuum Trial ) : Study Protocol for a Randomized Controlled Trial

Derek J. Roberts (robertdj@ucalgary.ca) Craig N. Jenne (cnjenne@ucalgary.ca) Chad G. Ball (ball.chad@gmail.com) Corina Tiruta (corina.tiruta@albertahealthservices.ca) Caroline Leger (cleger@ucalgary.ca) Zhengwen Xiao (jxiao@ualberta.ca) Peter D. Faris (peter.faris@albertahealthservices.ca) Paul B. McBeth (pmcbeth@gmail.com) Christopher J. Doig (cdoig@ucalgary.ca) Christine R. Skinner (christine.skinner@albertahealthservices.ca) Stacy G. Ruddell (stacy.ruddell@albertahealthservices.ca) Paul Kubes (pkubes@ucalgary.ca) Andrew W. Kirkpatrick (andrew.kirkpatrick@albertahealthservices.ca)
Molecular Virology of Hepatitis E Virus

Abstract Hepatitis E virus (HEV) is the causative agent of hepatitis E. It is a nonenveloped virus with a ∼7.2 kilobases positive-stranded RNA genome. The molecular virology of HEV is getting better understood with the development of replicons and in vitro infection systems, and the discovery of related viruses that infect animal species other than humans. This review focuses on the virology of HEV and updates the current knowledge on the HEV genome and its constituent proteins—ORF1, ORF2, and ORF3, and the viral life cycle.
A Subjective Measure of Complexity

This article presents a quantitative measure of complexity, subjectively understood as a property of the relationship between a system and its observer instead of as a property of the system itself. Within this framework, complexity is quantified by assuming to know the mental categories and the mental model by which a system is represented in the mind of its observer. It is argued that this subjectivist concept of complexity is not in contrast with objective measures of complexity introduced in particular domains, but generalizes complexity to domains where no objective measure is feasible. An extensive numerical example is presented and thoroughly discussed.
Mining 911 Calls in New York City: Temporal Patterns, Detection, and Forecasting

The New York Police Department (NYPD) is tasked with responding to a wide range of incidents that are reported through the city’s 911 emergency hotline. Currently, response resources are distributed within police precincts on the basis of high-level summary statistics and expert reasoning. In this paper, we describe our first steps towards a better understanding of 911 call activity: temporal behavioral clustering, predictive models of call activity, and anomalous event detection. In practice, the proposed techniques provide decision makers granular information on resource allocation needs across precincts and are important components of an overall data-driven resource allocation policy.
Cocaine exposure thoughout adolescence: a hormonal, neurochemical and behavioural study in the rat.

Throughout adolescence, the neurobiological systems are still undergoing important development rearrangements, associated to continuous plastic events that result from an integrated process of overproduction and elimination of synapses, evolution of the neurotransmitter systems and progressive myelination. Hormonal levels are also changed dramatically during this period as a result of the onset of puberty. Concomitant to these changes in the brain and hormonal status, significant transitions occur in cognitive, psychological and social competences. At this time, environmental factors may have a strong impact on the unique neurobiological and psycho-physiological profile of adolescents. Epidemiological data indicate that experiences with drugs of abuse and the onset of addictive disorders are primarily concentrated in the adolescence and early adulthood. However, studies on the effects of drugs of abuse, have primarily been conducted in adult animal models and little is known regarding the effects that these drugs on the adolescent. The objective of the present study was to contribute to further characterize the effects of exposure to drugs of abuse at this key developing time, using an animal model of exposure to cocaine. Experimental protocols were developed to assess short and long-term neurochemical, hormonal and behavioural effects of chronic cocaine exposure, throughout adolescence, in a rat model. Male and female Wistar rats were daily injected intraperitoneally with 3 doses of 15 mg/kg per body weight of cocaine hydrochloride, in 0.9% NaCl solution, from postnatal day (PND) 35 to PND 50. Controls were given isovolumetric 0.9% NaCl solution following the same experimental protocol. The anxiety-like behaviour was evaluated using the elevated plus maze test (EPM) in male rats, 2, 5 and 10 days after cocaine withdrawal, and in female rats, 2 days after withdrawal. The depressive-like behaviour was evaluated using the forced swim test (FST) both in male and female rats, 3 days after cocaine withdrawal. The aggressive behaviour was evaluated in male rats, 10 days after withdrawal, using the resident-intruder paradigm. The levels of neurotransmitters were analysed after each behavioural test and at 30 minutes, 1, 5 and 10 days after the last administration of cocaine, through measuring levels of dopamine (DA), serotonin (5-HT) and its metabolites (3,4-dihydroxyphenylacetic acid, DOPAC; homovanilic acid, HVA; 5hydroxyindoleacetic acid, 5-HIAA), by high performance liquid chromatography with electrochemical detection (HPLC-EC), in the ventral mesencephalon (SN-VTA), the dorsal raphe nucleus, the nucleus accumbens (Nac), the dorsal striatum, the prefrontal cortex, the amygdala, the hippocampus, the hypothalamus and the cerebellum. The plasma levels of adrenocorticotropic hormone (ACTH), corticosterone, testosterone and
Proprioceptive discharges from stretch‐receptors in the knee‐joint of the cat

The capsules of mammalian synovial joints are known to contain a variety of sense-organs (for references see Samuel, 1948). Little is known, however, about the precise function of any of these sense-organs. This is rather surprising, in view of the importance of the joints in health, and in view of the prevalence of diseases of the joints which are both crippling and painful. The appreciation ofthe relative positions of different parts ofthe body is exceedingly precise in man, even without the help of the eyes. For example, if the eyes are closed and a small object is put down with one hand it is possible, still with the eyes closed, to pick the object up again, with either hand. Presumably the position of the hand is deduced from an assessment of the angles of the various joints. This implies that there must be available very accurate information about the relative positions of the bones forming each joint. Stopford (1921) concluded, from a study of human peripheral-nerve lesions, that, although information about movements of the fingers can be derived from endings in muscles and tendons, accurate localization of the fingers depends on afferent impulses from the phalangeal joints. Various physiological responses have from time to time been attributed to impulses in nerves from the joints. Comroe & Schmidt (1943), for example, described effects on respiration produced by passive movements of the limbs. They showed that changes in respiration could still be observed on moving the knee of the dog after cutting the tendons of surrounding muscles, and that the effect was abolished by denervating the knee-joint. The nerve-impulses producing the changes in respiration must therefore arise in the joint. Impulses from sense-organs in the joints have occasionally been observed, but the discharges have never been analysed in detail. Adrian & Umrath (1929) mentioned that they observed impulses in the sciatic nerve of a frog on movement of the knee-joint after all muscular branches of the nerve had been cut. Gardner, who has made an important contribution to our knowledge of
Regulation of apoptosis by modified naringenin derivatives in human colorectal carcinoma RKO cells

Flavonoids are micronutrients that are widely detected in foods of plant origin and have been ascribed pharmacological properties. Several biological functions of flavonoids have been thus far identified, whereas there currently exists a lack of evidence to support the relationship between the structure‐activity relationship and apoptosis‐inducing activity. In an attempt to determine the importance of the OH group or substitution of the 5‐ or 7‐carbon in the diphenylpropane skeleton of flavonoids, we selected 14 different flavonoids with different structures, particularly with regard to the 5‐ or 7‐carbon, and found that naringenin treatment caused a slight decrease in the cell viability of the human colorectal carcinoma RKO cells. Next, in order to characterize the effects of specific substitutions of the 7‐carbon of naringenin on apoptosis‐regulatory activities, and in an attempt to develop anti‐proliferative flavonoid derivatives that would be more effective against colon cancer, we originally synthesized several modified naringenin derivatives (MNDs) including 7‐O‐benzyl naringenin (KUF‐1) and 7‐O‐(m‐metoxybenzyl) naringenin (KUF‐2). Treatment with KUF‐1 or KUF‐2 resulted in significant apoptosis‐inducing effects concomitant with losses in mitochondrial membrane potential, caspase activation, intracellular ROS production, and sustained ERK activation. Our data show that KUF‐1 or KUF‐2 regulate the apoptosis of RKO cells via intracellular ROS production coupled with the concomitant activation of the ERK signaling pathway, thereby implying that hydroxylation or substitution at C7 is critical for the apoptosis‐inducing activity of flavonoids. J. Cell. Biochem. 104: 259–273, 2008. © 2007 Wiley‐Liss, Inc.
Multilingual Knowledge in Aligned Wiktionary and OmegaWiki for Translation Applications

Multilingual lexical-semantic resources play an important role in translation applications. However, multilingual resources with sufficient quality and coverage are rare as the effort of manually constructing such a resource is substantial. In recent years, the emergence of Web 2.0 has opened new possibilities for constructing large-scale lexical-semantic resources. We identified Wiktionary and Omega­Wiki as two important multilingual initiatives where a community of users (“crowd”) collaboratively edits and refines the lexical in­for­ma­tion. They seem especially appropriate in the multilingual domain as users from all languages and cultures can easily contribute. However, despite their advantages such as open access and coverage of multiple languages, these resources have hardly been systematically investigated and utilized until now. Therefore, the goals of our contribution are threefold: (1) We analyze how these resources emerged and characterize their content and structure; (2) We propose an alignment at the word sense level to exploit the complementary in­for­ma­tion contained in both resources for increased coverage; (3) We describe a mapping of the resources to a standardized, unified model (UBY-LMF) thus creating a large freely available multilingual resource designed for easy integration into applications such as machine translation or computer-aided translation en­vi­ron­ments.
Are Cohesive Features Relevant for Text Readability Evaluation?

This paper investigates the effectiveness of 65 cohesion-based variables that are commonly used in the literature as predictive features to assess text readability. We evaluate the efficiency of these variables across narrative and informative texts intended for an audience of L2 French learners. In our experiments, we use a French corpus that has been both manually and automatically annotated as regards to co-reference and anaphoric chains. The efficiency of the 65 variables for readability is analyzed through a correlational analysis and some modelling experiments.
APDB: a web server to evaluate the accuracy of sequence alignments using structural information

UNLABELLED The APDB webserver uses structural information to evaluate the alignment of sequences with known structures. It returns a score correlated to the overall alignment accuracy as well as a local evaluation. Any sequence alignment can be analyzed with APDB provided it includes at least two proteins with known structures. Sequences without a known structure are simply ignored and do not contribute to the scoring procedure. AVAILABILITY APDB is part of the T-Coffee suite of tools for alignment analysis, it is available on www.tcoffee. org. A stand-alone version of the package is also available as a freeware open source from the same address.
The graft-versus-tumor potential of allogeneic cell therapy: an update on donor leukocyte infusions and nonmyeloablative allogeneic stem cell transplantation.

THE BEST, IF NOT ONLY, CURATIVE THERAPY for many patients with hematologic malignancies is allogeneic stem cell transplantation (SCT). It is now generally accepted that successful allogeneic SCT is dependent not only on the intensive conditioning therapy, but also on the anti-leukemic properties of the donor graft. This very important “graft-versus-leukemia” (GVL) effect is independent of the conditioning regimen and it is mediated, at least in part, by mature donor T cells contained in the stem cell graft. In fact, the rationale for some of the earliest trials of bone marrow transplantation were based on the use of allogeneic bone marrow as “adoptive immunotherapy” to destroy residual leukemia cells, and not just as a convenient source for hematopoietic “rescue” after myeloablative therapy (1). Unfortunately, despite many advances in conditioning regimens and supportive care, regimen-related toxicity, relapse, and graft-versus-host disease (GVHD) remain the major obstacles to successful allogeneic SCT. However, the ability to harness the GVL activity of allogeneic donor cells has provided the foundation for newer, safer approaches of allogeneic cell therapy (ACT) that begin to address problems such as relapse, conditioning regimen toxicity, and GVHD. In the past, the only curative therapy for relapsed leukemia after allogeneic SCT had been second SCT, but only at the expense of extensive morbidity, mortality, and very high relapse rates (2,3). Given conclusive preclinical data for important GVL activity and the indirect evidence for GVL reactions in the clinical setting, it was logical to test the potential for donor leukocyte infusions (DLI) to provide antileukemia activity for patients who relapse after allogeneic SCT. It has now been convincingly demonstrated that donor leukocytes can induce a direct GVL reaction in some patients with relapsed leukemia after allogeneic SCT and restore durable complete remissions without the need for any other conditioning therapy. This represents one of the best examples of successful adoptive immunotherapy and demonstrates that it is now possible to exploit the potent immunological properties of the human immune system for clinical benefit. The use of DLI for relapsed leukemia has led to trials using allogeneic adoptive immunotherapy as primary cancer therapy, either as primary DLI or with the use of nonmyeloablative conditioning and allogeneic SCT. Although many issues remain unsettled, the potential to harness the more general “graftversus-tumor” (GVT) activity of allogeneic donor cells may provide a new paradigm for allogeneic cell transplantation and the immunotherapy of cancer.
Functional and neural mechanisms of interval timing

Foreword, Robert Rousseau Introduction: The Persistence of Time, Warren H. Meck FUNCTIONAL MECHANISMS A Concise Introduction to Scalar Timing Theory, Russell M. Church General Learning Models: Timing without a Clock, John W. Hopson Nonlinearities in Sensitivity to Time: Implications for Oscillator-Based Representations of Interval and Circadian Clocks, Jonathon D. Crystal Toward a Unified Theory of Animal Event Timing, Thomas T. Hills Interval Timing and Optimal Foraging, Melissa Bateson Nonverbal Representations of Time and Number in Animals and Human Infants, Elizabeth M. Brannon and Jamie D. Roitman Temporal Experience and Timing in Children, Sylvie Droit-Volet Modality Differences in Interval Timing: Attention, Clock Speed, and Memory, Trevor B. Penney Attentional Time-Sharing in Interval Timing, Claudette Fortin Grandfather's Clock: Attention and Interval Timing in Older Adults, Cindy Lustig NEURAL MECHANISMS Neurogenetics of Interval Timing, Munire Ozlem Cevik Dopaminergic Mechanisms of Interval Timing and Attention, Catalin V. Buhusi Electrophysiological Correlates of Interval Timing, Shogo Sakata and Keiichi Onoda Importance of Frontal Motor Cortex in Divided Attention and Simultaneous Temporal Processing, Kevin C.H. Pang and J. Devin McAuley Integration of Behavior and Timing: Anatomically Separate Systems or Distributed Processing? Matthew S. Matell, Warren H. Meck, and Miguel A.L. Nicolelis Time Flies and May Also Sing: Cortico-Striatal Mechanisms of Interval Timing and Birdsong, Christopher J. MacDonald and Warren H. Meck Neuroimaging Approaches to the Study of Interval Timing, Sean C. Hinton Electrophysiological Evidence for Specific Processing of Temporal Information in Humans, Viviane Pouthas Cerebellar and Basal Ganglia Contributions to Interval Timing, Jorn Diedrichsen, Richard B. Ivry, and Jeff Pressing Interval Timing in the Dopamine-Depleted Basal Ganglia: From Empirical Data to Timing Theory, Chara Malapani and Brian C. Rakitin Overview: An Image of Human Neural Timing, Penelope A. Lewis and R. Chris Miall Afterword: Timing in the New Millennium, Where Are We Now? Francoise Macar Index
Nonlinear model-based control of two-phase flow in risers by feedback linearization

Abstract Active control of the production choke valve is the recommended solution to prevent severe slugging flow conditions at offshore oilfields. The slugging flow constitutes an unstable and highly nonlinear system; the gain of the system changes drastically for different operating points. Although PI and PID controllers are the most widely used controllers in the industry, they need to be re-tuned for different operating conditions. The focus of this paper is to design a model-based nonlinear controller in order to counteract nonlinearities of the system. Feedback linearization based on the riser-base pressure and the topside pressure was used for the control design. Stability and convergence of the closed-loop system was verified in theory as well as by experiments on a test rig.
Proline cis/trans-Isomerase Pin1 Regulates Peroxisome Proliferator-activated Receptor γ Activity through the Direct Binding to the Activation Function-1 Domain*

The important roles of a nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) are widely accepted in various biological processes as well as metabolic diseases. Despite the worldwide quest for pharmaceutical manipulation of PPARγ activity through the ligand-binding domain, very little information about the activation mechanism of the N-terminal activation function-1 (AF-1) domain. Here, we demonstrate the molecular and structural basis of the phosphorylation-dependent regulation of PPARγ activity by a peptidyl-prolyl isomerase, Pin1. Pin1 interacts with the phosphorylated AF-1 domain, thereby inhibiting the polyubiquitination of PPARγ. The interaction and inhibition are dependent upon the WW domain of Pin1 but are independent of peptidyl-prolyl cis/trans-isomerase activity. Gene knockdown experiments revealed that Pin1 inhibits the PPARγ-dependent gene expression in THP-1 macrophage-like cells. Thus, our results suggest that Pin1 regulates macrophage function through the direct binding to the phosphorylated AF-1 domain of PPARγ.
Approximate Bayesian computation, stochastic algorithms and non-local means for complex noise models

In this paper, we present a stochastic NL-means-based de-noising algorithm for generalized non-parametric noise models. First, we provide a statistical interpretation to current patch-based neighborhood filters and justify the Bayesian inference that needs to explicitly accounts for discrepancies between the model and the data. Furthermore, we investigate the Approximate Bayesian Computation (ABC) rejection method combined with density learning techniques for handling situations where the posterior is intractable or too prohibitive to calculate. We demonstrate our stochastic Gamma NL-means (SGNL) on real images corrupted by non-Gaussian noise.
Network Connectivity Proxy: Architecture, Implementation, and Performance Analysis

Several studies in the last decade have pointed out that many devices, such as computers, are often left powered on even when idle, just to make them available and reachable on the network, leading to large energy waste. The concept of network connectivity proxy (NCP) has been proposed as an effective means to improve energy efficiency. It impersonates the presence of networked devices that are temporally unavailable, by carrying out background networking routines on their behalf. Hence, idle devices could be put into low-power states and save energy. Several architectural alternatives and the applicability of this concept to different protocols and applications have been investigated. However, there is no clear understanding of the limitations and issues of this approach in current networking scenarios. This paper extends the knowledge about the NCP by defining an extended set of tasks that the NCP can carry out, by introducing a suitable communication interface to control NCP operation, and by designing, implementing, and evaluating a functional prototype.
How Does Technology-Enabled Active Learning Affect Undergraduate Students' Understanding of Electromagnetism Concepts?

Educational technology supports meaningful learning and enables the presentation of spatial and dynamic images, which portray relationships among complex concepts. The Technology-Enabled Active Learning (TEAL) Project at the Massachusetts Institute of Technology (MIT) involves media-rich software for simulation and visualization in freshman physics carried out in a specially redesigned classroom to facilitate group interaction. These technology-based learning materials are especially useful in electromagnetism to help students conceptualize phenomena and processes. This study analyzes the effects of the unique learning environment of the TEAL project on students' cognitive and affective outcomes. The assessment of the project included examining students' conceptual understanding before and after studying electromagnetism in a media-rich environment. We also investigated the effect of this environment on students' preferences regarding the various teaching methods. As part of the project, we developed pre- and posttests consisting of conceptual questions from standardized tests, as well as questions designed to assess the effect of visualizations and experiments. The research population consisted of 811 undergraduate students. It consisted of a small- and a large-scale experimental groups and a control group. TEAL students improved their conceptual understanding of the subject matter to a significantly higher extent than their control group peers. A majority of the students in the small-scale experiment noted that they would recommend the TEAL course to fellow students, indicating the benefits of interactivity, visualization, and hands-on experiments, which the technology helped enable. In the large-scale implementation students expressed both positive and negative attitudes in the course survey.